title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=843 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: Trophic niches reflect compositional differences in microbiota among Caribbean sea urchins link: https://peerj.com/articles/12084 last-modified: 2021-08-31 description: Sea urchins play a critical role in marine ecosystems, as they actively participate in maintaining the balance between coral and algae. We performed the first in-depth survey of the microbiota associated with four free-living populations of Caribbean sea urchins: Lytechinus variegatus, Echinometra lucunter, Tripneustes ventricosus, and Diadema antillarum. We compared the influence of the collection site, echinoid species and trophic niche to the composition of the microbiota. This dataset provides a comprehensive overview to date, of the bacterial communities and their ecological relevance associated with sea urchins in their natural environments. A total of sixty-samples, including surrounding reef water and seagrass leaves underwent 16S rRNA gene sequencing (V4 region) and high-quality reads were analyzed with standard bioinformatic approaches. While water and seagrass were dominated by Cyanobacteria such as Prochlorococcus and Rivularia respectively, echinoid gut samples had dominant Bacteroidetes, Proteobacteria and Fusobacteria. Propionigenium was dominant across all species’ guts, revealing a host-associated composition likely responsive to the digestive process of the animals. Beta-diversity analyses showed significant differences in community composition among the three collection sites, animal species, and trophic niches. Alpha diversity was significantly higher among L. variegatus samples compared to the other species. L. variegatus also displayed an increased abundance of Planctomycetes and Cyanobacterial OTUs. The bacterial community of this herbivorous echinoid reflected similarities to the microfilm community found on Thalassia testudinum leaves; a very abundant seagrass and its main food resource. The results of this study elaborate on the microbial ecology of four important Caribbean echinoids, confirming that selection on the microbial community is trophic-niche dependent. creator: Ruber Rodríguez-Barreras creator: Eduardo L. Tosado-Rodríguez creator: Filipa Godoy-Vitorino uri: https://doi.org/10.7717/peerj.12084 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Rodríguez-Barreras et al. title: Genomic comparison of non-photosynthetic plants from the family Balanophoraceae with their photosynthetic relatives link: https://peerj.com/articles/12106 last-modified: 2021-08-31 description: The plant family Balanophoraceae consists entirely of species that have lost the ability to photosynthesize. Instead, they obtain nutrients by parasitizing other plants. Recent studies have revealed that plastid genomes of Balanophoraceae exhibit a number of interesting features, one of the most prominent of those being a highly elevated AT content of nearly 90%. Additionally, the nucleotide substitution rate in the plastid genomes of Balanophoraceae is an order of magnitude greater than that of their photosynthetic relatives without signs of relaxed selection. Currently, there are no definitive explanations for these features. Given these unusual features, we hypothesised that the nuclear genomes of Balanophoraceae may also provide valuable information in regard to understanding the evolution of non-photosynthetic plants. To gain insight into these genomes, in the present study we analysed the transcriptomes of two Balanophoraceae species (Rhopalocnemis phalloides and Balanophora fungosa) and compared them to the transcriptomes of their close photosynthetic relatives (Daenikera sp., Dendropemon caribaeus, and Malania oleifera). Our analysis revealed that the AT content of the nuclear genes of Balanophoraceae did not markedly differ from that of the photosynthetic relatives. The nucleotide substitution rate in the genes of Balanophoraceae is, for an unknown reason, several-fold larger than in the genes of photosynthetic Santalales; however, the negative selection in Balanophoraceae is likely stronger. We observed an extensive loss of photosynthesis-related genes in the Balanophoraceae family members. Additionally, we did not observe transcripts of several genes whose products function in plastid genome repair. This implies their loss or very low expression, which may explain the increased nucleotide substitution rate and AT content of the plastid genomes. creator: Mikhail I. Schelkunov creator: Maxim S. Nuraliev creator: Maria D. Logacheva uri: https://doi.org/10.7717/peerj.12106 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 Schelkunov et al. title: Ciprofloxacin reduces tenocyte viability and proteoglycan synthesis in short-term explant cultures of equine tendon link: https://peerj.com/articles/12003 last-modified: 2021-08-30 description: Fluoroquinolones are an effective, broad-spectrum antibiotic used to treat an array of bacterial infections. However, they are associated with an increased risk of tendinopathy and tendon rupture even after discontinuation of treatment. This condition is known as fluoroquinolone-associated tendinopathy, the underlying mechanisms of which are poorly understood. While many factors may be involved in the pathophysiology of tendinopathies in general, changes in tenocyte metabolism and viability, as well as alteration of proteoglycan metabolism are prominent findings in the scientific literature. This study investigated the effects of ciprofloxacin, a common fluoroquinolone, on cell viability, proteoglycan synthesis, and proteoglycan mRNA expression in equine superficial digital flexor tendon explants after 96 h treatment with between 1–300 µg/mL ciprofloxacin, and again after 8 days discontinuation of treatment. Ciprofloxacin caused significant reductions in cell viability by between 25–33% at all dosages except 10 µg/mL, and viability decreased further after 8 days discontinuation of treatment. Proteoglycan synthesis significantly decreased by approximately 50% in explants treated with 100 µg/mL and 300 µg/mL, however this effect reversed after 8 days in the absence of treatment. No significant mRNA expression changes were observed after the treatment period with the exception of versican which was down-regulated at the highest concentration of ciprofloxacin. After the recovery period, aggrecan, biglycan and versican genes were all significantly downregulated in explants initially treated with 1–100 µg/mL. Results from this study corroborate previously reported findings of reduced cell viability and proteoglycan synthesis in a whole tissue explant model and provide further insight into the mechanisms underlying fluoroquinolone-associated tendinopathy and rupture. This study further demonstrates that certain ciprofloxacin induced cellular changes are not rapidly reversed upon cessation of treatment which is a novel finding in the literature. creator: Stuart James creator: Johannes Schuijers creator: John Daffy creator: Jill Cook creator: Tom Samiric uri: https://doi.org/10.7717/peerj.12003 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 James et al. title: The distribution of benthic amphipod crustaceans in Indonesian seas link: https://peerj.com/articles/12054 last-modified: 2021-08-30 description: Amphipod crustaceans are an essential component of tropical marine biodiversity. However, their distribution and biogeography have not been analysed in one of the world’s largest tropical countries nested in the Coral Triangle, Indonesia. We collected and identified amphipod crustaceans from eight sites in Indonesian waters and combined the results with data from 32 additional sites in the literature. We analysed the geographic distribution of 147 benthic amphipod crustaceans using cluster analysis and the ‘Bioregions Infomaps’ neural network method of biogeographic discrimination. We found five groups of benthic amphipod crustaceans which show relationships with sampling methods, depth, and substrata. Neural network biogeographic analysis indicated there was only one biogeographic region that matched with the global amphipod regions and marine biogeographic realms defined for all marine taxa. There was no support for Wallaces or other lines being marine biogeographic boundaries in the region. Species richness was lower than expected considering the region is within the Coral Triangle. We hypothesise that this low richness might be due to the intense fish predation which may have limited amphipod diversification. The results indicated that habitat rather than biogeography determines amphipod distribution in Indonesia. Therefore, future research needs to sample more habitats, and consider habitat in conservation planning. creator: Tri Arfianti creator: Mark John Costello uri: https://doi.org/10.7717/peerj.12054 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Arfianti and Costello title: Wedge-tailed Shearwater (Ardenna pacifica) nesting success in human-dominated coastal environments link: https://peerj.com/articles/12096 last-modified: 2021-08-30 description: Many seabird populations are declining globally, but successful conservation efforts have led to population expansion of some species into human-dominated landscapes. Thus, there is an increased potential for direct human and seabird interactions for certain species in human-occupied areas, with nest-site characteristics potentially affecting the susceptibility of nests to human disturbance. We assessed the effect of human activity and nest-site characteristics on Wedge-tailed Shearwater (Ardenna pacifica, ʻuaʻu kani) nesting success at two breeding colonies, one with human exposure and one without, located in Kailua, Oʻahu, Hawaiʻi. Human activity was measured by recording the frequency of people who entered a 5 m buffer around each nest. Nests were checked every two to three days to monitor nest success. The effect of human activity and nest-site characteristics on nesting success was determined using a variety of combinations of variables within binomial logistic regression models and AICc model selection. Nest-site characteristics among nests at both sites and human activity at the human-exposed site did not show a significant effect on nesting success. Our results suggest Wedge-tailed Shearwaters may experience some tolerance of human activity immediately around their nests—as long as burrow collapse does not occur. Given the small sample sizes and a single season of data collection, additional studies are needed to better understand the effect of human disturbance on Wedge-tailed Shearwaters. Infrastructure, such as fencing and signage, may be effective at reducing human-caused nest failure and may allow humans and disturbance-tolerant seabird species to coexist in shared coastal environments. creator: Jessica L. Idle creator: Chad J. Wilhite creator: Kristen C. Harmon creator: Brooke Friswold creator: Melissa R. Price uri: https://doi.org/10.7717/peerj.12096 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Idle et al. title: When size matters: the first comprehensive anatomical study of a species of “Condylocardiidae”, an extremely miniaturized bivalve link: https://peerj.com/articles/12108 last-modified: 2021-08-30 description: ‘Miniaturization’ is a widespread phenomenon among the Metazoa. In the molluscan class Bivalvia, records of miniaturization are numerous. Among the Archiheterodonta, Warrana besnardi (Klappenbach, 1963) has attracted attention for its tiny size, which does not exceed 1.5 mm in shell length, and because it belongs to a group with limited anatomical information and often-debated status, the “Condylocardiidae” (which recent molecular studies place deeply nested within the family Carditidae). All species of Warrana Laseron, 1953 are small-bodied, and so miniaturization presumably occurred from a large-bodied ancestor within the Carditidae sensu lato. South American W. besnardi is here studied in detail. Its small size and the enlargement of the anterodorsal region during growth, reflects (and likely led) to infaunal habit, living as a burrowing bivalve that passively feeds on deposit particles entering the pallial cavity anteriorly. Mantle glands, previously reported as a common feature of other archiheterodonts, are missing in W. besnardi, but spongiform tissue in the antero-ventral portion of the mantle lobes presumably represents a blood sinus that might compensate for the great reduction of the ctenidia. Lecithotrophy is reported, with yolky oocytes bearing a thick non-cellular capsule layer; brooding was not observed, and it is here hypothesized that the extreme miniaturization, with the great reduction of ctenidia, is responsible for a shift in the reproductive mode of condylocardiids, contrasting with the commonly reported ovoviviparity of the carditids. creator: Flávio Dias Passos creator: Alan Rodrigo Batistão creator: Rüdiger Bieler uri: https://doi.org/10.7717/peerj.12108 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 Passos et al. title: Anti-clustering in the national SARS-CoV-2 daily infection counts link: https://peerj.com/articles/11856 last-modified: 2021-08-27 description: The noise in daily infection counts of an epidemic should be super-Poissonian due to intrinsic epidemiological and administrative clustering. Here, we use this clustering to classify the official national SARS-CoV-2 daily infection counts and check for infection counts that are unusually anti-clustered. We adopt a one-parameter model of $\phi _i^{\prime}$ϕi′ infections per cluster, dividing any daily count ni into $n_i/ _i^{\prime}$ni/ϕi′ ‘clusters’, for ‘country’ i. We assume that ${n_i}/\phi _i^{\prime}$ni/ϕi′ on a given day j is drawn from a Poisson distribution whose mean is robustly estimated from the four neighbouring days, and calculate the inferred Poisson probability $P_{ij}^{\prime}$Pij′ of the observation. The $P_{ij}^{\prime}$Pij′ values should be uniformly distributed. We find the value $\phi_i$ϕi that minimises the Kolmogorov–Smirnov distance from a uniform distribution. We investigate the (ϕi, Ni) distribution, for total infection count Ni. We consider consecutive count sequences above a threshold of 50 daily infections. We find that most of the daily infection count sequences are inconsistent with a Poissonian model. Most are found to be consistent with the ϕi model. The 28-, 14- and 7-day least noisy sequences for several countries are best modelled as sub-Poissonian, suggesting a distinct epidemiological family. The 28-day least noisy sequence of Algeria has a preferred model that is strongly sub-Poissonian, with $\phi _i^{28} < 0.1$ϕi28<0.1. Tajikistan, Turkey, Russia, Belarus, Albania, United Arab Emirates and Nicaragua have preferred models that are also sub-Poissonian, with $\phi _i^{28} < 0.5$ϕi28<0.5. A statistically significant (Pτ < 0.05) correlation was found between the lack of media freedom in a country, as represented by a high Reporters sans frontieres Press Freedom Index (PFI2020), and the lack of statistical noise in the country’s daily counts. The ϕi model appears to be an effective detector of suspiciously low statistical noise in the national SARS-CoV-2 daily infection counts. creator: Boudewijn F. Roukema uri: https://doi.org/10.7717/peerj.11856 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 Roukema title: Genetic diversity and structure of one of the most endangered freshwater fish species in Mexico: Tlaloc hildebrandi (Miller, 1950) and recognition of its evolutionarily significant units link: https://peerj.com/articles/11952 last-modified: 2021-08-27 description: The endangered Chiapas killifish Tlaloc hildebrandi is an endemic freshwater species that lives in four subbasins of the Grijalva and Usumacinta basins, and one of the most geographically restricted species of the Produndulidae family. The species was originally described as endemic to springs in the high limestone plateau in San Cristóbal de Las Casas in the Río Amarillo subbasin (upper Grijalva basin). However, it was recently recorded in the Jataté and Tzaconejá subbasins in the upper Usumacinta basin, thereby expanding its known distribution range. The discovery of these populations is relevant not only for the conservation of the species but also for a better understanding of its evolutionary history. Currently, the scarce populations of T. hildebrandi, found in only a few localities in the Grijalva and Usumacinta basins, are fragmented and living under unfavorable conditions. Here, we analyzed three mitochondrial (mt-atp8&6 and mt-nd2) and one nuclear (nuc-s7) marker in order to assess the genetic diversity and population structure of T. hildebrandi. We found that, in comparison with other endangered freshwater fish species from Mexico, T. hildebrandi showed a lower level of genetic diversity (mt-nd2: h = 0.469, π = 0.0009; mt-atp8&6: h = 0.398, π = 0.001; and nuc-S7: h = 0.433, π = 0.001). Moreover, the analyzed populations exhibited a strong genetic structure in accordance with their geographic distribution, and can be placed into three genetic clusters: (1) Amarillo plus Chenhaló in the upper Grijalva basin, (2) Jataté, and (3) Tzaconejá, both in the upper Usumacinta basin. On the basis of our results, we propose the recognition of at least three evolutionarily significant units (ESUs) for the species and the urgent implementation of ex situ and in situ conservation and management efforts that consider the genetic background of the species. creator: Rosa G. Beltrán-López creator: Alfonso A. González-Díaz creator: Miriam Soria-Barreto creator: Marco Antonio Garduño-Sánchez creator: Carmela Xochitla-Castrejón creator: Rocío Rodiles-Hernández creator: Claudia Patricia Ornelas-García uri: https://doi.org/10.7717/peerj.11952 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 Beltrán-López et al. title: Low winter precipitation, but not warm autumns and springs, threatens mountain butterflies in middle-high mountains link: https://peerj.com/articles/12021 last-modified: 2021-08-27 description: Low-elevation mountains represent unique model systems to study species endangered by climate warming, such as subalpine and alpine species of butterflies. We aimed to test the effect of climate variables experienced by Erebia butterflies during their development on adult abundances and phenology, targeting the key climate factors determining the population dynamics of mountain insects. We analysed data from a long-term monitoring of adults of two subalpine and alpine butterfly species, Erebia epiphron and E. sudetica (Nymphalidae: Satyrinae) in the Jeseník Mts and Krkonoše Mts (Czech Republic). Our data revealed consistent patterns in their responses to climatic conditions. Lower precipitation (i.e., less snow cover) experienced by overwintering larvae decreases subsequent adult abundances. Conversely, warmer autumns and warmer and drier springs during the active larval phase increase adult abundances and lead to earlier onset and extended duration of the flight season. The population trends of these mountain butterflies are stable or even increasing. On the background of generally increasing temperatures within the mountain ranges, population stability indicates dynamic equilibrium of positive and detrimental consequences of climate warming among different life history stages. These contradictory effects warn against simplistic predictions of climate change consequences on mountain species based only on predicted increases in average temperature. Microclimate variability may facilitate the survival of mountain insect populations, however the availability of suitable habitats will strongly depend on the management of mountain grasslands. creator: Martin Konvicka creator: Tomas Kuras creator: Jana Liparova creator: Vit Slezak creator: Dita Horázná creator: Jan Klečka creator: Irena Kleckova uri: https://doi.org/10.7717/peerj.12021 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 Konvicka et al. title: The stability of soil organic carbon across topographies in a tropical rainforest link: https://peerj.com/articles/12057 last-modified: 2021-08-27 description: Mechanisms of soil organic carbon (SOC) stability are still unclear in forest ecosystems. In order to unveil the influences of topography on the SOC stability, a 60ha dynamic plot of a tropical montane rainforest was selected in Jianfengling, in Hainan Island, China and soil was sampled from 60 quadrats. The chemical fractions of the SOC were detected with 13C CPMAS/NMR and path analyses explore the mechanisms of SOC stability in different topographies. The chemical fractions of the SOC comprised alkyl carbon > O-alkyl carbon > carboxyl carbon > aromatic carbon. The decomposition index (DI) values were greater than 1 in the different topographies, with an average DI value was 1.29, which indicated that the SOC in the study area was stable. Flat and top areas (together named RF) had more favorable nutrients and silt contents compared with steep and slight steep areas (together named RS). The influencing factors of SOC stability varied across the topographies, where SOC, soil moisture (SM) and ammoniacal nitrogen (NH4+-N, AN) were the main influencing factors in the RF, while SM and AN were the main factors in the RS. Greater SOC and AN strengthened the SOC stability, while higher soil moisture lowered SOC stability. The inertia index was higher in the RS than the RF areas, indicating that local topography significantly affects SOC content and SOC stability by changing soil environmental factors. Topography cannot be neglected in considering SOC stability and future C budgets. creator: Yamin Jiang creator: Huai Yang creator: Qiu Yang creator: Wenjie Liu creator: Zhaolei Li creator: Wei Mao creator: Xu Wang creator: Zhenghong Tan uri: https://doi.org/10.7717/peerj.12057 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Jiang et al.