Coral-algal interactions at Weizhou Island in the northern South China Sea: variations by taxa and the exacerbating impact of sediments trapped in turf algae
Competitive interactions between corals and benthic algae are increasingly frequent on degrading coral reefs, but the processes and mechanisms surrounding the interactions, as well as the exacerbating effects of sediments trapped in turf algae, are poorly described. We surveyed the frequency, proportion, and outcomes of interactions between benthic algae (turf algae and macroalgae) and 631 corals (genera: Porites, Favites, Favia, Platygyra, and Pavona) on a degenerating reef in the northern South China Sea, with a specific focus on the negative effects of algal contact on corals. Our data indicated that turf algae were the main algal competitors for each surveyed coral genus and the proportion of algal contact along the coral edges varied significantly among the coral genera and the algal types. The proportions of algal wins between corals and turf algae or macroalgae differed significantly among coral genera. Compared to macroalgae, turf algae consistently yielded more algal wins and fewer coral wins on all coral genera. Amongst the coral genera, Porites was the most easily damaged by algal competition. The proportions of turf algal wins on the coral genera increased 1.1–1.9 times in the presence of sediments. Furthermore, the proportions of algal wins on massive and encrusting corals significantly increased with the combination of sediments and turf algae as the algal type. However, the variation in proportions of algal wins between massive and encrusting corals disappeared as sediments became trapped in turf algae. Sediments bound within turf algae further induced damage to corals and reduced the competitive advantage of the different coral growth forms in their competitive interactions with adjacent turf algae.
Liao et al. (2019) Coral-algal interactions at Weizhou Island in the northern South China Sea: variations by taxa and the exacerbating impact of sediments trapped in turf algae. PeerJ 7:e6590 https://doi.org/10.7717/peerj.6590
Assessing alignment-based taxonomic classification of ancient microbial DNA
The field of palaeomicrobiology—the study of ancient microorganisms—is rapidly growing due to recent methodological and technological advancements. It is now possible to obtain vast quantities of DNA data from ancient specimens in a high-throughput manner and use this information to investigate the dynamics and evolution of past microbial communities. However, we still know very little about how the characteristics of ancient DNA influence our ability to accurately assign microbial taxonomies (i.e. identify species) within ancient metagenomic samples. Here, we use both simulated and published metagenomic data sets to investigate how ancient DNA characteristics affect alignment-based taxonomic classification. We find that nucleotide-to-nucleotide, rather than nucleotide-to-protein, alignments are preferable when assigning taxonomies to short DNA fragment lengths routinely identified within ancient specimens (<60 bp). We determine that deamination (a form of ancient DNA damage) and random sequence substitutions corresponding to ∼100,000 years of genomic divergence minimally impact alignment-based classification. We also test four different reference databases and find that database choice can significantly bias the results of alignment-based taxonomic classification in ancient metagenomic studies. Finally, we perform a reanalysis of previously published ancient dental calculus data, increasing the number of microbial DNA sequences assigned taxonomically by an average of 64.2-fold and identifying microbial species previously unidentified in the original study. Overall, this study enhances our understanding of how ancient DNA characteristics influence alignment-based taxonomic classification of ancient microorganisms and provides recommendations for future palaeomicrobiological studies.
Eisenhofer et al. (2019) Assessing alignment-based taxonomic classification of ancient microbial DNA. PeerJ 7:e6594 https://doi.org/10.7717/peerj.6594
Microgeographic variation in body condition of three Mexican garter snakes in central Mexico
Background Geographic variation in body size and condition can reveal differential local adaptation to resource availability or climatic factors. Body size and condition are related to fitness in garter snakes (Thamnophis), thus good body condition may increase survival, fecundity in females, and mating success in males. Phylogenetically related species in sympatry are predicted to exhibit similar body condition when they experience similar environmental conditions. We focused on interspecific and geographical variation in body size and condition in three sympatric Mexican garter snakes from the highlands of Central Mexico. Methods We assessed SVL, mass, and body condition (obtained from Major axis linear regression of ln-transformed body mass on ln-transformed SVL) in adults and juveniles of both sexes of Thamnophis eques, T. melanogaster, and T. scalaris sampled at different locations and ranges from 3–11 years over a 20-year period. Results We provide a heterogeneous pattern of sexual and ontogenic reproductive status variations of body size and condition among local populations. Each garter snake species shows locations with good and poor body condition; juvenile snakes show similar body condition between populations, adults show varying body condition between populations, and adults also show sex differences in body condition. We discuss variations in body condition as possibly related to the snakes’ life cycle differences.
Valencia-Flores et al. (2019) Microgeographic variation in body condition of three Mexican garter snakes in central Mexico. PeerJ 7:e6601 https://doi.org/10.7717/peerj.6601
Seroprevalence and risk factors of Toxoplasma gondii infection in children with leukemia in Shandong Province, Eastern China: a case—control prospective study
Limited information is available concerning the epidemiology of Toxoplasma gondii infection in children with leukemia in Eastern China. Therefore, a case-control study was conducted to estimate the seroprevalence of toxoplasmosis in this patient group and to identify risk factors and possible routes of infection. Serum samples were collected from 339 children with leukemia and 339 age matched health control subjects in Qingdao from September 2014 to March 2018. Enzyme linked immunoassays were used to screen anti- T. gondii IgG and anti- T. gondii IgM antibodies. Forty-eight (14.2%) children with leukemia and 31 (9.1%) control subjects were positive for anti-T. gondii IgG antibodies (P < 0.05), while 13 (3.8%) patients and 14 (4.1%) controls were positive for anti-T. gondii IgM antibodies (P = 0.84). Multivariate analysis showed exposure to soil and a history of blood transfusion were risk factors for T. gondii infection. Compared with IgG, patients with a history of blood transfusion were more likely to present anti- T. gondii IgM (P = 0.003). Moreover, patients with chronic lymphocytic leukemia and acute lymphocytic leukemia had higher T. gondii seroprevalence in comparison to control subjects (P = 0.002 and P = 0.016, respectively). The results indicated that the seroprevalence of T. gondii infection in children with leukemia is higher than that of healthy children in Eastern China. This information may be used to guide future research and clinical management, and further studies are necessary to elucidate the role of T. gondii in children with leukemia.
Zhou et al. (2019) Seroprevalence and risk factors of Toxoplasma gondii infection in children with leukemia in Shandong Province, Eastern China: a case—control prospective study. PeerJ 7:e6604 https://doi.org/10.7717/peerj.6604
A new ancient lineage of frog (Anura: Nyctibatrachidae: Astrobatrachinae subfam. nov.) endemic to the Western Ghats of Peninsular India
The Western Ghats (WG) is an escarpment on the west coast of Peninsular India, housing one of the richest assemblages of frogs in the world, with three endemic families. Here, we report the discovery of a new ancient lineage from a high-elevation massif in the Wayanad Plateau of the southern WG. Phylogenetic analysis reveals that the lineage belongs to Natatanura and clusters with Nyctibatrachidae, a family endemic to the WG/Sri Lanka biodiversity hotspot. Based on geographic distribution, unique morphological traits, deep genetic divergence, and phylogenetic position that distinguishes the lineage from the two nyctibatrachid subfamilies Nyctibatrachinae Blommers-Schlösser, 1993 and Lankanectinae Dubois & Ohler, 2001, we erect a new subfamily Astrobatrachinae subfam. nov. (endemic to the WG, Peninsular India), and describe a new genus Astrobatrachus gen. nov. and species, Astrobatrachus kurichiyana sp. nov. The discovery of this species adds to the list of deeply divergent and monotypic or depauperate lineages with narrow geographic ranges in the southern massifs of the WG. The southern regions of the WG have long been considered geographic and climatic refugia, and this new relict lineage underscores their evolutionary significance. The small range of this species exclusively outside protected areas highlights the significance of reserve forest tracts in the WG in housing evolutionary novelty. This reinforces the need for intensive sampling to uncover new lineages and advance our understanding of the historical biogeography of this ancient landmass.
Vijayakumar et al. (2019) A new ancient lineage of frog (Anura: Nyctibatrachidae: Astrobatrachinae subfam. nov.) endemic to the Western Ghats of Peninsular India. PeerJ 7:e6457 https://doi.org/10.7717/peerj.6457
Habitat differentiation and conservation gap of Magnolia biondii, M. denudata, and M. sprengeri in China
The flower buds of Magnolia biondii, M. denudata, and M. sprengeri are the materials of Xinyi, a traditional Chinese medicine. The harvest of flower buds and habitat fragmentation caused by human disturbance heavily threatens the natural regeneration and survival of these three Magnolia species. With the aim to support the conservation and improve the effectiveness of conservation, we performed an assessment on habitat suitability, influences of environmental variables on habitat suitability, and the conservation gap of these three Magnolia species, based on the Maxent modeling method. The results indicated that: (1) altitude, annual mean temperature, extreme temperature, temperature fluctuation, annual precipitation, and extreme precipitation are the most influential environmental variables for the distribution of M. sprengeri, M. biondii, and M. denudata; (2) obvious habitat differentiations were observed among M. biondii, M. denudata, and M. sprengeri. M. sprengeri tends to be located in further northern areas with higher altitudes, lower temperatures, and lower precipitation compared to M. biondii and M. denudata; and (3) a large proportion of suitable habitats have been left without protection. Woodland and forest shared the largest area out of the suitable habitats. However, grassland, agricultural land, residential land, and mining and industry areas also occupied large areas of suitable habitats.
Song et al. (2019) Habitat differentiation and conservation gap of Magnolia biondii, M. denudata, and M. sprengeri in China. PeerJ 6:e6126 https://doi.org/10.7717/peerj.6126
Determination of two fluoroquinolones and their combinations with hyaluronan effect in in vitro canine cartilage explants
Background Previous studies reported the effect of enrofloxacin (Enro) and marbofloxacin (Mar) on cell death and alteration of the key genes involved in catabolic and anabolic processes and demonstrated the beneficial effects of hyaluronan (HA) combined with fluoroquinolones (FQs) on primary canine chondrocytes. This study further determines the effects of these treatments on canine cartilage explants in both normal and interleukin-1 beta (IL-1β)-stimulated conditions. Methods We examined sulfate glycosaminoglycan (s-GAG) release, uronic acid (UA) content, and safranin-O staining, as well as the expression patterns of inflammatory, extracellular matrix (ECM) component and enzymes. Results Enro treatment alone effectively stimulated proteoglycan anabolism by increasing UA content and glycosaminoglycans (GAGs) in normal and pre-IL-1β-stimulated explant, whereas Mar showed opposite results. The combination of HA and FQs increased s-GAG release and UA content in normal explants in addition to effective down-regulated expression of MMP3. HA reduced the adverse effects of Mar by enhancing UA and GAG contents in both normal and pre-IL-1β-explants. Moreover, HA effectively induced HAS1and ACANup-regulation and reduced MMP9, TNF, PTGS2,and NFKB1 expression for a long term. Discussion Our results suggest the direct effects of Enro and Mar may selectively stimulate the conditioned explants to express MMP-codinggenes and promote gene expression involved in matrix production, pro-inflammatory cytokines, and cell degradation in different directions. HA successfully reduced the adverse effects of FQs by enhancing s-GAG and UA contents and down-regulated expression of MMPs.
Siengdee et al. (2019) Determination of two fluoroquinolones and their combinations with hyaluronan effect in in vitro canine cartilage explants. PeerJ 7:e6553 https://doi.org/10.7717/peerj.6553
The effects of Solidago canadensis water extracts on maize seedling growth in association with the biomass allocation pattern
Background Solidago canadensis L. is an aggressive exotic plant species in China that has potential allelopathic effects on competing plant species. Effects of hormesis are frequently observed in studies of allelopathy; however, the mechanisms of such effects need to be elucidated. Allelopathic compounds may affect the growth of recipient plants via alteration of biomass allocation patterns or photosynthetic capacity. The aim of this study was to determine how water extracts from S. canadensis affected the shoot and root growth of recipient plants and whether the underlying mechanism was related to the biomass allocation pattern or photosynthetic gas exchange capacity. Methods The water extracts from S. canadensis shoots at 12 different concentrations in the range of 0–0.25 g/ml were applied thrice in 9 days to maize seedlings cultivated in silica sand. The growth (shoot height, leaf length and area and root length) and biomass accumulation and allocation (specific leaf area (SLA), leaf area ratio (LAR) and leaf mass ratio (LMR)) were compared among maize seedlings exposed to different treatment concentrations. Gas exchange (photosynthetic light response curve) was measured and compared among maize seedlings exposed to three concentrations of water extract (0, 0.0125 and 0.2 g/ml) before and after the first application, and seedling growth was measured after the third and final application. Results The growth of seedlings (shoot height, leaf length and area and root length) was promoted at concentrations below 0.125 g/ml and inhibited at concentrations above this level (P < 0.05). The pattern of change in biomass accumulation and allocation was similar to that of shoot growth, but biomass accumulation and allocation was not significantly affected by the water extract treatments (P > 0.05). The water extract treatments did not significantly affect the photosynthetic capacity (P > 0.05), but the dark respiration rate was higher in the low-dose treatment than that in the high-dose treatment. Shoot height was positively correlated with the biomass allocation indicators SLA and LAR (P < 0.05) but not with LMR (P > 0.05). Conclusions The results suggested that the effects of the water extracts from S. canadensis were highly dependent on the concentration, with the growth of maize seedlings promoted at low concentrations of water extracts. The effects of the water extracts on the growth of maize seedlings were mainly due to the effects on the LAR, the allocation to leaf area growth, whereas the effects of the water extracts on leaf gas exchange capacity cannot explain variation of seedling growth. Thus, the stimulation of plant growth was very likely due to increased biomass allocation towards the shoot.
Ye et al. (2019) The effects of Solidago canadensis water extracts on maize seedling growth in association with the biomass allocation pattern. PeerJ 7:e6564 https://doi.org/10.7717/peerj.6564
Anywhere but here: local conditions motivate dispersal in Daphnia
Dispersal is fundamental to population dynamics. However, it is increasingly apparent that, despite most models treating dispersal as a constant, many organisms make dispersal decisions based upon information gathered from the environment. Ideally, organisms would make fully informed decisions, with knowledge of both intra-patch conditions (conditions in their current location) and extra-patch conditions (conditions in alternative locations). Acquiring information is energetically costly, however, and extra-patch information will typically be costlier to obtain than intra-patch information. As a consequence, theory suggests that organisms will often make partially informed dispersal decisions, utilising intra-patch information only. We test this proposition in an experimental two-patch system using populations of the aquatic crustacean, Daphnia carinata. We manipulated conditions (food availability) in the population’s home patch, and in its alternative patch. We found that D. carinata made use of intra-patch information (resource availability in the home patch induced a 10-fold increase in dispersal probability) but either ignored or were incapable of using of extra-patch information (resource availability in the alternative patch did not affect dispersal probability). We also observed a small apparent increase in dispersal in replicates with higher population densities, but this effect was smaller than the effect of resource constraint, and not found to be significant. Our work highlights the considerable influence that information can have on dispersal probability, but also that dispersal decisions will often be made in only a partially informed manner. The magnitude of the response we observed also adds to the growing chorus that condition-dependence may be a significant driver of variation in dispersal.
Erm et al. (2019) Anywhere but here: local conditions motivate dispersal in Daphnia. PeerJ 7:e6599 https://doi.org/10.7717/peerj.6599
Quality-of-life among Syrian refugees residing outside camps in Jordan relative to Jordanians and other countries
Background Since the beginning of the Syrian humanitarian crisis, Syrians sought refuge in many safer countries. Many aspects of Syrian refugees’ lives have been affected, hence affecting the overall quality of their lives. However, only one study has investigated their quality of life (QOL). The aim of this study was to assess the QOL of Syrian refugees residing outside camps in Jordan and compare it to the QOL of Jordanians and to other refugees and populations around the globe. Methods Data were obtained from Syrian refugees residing outside camps in Jordan, and from two Jordanian groups; low socioeconomic status (LSES) Jordanians and average socioeconomic status (ASES) Jordanians in 2017. A total of 661 Syrians, 208 LSES Jordanians and 714 ASES Jordanians, aged between 18 and 75 years were included. The World Health Organization Quality of Life instrument (WHOQOL-BREF) questionnaire was used as the QOL assessment tool. Analysis of Variance “ANOVA” and post hoc Tukey-Honest tests were used to find the differences between the means of QOL questions in the three groups (Syrians, ASES, and LSES). Stepwise multivariate linear regression was performed for each domain to determine the most associated risk factors. Results No significant difference was found between Syrian refugees and LSES Jordanians in the physical health domain. Syrian refugees scored significantly lower than LSES Jordanians in the psychological health and social relationship domain. Syrian refugees scored significantly higher than LSES Jordanians in the environmental domain. ASES Jordanians scored significantly higher than the other two groups in all domains, with all its scores above the average. Discussion Despite the support Jordan provides to the Syrian refugees, they still seem to suffer from poor psychological health, social relationships and environmental domains, with scores below 50 on (0–100) scale. Nonetheless, no significant difference was found between Syrian refugees and LSES Jordanians in the physical health domain, furthermore they scored significantly higher than LSES Jordanians in the environmental domain despite both scoring below 50 on (0–100) scale in this domain. Physical, psychological, and social domains were mainly affected by having a job, having higher income, and being married and free from diseases.
Abdo et al. (2019) Quality-of-life among Syrian refugees residing outside camps in Jordan relative to Jordanians and other countries. PeerJ 7:e6454 https://doi.org/10.7717/peerj.6454