title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=1485 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: Improving remote estimation of winter crops gross ecosystem production by inclusion of leaf area index in a spectral model link: https://peerj.com/articles/5613 last-modified: 2018-09-21 description: The hysteresis of the seasonal relationships between vegetation indices (VIs) and gross ecosystem production (GEP) results in differences between these relationships during vegetative and reproductive phases of plant development cycle and may limit their applicability for estimation of croplands productivity over the entire season. To mitigate this problem and to increase the accuracy of remote sensing-based models for GEP estimation we developed a simple empirical model where greenness-related VIs are multiplied by the leaf area index (LAI). The product of this multiplication has the same seasonality as GEP, and specifically for vegetative periods of winter crops, it allowed the accuracy of GEP estimations to increase and resulted in a significant reduction of the hysteresis of VIs vs. GEP. Our objective was to test the multiyear relationships between VIs and daily GEP in order to develop more general models maintaining reliable performance when applied to years characterized by different climatic conditions. The general model parametrized with NDVI and LAI product allowed to estimate daily GEP of winter and spring crops with an error smaller than 14%, and the rate of GEP over- (for spring barley) or underestimation (for winter crops and potato) was smaller than 25%. The proposed approach may increase the accuracy of crop productivity estimation when greenness VIs are saturating early in the growing season. creator: Radosław Juszczak creator: Bogna Uździcka creator: Marcin Stróżecki creator: Karolina Sakowska uri: https://doi.org/10.7717/peerj.5613 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Juszczak et al. title: Genomic organization, gene expression and activity profile of Marinobacter hydrocarbonoclasticus denitrification enzymes link: https://peerj.com/articles/5603 last-modified: 2018-09-21 description: BackgroundDenitrification is one of the main pathways of the N-cycle, during which nitrate is converted to dinitrogen gas, in four consecutive reactions that are each catalyzed by a different metalloenzyme. One of the intermediate metabolites is nitrous oxide, which has a global warming impact greater then carbon dioxide and which atmospheric concentration has been increasing in the last years. The four denitrification enzymes have been isolated and biochemically characterized from Marinobacter hydrocarbonoclasticus in our lab.MethodsBioinformatic analysis of the M. hydrocarbonoclasticus genome to identify the genes involved in the denitrification pathway. The relative gene expression of the gene encoding the catalytic subunits of those enzymes was analyzed during the growth under microoxic conditions. The consumption of nitrate and nitrite, and the reduction of nitric oxide and nitrous oxide by whole-cells was monitored during anoxic and microoxic growth in the presence of 10 mM sodium nitrate at pH 7.5.ResultsThe bioinformatic analysis shows that genes encoding the enzymes and accessory factors required for each step of the denitrification pathway are clustered together. An unusual feature is the co-existence of genes encoding a q- and a c-type nitric oxide reductase, with only the latter being transcribed at similar levels as the ones encoding the catalytic subunits of the other denitrifying enzymes, when cells are grown in the presence of nitrate under microoxic conditions. Using either a batch- or a closed system, nitrate is completely consumed in the beginning of the growth, with transient formation of nitrite, and whole-cells can reduce nitric oxide and nitrous oxide from mid-exponential phase until being collected (time-point 50 h).DiscussionM. hydrocarbonoclasticus cells can reduce nitric and nitrous oxide in vivo, indicating that the four denitrification steps are active. Gene expression profile together with promoter regions analysis indicates the involvement of a cascade regulatory mechanism triggered by FNR-type in response to low oxygen tension, with nitric oxide and nitrate as secondary effectors, through DNR and NarXL, respectively. This global characterization of the denitrification pathway of a strict marine bacterium, contributes to the understanding of the N-cycle and nitrous oxide release in marine environments. creator: Cíntia Carreira creator: Olga Mestre creator: Rute F. Nunes creator: Isabel Moura creator: Sofia R. Pauleta uri: https://doi.org/10.7717/peerj.5603 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Carreira et al. title: The genetic status of the Hungarian brown trout populations: exploration of a blind spot on the European map of Salmo trutta studies link: https://peerj.com/articles/5152 last-modified: 2018-09-21 description: BackgroundAnalyses of the control region sequences of European brown trout populations’ mitrochondrial DNA have revealed five main evolutionary lineages (Atlantic, Danubian, Mediterranean, Adriatic, Marble) mostly relating to the main water basins; however, the hybridization between lineages were increasingly reported. Due to the hydrogeography of Hungary, wild populations should theoretically belong to the Danubian lineage, however, this has not been verified by genetic studies.MethodsIn our study multiple molecular marker sets (mitochondrial sequence, microsatellites, PCR-RFLP of nuclear markers and sex marker) were used to investigate the genetic composition and population genetics of the brown trout populations in two broodstocks, six wild streams in Hungary and one Serbian population.ResultsThe admixture of Atlantic and Danubian lineages in these populations, except the Serbian population with pure Danubian origin, was observed by control region sequences of mitochondrial DNA and PCR-RFLP markers in the nuclear genome, and one unpublished Danubian haplotype was found in Hungarian populations. A sex-specific marker revealed equal gender ratio in broodstocks and Kemence stream, whereas in other wild streams the proportion of female individuals were less than 50%. Structure and principal component analyses based on the alleles of microsatellite loci also revealed overlapping populations, however the populations were still significantly different from each other and were mostly in Hardy-Weinberg equilibrium.DiscussionStocking and migration can have a significant genetic impact on trout populations of wild streams, however there are no guidelines or common practices for stocking of small streams in Hungary, thus the genetic background of these populations should be considered when developing conservation actions. creator: Ágnes Ősz creator: Ákos Horváth creator: György Hoitsy creator: Dóra Kánainé Sipos creator: Szilvia Keszte creator: Anna Júlia Sáfrány creator: Saša Marić creator: Csaba Palkó creator: Balázs Tóth creator: Béla Urbányi creator: Balázs Kovács uri: https://doi.org/10.7717/peerj.5152 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Ősz et al. title: Characterization of retinal regeneration in adult zebrafish following multiple rounds of phototoxic lesion link: https://peerj.com/articles/5646 last-modified: 2018-09-20 description: Müller glia in the zebrafish retina respond to retinal damage by re-entering the cell cycle, which generates large numbers of retinal progenitors that ultimately replace the lost neurons. In this study we compared the regenerative outcomes of adult zebrafish exposed to one round of phototoxic treatment with adult zebrafish exposed to six consecutive rounds of phototoxic treatment. We observed that Müller glia continued to re-enter the cell cycle to produce clusters of retinal progenitors in zebrafish exposed to multiple rounds of phototoxic light. Some abnormalities were noted, however. First, we found that retinas exposed to multiple rounds of damage exhibited a greater loss of photoreceptors at 36 hours of light damage than retinas that were exposed to their first round of light damage. In addition, we found that Müller glia appeared to have an increase in the acute gliotic response in retinas exposed to multiple rounds of light treatment. This was evidenced by cellular hypertrophy, changes in GFAP cellular localization, and transient increases in stat3 and gfap expression. Finally, following the sixth round of phototoxic lesion, we observed a significant increase in mis-localized HuC/D-positive amacrine and ganglion cells in the inner plexiform layer and outer retina, and a decreased number of regenerated blue cone photoreceptors. These data add to recent findings that retinal regeneration in adult zebrafish occurs concomitant with Müller glia reactivity and can result in the generation of aberrant neurons. These data are also the first to demonstrate that Müller glia appear to modify their phenotype in response to multiple rounds of phototoxic lesion, exhibiting an increase in acute gliosis while maintaining a remarkable capacity for long-term regeneration of photoreceptors. creator: Alexandra H. Ranski creator: Ashley C. Kramer creator: Gregory W. Morgan creator: Jennifer L. Perez creator: Ryan Thummel uri: https://doi.org/10.7717/peerj.5646 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Ranski et al. title: Preliminary analysis of New Zealand scampi (Metanephrops challengeri) diet using metabarcoding link: https://peerj.com/articles/5641 last-modified: 2018-09-20 description: Deep sea lobsters are highly valued for seafood and provide the basis of important commercial fisheries in many parts of the world. Despite their economic significance, relatively little is known about their natural diets. Microscopic analyses of foregut content in some species have suffered from low taxonomic resolution, with many of the dietary items difficult to reliably identify as their tissue is easily digested. DNA metabarcoding has the potential to provide greater taxonomic resolution of the diet of the New Zealand scampi (Metanephrops challengeri) through the identification of gut contents, but a number of methodological concerns need to be overcome first to ensure optimum DNA metabarcoding results. In this study, a range of methodological parameters were tested to determine the optimum protocols for DNA metabarcoding, and provide a first view of M. challengeri diet. Several PCR protocols were tested, using two universal primer pairs targeting the 18S rRNA and COI genes, on DNA extracted from both frozen and ethanol preserved samples for both foregut and hindgut digesta. The selection of appropriate DNA polymerases, buffers and methods for reducing PCR inhibitors (including the use of BSA) were found to be critical. Amplification from frozen or ethanol preserved gut contents appeared similarly dependable. The COI gene was found to be more effective than 18S rRNA gene for identifying large eukaryotic taxa from the digesta; however, it was less successfully amplified. The 18S rRNA gene was more easily amplified, but identified mostly smaller marine organisms such as plankton and parasites. This preliminary analysis of the diet of M. challengeri identified a range of species (13,541 reads identified as diet), which included the ghost shark (Hydrolagus novaezealandiae), silver warehou (Seriolella punctata), tall sea pen (Funiculina quadrangularis) and the salp (Ihlea racovitzai), suggesting that they have a varied diet, with a high reliance on scavenging a diverse range of pelagic and benthic species from the seafloor. creator: Aimee L. van der Reis creator: Olivier Laroche creator: Andrew G. Jeffs creator: Shane D. Lavery uri: https://doi.org/10.7717/peerj.5641 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 van der Reis et al. title: An examination of the Devonian fishes of Michigan link: https://peerj.com/articles/5636 last-modified: 2018-09-20 description: We surveyed the taxa, ecosystems, and localities of the Devonian fishes of Michigan to provide a framework for renewed study, to learn about the diversity and number of these fishes, and to investigate their connection to other North American faunas. Nineteen genera of fishes have been found in the Middle and Late Devonian deposits of Michigan, of which thirteen are ‘placoderms’ represented by material ranging from articulated head shields to ichthyoliths. As expected from the marine nature of these deposits, ‘placoderms’ are overwhelmingly arthrodire in nature, but two genera of ptyctodonts have been reported along with less common petalichthyid material. The remaining fish fauna consists of fin-spines attributed to ‘acanthodians’, two genera of potential crown chondrichthyans, an isolated dipnoan, and onychodont teeth/jaw material. There was an apparent drop in fish diversity and fossil abundance between Middle and Late Devonian sediments. This pattern may be attributed to a paucity of Late Devonian sites, along with a relative lack of recent collection efforts at existing outcrops. It may also be due to a shift towards open water pelagic environments at Late Devonian localities, as opposed to the nearshore reef fauna preserved in the more numerous Middle Devonian localities. The Middle Devonian vertebrate fauna in Michigan shows strong connections with same-age assemblages from Ohio and New York. Finally, we document the presence of partially articulated vertebrate remains associated with benthic invertebrates, an uncommon occurrence in Devonian strata outside of North America. We anticipate this new survey will guide future field work efforts in an undersampled yet highly accessible region that preserves an abundance of fishes from a critical interval in marine vertebrate evolution. creator: Jack Stack creator: Lauren Sallan uri: https://doi.org/10.7717/peerj.5636 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Stack and Sallan title: Gαq and Phospholipase Cβ signaling regulate nociceptor sensitivity in Drosophila melanogaster larvae link: https://peerj.com/articles/5632 last-modified: 2018-09-20 description: Drosophila melanogaster larvae detect noxious thermal and mechanical stimuli in their environment using polymodal nociceptor neurons whose dendrites tile the larval body wall. Activation of these nociceptors by potentially tissue-damaging stimuli elicits a stereotyped escape locomotion response. The cellular and molecular mechanisms that regulate nociceptor function are increasingly well understood, but gaps remain in our knowledge of the broad mechanisms that control nociceptor sensitivity. In this study, we use cell-specific knockdown and overexpression to show that nociceptor sensitivity to noxious thermal and mechanical stimuli is correlated with levels of Gαq and phospholipase Cβ signaling. Genetic manipulation of these signaling mechanisms does not result in changes in nociceptor morphology, suggesting that changes in nociceptor function do not arise from changes in nociceptor development, but instead from changes in nociceptor activity. These results demonstrate roles for Gαq and phospholipase Cβ signaling in facilitating the basal sensitivity of the larval nociceptors to noxious thermal and mechanical stimuli and suggest future studies to investigate how these signaling mechanisms may participate in neuromodulation of sensory function. creator: Joshua A. Herman creator: Adam B. Willits creator: Andrew Bellemer uri: https://doi.org/10.7717/peerj.5632 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Herman et al. title: Gap analysis and implications for seasonal management on a local scale link: https://peerj.com/articles/5622 last-modified: 2018-09-20 description: BackgroundIdentifying biodiversity hotspots on a local scale, using multiple data sources, and ecological niche modeling, has the potential to contribute to more effective nature reserve management.MethodsIn this study, we used infrared-triggered camera trapping, field surveys, and interviews to create a dataset on the distribution of species (mammals and birds) in Hebei Wulingshan Nature Reserve (Hebei Province, China).ResultsWe identified 101 species (14 orders, 38 families), 64 of which (2,142 effective records) were selected for environmental niche modeling. All results were reclassified into three groups: “priority areas” (areas including the potential distributions of over 80% of species), “important areas” (those with 50% of species), and “normal areas” (all other areas). Our results show that priority areas (1.31–1.82 km2) and important areas (7.73–21.44 km2) for conservation were mainly covered by the core and experimental zones of the reserve; additionally, a kilometer-wide margin around the outside of the nature reserve seems to be important to maintaining biodiversity.DiscussionWe close by suggesting some actions for enhancing conservation of biodiversity in the reserve, including monitoring, strengthen law enforcements, introducing popular science, and co-operating with local people. creator: Li Yang creator: Baofeng Zhang creator: Xinrui Wang creator: Yueheng Ren creator: Jinlin Chen creator: Chao Zhang creator: Yongpeng Xia creator: Yuankun Li creator: Jianguo Sun creator: Jiangang Guo creator: Weijia Wang creator: XiaoFeng Luan uri: https://doi.org/10.7717/peerj.5622 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2018 Yang et al. title: Effect of floods on the δ13C values in plant leaves: a study of willows in Northeastern Siberia link: https://peerj.com/articles/5374 last-modified: 2018-09-20 description: Although stable carbon isotopic composition (δ13C) of plants has been widely used to indicate different water regimes in terrestrial ecosystems over the past four decades, the changes in the plant δ13C value under waterlogging have not been sufficiently clarified. With the enhanced global warming in recent years, the increasing frequency and severity of river floods in Arctic regions lead to more waterlogging on willows that are widely distributed in river lowland. To investigate the δ13C changes in plants under different water conditions (including waterlogging), we measured the δ13C values in the leaves of willows with three species, Salix boganidensis, S. glauca, and S. pulchra, and also monitored changes in plant physiology, under several major flooding conditions in Northeastern Siberia. The foliar δ13C values of willows varied, ranging from −31.6 to −25.7‰ under the different hydrological status, which can be explained by: (i) under normal conditions, the foliar δ13C values decrease from dry (far from a river) to wet (along a river bank) areas; (ii) the δ13C values increase in frequently waterlogged areas owing to stomatal closure; and (iii) after prolonged flooding periods, the δ13C values again decrease, probably owing to the effects of not only the closure of stomata but also the reduction of foliar photosynthetic ability under long period of waterlogging. Based on these results, we predict that plant δ13C values are strongly influenced by plant physiological responses to diverse hydrological conditions, particularly the long periods of flooding, as occurs in Arctic regions. creator: Rong Fan creator: Tomoki Morozumi creator: Trofim C. Maximov creator: Atsuko Sugimoto uri: https://doi.org/10.7717/peerj.5374 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2018 Fan et al. title: Spatial and temporal variations of aridity shape dung beetle assemblages towards the Sahara desert link: https://peerj.com/articles/5210 last-modified: 2018-09-20 description: BackgroundAssemblage responses to environmental gradients are key to understand the general principles behind the assembly and functioning of communities. The spatially and temporally uneven distribution of water availability in drylands creates strong aridity gradients. While the effects of spatial variations of aridity are relatively well known, the influence of the highly-unpredictable seasonal and inter-annual precipitations on dryland communities has been seldom addressed.AimsHere, we study the seasonal and inter-annual responses of dung beetle (Coleoptera, Scarabaeidae) communities to the variations of water availability along a semiarid region of the Mediterranean.MethodsWe surveyed a 400 km linear transect along a strong aridity gradient from the Mediterranean coast to the Sahara (Eastern Morocco), during four sampling campaigns: two in the wet season and two in the dry season. We measured species richness, abundance and evenness. Variations in community composition between sites, seasons and years were assessed through beta diversity partitioning of dissimiliarity metrics based on species occurrences and abundances. The effects of climate, soil, vegetation and dung availability were evaluated using Spearman-rank correlations, general linear regressions and partial least-squares generalized linear regressions for community structure, and non-metric multi-dimensional scaling, Permutational Analysis of Variance (PERMANOVA) and distance-based RDA variation partitioning for compositional variations.ResultsDung beetle abundance and species richness showed large seasonal variations, but remained relatively similar between years. Indeed, aridity and its interaction with season and year were the strongest correlates of variations in species richness and composition. Increasing aridity resulted in decreasing species richness and an ordered replacement of species, namely the substitution of the Mediterranean fauna by desert assemblages dominated by saprophagous and generalist species both in space towards the Sahara and in the dry season.DiscussionOur study shows that aridity determines composition in dung beetle communities, filtering species both in space and time. Besides the expected decrease in species richness, such environmental filtering promotes a shift towards generalist and saprophagous species in arid conditions, probably related to changes in resource quality along the transect and through the year. Our results highlight the importance of considering the effects of the highly-unpredictable seasonal and inter-annual variations in precipitation when studying dryland communities. creator: Indradatta deCastro-Arrazola creator: Joaquín Hortal creator: Marco Moretti creator: Francisco Sánchez-Piñero uri: https://doi.org/10.7717/peerj.5210 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2018 deCastro-Arrazola et al.