Anthropogenic impacts in protected areas: assessing the efficiency of conservation efforts using Mediterranean ant communities
In countries with high levels of urbanization, protected areas are often subject to human disturbance. In addition to dealing with fragmentation, land managers also have to confront the loss of characteristic ecosystems due to biotic homogenization, which is the increasing similarity of species assemblages among geographically separate regions. Using ants as a model system, we explored whether anthropogenic factors negatively affect biodiversity of protected areas of a regional network. We first analysed the effect of fragmentation and human activity on ant biodiversity within protected areas. Secondly, we tested whether homogenization could occur among protected areas. We sampled 79 plots in the most common habitats of 32 protected areas in southern Spain and calculated ant community richness and diversity indices, endemic richness, and Bray–Curtis similarity indices (between pairs of plots). We related these indices with patch fragmentation and human disturbance variables, taking into account environmental, spatial and landscape covariates. We used ANOSIM to test for differences between similarity indices, specifically among levels of anthropogenic disturbance. Species richness was positively correlated with the distance from the border of the protected areas and the number of endemic species was negatively correlated with the degree of fragmentation. Ant communities were similar within each protected area but differed across regions. Human disturbance was not correlated with community similarity among sampling points. Our approach suggests how the ability of European protected areas to sustain biodiversity is limited because they remain susceptible to anthropogenic impacts. Although ant communities maintained their biological distinctiveness, we reveal how fragmentation within protected areas is important for community richness and endemism maintenance.
Angulo et al. (2016) Anthropogenic impacts in protected areas: assessing the efficiency of conservation efforts using Mediterranean ant communities. PeerJ 4:e2773 https://doi.org/10.7717/peerj.2773
Blood circulation in the ascidian tunicate Corella inflata (Corellidae)
The body of the ascidian tunicate Corella inflata is relatively transparent. Thus, the circulatory system can be visualized by injecting high molecular weight fluorescein labeled dextran into the heart or the large vessels at the ends of the heart without surgery to remove the body wall. In addition, after staining with neutral red, the movement of blood cells can be easily followed to further characterize the circulatory system. The heart is two gently curved concentric tubes extending across the width of the animal. The inner myocardial tube has a partial constriction approximately in the middle. As in other tunicates, the heart is peristaltic and periodically reverses direction. During the branchial phase blood leaves the anterior end of the heart by two asymmetric vessels that connect to the two sides of the branchial basket. Blood then flows in both transverse directions through a complex system of ducts in the basket into large ventral and dorsal vessels which carry blood back to the visceral organs in the posterior of the animal. During the visceral phase blood leaves the posterior end of the heart in two vessels that repeatedly bifurcate and fan into the stomach and gonads. Blood velocity, determined by following individual cells in video frames, is high and pulsatory near the heart. A double peak in velocity at the maximum may be due to the constriction in the middle of the heart tube. Blood velocity progressively decreases with distance from the heart. In peripheral regions with vessels of small diameter blood cells frequently collide with vessel walls and cell motion is erratic. The estimated volume of blood flow during each directional phase is greater than the total volume of the animal. Circulating blood cells are confined to vessels or ducts in the visible parts of the animal and retention of high molecular weight dextran in the vessels is comparable to that seen in vertebrates. These are characteristics of a closed circulatory system.
Konrad (2016) Blood circulation in the ascidian tunicate Corella inflata (Corellidae). PeerJ 4:e2771 https://doi.org/10.7717/peerj.2771
Distribution and characteristic of nitrite-dependent anaerobic methane oxidation bacteria by comparative analysis of wastewater treatment plants and agriculture fields in northern China
Nitrite-dependent anaerobic methane oxidation (n-damo) is a recently discovered biological process which has been arousing global attention because of its potential in minimizing greenhouse gases emissions. In this study, molecular biological techniques and potential n-damo activity batch experiments were conducted to investigate the presence and diversity of M. oxyfera bacteria in paddy field, corn field, and wastewater treatment plant (WWTP) sites in northern China, as well as lab-scale n-damo enrichment culture. N-damo enrichment culture showed the highest abundance of M. oxyfera bacteria, and positive correlation was observed between potential n-damo rate and abundance of M. oxyfera bacteria. Both paddy field and corn field sites were believed to be better inoculum than WWTP for the enrichment of M. oxyfera bacteria due to their higher abundance and the diversity of M. oxyfera bacteria. Comparative analysis revealed that long biomass retention time, low NH ${}_{4}^{+}$ 4 + and high NO ${}_{2}^{-}$ 2 − content were suitable for the growth of M. oxyfera bacteria.
Hu et al. (2016) Distribution and characteristic of nitrite-dependent anaerobic methane oxidation bacteria by comparative analysis of wastewater treatment plants and agriculture fields in northern China. PeerJ 4:e2766 https://doi.org/10.7717/peerj.2766
Probabilistic adaptation in changing microbial environments
Microbes growing in animal host environments face fluctuations that have elements of both randomness and predictability. In the mammalian gut, fluctuations in nutrient levels and other physiological parameters are structured by the host’s behavior, diet, health and microbiota composition. Microbial cells that can anticipate environmental fluctuations by exploiting this structure would likely gain a fitness advantage (by adapting their internal state in advance). We propose that the problem of adaptive growth in structured changing environments, such as the gut, can be viewed as probabilistic inference. We analyze environments that are “meta-changing”: where there are changes in the way the environment fluctuates, governed by a mechanism unobservable to cells. We develop a dynamic Bayesian model of these environments and show that a real-time inference algorithm (particle filtering) for this model can be used as a microbial growth strategy implementable in molecular circuits. The growth strategy suggested by our model outperforms heuristic strategies, and points to a class of algorithms that could support real-time probabilistic inference in natural or synthetic cellular circuits.
Katz et al. (2016) Probabilistic adaptation in changing microbial environments. PeerJ 4:e2716 https://doi.org/10.7717/peerj.2716
Functional characterisation of phagocytes in the Pacific oyster Crassostrea gigas
Invertebrates lack canonical adaptive immunity and mainly rely on innate immune system to fight against pathogens. The phagocytes, which could engulf and kill microbial pathogens, are likely to be of great importance and have to undertake significant roles in invertebrate immune defense. In the present study, flow cytometry combined with histological and lectin staining was employed to characterise functional features of phagocytes in the Pacific oyster Crassostrea gigas. Based on the cell size and cellular contents, haemocytes were categorised into three cell types, i.e., granulocytes, semigranulocytes and agranulocytes. Agranulocytes with smaller cell volume and lower cytoplasmic-to-nuclear ratio did not show phagocytic activity, while semigranulocytes and agranulocytes exhibited larger cell volume, higher cytoplasmic-to-nuclear ratio and phagocytic activity. In addition, granulocytes with higher side scatter (SSC) exhibited higher phagocytic activity than that of semigranulocytes. When β-integrin and lectin-like receptors were blocked by RGD tripeptide and carbohydrates, respectively, the phagocytic activity of both granulocytes and semigranulocytes was significantly inhibited, indicating that β-integrin and certain lectin-like receptors were involved in phagocytosis towards microbes. Moreover, lipopolysaccharide but not peptidylglycan could enhance phagocytic activity of granulocytes and semigranulocytes towards Vibrio splendidus and Staphylococcus aureus. Lectin staining analysis revealed that Lycopersicon esculentum lectin (LEL), binding the epitope polylactosamine, was highly distributed on the extracellular cell surface of phagocytes, and could be utilized as a potential molecular marker to differentiate phagocytes from non-phagocytic haemocytes. The results, collectively, provide knowledge on the functional characters of oyster phagocytes, which would contribute to deep investigation of cell typing and cellular immunity in bivalves.
Jiang et al. (2016) Functional characterisation of phagocytes in the Pacific oyster Crassostrea gigas. PeerJ 4:e2590 https://doi.org/10.7717/peerj.2590
Age-congruency and contact effects in body expression recognition from point-light displays (PLD)
Recognition of older people’s body expressions is a crucial social skill. We here investigate how age, not just of the observer, but also of the observed individual, affects this skill. Age may influence the ability to recognize other people’s body expressions by changes in one’s own ability to perform certain action over the life-span (i.e., an own-age bias may occur, with best recognition for one’s own age). Whole body point light displays of children, young adults and older adults (>70 years) expressing six different emotions were presented to observers of the same three age-groups. Across two variations of the paradigm, no evidence for the predicted own-age bias (a cross-over interaction between one’s own age and the observed person’s age) was found. Instead, experience effects were found with children better recognizing older actors’ expressions of ‘active emotions,’ such as anger and happiness with greater exposure in daily life. Together, the findings suggest that age-related changes in one own’s mobility only influences body expression categorization in young children who interact frequently with older adults.
Pollux et al. (2016) Age-congruency and contact effects in body expression recognition from point-light displays (PLD). PeerJ 4:e2796 https://doi.org/10.7717/peerj.2796
Species interactions in an Andean bird–flowering plant network: phenology is more important than abundance or morphology
Biological constraints and neutral processes have been proposed to explain the properties of plant–pollinator networks. Using interactions between nectarivorous birds (hummingbirds and flowerpiercers) and flowering plants in high elevation forests (i.e., “elfin” forests) of the Andes, we explore the importance of biological constraints and neutral processes (random interactions) to explain the observed species interactions and network metrics, such as connectance, specialization, nestedness and asymmetry. In cold environments of elfin forests, which are located at the top of the tropical montane forest zone, many plants are adapted for pollination by birds, making this an ideal system to study plant–pollinator networks. To build the network of interactions between birds and plants, we used direct field observations. We measured abundance of birds using mist-nets and flower abundance using transects, and phenology by scoring presence of birds and flowers over time. We compared the length of birds’ bills to flower length to identify “forbidden interactions”—those interactions that could not result in legitimate floral visits based on mis-match in morphology. Diglossa flowerpiercers, which are characterized as “illegitimate” flower visitors, were relatively abundant. We found that the elfin forest network was nested with phenology being the factor that best explained interaction frequencies and nestedness, providing support for biological constraints hypothesis. We did not find morphological constraints to be important in explaining observed interaction frequencies and network metrics. Other network metrics (connectance, evenness and asymmetry), however, were better predicted by abundance (neutral process) models. Flowerpiercers, which cut holes and access flowers at their base and, consequently, facilitate nectar access for other hummingbirds, explain why morphological mis-matches were relatively unimportant in this system. Future work should focus on how changes in abundance and phenology, likely results of climate change and habitat fragmentation, and the role of nectar robbers impact ecological and evolutionary dynamics of plant–pollinator (or flower-visitor) interactions.
Gonzalez et al. (2016) Species interactions in an Andean bird–flowering plant network: phenology is more important than abundance or morphology. PeerJ 4:e2789 https://doi.org/10.7717/peerj.2789
One-year mortality after severe COPD exacerbation in Bulgaria
Introduction One-year mortality in COPD patients is reported to be between 4% and 43%, depending on the group examined. Aim To examine the one-year mortality in COPD patients after severe exacerbation and the correlation between mortality and patients’ characteristics and comorbidities. Methods A total of 152 COPD patients hospitalized for severe exacerbation were assessed for vitamin D status, diabetes mellitus (DM), arterial hypertension (AH), and metabolic syndrome (MS). Data were gathered about smoking status and number of exacerbations in previous year. CAT and mMRC questionnaires were completed by all patients. Pre- and post-bronchodilatory spirometry was performed. One-year mortality was established from national death register. Results One-year mortality is 7.2%. DM, MS, and VD are not predictors for one-year mortality. However there is a trend for increased mortality in patients with AH (9.5% vs. 2.1%, p = 0.107). There is increased mortality in patients with mMRC > 2 (11.1 vs. 0%, p = 0.013). The presence of severe exacerbation in the previous year is a risk factor for mortality (12.5% vs. 1.4%, p = 0.009). There is a trend for increased mortality in the group with FEV1 < 50% (11.5 vs. 4.4%, p = 0.094). Cox regression shows 3.7% increase in mortality rate for 1% decrease in FEV1, 5.2% for 1% decrease in PEF, 7.8% for one year age increase and 8.1% for 1 CAT point increase (all p < 0.05). Conclusions This study finds relatively low one-year mortality in COPD patients after surviving severe exacerbation. Grade C and FEV1 > 80% may be factors for good prognosis. Risk factors for increased mortality are age, FEV1 value, severe exacerbation in previous year and reduced quality of life.
Mekov et al. (2016) One-year mortality after severe COPD exacerbation in Bulgaria. PeerJ 4:e2788 https://doi.org/10.7717/peerj.2788
Diet of the endangered big-headed turtle Platysternon megacephalum
Populations of the big-headed turtle Platysternon megacephalum are declining at unprecedented rates across most of its distribution in Southeast Asia owing to unsustainable harvest for pet, food, and Chinese medicine markets. Research on Asian freshwater turtles becomes more challenging as populations decline and basic ecological information is needed to inform conservation efforts. We examined fecal samples collected from P. megacephalum in five streams in Hong Kong to quantify the diet, and we compared the germination success of ingested and uningested seeds. Fruits, primarily of Machilus spp., were most frequently consumed, followed by insects, plant matter, crabs and mollusks. The niche breadth of adults was wider than that of juveniles. Diet composition differed between sites, which may be attributable to the history of illegal trapping at some sites, which reduced the proportion of larger and older individuals. Digestion of Machilus spp. fruits by P. megacephalum enhanced germination success of seeds by about 30%. However, most digested seeds are likely defecated in water in this highly aquatic species, which limits the potential benefit to dispersal. The results of our study can be used by conservation-related captive breeding programs to ensure a more optimal diet is provided to captive P. megacephalum.
Sung et al. (2016) Diet of the endangered big-headed turtle Platysternon megacephalum. PeerJ 4:e2784 https://doi.org/10.7717/peerj.2784
Diversity, taxonomic composition, and functional aspects of fungal communities in living, senesced, and fallen leaves at five sites across North America
Background Fungal endophytes inhabit symptomless, living tissues of all major plant lineages to form one of earth’s most prevalent groups of symbionts. Many reproduce from senesced and/or decomposing leaves and can produce extracellular leaf-degrading enzymes, blurring the line between symbiotrophy and saprotrophy. To better understand the endophyte–saprotroph continuum we compared fungal communities and functional traits of focal strains isolated from living leaves to those isolated from leaves after senescence and decomposition, with a focus on foliage of woody plants in five biogeographic provinces ranging from tundra to subtropical scrub forest. Methods We cultured fungi from the interior of surface-sterilized leaves that were living at the time of sampling (i.e., endophytes), leaves that were dead and were retained in plant canopies (dead leaf fungi, DLF), and fallen leaves (leaf litter fungi, LLF) from 3–4 species of woody plants in each of five sites in North America. Our sampling encompassed 18 plant species representing two families of Pinophyta and five families of Angiospermae. Diversity and composition of fungal communities within and among leaf life stages, hosts, and sites were compared using ITS-partial LSU rDNA data. We evaluated substrate use and enzyme activity by a subset of fungi isolated only from living tissues vs. fungi isolated only from non-living leaves. Results Across the diverse biomes and plant taxa surveyed here, culturable fungi from living leaves were isolated less frequently and were less diverse than those isolated from non-living leaves. Fungal communities in living leaves also differed detectably in composition from communities in dead leaves and leaf litter within focal sites and host taxa, regardless of differential weighting of rare and abundant fungi. All focal isolates grew on cellulose, lignin, and pectin as sole carbon sources, but none displayed ligninolytic or pectinolytic activity in vitro. Cellulolytic activity differed among fungal classes. Within Dothideomycetes, activity differed significantly between fungi from living vs. non-living leaves, but such differences were not observed in Sordariomycetes. Discussion Although some fungi with endophytic life stages clearly persist for periods of time in leaves after senescence and incorporation into leaf litter, our sampling across diverse biomes and host lineages detected consistent differences between fungal assemblages in living vs. non-living leaves, reflecting incursion by fungi from the leaf exterior after leaf death and as leaves begin to decompose. However, fungi found only in living leaves do not differ consistently in cellulolytic activity from those fungi detected thus far only in dead leaves. Future analyses should consider Basidiomycota in addition to the Ascomycota fungi evaluated here, and should explore more dimensions of functional traits and persistence to further define the endophytism-to-saprotrophy continuum.
U’Ren et al. (2016) Diversity, taxonomic composition, and functional aspects of fungal communities in living, senesced, and fallen leaves at five sites across North America. PeerJ 4:e2768 https://doi.org/10.7717/peerj.2768