title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=1318 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: Variation in denitrifying bacterial communities along a primary succession in the Hailuogou Glacier retreat area, China link: https://peerj.com/articles/7356 last-modified: 2019-08-14 description: BackgroundThe Hailuogou Glacier is located at the Gongga Mountain on the southeastern edge of the Tibetan Plateau, and has retreated continuously as a result of global warming. The retreat of the Hailuogou Glacier has left behind a primary succession along soil chronosequences. Hailuogou Glacier’s retreated area provides an excellent living environment for the colonization of microbes and plants, making it an ideal model to explore plant successions, microbial communities, and the interaction of plants and microbes during the colonization process. However, to date, the density of the nitrogen cycling microbial communities remain unknown, especially for denitrifiers in the primary succession of the Hailuogou Glacier. Therefore, we investigated the structural succession and its driving factors for denitrifying bacterial communities during the four successional stages (0, 20, 40, and 60 years).MethodsThe diversity, community composition, and abundance of nosZ-denitrifiers were determined using molecular tools, including terminal restriction fragment length polymorphism and quantitative polymerase chain reactions (qPCR).ResultsnosZ-denitrifiers were more abundant and diverse in soils from successional years 20–60 compared to 0–5 years, and was highest in Site3 (40 years). The denitrifying bacterial community composition was more complex in older soils (40–60 years) than in younger soils (≤20 years). The terminal restriction fragments (T-RFs) of Azospirillum (90 bp) and Rubrivivax (95 bp) were dominant in soisl during early successional stages (0–20 years) and in the mature phase (40–60 years), respectively. Specific T-RFs of Bradyrhizobium (100 bp) and Pseudomonas (275 bp) were detected only in Site3 and Site4, respectively. Moreover, the unidentified 175 bp T-RFs was detected only in Site3. Of the abiotic factors that were measured in this study, soil available phosphorus, available potassium and denitrifying enzyme activity (DEA) correlated significantly with the community composition of nosZ-denitrifiers (P < 0.05 by Monte Carlo permutation test within RDA analysis). creator: Yan Bai creator: Xiying Huang creator: Xiangrui Zhou creator: Quanju Xiang creator: Ke Zhao creator: Xiumei Yu creator: Qiang Chen creator: Hao Jiang creator: Tashi Nyima creator: Xue Gao creator: Yunfu Gu uri: https://doi.org/10.7717/peerj.7356 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2019 Bai et al. title: Application of the Ostrom framework in the analysis of a social-ecological system with multiple resources in a marine protected area link: https://peerj.com/articles/7374 last-modified: 2019-08-14 description: The framework proposed by Ostrom (2009) has become one of the most utilized tools to address the complexity of social-ecological systems. Most cases use this framework to analyze the systems from the perspective of a single resource unit. However, the livelihoods in several coastal communities are diverse, so that the users interact with multiple common-pool resources, which makes their analysis difficult. In this sense, it is important to identify the key elements of management to achieve the sustainable use of the resources. In this study, we were able to do this in a coastal community where commercial fishing, ecotourism, and recreational fishing coexist. The system of interest, located in the state of Quintana Roo, Mexico, was subdivided by resource type using a multi-method approach to data collection including surveys, interviews, and records review. A conceptual map was developed that shows how the second-tier variables are integrated through the governance and actors with the biophysical system. The actors involved in lobster fishing achieved a more complex governance system, followed by the ecotourism and recreational fishing; the complexity of the governance was related with the equity level of the actors. The analysis revealed the research gaps to develop management strategies and improve the sustainability of the system. creator: Leopoldo E. Palomo creator: Alvaro Hernández-Flores uri: https://doi.org/10.7717/peerj.7374 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2019 Palomo and Hernández-Flores title: Latitudinal variation in phlorotannin contents from Southwestern Atlantic brown seaweeds link: https://peerj.com/articles/7379 last-modified: 2019-08-14 description: Phlorotannins are primary and/or secondary metabolites found exclusively in brown seaweeds, but their geographic distribution and abundance dynamic are not very well understood. In this study we evaluated the phlorotannin concentrations among and within-species of brown seaweeds in a broad latitudinal context (range of 21°) along the Brazilian coast (Southwestern Atlantic), using the Folin-Ciocalteau colorimetric method. In almost all species (16 out of 17) very low phlorotannin concentrations were found (<2.0%, dry weight for the species), confirming reports of the typical amounts of these chemicals in tropical brown seaweeds, but with significantly distinct values among seven different and probably highly structured populations. In all 17 seaweed species (but a total of 25 populations) analyzed there were significant differences on the amount of phlorotannins in different individuals (t-test, p < 0.01), with coefficients of variation (CV) ranging from 5.2% to 65.3%. The CV, but not the total amount of phlorotannins, was significantly correlated with latitude, and higher values of both these variables were found in brown seaweeds collected at higher latitudes. These results suggest that brown seaweeds from higher latitudes can produce phlorotannins in a wider range of amounts and probably as response to environmental variables or stimuli, compared to low latitude algae. creator: Glaucia Ank creator: Bernardo Antônio Perez da Gama creator: Renato Crespo Pereira uri: https://doi.org/10.7717/peerj.7379 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2019 Ank et al. title: Borneo coral reefs subject to high sediment loads show evidence of resilience to various environmental stressors link: https://peerj.com/articles/7382 last-modified: 2019-08-14 description: For reefs in South East Asia the synergistic effects of rapid land development, insufficient environmental policies and a lack of enforcement has led to poor water quality and compromised coral health from increased sediment and pollution. Those inshore turbid coral reefs, subject to significant sediment inputs, may also inherit some resilience to the effects of thermal stress and coral bleaching. We studied the inshore turbid reefs near Miri, in northwest Borneo through a comprehensive assessment of coral cover and health in addition to quantifying sediment-related parameters. Although Miri’s Reefs had comparatively low coral species diversity, dominated by massive and encrusting forms of Diploastrea, Porites, Montipora, Favites, Dipsastrea and Pachyseris, they were characterized by a healthy cover ranging from 22 to 39%. We found a strong inshore to offshore gradient in hard coral cover, diversity and community composition as a direct result of spatial differences in sediment at distances <10 km. As well as distance to shore, we included other environmental variables like reef depth and sediment trap accumulation and particle size that explained 62.5% of variation in benthic composition among sites. Miri’s reefs showed little evidence of coral disease and relatively low prevalence of compromised health signs including bleaching (6.7%), bioerosion (6.6%), pigmentation response (2.2%), scars (1.1%) and excessive mucus production (0.5%). Tagged colonies of Diploastrea and Pachyseris suffering partial bleaching in 2016 had fully (90–100%) recovered the following year. There were, however, seasonal differences in bioerosion rates, which increased five-fold after the 2017 wet season. Differences in measures of coral physiology, like that of symbiont density and chlorophyll a for Montipora, Pachyseris and Acropora, were not detected among sites. We conclude that Miri’s reefs may be in a temporally stable state given minimal recently dead coral and a limited decline in coral cover over the last two decades. This study provides further evidence that turbid coral reefs exposed to seasonally elevated sediment loads can exhibit relatively high coral cover and be resilient to disease and elevated sea surface temperatures. creator: Nicola Browne creator: Christina Braoun creator: Jennifer McIlwain creator: Ramasamy Nagarajan creator: Jens Zinke uri: https://doi.org/10.7717/peerj.7382 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2019 Browne et al. title: Comprehensive classification of the plant non-specific lipid transfer protein superfamily towards its sequence–structure–function analysis link: https://peerj.com/articles/7504 last-modified: 2019-08-14 description: BackgroundNon-specific Lipid Transfer Proteins (nsLTPs) are widely distributed in the plant kingdom and constitute a superfamily of related proteins. Several hundreds of different nsLTP sequences—and counting—have been characterized so far, but their biological functions remain unclear. It has been clear for years that they present a certain interest for agronomic and nutritional issues. Deciphering their functions means collecting and analyzing a variety of data from gene sequence to protein structure, from cellular localization to the physiological role. As a huge and growing number of new protein sequences are available nowadays, extracting meaningful knowledge from sequence–structure–function relationships calls for the development of new tools and approaches. As nsLTPs show high evolutionary divergence, but a conserved common right handed superhelix structural fold, and as they are involved in a large number of key roles in plant development and defense, they are a stimulating case study for validating such an approach.MethodsIn this study, we comprehensively investigated 797 nsLTP protein sequences, including a phylogenetic analysis on canonical protein sequences, three-dimensional structure modeling and functional annotation using several well-established bioinformatics programs. Additionally, two integrative methodologies using original tools were developed. The first was a new method for the detection of (i) conserved amino acid residues involved in structure stabilization and (ii) residues potentially involved in ligand interaction. The second was a structure–function classification based on the evolutionary trace display method using a new tree visualization interface. We also present a new tool for visualizing phylogenetic trees.ResultsFollowing this new protocol, an updated classification of the nsLTP superfamily was established and a new functional hypothesis for key residues is suggested. Lastly, this work allows a better representation of the diversity of plant nsLTPs in terms of sequence, structure and function. creator: Cécile Fleury creator: Jérôme Gracy creator: Marie-Françoise Gautier creator: Jean-Luc Pons creator: Jean-François Dufayard creator: Gilles Labesse creator: Manuel Ruiz creator: Frédéric de Lamotte uri: https://doi.org/10.7717/peerj.7504 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2019 Fleury et al. 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.