Impact of land reclamation and agricultural water regime on the distribution and conservation status of the endangered Dryophytes suweonensis
Knowledge about the distribution and habitat preferences of a species is critical for its conservation. The Suweon Treefrog (Dryophytes suweonensis) is an endangered species endemic to the Republic of Korea. We conducted surveys from 2014 to 2016 at 890 potentially suitable sites across the entire range of the species in South Korea. We then assessed whether D. suweonensis was found in the current and ancestral predicted ranges, reclaimed and protected areas, and how the presence of agricultural floodwater affected its occurrence. Our results describe a 120 km increase in the southernmost known distribution of the species, and the absence of the species at lower latitudes. We then demonstrate a putative constriction on the species ancestral range due to urban encroachment, and provide evidence for a significant increase in its coastal range due to the colonisation of reclaimed land by the species. In addition, we demonstrate that D. suweonensis is present in rice fields that are flooded with water originating from rivers as opposed to being present in rice fields that are irrigated from underground water. Finally, the non-overlap of protected areas and the occurrence of the species shows that only the edge of a single site where D. suweonensis occurs is legally protected. Based on our results and the literature, we suggest the design of a site fitting all the ecological requirements of the species, and suggest the use of such sites to prevent further erosion in the range of D. suweonensis.
Borzée et al. (2017) Impact of land reclamation and agricultural water regime on the distribution and conservation status of the endangered Dryophytes suweonensis. PeerJ 5:e3872 https://doi.org/10.7717/peerj.3872
Accuracy of microbial community diversity estimated by closed- and open-reference OTUs
Next-generation sequencing of 16S ribosomal RNA is widely used to survey microbial communities. Sequences are typically assigned to Operational Taxonomic Units (OTUs). Closed- and open-reference OTU assignment matches reads to a reference database at 97% identity (closed), then clusters unmatched reads using a de novo method (open). Implementations of these methods in the QIIME package were tested on several mock community datasets with 20 strains using different sequencing technologies and primers. Richness (number of reported OTUs) was often greatly exaggerated, with hundreds or thousands of OTUs generated on Illumina datasets. Between-sample diversity was also found to be highly exaggerated in many cases, with weighted Jaccard distances between identical mock samples often close to one, indicating very low similarity. Non-overlapping hyper-variable regions in 70% of species were assigned to different OTUs. On mock communities with Illumina V4 reads, 56% to 88% of predicted genus names were false positives. Biological inferences obtained using these methods are therefore not reliable.
Edgar (2017) Accuracy of microbial community diversity estimated by closed- and open-reference OTUs. PeerJ 5:e3889 https://doi.org/10.7717/peerj.3889
Exceptional soft tissues preservation in a mummified frog-eating Eocene salamander
Fossils are almost always represented by hard tissues but we present here the exceptional case of a three-dimensionally preserved specimen that was ‘mummified’ (likely between 40 and 34 million years ago) in a terrestrial karstic environment. This fossil is the incomplete body of a salamander, Phosphotriton sigei, whose skeleton and external morphology are well preserved, as revealed by phase-contrast synchrotron X-ray microtomography. In addition, internal structures composed of soft tissues preserved in three dimensions are now identified: a lung, the spinal cord, a lumbosacral plexus, the digestive tract, muscles and urogenital organs that may be cloacal glands. These are among the oldest known cases of three-dimensional preservation of these organs in vertebrates and shed light on the ecology of this salamander. Indeed, the digestive tract contains remains of a frog, which represents the only known case of an extinct salamander that fed on a frog, an extremely rare type of predation in extant salamanders. These new data improve our scarce knowledge on soft tissue anatomy of early urodeles and should prove useful for future biologists and palaeontologists working on urodele evolutionary biology. We also suggest that the presence of bat guano and carcasses represented a close source of phosphorus, favouring preservation of soft tissues. Bone microanatomy indicates that P. sigei was likely amphibious or terrestrial, and was probably not neotenic.
Tissier et al. (2017) Exceptional soft tissues preservation in a mummified frog-eating Eocene salamander. PeerJ 5:e3861 https://doi.org/10.7717/peerj.3861
Alpha-arylphorin is a mitogen in the Heliothis virescens midgut cell secretome upon Cry1Ac intoxication
Insecticidal crystal (Cry) proteins produced by the bacterium Bacillus thuringiensis (Bt) target cells in the midgut epithelium of susceptible larvae. While the mode of action of Cry toxins has been extensively investigated, the midgut response to Cry intoxication and its regulation are not well characterized. In this work, we describe the secreted proteome (secretome) of primary mature midgut cell cultures from Heliothis virescens larvae after exposure to Cry1Ac toxin compared to control buffer treatment. The Cry1Ac-induced secretome caused higher proliferation and differentiation and an overall reduction in total cell mortality over time in primary H. virescens midgut stem cell cultures when compared to treatment with control buffer secretome. Differential proteomics identified four proteins with significant differences in abundance comparing Cry1Ac-treated and control secretomes. The most significant difference detected in the Cry1Ac secretome was an arylphorin subunit alpha protein not detected in the control secretome. Feeding of purified alpha-arylphorin to H. virescens larvae resulted in midgut hyperplasia and significantly reduced susceptibility to Cry1Ac toxin compared to controls. These data identify alpha-arylphorin as a protein with a new putative role in the midgut regeneration process in response to Cry1Ac intoxication and possibly pathogen/abiotic stress, identifying alpha-arylphorin as a potential gene to target with insecticidal gene silencing for pest control.
Castagnola et al. (2017) Alpha-arylphorin is a mitogen in the Heliothis virescens midgut cell secretome upon Cry1Ac intoxication. PeerJ 5:e3886 https://doi.org/10.7717/peerj.3886
Perch, Perca fluviatilis show a directional preference for, but do not increase attacks toward, prey in response to water-borne cortisol
In freshwater environments, chemosensory cues play an important role in predator-prey interactions. Prey use a variety of chemosensory cues to detect and avoid predators. However, whether predators use the chemical cues released by disturbed or stressed prey has received less attention. Here we tested the hypothesis that the disturbance cue cortisol, in conjunction with visual cues of prey, elevates predatory behavior. We presented predators (perch, Perca fluviatilis) with three chemosensory choice tests and recorded their location, orientation, and aggressive behavior. We compared the responses of predators when provided with (i) visual cues of prey only (two adjacent tanks containing sticklebacks); (ii) visual and natural chemical cues of prey vs. visual cues only; and (iii) visual cues of prey with cortisol vs. visual cues only. Perch spent a significantly higher proportion of time in proximity to prey, and orientated toward prey more, when presented with a cortisol stimulus plus visual cues, relative to presentations of visual and natural chemical cues of prey, or visual cues of prey only. There was a trend that perch directed a higher proportion of predatory behaviors (number of lunges) toward sticklebacks when presented with a cortisol stimulus plus visual cues, relative to the other chemosensory conditions. But they did not show a significant increase in total predatory behavior in response to cortisol. Therefore, it is not clear whether water-borne cortisol, in conjunction with visual cues of prey, affects predatory behavior. Our results provide evidence that cortisol could be a source of public information about prey state and/or disturbance, but further work is required to confirm this.
Henderson et al. (2017) Perch, Perca fluviatilis show a directional preference for, but do not increase attacks toward, prey in response to water-borne cortisol. PeerJ 5:e3883 https://doi.org/10.7717/peerj.3883
Segmentation and classification of colon glands with deep convolutional neural networks and total variation regularization
Segmentation of histopathology sections is a necessary preprocessing step for digital pathology. Due to the large variability of biological tissue, machine learning techniques have shown superior performance over conventional image processing methods. Here we present our deep neural network-based approach for segmentation and classification of glands in tissue of benign and malignant colorectal cancer, which was developed to participate in the GlaS@MICCAI2015 colon gland segmentation challenge. We use two distinct deep convolutional neural networks (CNN) for pixel-wise classification of Hematoxylin-Eosin stained images. While the first classifier separates glands from background, the second classifier identifies gland-separating structures. In a subsequent step, a figure-ground segmentation based on weighted total variation produces the final segmentation result by regularizing the CNN predictions. We present both quantitative and qualitative segmentation results on the recently released and publicly available Warwick-QU colon adenocarcinoma dataset associated with the GlaS@MICCAI2015 challenge and compare our approach to the simultaneously developed other approaches that participated in the same challenge. On two test sets, we demonstrate our segmentation performance and show that we achieve a tissue classification accuracy of 98% and 95%, making use of the inherent capability of our system to distinguish between benign and malignant tissue. Our results show that deep learning approaches can yield highly accurate and reproducible results for biomedical image analysis, with the potential to significantly improve the quality and speed of medical diagnoses.
Kainz et al. (2017) Segmentation and classification of colon glands with deep convolutional neural networks and total variation regularization. PeerJ 5:e3874 https://doi.org/10.7717/peerj.3874
Development and validation of near-infrared spectroscopy for the prediction of forage quality parameters in Lolium multiflorum
Italian ryegrass (Lolium multiflorum) is an important cool-season, annual forage crop for the grassland rotation system in Southern China. The primary aim of breeding programs is always to seek to improve forage quality in the animal productivity system; however, it is time- and labor-consuming when analyzed excessive large number of samples. The main objectives of this study were to construct near-infrared reflectance spectroscopy (NIRS) models to predict the forage chemistry quality of Italian ryegrass including the concentrations of crude protein (CP), acid detergent fiber (ADF), neutral detergent fiber (NDF), and water soluble carbohydrate (WSC). The results showed that a broader range of CP, NDF, ADF and WSC contents (%DM) were obtained (4.45–30.60, 21.29–60.47, 11.66–36.17 and 3.95–51.52, respectively) from the samples selected for developing NIRS models. In addition, the critical wavelengths identified in this study to construct optimal NIRS models were located in 4,247–6,102 and 4,247–5,450 cm-1 for CP and NDF content, and both wavelengths 5,446–6,102 and 4,247–4,602 cm-1 could for ADF and WSC. Finally, the optimal models were developed based on the laboratory data and the spectral information by partial least squares (PLS) regression, with relatively high coefficients of determination (R2CV, CP = 0.99, NDF = 0.94, ADF = 0.92, WSC = 0.88), ratio of prediction to devitation (RPD, CP = 8.58, NDF = 4.25, ADF = 3.64, WSC = 3.10). The further statistics of prediction errors relative to laboratory (PRL) and the range error ratio (RER) give excellent assessments of the models with the PRL ratios lower than 2 and the RER values greater than 10. The NIRS models were validated using a completely independent set of samples and have coefficients of determination (R2V, CP = 0.99, NDF = 0.91, ADF = 0.95, WSC = 0.91) and ratio of prediction to deviation (RPD, CP = 9.37, NDF = 3.44, ADF = 4.40, WSC = 3.39). The result suggested that routine screening for forage quality parameters with large numbers of samples is available with the NIRS model in Italian ryegrass breeding programs, as well as facilitating graziers to monitor the forage development stage for improving grazing efficiency.
Yang et al. (2017) Development and validation of near-infrared spectroscopy for the prediction of forage quality parameters in Lolium multiflorum. PeerJ 5:e3867 https://doi.org/10.7717/peerj.3867
Assessment on the coupling effects of drip irrigation and organic fertilization based on entropy weight coefficient model
Water and fertilizer are two important factors influencing crop growth, development and yield formation. To investigate their combined effects on the soil-plant system, and to find out the optimal water and organic fertilizer coupling strategy for tomato (Solanum lycopersicum L), an experiment was carried out from May to October in 2016 in the south of China. The experiment consisted of three drip irrigation quotas (150, 180, 210 m3/ha) and three organic fertilizer application amounts (2,800, 3,600, 4,400 kg/ha). A water-fertilizer treatment (abbreviated as CK) that is in line with local practice was used for comparison. The tomato marketable yield, sugar/acid ratio (SAR) and irrigation water use efficiency (IWUE), as well as the soil salinity and available nutrient concentrations were measured. The results showed that the marketable yield was highly significantly (p < 0.01) affected by irrigation or fertilization. The SAR of tomato were significantly (p < 0.05) affected by irrigation or/and fertilization. The fertilization had an highly significant (p < 0.01) effect on the concentrations of soil nutrients (N, P, K), while the coupling effect of irrigation and fertilization was not pronounced. According to the multi-index analysis and the computed result by the entropy weight coefficient model, a 180 m3/ha irrigation quota in combination with 4,400 kg/ha organic fertilizer application amount was the optimal water-fertilizer coupling strategy which owned the most satisfactory comprehensive benefits. The marketable yield, SAR and IWUE under this optimal strategy were 122.4 t/ha, 9.2, 32.4 kg/m3, respectively, and by 28.0%, 29.6% and 28.1% higher compared to that under CK.
Zhong et al. (2017) Assessment on the coupling effects of drip irrigation and organic fertilization based on entropy weight coefficient model. PeerJ 5:e3855 https://doi.org/10.7717/peerj.3855
A preliminary survey of zoantharian endosymbionts shows high genetic variation over small geographic scales on Okinawa-jima Island, Japan
Symbiotic dinoflagellates (genus Symbiodinium) shape the responses of their host reef organisms to environmental variability and climate change. To date, the biogeography of Symbiodinium has been investigated primarily through phylogenetic analyses of the ribosomal internal transcribed spacer 2 region. Although the marker can approximate species-level diversity, recent work has demonstrated that faster-evolving genes can resolve otherwise hidden species and population lineages, and that this diversity is often distributed over much finer geographical and environmental scales than previously recognized. Here, we use the noncoding region of the chloroplast psbA gene (psbAncr) to examine genetic diversity among clade C Symbiodinium associating with the common reef zoantharian Palythoa tuberculosa on Okinawa-jima Island, Japan. We identify four closely related Symbiodinium psbAncr lineages including one common generalist and two potential specialists that appear to be associated with particular microhabitats. The sea surface temperature differences that distinguish these habitats are smaller than those usually investigated, suggesting that future biogeographic surveys of Symbiodinium should incorporate fine scale environmental information as well as fine scale molecular data to accurately determine species diversity and their distributions.
Noda et al. (2017) A preliminary survey of zoantharian endosymbionts shows high genetic variation over small geographic scales on Okinawa-jima Island, Japan. PeerJ 5:e3740 https://doi.org/10.7717/peerj.3740
Framework for community functioning: synthesis of stress gradient and resource partitioning concepts
To understand how communities function and generate abundance, I develop a framework integrating elements from the stress gradient and resource partitioning concepts. The framework suggests that guild abundance depends on environmental and spatial factors but also on inter-guild interactions (competitor or facilitator richness), which can alter the fundamental niche of constituent species in negative (competition) or positive direction (facilitation). Consequently, the environmental and spatial mechanisms driving guild abundance would differ across guilds and interaction modes. Using continental data on stream diatoms and physico-chemistry, the roles of these mechanisms were tested under three interaction modes—shared preference, distinct preference, and facilitative, whereby pairs of guilds exhibited, respectively, a dominance-tolerance tradeoff along a eutrophication gradient, specialization along a pH gradient, or a donor-recipient relationship along a nitrogen gradient. Representative of the shared preference mode were the motile (dominant) and low profile (tolerant) guilds, of the distinct preference mode—the acidophilous and alkaliphilous (low profile) guilds, and of the facilitative mode—nitrogen fixers (donors) and motile species (recipients). In each mode, the influences of environment, space (latitude and longitude), and competitor or facilitator richness on guild density were assessed by variance partitioning. Pure environment constrained most strongly the density of the dominant, the acidophilous, and the recipient guild in the shared preference, distinct preference, and facilitative mode, respectively, while spatial effects were important only for the low profile guild. Higher competitor richness was associated with lower density of the tolerant guild in the shared preference mode, both guilds in the distinct preference mode, and the donor guild in the facilitative mode. Conversely, recipient density in the facilitative mode increased with donor richness in stressful nitrogen-poor environments. Thus, diatom guild abundance patterns were determined primarily by biotic and/or environmental impacts and, with the exception of the low profile guild, were insensitive to spatial effects. This framework identifies major sources of variability in diatom guild abundance with implications for the understanding of biodiversity-ecosystem functioning.
Passy (2017) Framework for community functioning: synthesis of stress gradient and resource partitioning concepts. PeerJ 5:e3885 https://doi.org/10.7717/peerj.3885