Bacterial community associated with worker honeybees (Apis mellifera) affected by European foulbrood
Background Melissococcus plutonius is an entomopathogenic bacterium that causes European foulbrood (EFB), a honeybee (Apis mellifera L.) disease that necessitates quarantine in some countries. In Czechia, positive evidence of EFB was absent for almost 40 years, until an outbreak in the Krkonose Mountains National Park in 2015. This occurrence of EFB gave us the opportunity to study the epizootiology of EFB by focusing on the microbiome of honeybee workers, which act as vectors of honeybee diseases within and between colonies. Methods The study included worker bees collected from brood combs of colonies (i) with no signs of EFB (EFB0), (ii) without clinical symptoms but located at an apiary showing clinical signs of EFB (EFB1), and (iii) with clinical symptoms of EFB (EFB2). In total, 49 samples from 27 honeybee colonies were included in the dataset evaluated in this study. Each biological sample consisted of 10 surface-sterilized worker bees processed for DNA extraction. All subjects were analyzed using conventional PCR and by metabarcoding analysis based on the 16S rRNA gene V1–V3 region, as performed through Illumina MiSeq amplicon sequencing. Results The bees from EFB2 colonies with clinical symptoms exhibited a 75-fold-higher incidence of M. plutonius than those from EFB1 asymptomatic colonies. Melissococcus plutonius was identified in all EFB1 colonies as well as in some of the control colonies. The proportions of Fructobacillus fructosus, Lactobacillus kunkeei, Gilliamella apicola, Frischella perrara, and Bifidobacterium coryneforme were higher in EFB2 than in EFB1, whereas Lactobacillus mellis was significantly higher in EFB2 than in EFB0. Snodgrassella alvi and L. melliventris, L. helsingborgensis and, L. kullabergensis exhibited higher proportion in EFB1 than in EFB2 and EFB0. The occurrence of Bartonella apis and Commensalibacter intestini were higher in EFB0 than in EFB2 and EFB1. Enterococcus faecalis incidence was highest in EFB2. Conclusions High-throughput Illumina sequencing permitted a semi-quantitative analysis of the presence of M. plutonius within the honeybee worker microbiome. The results of this study indicate that worker bees from EFB-diseased colonies are capable of transmitting M. plutonius due to the greatly increased incidence of the pathogen. The presence of M. plutonius sequences in control colonies supports the hypothesis that this pathogen exists in an enzootic state. The bacterial groups synergic to both the colonies with clinical signs of EFB and the EFB-asymptomatic colonies could be candidates for probiotics. This study confirms that E. faecalis is a secondary invader to M. plutonius; however, other putative secondary invaders were not identified in this study.
Erban et al. (2017) Bacterial community associated with worker honeybees (Apis mellifera) affected by European foulbrood. PeerJ 5:e3816 https://doi.org/10.7717/peerj.3816
Diversity of cultivated aerobic poly-hydrolytic bacteria in saline alkaline soils
Alkaline saline soils, known also as “soda solonchaks”, represent a natural soda habitat which differs from soda lake sediments by higher aeration and lower humidity. The microbiology of soda soils, in contrast to the more intensively studied soda lakes, remains poorly explored. In this work we investigate the diversity of culturable aerobic haloalkalitolerant bacteria with various hydrolytic activities from soda soils at different locations in Central Asia, Africa, and North America. In total, 179 pure cultures were obtained by using media with various polymers at pH 10 and 0.6 M total Na+. According to the 16S rRNA gene sequence analysis, most of the isolates belonged to Firmicutes and Actinobacteria. Most isolates possessed multiple hydrolytic activities, including endoglucanase, xylanase, amylase and protease. The pH profiling of selected representatives of actinobacteria and endospore-forming bacteria showed, that the former were facultative alkaliphiles, while the latter were mostly obligate alkaliphiles. The hydrolases of selected representatives from both groups were active at a broad pH range from six to 11. Overall, this work demonstrates the presence of a rich hydrolytic bacterial community in soda soils which might be explored further for production of haloalkalistable hydrolases.
Sorokin et al. (2017) Diversity of cultivated aerobic poly-hydrolytic bacteria in saline alkaline soils. PeerJ 5:e3796 https://doi.org/10.7717/peerj.3796
Ecomorphological characterization of murines and non-arvicoline cricetids (Rodentia) from south-western Europe since the latest Middle Miocene to the Mio-Pliocene boundary (MN 7/8–MN13)
Rodents are the most speciose group of mammals and display a great ecological diversity. Despite the greater amount of ecomorphological information compiled for extant rodent species, studies usually lack of morphological data on dentition, which has led to difficulty in directly utilizing existing ecomorphological data of extant rodents for paleoecological reconstruction because teeth are the most common or often the only micromammal fossils. Here, we infer the environmental ranges of extinct rodent genera by extracting habitat information from extant relatives and linking it to extinct taxa based on the phenogram of the cluster analysis, in which variables are derived from the principal component analysis on outline shape of the upper first molars. This phenotypic “bracketing” approach is particularly useful in the study of the fossil record of small mammals, which is mostly represented by isolated teeth. As a case study, we utilize extinct genera of murines and non-arvicoline cricetids, ranging from the Iberoccitanian latest middle Miocene to the Mio-Pliocene boundary, and compare our results thoroughly with previous paleoecological reconstructions inferred by different methods. The resultant phenogram shows a predominance of ubiquitous genera among the Miocene taxa, and the presence of a few forest specialists in the two rodent groups (Murinae and Cricetidae), along with the absence of open environment specialists in either group of rodents. This appears to be related to the absence of enduring grassland biomes in the Iberian Peninsula during the late Miocene. High consistency between our result and previous studies suggests that this phenotypic “bracketing” approach is a very useful tool.
Gomez Cano et al. (2017) Ecomorphological characterization of murines and non-arvicoline cricetids (Rodentia) from south-western Europe since the latest Middle Miocene to the Mio-Pliocene boundary (MN 7/8–MN13). PeerJ 5:e3646 https://doi.org/10.7717/peerj.3646
Rootstock influence on iron uptake responses in Citrus leaves and their regulation under the Fe paradox effect
Background and aims This work evaluates the regulation of iron uptake responses in Citrus leaves and their involvement in the Fe paradox effect. Methods Experiments were performed in field-grown ‘Navelina’ trees grafted onto two Cleopatra mandarin × Poncirus trifoliata (L.) Raf. hybrids with different Fe-chlorosis symptoms: 030146 (non-chlorotic) and 030122 (chlorotic). Results Chlorotic leaves were smaller than non-chlorotic ones for both dry weight (DW) and area basis, and exhibited marked photosynthetic state affection, but reduced catalase and peroxidase enzymatic activities. Although both samples had a similar total Fe concentration on DW, it was lower in chlorotic leaves when expressed on an area basis. A similar pattern was observed for the total Fe concentration in the apoplast and cell sap and in active Fe (Fe2+) concentration. FRO2 gene expression and ferric chelate reductase (FC-R) activity were also lower in chlorotic samples, while HA1 and IRT1 were more induced. Despite similar apoplasmic pH, K+/Ca2+ was higher in chlorotic leaves, and both citrate and malate concentrations in total tissue and apoplast fluid were lower. Conclusion (1) The rootstock influences Fe acquisition system in the leaf; (2) the increased sensitivity to Fe-deficiency as revealed by chlorosis and decreased biomass, was correlated with lower FC-R activity and lower organic acid level in leaf cells, which could cause a decreased Fe mobility and trigger other Fe-stress responses in this organ to enhance acidification and Fe uptake inside cells; and (3) the chlorosis paradox phenomenon in citrus likely occurs as a combination of a marked FC-R activity impairment in the leaf and the strong growth inhibition in this organ.
Martinez-Cuenca et al. (2017) Rootstock influence on iron uptake responses in Citrus leaves and their regulation under the Fe paradox effect. PeerJ 5:e3553 https://doi.org/10.7717/peerj.3553
Filtering out parasites: sand crabs (Lepidopa benedicti) are infected by more parasites than sympatric mole crabs (Emerita benedicti)
Two digging decapod crustaceans, the sand crab species Lepidopa benedicti and the mole crab species Emerita benedicti, both live in the swash zone of fine sand beaches. They were examined for two parasites that infect decapod crustaceans in the region, an unidentified nematode previously shown to infect L. benedicti, and cestode tapeworm larvae, Polypocephalus sp., previously shown to infect shrimp (Litopenaeus setiferus). Lepidopa benedicti were almost always infected with both parasite species, while E. benedicti were rarely infected with either parasite species. This difference in infection pattern suggests that tapeworms are ingested during sediment feeding in L. benedicti, which E. benedicti avoid by filter feeding. Larger L. benedicti had more Polypocephalus sp. larvae. The thoracic ganglia, which make up the largest proportion of neural tissue, contained the largest numbers of Polypocephalus sp. larvae. Intensity of Polypocephalus sp. infection was not correlated with how long L. benedicti remained above sand in behavioural tests, suggesting that Polypocephalus sp. do not manipulate the sand crabs in a way that facilitates trophic transmission of the parasite. Litopenaeus setiferus may be a primary host for Polypocephalus sp., and L. benedict may be a secondary, auxiliary host.
Faulkes (2017) Filtering out parasites: sand crabs (Lepidopa benedicti) are infected by more parasites than sympatric mole crabs (Emerita benedicti). PeerJ 5:e3852 https://doi.org/10.7717/peerj.3852
Functional modularity in lake-dwelling characin fishes of Mexico
Modular evolution promotes evolutionary change, allowing independent variation across morphological units. Recent studies have shown that under contrasting ecological pressures, patterns of modularity could be related to divergent evolution. The main goal of the present study was to evaluate the presence of modular evolution in two sister lacustrine species, Astyanax aeneus and A. caballeroi, which are differentiated by their trophic habits. Two different datasets were analyzed: (1) skull X-rays from 73 specimens (35 A. aeneus and 38 A. caballeroi) to characterize skull variation patterns, considering both species and sex effects. For this dataset, three different modularity hypotheses were tested, previously supported in other lacustrine divergent species; (2) a complete body shape dataset was also tested for four modularity hypotheses, which included a total of 196 individuals (110 Astyanax aeneus and 86 A. caballeroi). Skull shape showed significant differences among species and sex (P < 0.001), where Astyanax caballeroi species showed an upwardly projected mandible and larger preorbital region. For the skull dataset, the modularity hypothesis ranked first included three partitioning modules. While for the complete body dataset the best ranked hypothesis included two modules (head vs the rest of the body), being significant only for A. caballeroi.
Ornelas-García et al. (2017) Functional modularity in lake-dwelling characin fishes of Mexico. PeerJ 5:e3851 https://doi.org/10.7717/peerj.3851
The Dark Cube: dark character profiles and OCEAN
Background The Big Five traits (i.e., openness, conscientiousness, extraversion, agreeableness, and neuroticism: OCEAN) have been suggested to provide a meaningful taxonomy for studying the Dark Triad: Machiavellianism, narcissism, and psychopathy. Nevertheless, current research consists of mixed and inconsistent associations between the Dark Triad and OCEAN. Here we used the Dark Cube (Garcia & Rosenberg, 2016), a model of malevolent character theoretically based on Cloninger’s biopsychosocial model of personality and in the assumption of a ternary structure of malevolent character. We use the dark cube profiles to investigate differences in OCEAN between individuals who differ in one dark character trait while holding the other two constant (i.e., conditional relationships). Method Participants (N = 330) responded to the Short Dark Triad Inventory and the Big Five Inventory and were grouped according to the eight possible combinations using their dark trait scores (M, high Machiavellianism; m, low Machiavellianism; N, high narcissism; n, low narcissism; P, high psychopathy; p, low psychopathy): MNP “maleficent”, MNp “manipulative narcissistic”, MnP “anti-social”, Mnp “Machiavellian”, mNP “psychopathic narcissistic”, mNp “narcissistic”, mnP “psychopathic”, and mnp “benevolent”. Results High narcissism-high extraversion and high psychopathy-low agreeableness were consistently associated across comparisons. The rest of the comparisons showed a complex interaction. For example, high Machiavellianism-high neuroticism only when both narcissism and psychopathy were low (Mnp vs. mnp), high narcissism-high conscientiousness only when both Machiavellianism and psychopathy were also high (MNP vs. MnP), and high psychopathy-high neuroticism only when Machiavellianism was low and narcissism was high (mNP vs. mNp). Conclusions We suggest that the Dark Cube is a useful tool in the investigation of a consistent Dark Triad Theory. This approach suggests that the only clear relationships were narcissism-extraversion and psychopathy-agreeableness and that the malevolent character traits were associated to specific OCEAN traits only under certain conditions. Hence, explaining the mixed and inconsistent linear associations in the Dark Triad literature.
Garcia et al. (2017) The Dark Cube: dark character profiles and OCEAN. PeerJ 5:e3845 https://doi.org/10.7717/peerj.3845
Are diversification rates and chromosome evolution in the temperate grasses (Pooideae) associated with major environmental changes in the Oligocene-Miocene?
The Pooideae are a highly diverse C3 grass subfamily that includes some of the most economically important crops, nested within the highly speciose core-pooid clade. Here, we build and explore the phylogeny of the Pooideae within a temporal framework, assessing its patterns of diversification and its chromosomal evolutionary changes in the light of past environmental transformations. We sequenced five plastid DNA loci, two coding (ndhF, matk) and three non-coding (trnH-psbA, trnT-L and trnL-F), in 163 Poaceae taxa, including representatives for all subfamilies of the grasses and all but four ingroup Pooideae tribes. Parsimony and Bayesian phylogenetic analyses were conducted and divergence times were inferred in BEAST using a relaxed molecular clock. Diversification rates were assessed using the MEDUSA approach, and chromosome evolution was analyzed using the chromEvol software. Diversification of the Pooideae started in the Late-Eocene and was especially intense during the Oligocene-Miocene. The background diversification rate increased significantly at the time of the origin of the Poodae + Triticodae clade. This shift in diversification occurred in a context of falling temperatures that potentially increased ecological opportunities for grasses adapted to open areas around the world. The base haploid chromosome number n = 7 has remained stable throughout the phylogenetic history of the core pooids and we found no link between chromosome transitions and major diversification events in the Pooideae.
Pimentel et al. (2017) Are diversification rates and chromosome evolution in the temperate grasses (Pooideae) associated with major environmental changes in the Oligocene-Miocene?. PeerJ 5:e3815 https://doi.org/10.7717/peerj.3815
Spontaneous reoccurrence of “scooping”, a wild tool-use behaviour, in naïve chimpanzees
Modern human technological culture depends on social learning. A widespread assumption for chimpanzee tool-use cultures is that they, too, are dependent on social learning. However, we provide evidence to suggest that individual learning, rather than social learning, is the driver behind determining the form of these behaviours within and across individuals. Low-fidelity social learning instead merely facilitates the reinnovation of these behaviours, and thus helps homogenise the behaviour across chimpanzees, creating the population-wide patterns observed in the wild (what here we call “socially mediated serial reinnovations”). This is the main prediction of the Zone of Latent Solutions (ZLS) hypothesis. This study directly tested the ZLS hypothesis on algae scooping, a wild chimpanzee tool-use behaviour. We provided naïve chimpanzees (n = 14, Mage = 31.33, SD = 10.09) with ecologically relevant materials of the wild behaviour but, crucially, without revealing any information on the behavioural form required to accomplish this task. This study found that naïve chimpanzees expressed the same behavioural form as their wild counterparts, suggesting that, as the ZLS theory predicts, individual learning is the driver behind the frequency of this behavioural form. As more behaviours are being found to be within chimpanzee’s ZLS, this hypothesis now provides a parsimonious explanation for chimpanzee tool cultures.
Bandini et al. (2017) Spontaneous reoccurrence of “scooping”, a wild tool-use behaviour, in naïve chimpanzees. PeerJ 5:e3814 https://doi.org/10.7717/peerj.3814
Selected nutritional habits of teenagers associated with overweight and obesity
Introduction A balanced diet is at the heart of healthy growth and development of children and youth, whereas inappropriate eating habits considerably influence the incidence of disorders connected with nutrition, including overweight and obesity. This paper aims at studying nutritional factors of 18-year-old secondary school youth in the urban environment and their effect on the incidence of overweight and obesity. Materials and methods The survey was conducted among 1,999 secondary school students chosen at random. The research tool consisted an original survey questionnaire. The measurements of respondents’ height and body mass provided data for calculating the body mass index. Results and conclusion The percentage of youth with deficient body mass was estimated at 8.4%. The percentage of normal weight students in the surveyed group was estimated at 77.6%. Overweight and obesity characterized 14.0% of the total number. As many as 21.8% of overweight and obese respondents would eat one or two meals as opposed to 16.8% of normal weight students. Three-fourths of the surveyed students would eat breakfast regardless of their nutritional habits. Lunch is eaten by 52.9% of normal weight 18-year-olds and 46.1% of overweight and obese students. The analysis of mealtimes suggests that overweight and obese students would have their breakfast and dinner at later hours than the rest of the surveyed. More than half of the participating students failed to eat lunch (53.9%), and one in four students within this group resigned from supper. Girls would eat fruit and vegetables more frequently than boys several times a day. The percentage of persons in the surveyed groups who would eat fast foods on a daily basis was similar regardless of their nutritional status. Sweetened carbonated beverages would be drunk more often by overweight and obese boys (81.2%) as compared with boys with proper body mass (75.8%). The same type of beverages would be popular with two-thirds of girls, and this result was similar regardless of their nutritional status. About 44.2% of overweight and obese girls and 20% of girls with proper body mass attempted to lose weight, and 5.7% of boys tried to go on a diet. Eating limitations were declared by 16.5% of overweight and obese boys and ca. 3% of normal weight boys. Conclusion Within the surveyed group of youth, it was possible to indicate eating errors primarily consisting in irregular eating, too low a number of meals during the day, particularly skipping breakfast, which took place more frequently among overweight and obese students rather than normal weight ones. The survey points to the insufficient intake of vegetables and fruit as opposed to salty and sweet meals. It is essential to convey the knowledge on the causes of overweight and obesity as well as rules of a healthy diet as factors preventing civilization diseases.
Zalewska et al. (2017) Selected nutritional habits of teenagers associated with overweight and obesity. PeerJ 5:e3681 https://doi.org/10.7717/peerj.3681