title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=1131 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: Meiofaunal communities and nematode diversity characterizing the Secca delle Fumose shallow vent area (Gulf of Naples, Italy) link: https://peerj.com/articles/9058 last-modified: 2020-05-29 description: Hydrothermal venting is rather prevalent in many marine areas around the world, and marine shallow vents are relatively abundant in the Mediterranean Sea, especially around Italy. However, investigations focusing on the characterization of meiofaunal organisms inhabiting shallow vent sediments are still scant compared to that on macrofauna. In the present study, we investigated the meiobenthic assemblages and nematode diversity inhabiting the Secca delle Fumose (SdF), a shallow water vent area located in the Gulf of Naples (Italy). In this area, characterized by a rapid change in the environmental conditions on a relative small spatial scale (i.e., 100 m), we selected four sampling sites: one diffusive emission site (H); one geyser site (G) and two inactive sites (CN, CS). Total meiofauna abundance did not vary significantly between active and inactive sites and between surface and deeper sediment layers due to a high inter-replicate variability, suggesting a pronounced spatial-scale patchiness in distribution of meiofauna. Nematofauna at site H presented the typical features of deep-sea vents with low structural and functional diversity, high biomass and dominance of few genera (i.e., Oncholaimus; Daptonema) while from site G we reported diversity values comparable to that of the inactive sites. We hypothesized that site G presented a condition of “intermediate disturbance” that could maintain a high nematode diversity. Environmental features such as sediment temperature, pH, total organic carbon and interstitial waters ions were found to be key factors influencing patterns of meiofauna and nematofauna assemblages at SdF. Even though the general theory is that nematodes inhabiting shallow vent areas include a subset of species that live in background sediments, this was not the case for SdF vent area. Due to a marked change in nematode composition between all sites and to the presence of many exclusive species, every single investigated site was characterized by a distinct nematofauna reflecting the high spatial heterogeneity of SdF. creator: Elisa Baldrighi creator: Daniela Zeppilli creator: Luca Appolloni creator: Luigia Donnarumma creator: Elena Chianese creator: Giovanni Fulvio Russo creator: Roberto Sandulli uri: https://doi.org/10.7717/peerj.9058 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Baldrighi et al. title: Mountain goat survival and mortality during a period of increased puma abundance in the Black Hills, South Dakota link: https://peerj.com/articles/9143 last-modified: 2020-05-29 description: We investigated survival and cause-specific mortality for a mountain goat (Oreamnos americanus) population during a period when the puma (Puma concolor) population was growing in the Black Hills, South Dakota, 2006–2018. We obtained survival data from 47 adult goats (n = 33 females, n = 14 males). Annual survival varied from 0.538 (95% CI [0.285–0.773]) to 1.00 (95% CI [1.00–1.00]) and puma predation was the primary cause-specific mortality factor over a 12-year period. Cumulative hectares of mountain pine beetle (Dendroctonus ponderosae) disturbance was a covariate of importance (wi = 0.972; β = 0.580, 95% CI [0.302–0.859]) influencing survival. To our knowledge, this is the first account of puma being the primary mortality factor of mountain goats over a long-term study. The Black Hills system is unique because we could examine the expanded realized niche of puma in the absence of other large carnivores and their influence on mountain goats. We hypothesize that puma were being sustained at higher densities due to alternate prey sources (e.g., white-tailed deer; Odocoileous virginianus) and this small population of mountain goats was susceptible to predation by one or several specialized puma in the Black Hills. However, we also hypothesize a changing landscape with increased tree mortality due to insect infestation provided conditions for better predator detection by goats and increased survival. Alternatively, open canopy conditions may have increased understory forage production potentially increasing mountain goat survival but we did not evaluate this relationship. Survival and mortality rates of mountain goats should continue to be monitored as this small population may be highly susceptible to population declines due to slow growth rates. creator: Chadwick P. Lehman creator: Eric M. Rominger creator: Brady Y. Neiles uri: https://doi.org/10.7717/peerj.9143 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Lehman et al. title: Proliferating activity in a bryozoan lophophore link: https://peerj.com/articles/9179 last-modified: 2020-05-29 description: Bryozoans are small benthic colonial animals; their colonies consist of zooids which are composed of a cystid and polypide. According to morphological and molecular data, three classes of bryozoans are recognized: Phylactolaemata, Gymnolaemata and Stenolaemata. Bryozoans are active suspension feeders and their feeding apparatus, the lophophore, is fringed with a single row of ciliated tentacles. In gymnolaemates, the lophophore is bell-shaped and its tentacles may be equal in length (equitentacled lophophores) or some tentacles may be longer than others (obliquely truncated lophophores). In encrusting colonies, polypides with obliquely truncated lophophores usually border specific sites of excurrent water outlets (colony periphery and chimneys) where depleted water has to be removed. It is known that during colony astogeny, colony-wide water currents rearrange: new chimneys are formed and/or location of the chimneys within a given colony changes with time. Such rearrangement requires remodeling of the lophophore shape and lengthening of some tentacles in polypides surrounding water outlets. However, proliferating activity has not been described for bryozoans. Here, we compared the distribution of S-phase and mitotic cells in young and adult polypides in three species of Gymnolaemata. We tested the hypothesis that tentacle growth/elongation is intercalary and cell proliferation takes place somewhere at the lophophore base because such pattern does not interfere with the feeding process. We also present a detailed description of ultrastructure of two parts of the lophophore base: the oral region and ciliated pits, and uncover the possible function of the latter. The presence of stem cells within the ciliated pits and the oral region of polypides provide evidence that both sites participate in tentacle elongation. This confirms the suggested hypothesis about intercalary tentacle growth which provides a potential to alter a lophophore shape in adult polypides according to rearrangement of colony wide water currents during colony astogeny. For the first time deuterosome-like structures were revealed during kinetosome biogenesis in the prospective multiciliated epithelial cells in invertebrates. Tentacle regeneration experiments in Electra pilosa demonstrated that among all epidermal cell types, only non-ciliated cells at the abfrontal tentacle surface are responsible for wound healing. Ciliated cells on the frontal and lateral tentacle surfaces are specialized and unable to proliferate, not even under wound healing. Tentacle regeneration in E. pilosa is very slow and similar to the morphallaxis type. We suggest that damaged tentacles recover their length by a mechanism similar to normal growth, powered by proliferation of cells both within ciliated pits and the oral region. creator: Natalia Shunatova creator: Ilya Borisenko uri: https://doi.org/10.7717/peerj.9179 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Shunatova and Borisenko title: Future sea-level rise drives rocky intertidal habitat loss and benthic community change link: https://peerj.com/articles/9186 last-modified: 2020-05-29 description: The impacts of sea-level rise (SLR) are likely to be the greatest for ecosystems that exist at the land-sea interface, where small changes in sea-level could result in drastic changes in habitat availability. Rocky intertidal ecosystems possess a number of characteristics which make them highly vulnerable to changes in sea-level, yet our understanding of potential community-scale responses to future SLR scenarios is limited. Combining remote-sensing with in-situ large-area imaging, we quantified habitat extent and characterized the biological community at two rocky intertidal study locations in California, USA. We then used a model-based approach to estimate how a range of SLR scenarios would affect total habitat area, areal extent of dominant benthic space occupiers, and numerical abundance of invertebrates. Our results suggest that SLR will reduce total available rocky intertidal habitat area at our study locations, leading to an overall decrease in areal extent of dominant benthic space occupiers, and a reduction in invertebrate abundances. As large-scale environmental changes, such as SLR, accelerate in the next century, more extensive spatially explicit monitoring at ecologically relevant scales will be needed to visualize and quantify their impacts to biological systems. creator: Nikolas J. Kaplanis creator: Clinton B. Edwards creator: Yoan Eynaud creator: Jennifer E. Smith uri: https://doi.org/10.7717/peerj.9186 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Kaplanis et al. title: Recent advances in the contribution of noncoding RNAs to cisplatin resistance in cervical cancer link: https://peerj.com/articles/9234 last-modified: 2020-05-29 description: Cervical cancer (CC) remains a major disease burden on the female population worldwide. Chemotherapy with cisplatin (cis-diamminedichloroplatinum (II); CDDP) and related drugs are the main treatment option for CC; however, their efficacy is limited by the development of drug resistance. Noncoding RNAs (ncRNAs) have been found to play critical roles in numerous physiological and pathological cellular processes, including drug resistance of cancer cells. In this review, we describe some of the ncRNAs, including miRNAs, lncRNAs and circRNAs, that are involved in the sensitivity/resistance of CC to CDDP-based chemotherapy and discuss their mechanisms of action. We also describe some ncRNAs that could be therapeutic targets to improve the sensitivity of CC to CDDP-based chemotherapy. creator: Xin Wen creator: Shui Liu creator: Jiyao Sheng creator: Manhua Cui uri: https://doi.org/10.7717/peerj.9234 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Wen et al. title: Decreased inhibitory control after partial sleep deprivation in individuals reporting binge eating: preliminary findings link: https://peerj.com/articles/9252 last-modified: 2020-05-29 description: BackgroundPoor executive functions are associated with dysregulated eating and greater caloric intake in healthy samples. In parallel, findings suggested that sleep deprivation impairs executive functions.MethodsWe investigated whether partial sleep deprivation impairs executive functions in individuals reporting binge eating (BE, N = 14) and healthy controls (C, N = 13). Switch cost and backward inhibition were measured using the Task Switching Paradigm after a habitual night of sleep and after a night of partial sleep deprivation.ResultsResults showed a Night by Group interaction on the backward inhibition. The two groups differed in the habitual night, evidencing higher inhibitory control in BE compared to C. Additionally, after partial sleep deprivation, compared to the habitual night, backward inhibition decreased in BE group. This preliminary study was the first to explore the impact of sleep deprivation on executive functions in participants reporting binge eating and healthy controls, thus highlighting their potential role in influencing eating behavior. creator: Silvia Cerolini creator: Andrea Ballesio creator: Fabio Ferlazzo creator: Fabio Lucidi creator: Caterina Lombardo uri: https://doi.org/10.7717/peerj.9252 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Cerolini et al. title: Uncovering the species diversity of subterranean rodents at the end of the World: three new species of Patagonian tuco-tucos (Rodentia, Hystricomorpha, Ctenomys) link: https://peerj.com/articles/9259 last-modified: 2020-05-29 description: Ctenomys Blainville 1826 is one of the most diverse genera of South American caviomorph rodents. Currently, six species of this genus are reported from Patagonia, south of 42°S. In this contribution, we assessed the taxonomic status of several populations from eastern and central Chubut province, northern Patagonia. Based on phylogenetic analyses of DNA sequences, morphology assessment (qualitative and quantitative), and previously published karyological data, we describe three new species of this genus, one formed by two subspecies, endemic to northern Patagonia. In addition, we include C. coyhaiquensis Kelt and Gallardo 1994 into the synonymy of C. sericeus J.A. Allen 1903. Finally, we discussed the need for additional integrative approaches, including field collection of specimens, to better understand the diversity of this highly speciose rodent genus. creator: Pablo Teta creator: Guillermo D’Elía uri: https://doi.org/10.7717/peerj.9259 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Teta et al. title: Isotopic biomonitoring of anthropic carbon emissions in a megalopolis link: https://peerj.com/articles/9283 last-modified: 2020-05-29 description: Atmospheric pollution has become a serious threat for human health and the environment. However, the deployment, operation and maintenance of monitoring networks can represent a high cost for local governments. In certain locations, the use of naturally occurring plants for monitoring pollution can be a useful supplement of existing monitoring networks, and even provide information when other types of monitoring are lacking. In this work, we (i) determined the tissue carbon content and the δ13C values for the epiphytic CAM bromeliad Tillandsia recurvata and the relationship of both parameters with the existing CO concentrations in the Valley of Mexico basin and (ii) mapped the spatial distribution of such elemental and isotopic composition for this plant within the basin, in order to assess its potential as an atmospheric biomonitor of carbon monoxide, a pollutant with important repercussions on public health. The CO concentrations in the basin ranged from 0.41 ppm at rural locations to 0.81 ppm at urban sites. The carbon content of T. recurvata, which averaged 42.9 ± 0.34% (dry weight), was not influenced by the surrounding CO concentration. In contrast, the δ13C depended on the sites where the plants were collected. For example, the values were −13.2‰ in rural areas and as low as –17.5‰ in an urban site. Indeed, the isotopic values had a positive linear relationship with the atmospheric CO concentrations. Given the close relationship observed between the isotopic composition of T. recurvata with the CO concentrations in the Valley of Mexico, the δ13C values can be useful for the detection of atmospheric carbonaceous emissions. creator: Edison A. Díaz-Álvarez creator: Erick de la Barrera uri: https://doi.org/10.7717/peerj.9283 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Díaz-Álvarez and de la Barrera title: Farming by soil in Europe: status and outlook of cropping systems under different pedoclimatic conditions link: https://peerj.com/articles/8984 last-modified: 2020-05-28 description: BackgroundDespite of the importance of soils in agronomy, to date no comprehensive assessment of cropping in Europe has been performed from the viewpoint of the soil variability and its relationship to cropping patterns. In order to fill this knowledge gap, we studied the cropping patterns in different soils of European climate zones with regards to the shares of their crop types in a comparative manner. The study highlights the main features of farming by soil in Europe. Farming by soil in this context means the consideration of soil characteristics when selecting crop types and cropping patterns.MethodsWe first assessed the dissimilarity between the cropping compositions of different pedoclimatic zones in Europe. Next, we assessed the differences of crop distribution in the climate zones by soil types and main crop types by analyzing the degree of association of crops to soil types. A detailed country scale assessment was performed using crops-specific soil productivity maps and land use survey data from Hungary.ResultsResults suggest that, in general, farmers consciously take pedoclimatic condition of farming into account when selecting their cropping patterns. In other words, farming by soil is a common practice in the different climatic regions of Europe. However, we have strong reasons to believe that soil suitability-based cropping is not practiced to its full potential over the continent. For example, the findings of our European assessment suggest that production areas of legumes are not always optimized for the local pedoclimatic conditions in some zones. These findings also underline that economic drivers are decisive, when farmers adopt their cropping (eg. oil crops on Albeluvsiols in Europe). Win-win situations of economic considerations and soil suitability based management are observed in all pedoclimatic zones of Europe. The country analysis shows that cropping is progressively practiced on more suitable areas, depending also the crop tolerance to variable pedoclimatic conditions In conclusion, we can assume that pedoclimatic conditions of cropping are respected in most of Europe and farmers crops according to edaphic conditions whenever economic considerations do not override the ecological concerns of farming. creator: Gergely Tóth creator: Tamás Kismányoky creator: Piroska Kassai creator: Tamás Hermann creator: Oihane Fernandez-Ugalde creator: Brigitta Szabó uri: https://doi.org/10.7717/peerj.8984 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Tóth et al. title: Characterization of biofilm production in different strains of Acinetobacter baumannii and the effects of chemical compounds on biofilm formation link: https://peerj.com/articles/9020 last-modified: 2020-05-28 description: Acinetobacter baumannii, an important emerging pathogen of nosocomial infections, is known for its ability to form biofilms. Biofilm formation increases the survival rate of A. baumannii on dry surfaces and may contribute to its persistence in the hospital environment, which increases the probability of nosocomial infections and outbreaks. This study was undertaken to characterize the biofilm production of different strains of A. baumannii and the effects of chemical compounds, especially antibiotics, on biofilm formation. In this study, no statistically significant relationship was observed between the ability to form a biofilm and the antimicrobial susceptibility of the A. baumannii clinical isolates. Biofilm formation caused by A. baumannii ATCC 17978 after gene knockout of two-component regulatory system gene baeR, efflux pump genes emrA/emrB and outer membrane coding gene ompA revealed that all mutant strains had less biofilm formation than the wild-type strain, which was further supported by the images from scanning electron microscopy and confocal laser scanning microscopy. The addition of amikacin, colistin, LL-37 or tannic acid decreased the biofilm formation ability of A. baumannii. In contrast, the addition of lower subinhibitory concentration tigecycline increased the biofilm formation ability of A. baumannii. Minimum biofilm eradication concentrations of amikacin, imipenem, colistin, and tigecycline were increased obviously for both wild type and multidrug resistant clinical strain A. baumannii VGH2. In conclusion, the biofilm formation ability of A. baumannii varied in different strains, involved many genes and could be influenced by many chemical compounds. creator: Ming-Feng Lin creator: Yun-You Lin creator: Chung-Yu Lan uri: https://doi.org/10.7717/peerj.9020 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Lin et al.