title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=1327 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: Conspicuous colours reduce predation rates in fossorial uropeltid snakes link: https://peerj.com/articles/7508 last-modified: 2019-08-14 description: Uropeltid snakes (Family Uropeltidae) are non-venomous, fossorial snakes that are found above ground occasionally, during which time they are exposed to predation. Many species are brightly coloured, mostly on the ventral surface, but these colours are expected to have no function below the ground. Observations have shown that the cephalic resemblance (resemblance to heads) of uropeltid tails may direct attacks of predators towards the hardened tails, thereby potentially increasing handling times for predators. Experiments have also shown that predators learn to avoid prey that are non-toxic and palatable but are difficult to capture, hard to process or require long handling time when such prey advertise their unprofitability through conspicuous colours. We here postulate that uropeltid snakes use their bright colours to signal long handling times associated with attack deflection to the tails, thereby securing reduced predation from predators that can learn to associate colour with handling time. Captive chicken experiments with dough models mimicking uropeltids indicate that attacks were more common on the tail than on the head. Field experiments with uropeltid clay models show that the conspicuous colours of these snakes decrease predation rates compared to cryptic models, but a novel conspicuous colour did not confer such a benefit. Overall, our experiments provide support for our hypothesis that the conspicuous colours of these snakes reduce predation, possibly because these colours advertise unprofitability due to long handling times. creator: Vivek Philip Cyriac creator: Ullasa Kodandaramaiah uri: https://doi.org/10.7717/peerj.7508 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2019 Cyriac and Kodandaramaiah title: Dynamics of a methanol-fed marine denitrifying biofilm: 1-Impact of environmental changes on the denitrification and the co-occurrence of Methylophaga nitratireducenticrescens and Hyphomicrobium nitrativorans link: https://peerj.com/articles/7497 last-modified: 2019-08-13 description: BackgroundThe biofilm of a methanol-fed denitrification system that treated a marine effluent is composed of multi-species microorganisms, among which Hyphomicrobium nitrativorans strain NL23 and Methylophaga nitratireducenticrescens strain JAM1 are the principal bacteria involved in the denitrifying activities. Here, we report the capacity of the denitrifying biofilm to sustain environmental changes, and the impact of these changes on the co-occurrence of H. nitrativorans and M. nitratireducenticrescens.MethodsIn a first set of assays, the original biofilm (OB) was cultivated in an artificial seawater (ASW) medium under anoxic conditions to colonize new carriers. The new formed biofilm was then subjected to short exposures (1–5 days) of a range of NaCl, methanol, nitrate (NO3−) and nitrite (NO2−) concentrations, and to different pHs and temperatures. In a second set of assays, the OB was cultivated in ASW medium for five weeks with (i) a range of NaCl concentrations, (ii) four combinations of NO3−/methanol concentrations and temperatures, (iii) NO2−, and (iv) under oxic conditions. Finally, the OB was cultivated for five weeks in the commercial Instant Ocean (IO) seawater. The growth of the biofilm and the dynamics of NO3− and NO2− were determined. The levels of M. nitratireducenticrescens and H. nitrativorans were measured by qPCR.ResultsIn the first set of assays, the biofilm cultures had the capacity to sustain denitrifying activities in most of the tested conditions. Inhibition occurred when they were exposed to high pH (10) or to high methanol concentration (1.5%). In the second set of assays, the highest specific denitrification rates occurred with the biofilm cultures cultivated at 64.3 mM NO3− and 0.45% methanol, and at 30 °C. Poor biofilm development occurred with the biofilm cultures cultivated at 5% and 8% NaCl. In all biofilm cultures cultivated in ASW at 2.75% NaCl, H. nitrativorans strain NL23 decreased by three orders of magnitude in concentrations compared to that found in OB. This decrease coincided with the increase of the same magnitude of a subpopulation of M. nitratireducenticrescens (strain GP59 as representative). In the biofilm cultures cultivated at low NaCl concentrations (0% to 1.0%), persistence of H. nitrativorans strain NL23 was observed, with the gradual increase in concentrations of M. nitratireducenticrescens strain GP59. High levels of H. nitrativorans strain NL23 were found in the IO biofilm cultures. The concentrations of M. nitratireducenticrescens strain JAM1 were lower in most of the biofilms cultures than in OB.ConclusionsThese results demonstrate the plasticity of the marine methylotrophic denitrifying biofilm in adapting to different environmental changes. The NaCl concentration is a crucial factor in the dynamics of H. nitrativorans strain NL23, for which growth was impaired above 1% NaCl in the ASW-based biofilm cultures in favor of M. nitratireducenticrescens strain GP59. creator: Geneviève Payette creator: Valérie Geoffroy creator: Christine Martineau creator: Richard Villemur uri: https://doi.org/10.7717/peerj.7497 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2019 Payette et al. title: Grazing effects on woody and herbaceous plant biodiversity on a limestone mountain in northern Tunisia link: https://peerj.com/articles/7296 last-modified: 2019-08-13 description: Mediterranean maquis vegetation is highly biodiverse, but widespread grazing poses a challenge for management and conservation. We sampled woody and herbaceous plants separately on a limestone mountain with strong mesic-xeric gradients in Tunisia’s Parc National de L’Ichkeul, assessed grazing pressure (on a scale of 1–3), and asked whether grazing had a significant effect on plant compositional abundance before and after controlling for environmental covariates. Sites on the more mesic lakeside face of the mountain were most compositionally unique, and forbs contributed most to the herbaceous beta-diversity on the mountain. We used variance partitioning to separate the collective and individual effects of the abiotic environment, grazing, human activity, and space on herbaceous and woody beta-diversity. However, the individual effect of grazing on overall plant community composition was confounded with space, due to the spatially autocorrelated grazing pressure on the mountain. Importantly, we found that herbaceous and woody communities responded differently to increasing levels of grazing intensity: herbaceous beta-diversity was highest between sites with no grazing pressure, while woody beta-diversity peaked under light grazing. Herbaceous community composition was sensitive to any intensity of grazing pressure, and biotic homogenization occured under moderate-to-high grazing pressure. On the other hand, woody community composition remained relatively similar under no to light grazing pressure, but differed under moderate-to-heavy grazing. Using a one-way permutational analysis of variance analysis, we showed that grazing had a significant effect when controlling for abiotic and spatial covariates. Our findings offer insight into the effects of grazing on maquis vegetation at Jebel Ichkeul, acting as a microcosm of similar conservation and management issues elsewhere in the Mediterranean. We suggest that a combination of monitoring and carefully controlled grazing may enhance plant diversity and maintain the region’s biodiverse maquis vegetation, potentially maintaining a key climate refugium for vulnerable endemic species. Importantly, our study provides a useful baseline of the plant assemblages at Jebel Ichkeul with which to compare future vegetation changes. creator: David Anthony Kirk creator: Katherine Hébert creator: Frank Barrie Goldsmith uri: https://doi.org/10.7717/peerj.7296 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2019 Kirk et al. title: Mitochondrial DNA in human identification: a review link: https://peerj.com/articles/7314 last-modified: 2019-08-13 description: Mitochondrial DNA (mtDNA) presents several characteristics useful for forensic studies, especially related to the lack of recombination, to a high copy number, and to matrilineal inheritance. mtDNA typing based on sequences of the control region or full genomic sequences analysis is used to analyze a variety of forensic samples such as old bones, teeth and hair, as well as other biological samples where the DNA content is low. Evaluation and reporting of the results requires careful consideration of biological issues as well as other issues such as nomenclature and reference population databases. In this work we review mitochondrial DNA profiling methods used for human identification and present their use in the main cases of humanidentification focusing on the most relevant issues for forensics. creator: António Amorim creator: Teresa Fernandes creator: Nuno Taveira uri: https://doi.org/10.7717/peerj.7314 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2019 Amorim et al. title: Developing sport expertise in youth sport: a decision training program in basketball link: https://peerj.com/articles/7392 last-modified: 2019-08-13 description: BackgroundThis study has analyzed the impact of applying a decision training program, in which video-feedback and questioning were used, on the development of decision-making, skill execution and procedural knowledge in basketball players.MethodsParticipants were eleven male players aged between 12 and 13 years old (Mage = 12.75, SDage = .65), who were assigned to an experimental or control group within a pre-test/intervention test/retention test quasi-experimental design. The decision training program was applied over 11 weeks. Throughout this intervention, players had to analyze the causes and reasons for the decision made, using video feedback and questioning to this end. Decision-making and skill execution variables were analyzed using the French & Thomas (1987) observation instrument, while a validated questionnaire was used to assess procedural knowledge in basketball.ResultsThe results reported that sport expertise improved in players from the experimental group, who had significantly higher intervention test scores for successful decisions and skill executions when compared to players in the control group. In the intra-group analysis, the experimental group significantly improved in the intervention test compared to the pre-test, in terms of some of the variables of decision-making, skill execution and procedural knowledge.DiscussionThese results reinforce the idea of including cognitive tools in training, such as video-feedback and questioning, to improve sport expertise in players’ formative stages, and presumably to improve their performance whilst maintaining decision training throughout time. creator: Alexander Gil-Arias creator: Luis Garcia-Gonzalez creator: Fernando Del Villar Alvarez creator: Damián Iglesias Gallego uri: https://doi.org/10.7717/peerj.7392 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2019 Gil-Arias et al. title: The effects of detraining and retraining periods on fat-mass and fat-free mass in elite male soccer players link: https://peerj.com/articles/7466 last-modified: 2019-08-13 description: The aim of the study was to examine the effects of a detraining period (DTP) (i.e., off-season) with an individually prescribed training program, and a retraining period (RTP) (i.e., pre-season) combining soccer and flywheel-based strength training on fat-free mass (FFM) and fat-mass (FM) in 10 elite professional male soccer players. The present study used a controlled repeated-measures research design to investigate the changes in FFM and FM using dual-energy X-ray absorptiometry. Whole body %FM increased (effect size (ES) = 0.87 ± 0.46) and FFM reduced after DTP (ES = −0.30 ± 0.19), returning to values comparable to the end of the previous season after RTP. At regional levels, arms, legs, and trunk %FM increased (ES = from 0.42 to 1.29) while trunk-FFM was reduced (ES = −0.40 ± 0.26) after DTP, returning to the values observed at the end of the previous season after RTP. Legs-FFM did not change after DTP, with a substantial increase after RTP in comparison with pre-season values (ES = 0.34 ± 0.29 and 0.53 ± 0.36 for the right and left leg, respectively). Despite the small sample size of the present study, the findings indicate that elite soccer players can be allowed 2 weeks of rest during a five-week DTP, since the changes in %FM and FFM were relatively small, and FM and FFM returned to the optimal initial values for competition after the proposed RTP during the pre-season. creator: Luis Suarez-Arrones creator: Pilar Lara-Lopez creator: Rafael Maldonado creator: Nacho Torreno creator: Moises De Hoyo creator: Fabio Yuzo Nakamura creator: Valter Di Salvo creator: Alberto Mendez-Villanueva uri: https://doi.org/10.7717/peerj.7466 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2019 Suarez-Arrones et al. title: Dynamics of a methanol-fed marine denitrifying biofilm: 2—impact of environmental changes on the microbial community link: https://peerj.com/articles/7467 last-modified: 2019-08-13 description: BackgroundThe biofilm of a methanol-fed, marine denitrification system is composed of a multi-species microbial community, among which Hyphomicrobium nitrativorans and Methylophaga nitratireducenticrescens are the principal bacteria involved in the denitrifying activities. To assess its resilience to environmental changes, the biofilm was cultivated in artificial seawater (ASW) under anoxic conditions and exposed to a range of specific environmental conditions. We previously reported the impact of these changes on the denitrifying activities and the co-occurrence of H. nitrativorans strain NL23 and M. nitratireducenticrescens in the biofilm cultures. Here, we report the impact of these changes on the dynamics of the overall microbial community of the denitrifying biofilm.MethodsThe original biofilm (OB) taken from the denitrification system was cultivated in ASW under anoxic conditions with a range of NaCl concentrations, and with four combinations of nitrate/methanol concentrations and temperatures. The OB was also cultivated in the commercial Instant Ocean seawater (IO). The bacterial diversity of the biofilm cultures and the OB was determined by 16S ribosomal RNA gene sequences. Culture approach was used to isolate other denitrifying bacteria from the biofilm cultures. The metatranscriptomes of selected biofilm cultures were derived, along with the transcriptomes of planktonic pure cultures of H. nitrativorans strain NL23 and M. nitratireducenticrescens strain GP59.ResultsHigh proportions of M. nitratireducenticrescens occurred in the biofilm cultures. H. nitrativorans strain NL23 was found in high proportion in the OB, but was absent in the biofilm cultures cultivated in the ASW medium at 2.75% NaCl. It was found however in low proportions in the biofilm cultures cultivated in the ASW medium at 0–1% NaCl and in the IO biofilm cultures. Denitrifying bacterial isolates affiliated to Marinobacter spp. and Paracoccus spp. were isolated. Up regulation of the denitrification genes of strains GP59 and NL23 occurred in the biofilm cultures compared to the planktonic pure cultures. Denitrifying bacteria affiliated to the Stappia spp. were metabolically active in the biofilm cultures.ConclusionsThese results illustrate the dynamics of the microbial community in the denitrifying biofilm cultures in adapting to different environmental conditions. The NaCl concentration is an important factor affecting the microbial community in the biofilm cultures. Up regulation of the denitrification genes of M. nitratireducenticrescens strain GP59 and H. nitrativorans strain NL23 in the biofilm cultures suggests different mechanisms of regulation of the denitrification pathway in the biofilm. Other denitrifying heterotrophic bacteria are present in low proportions, suggesting that the biofilm has the potential to adapt to heterotrophic, non-methylotrophic environments. creator: Richard Villemur creator: Geneviève Payette creator: Valérie Geoffroy creator: Florian Mauffrey creator: Christine Martineau uri: https://doi.org/10.7717/peerj.7467 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2019 Villemur et al. title: Vulnerability of small-scale fishers to benzene exposure and the current knowledge gap on benzene-exposure in Brazilian fishers link: https://peerj.com/articles/7483 last-modified: 2019-08-13 description: Fishers are a particularly vulnerable population, chronically exposed to many stresses, injuries and health conditions directly linked to their fishing activities. This includes benzene exposure through gasoline and diesel exhaust fumes. Benzene is a known carcinogen, and has been assessed in many worker groups, but reports on fisher benzene exposure are extremely scarce in the literature. This paper discusses benzene exposure in small-scale fishers and reflects on the current knowledge gap on benzene-exposure in Brazilian fishers. creator: Rachel Ann Hauser-Davis uri: https://doi.org/10.7717/peerj.7483 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2019 Hauser-Davis title: The effect of mangrove restoration on avian assemblages of a coastal lagoon in southern Mexico link: https://peerj.com/articles/7493 last-modified: 2019-08-13 description: BackgroundMangrove forests provide many ecosystem services, including the provision of habitat that supports avian biodiversity. However, hurricanes can knock down trees, alter hydrologic connectivity, and affect avian habitat. In 1995, Hurricanes Opal and Roxanne destroyed approximately 1,700 ha of mangrove forest in Laguna de Términos, Mexico. Since then, hydrological restoration has been implemented to protect the mangrove forest and its biodiversity.MethodsSince avian communities are often considered biological indicators of ecosystem quality, avian diversity and species relative abundance were evaluated as indicators of mangrove restoration success by comparing undisturbed mangrove patches with those affected by the hurricanes. Using bird surveys, similarity analyses, and generalized linear models, we evaluated the effects of water quality variables and forest structure on the relative abundance and diversity of the avian community in disturbed, restored, and undisturbed mangrove patches.ResultsHigher bird species richness and relative abundances were found in disturbed and restored sites compared to the undisturbed site. After restoration, values of frequency of flooding, water temperature, tree density, and the number of tree species were more similar to that of the undisturbed site than to the values of the disturbed one. Such variables influenced the relative abundance of bird guilds in the different habitat conditions. Furthermore, some insectivorous bird species, such as the Yellow Warbler and Tropical Kingbird, were found to be similarly abundant in both undisturbed and restored sites, but absent or very low in occurrence at the disturbed site.ConclusionsCollectively, our results strongly suggest that hydrologic restoration helps to enhance niche availability for different bird guilds, including water and canopy bird species. Our work can help inform management strategies that benefit avian communities in mangrove forests and wetland systems. creator: Julio Cesar Canales-Delgadillo creator: Rosela Perez-Ceballos creator: Mario Arturo Zaldivar-Jimenez creator: Martin Merino-Ibarra creator: Gabriela Cardoza creator: Jose-Gilberto Cardoso-Mohedano uri: https://doi.org/10.7717/peerj.7493 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2019 Canales-Delgadillo et al. title: Identification and functional analysis of LecRLK genes in Taxodium ‘Zhongshanshan’ link: https://peerj.com/articles/7498 last-modified: 2019-08-13 description: BackgroundLectin receptor-like protein kinases (LecRLKs) can transform external stimuli into intracellular signals and play important regulatory roles in plant development and response to environmental stressors. However, research on the LecRLK gene family of conifers has seldom been reported.MethodsPutative LecRLK genes were identified in the transcriptome of Taxodium ‘Zhongshanshan’. The classification, domain structures, subcellular localization prediction, and expression patterns of LecRLK genes, as well as co-expressed genes, were analyzed using bioinformatics methods. Fifteen representative genes were further selected for qRT-PCR analysis in six tissues and under five different environmental stressor conditions.ResultsIn total, 297 LecRLK genes were identified, including 155 G-type, 140 L-type, and 2 C-type. According to the classification, G-type and L-type LecRLK genes both can be organized into seven groups. The domain architecture of G-type proteins were more complex compared with that of L- and C-type proteins. Conservative motifs were found in G-type and L-type diverse lectin domains. Prediction and transient expression experiments to determine subcellular localization showed that LecRLKs were mainly concentrated in the cell membrane system, and some members were located at multiple sites at the same time. RNA-seq-based transcriptomics analysis suggested functional redundancy and divergence within each group. Unigenes co-expressed with LecRLKs in the transcriptome were found to be enriched in pathways related to signal transduction and environmental adaptation. Furthermore, qRT-PCR analysis of representative genes showed evidence of functional divergence between different groups.ConclusionsThis is the first study to conduct an identification and expression analysis of the LecRLK gene family in Taxodium. These results provide a basis for future studies on the evolution and function of this important gene family in Taxodium. creator: Jinbo Guo creator: Hao Duan creator: Lei Xuan creator: Ziyang Wang creator: Jianfeng Hua creator: Chaoguang Yu creator: Yunlong Yin creator: Mingzhi Li creator: Ying Yang uri: https://doi.org/10.7717/peerj.7498 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2019 Guo et al.