title: PeerJ
description:  Articles published in PeerJ
link: https://peerj.com/articles/index.rss3?journal=peerj&page=1508
creator: info@peerj.com PeerJ
errorsTo: info@peerj.com PeerJ
language: en

title: Can non-destructive DNA extraction of bulk invertebrate samples be used for metabarcoding?
link: https://peerj.com/articles/4980
last-modified: 2018-06-13
description: BackgroundHigh throughput DNA sequencing of bulk invertebrate samples or metabarcoding is becoming increasingly used to provide profiles of biological communities for environmental monitoring. As metabarcoding becomes more widely applied, new reference DNA barcodes linked to individual specimens identified by taxonomists are needed. This can be achieved through using DNA extraction methods that are not only suitable for metabarcoding but also for building reference DNA barcode libraries.MethodsIn this study, we test the suitability of a rapid non-destructive DNA extraction method for metabarcoding of freshwater invertebrate samples.ResultsThis method resulted in detection of taxa from many taxonomic groups, comparable to results obtained with two other tissue-based extraction methods. Most taxa could also be successfully used for subsequent individual-based DNA barcoding and taxonomic identification. The method was successfully applied to field-collected invertebrate samples stored for taxonomic studies in 70% ethanol at room temperature, a commonly used storage method for freshwater samples.DiscussionWith further refinement and testing, non-destructive extraction has the potential to rapidly characterise species biodiversity in invertebrate samples, while preserving specimens for taxonomic investigation.
creator: Melissa E. Carew
creator: Rhys A. Coleman
creator: Ary A. Hoffmann
uri: https://doi.org/10.7717/peerj.4980
license: http://creativecommons.org/licenses/by/4.0/
rights: ©2018 Carew et al.

title: Dynamic succession of substrate-associated bacterial composition and function during Ganoderma lucidum growth
link: https://peerj.com/articles/4975
last-modified: 2018-06-13
description: BackgroundGanoderma lucidum, a valuable medicinal fungus, is widely distributed in China. It grows alongside with a complex microbial ecosystem in the substrate. As sequencing technology advances, it is possible to reveal the composition and functions of substrate-associated bacterial communities.MethodsWe analyzed the bacterial community dynamics in the substrate during the four typical growth stages of G. lucidum using next-generation sequencing.ResultsThe physicochemical properties of the substrate (e.g. acidity, moisture, total nitrogen, total phosphorus and total potassium) changed between different growth stages. A total of 598,771 sequences from 12 samples were obtained and assigned to 22 bacterial phyla. Proteobacteria and Firmicutes were the dominant phyla. Bacterial community composition and diversity significantly differed between the elongation stage and the other three growth stages. LEfSe analysis revealed a large number of bacterial taxa (e.g. Bacteroidetes, Acidobacteria and Nitrospirae) with significantly higher abundance at the elongation stage. Functional pathway prediction uncovered significant abundance changes of a number of bacterial functional pathways between the elongation stage and other growth stages. At the elongation stage, the abundance of the environmental information processing pathway (mainly membrane transport) decreased, whereas that of the metabolism-related pathways increased.DiscussionThe changes in bacterial community composition, diversity and predicted functions were most likely related to the changes in the moisture and nutrient conditions in the substrate with the growth of G. lucidum, particularly at the elongation stage. Our findings shed light on the G. lucidum-bacteria-substrate relationships, which should facilitate the industrial cultivation of G. lucidum.
creator: Bo Zhang
creator: Lijuan Yan
creator: Qiang Li
creator: Jie Zou
creator: Hao Tan
creator: Wei Tan
creator: Weihong Peng
creator: Xiaolin Li
creator: Xiaoping Zhang
uri: https://doi.org/10.7717/peerj.4975
license: http://creativecommons.org/licenses/by/4.0/
rights: ©2018 Zhang et al.

title: Multi-omic profiling to assess the effect of iron starvation in Streptococcus pneumoniae TIGR4
link: https://peerj.com/articles/4966
last-modified: 2018-06-13
description: We applied multi-omics approaches (transcriptomics, proteomics and metabolomics) to study the effect of iron starvation on the Gram-positive human pathogen Streptococcus pneumoniae to elucidate global changes in the bacterium in a condition similar to what can be found in the host during an infectious episode. We treated the reference strain TIGR4 with the iron chelator deferoxamine mesylate. DNA microarrays revealed changes in the expression of operons involved in multiple biological processes, with a prevalence of genes coding for ion binding proteins. We also studied the changes in protein abundance by 2-DE followed by MALDI-TOF/TOF analysis of total cell extracts and secretome fractions. The main proteomic changes were found in proteins related to the primary and amino sugar metabolism, especially in enzymes with divalent cations as cofactors. Finally, the metabolomic analysis of intracellular metabolites showed altered levels of amino sugars involved in the cell wall peptidoglycan metabolism. This work shows the utility of multi-perspective studies that can provide complementary results for the comprehension of how a given condition can influence global physiological changes in microorganisms.
creator: Irene Jiménez-Munguía
creator: Mónica Calderón-Santiago
creator: Antonio Rodríguez-Franco
creator: Feliciano Priego-Capote
creator: Manuel J. Rodríguez-Ortega
uri: https://doi.org/10.7717/peerj.4966
license: http://creativecommons.org/licenses/by/4.0/
rights: ©2018 Jiménez-Munguía et al.

title: Long-term experimental in situ farming of Crambe crambe (Demospongiae: Poecilosclerida)
link: https://peerj.com/articles/4964
last-modified: 2018-06-13
description: BackgroundThe marine sponge Crambe crambe was chosen as an experimental model of sustainable shallow-water mariculture in the Sardinian Sea (Western Mediterranean) to provide biomass with high potential in applied research.MethodsExplants were cultured in four long-term experiments (19 and 31 months at ca. 2.5 m depth), to determine the suitability of new culture techniques by testing substrata and seeding time (season), and monitoring survival and growth. Explants were excised and grown in an experimental plant close to the wild donor sponge population. Percentage growth rate (GR%) was measured in terms of surface cover area, and explant survival was monitored in situ by means of a digital photo camera.ResultsExplant survival was high throughout the trial, ranging from 78.57% to 92.85% on travertine tiles and from 50% to 71.42% on oyster shells. A few instances of sponge regression were observed. Explant cover area correlated positively with season on two substrata, i.e., tiles and shells. The surface cover area and GR% of explants were measured in the starting phase and monitored up to the end of the trial. High GR% values were observed both on tiles (>21%) and on oyster shells (>15%).DiscussionThe data on the behaviour and life-style of cultured fragments, together with an increase >2,400% in cover area, demonstrate that in situ aquaculture is a viable and sustainable method for the shallow-water biomass supply of Crambe crambe.
creator: Andrea Padiglia
creator: Fabio D. Ledda
creator: Bachisio M. Padedda
creator: Roberto Pronzato
creator: Renata Manconi
uri: https://doi.org/10.7717/peerj.4964
license: http://creativecommons.org/licenses/by/4.0/
rights: ©2018 Padiglia et al.

title: Suitable oasis scales under a government plan in the Kaidu-Konqi River Basin of northwest arid region, China
link: https://peerj.com/articles/4943
last-modified: 2018-06-13
description: The Yanqi Basin and the Konqi River Basin of the Kaidu-Konqi River Basin were chosen as the study sites in this paper in order to investigate suitable scales of natural and artificial oases with a specified water resource and water quantity planned by the local government. Combined with remote-sensing images from 2013, water resources in 2013, 2025 and 2035, and weather and socioeconomic data, suitable scales of oases were analyzed. The results showed that: (1) The total available water quantities in the Yanqi Basin and the Konqi River Basin without river base flow, and the input of water into Bosten Lake and Tarim River, over high-, normal and low-flow periods, in 2025 and 2035, were 19.04 × 108 m3, 10.52 × 108 m3, 4.95 × 108 m3, 9.95 × 108 m3 and 9.95 × 108 m3, as well as 21.77 × 108 m3, 13.95 × 108 m3, 10.11 × 108 m3, 12.50 × 108 m3, and 9.74 × 108 m3. (2) The water demand of the natural oasis in the Yanqi Basin and the Konqi River Basin was 2.59 × 108 m3, and 4.59 × 108 m3, respectively. (3) The total water consumption of the artificial oasis in 2013, 2025, and 2035 were 10.51 × 108 m3, 10.99 × 108 m3 and 10.74 × 108 m3 in the Yanqi Basin, respectively, and 18.59 × 108 m3, 14.07 × 108 m3 and 13.30 × 108m3 in the Kongqi River Basin, respectively. (4) Under government planning, the optimal area in 2025 and 2035 should be 5,100.06 km2 and 5,096.15 km2 in the Yanqi Basin oases, and 6,008.53 km2 and 4,691.36 km2 in the Konqi River Basin oases, respectively, under the different inflow variations, and 4,972.71 km2 and 4,969.22 km2 in the Yanqi Basin oases, and 5,975.17 km2 and 4,665.67 km2 in the Kongqi River Basin oases, respectively, under the appropriate proportion. (5) The artificial oases in these basins should be greatly decreased in the future due to limited water resources.
creator: Aihong Fu
creator: Weihong Li
creator: Yaning Chen
creator: Yuting Liu
uri: https://doi.org/10.7717/peerj.4943
license: http://creativecommons.org/licenses/by/4.0/
rights: ©2018 Fu et al.

title: First use of molecular evidence to match sexes in the Monstrilloida (Crustacea: Copepoda), and taxonomic implications of the newly recognized and described, partly Maemonstrilla-like females of Monstrillopsis longilobata Lee, Kim & Chang, 2016
link: https://peerj.com/articles/4938
last-modified: 2018-06-13
description: Two forms of the monstrilloid copepod, one represented by males, the other by females, were dominant among the monstrilloids collected while sampling zooplankton with a light trap in southern coastal waters of Korea. Morphological examination revealed that the males are conspecific with the previously reported and rather specialized Korean species Monstrillopsis longilobata Lee, Kim & Chang, 2016, hitherto known only from males that have extremely long genital lappets. The females also show several diagnostic features of Monstrillopsis, such as prominent eyes, bilobed fifth legs with the inner lobe unarmed and reduced, and four urosomal somites. In addition, though, these females are extraordinary among all Monstrilloida in that their ovigerous spines are directed ventrally, not posteriorly as in most species or anteriorly as in those assigned to Maemonstrilla. Genetic divergence analyses based on partial mitochondrial cytochrome c oxidase subunit I, complete Internal Transcribed Spacer 1 (ITS1)–5.8S–ITS2, and partial 28S rRNA revealed little or no genetic divergence between the present males and females, thus demonstrating that they are mutually conspecific. The present report (1) provides the first morphological description of female M. longilobata with the proposal of a revised nomenclature for antennular setal armament; (2) presents the molecular evidence for conspecificity of the males and females; and (3) lists several morphological characteristics that are sexually dimorphic in this species, and thus likely also in other monstrilloids. Matters bearing on the validity of the genera Haemocera, Monstrillopsis, and Maemonstrilla are discussed.
creator: Donggu Jeon
creator: Donghyun Lim
creator: Wonchoel Lee
creator: Ho Young Soh
uri: https://doi.org/10.7717/peerj.4938
license: http://creativecommons.org/licenses/by/4.0/
rights: © 2018 Jeon et al.

title: Genetic differentiation, local adaptation and phenotypic plasticity in fragmented populations of a rare forest herb
link: https://peerj.com/articles/4929
last-modified: 2018-06-13
description: BackgroundDue to habitat loss and fragmentation, numerous forest species are subject to severe population decline. Investigating variation in genetic diversity, phenotypic plasticity and local adaptation should be a prerequisite for implementing conservation actions. This study aimed to explore these aspects in ten fragmented populations of Physospermum cornubiense in view of translocation measures across its Italian range.MethodsFor each population we collected environmental data on landscape (habitat size, quality and fragmentation) and local conditions (slope, presence of alien species, incidence of the herbivorous insect Metcalfa pruinosa and soil parameters). We measured vegetative and reproductive traits in the field and analysed the genetic population structure using ISSR markers (STRUCTURE and AMOVA). We then estimated the neutral (FST) and quantitative (PST) genetic differentiation of populations.ResultsThe populations exhibited moderate phenotypic variation. Population size (range: 16–655 individuals), number of flowering adults (range: 3–420 individuals) and inflorescence size (range: 5.0–8.4 cm) were positively related to Mg soil content. Populations’ gene diversity was moderate (Nei-H = 0.071–0.1316); STRUCTURE analysis identified five different clusters and three main geographic groups: upper, lower, and Apennine/Western Po plain. Fragmentation did not have an influence on the local adaptation of populations, which for all measured traits showed PST < FST, indicating convergent selection.DiscussionThe variation of phenotypic traits across sites was attributed to plastic response rather than local adaptation. Plant translocation from suitable source populations to endangered ones should particularly take into account provenance according to identified genetic clusters and specific soil factors.
creator: Rodolfo Gentili
creator: Aldo Solari
creator: Martin Diekmann
creator: Cecilia Duprè
creator: Gianna Serafina Monti
creator: Stefano Armiraglio
creator: Silvia Assini
creator: Sandra Citterio
uri: https://doi.org/10.7717/peerj.4929
license: http://creativecommons.org/licenses/by/4.0/
rights: ©2018 Gentili et al.

title: Tackling critical parameters in metazoan meta-barcoding experiments: a preliminary study based on coxI DNA barcode
link: https://peerj.com/articles/4845
last-modified: 2018-06-13
description: Nowadays DNA meta-barcoding is a powerful instrument capable of quickly discovering the biodiversity of an environmental sample by integrating the DNA barcoding approach with High Throughput Sequencing technologies. It mainly consists of the parallel reading of informative genomic fragment/s able to discriminate living entities. Although this approach has been widely studied, it still needs optimization in some necessary steps requested in its advanced accomplishment. A fundamental element concerns the standardization of bioinformatic analyses pipelines. The aim of the present study was to underline a number of critical parameters of laboratory material preparation and taxonomic assignment pipelines in DNA meta-barcoding experiments using the cytochrome oxidase subunit-I (coxI) barcode region, known as a suitable molecular marker for animal species identification. We compared nine taxonomic assignment pipelines, including a custom in-house method, based on Hidden Markov Models. Moreover, we evaluated the potential influence of universal primers amplification bias in qPCR, as well as the correlation between GC content with taxonomic assignment results. The pipelines were tested on a community of known terrestrial invertebrates collected by pitfall traps from a chestnut forest in Italy. Although the present analysis was not exhaustive and needs additional investigation, our results suggest some potential improvements in laboratory material preparation and the introduction of additional parameters in taxonomic assignment pipelines. These include the correct setup of OTU clustering threshold, the calibration of GC content affecting sequencing quality and taxonomic classification, as well as the evaluation of PCR primers amplification bias on the final biodiversity pattern. Thus, careful attention and further validation/optimization of the above-mentioned variables would be required in a DNA meta-barcoding experimental routine.
creator: Bachir Balech
creator: Anna Sandionigi
creator: Caterina Manzari
creator: Emiliano Trucchi
creator: Apollonia Tullo
creator: Flavio Licciulli
creator: Giorgio Grillo
creator: Elisabetta Sbisà
creator: Stefano De Felici
creator: Cecilia Saccone
creator: Anna Maria D’Erchia
creator: Donatella Cesaroni
creator: Maurizio Casiraghi
creator: Saverio Vicario
uri: https://doi.org/10.7717/peerj.4845
license: http://creativecommons.org/licenses/by/4.0/
rights: ©2018 Balech et al.

title: Surface electromyographic analysis of differential effects in kettlebell carries for the serratus anterior muscles
link: https://peerj.com/articles/5044
last-modified: 2018-06-12
description: The purpose of this study was to examine differences in the Electromyography (EMG) amplitude of the serratus anterior between 45° kettlebell carries and 90° kettlebell carries. Thirty-three men aged roughly between 19 and 23 and who were either college or professional baseball pitchers were chosen and randomly assigned to either perform the 45° kettlebell carry followed by the 90° kettlebell carry (n = 17) or the 90° kettlebell carry followed by the 45° kettlebell carry (n = 16). Each pitcher was instructed in the proper usage of the exercise and assigned a short break between the two carries. Changes in EMG amplitude were examined after proper band-pass filtering, normalization, and moving average-smoothing of the raw EMG signal. Differences of the EMG amplitude mean frequencies were examined between each subject’s individual carries and the clumped groups of all 45° and 90° carries. Among each individual comparison, eight pitchers had “large” Effect Size differences between the EMG amplitudes of their two carries, with seven of them signaling the 45° carry as the larger value. In addition, when examining the grouped mean differences of the EMG amplitudes, we found the 45° carries to be significantly higher (p-value of 0.018).
creator: Alex Caravan
creator: John O. Scheffey
creator: Sam J. Briend
creator: Kyle J. Boddy
uri: https://doi.org/10.7717/peerj.5044
license: http://creativecommons.org/licenses/by/4.0/
rights: © 2018 Caravan et al.

title: Taxonomy annotation and guide tree errors in 16S rRNA databases
link: https://peerj.com/articles/5030
last-modified: 2018-06-12
description: Sequencing of the 16S ribosomal RNA (rRNA) gene is widely used to survey microbial communities. Specialized 16S rRNA databases have been developed to support this approach including Greengenes, RDP and SILVA. Most taxonomy annotations in these databases are predictions from sequence rather than authoritative assignments based on studies of type strains or isolates. In this work, I investigated the taxonomy annotations and guide trees provided by these databases. Using a blinded test, I estimated that the annotation error rate of the RDP database is ∼10%. The branching orders of the Greengenes and SILVA guide trees were found to disagree at comparable rates with each other and with taxonomy annotations according to the training set (authoritative reference) provided by RDP, indicating that the trees have comparable quality. Pervasive conflicts between tree branching order and type strain taxonomies strongly suggest that the guide trees are unreliable guides to phylogeny. I found 249,490 identical sequences with conflicting annotations in SILVA v128 and Greengenes v13.5 at ranks up to phylum (7,804 conflicts), indicating that the annotation error rate in these databases is ∼17%.
creator: Robert Edgar
uri: https://doi.org/10.7717/peerj.5030
license: http://creativecommons.org/licenses/by/4.0/
rights: © 2018 Edgar