Porcine rotavirus C in pigs with gastroenteritis on Thai swine farms, 2011–2016
Swine are economically important food animals, but highly contagious porcine epidemic diarrhea virus (PEDV) and rotavirus can afflict pig herds and contribute significantly to piglet morbidity and mortality. While there have been studies on rotavirus group A (RVA) in Thailand, reports of rotavirus group C (RVC) are limited. Here, we aimed to identify the prevalence of RVC circulating on Thai commercial swine farms. We analyzed 769 feces and intestine mucosal contents of pigs affected with diarrhea between 2011 and 2016 using RT-PCR specific for the PEDV spike (S), rotavirus glycoprotein (G) VP7, and protease-sensitive protein (P) VP4 genes. We found that 6.6% (51/769) of samples tested positive for RVC, of which 11 samples were co-infected with RVA and four samples were co-infected with PEDV. Three samples tested positive for all three viruses. Phylogenetic analysis of the VP7 gene showed that the most frequent RVC genotype was G1, which grouped with the prototypic RVC Cowden strain. While G6 and G9 were also common, G3 was relatively rare. Analysis of the VP4 gene revealed that the most common P type was P[5], followed by P[4], P[7], and P[1]. In all, there were six G/P combinations (G6P[5], G1P[1], G1P[4], G1P[5], G9P[4], and G9P[7]), of which G6P[5] was the most predominant.
Tuanthap et al. (2018) Porcine rotavirus C in pigs with gastroenteritis on Thai swine farms, 2011–2016. PeerJ 6:e4724 https://doi.org/10.7717/peerj.4724
The brown anole dewlap revisited: do predation pressure, sexual selection, and species recognition shape among-population signal diversity?
Animal signalling structures are amongst the most variable characteristics, as they are subjected to a diversity of selection pressures. A well-known example of a diverse signalling system in the animal kingdom is the dewlap of Anolis lizards. Dewlap characteristics can vary remarkably among and within species, and also between sexes. Although a considerable amount of studies have attempted to disentangle the functional significance of the staggering dewlap diversity in Anolis, the underlying evolutionary processes remain elusive. In this study, we focus on the contribution of biotic selective pressures in shaping geographic variation in dewlap design (size, colour, and pattern) and dewlap display behaviour at the intraspecific level. Notably, we have tried to replicate and extend previously reported results hereof in both sexes of the brown anole lizard (Anolis sagrei). To do this, we assembled a dataset consisting of 17 A. sagrei heterogeneous island populations from the Caribbean and specifically tested whether predation pressure, sexual selection, or species recognition could explain interpopulational variation in an array of dewlap characteristics. Our findings show that in neither males nor females estimates of predation pressure (island size, tail break frequency, model attack rate, presence of predatory Leiocephalus lizards) or sexual selection (sexual size dimorphism) could explain variation in dewlap design. We did find that A. sagrei males from larger islands showed higher dewlap display intensities than males from smaller islands, but the direct connection with predation pressure remains ambiguous and demands further investigation. Last, we could show indirect support for species recognition only in males, as they are more likely to have a ‘spotted’ dewlap pattern when co-occurring with a higher number of syntopic Anolis species. In conclusion, we found overall limited support for the idea that the extensive interpopulational variability in dewlap design and use in A. sagrei is mediated by variation in their biotic environment. We propose a variety of conceptual and methodological explanations for this unexpected finding.
Baeckens et al. (2018) The brown anole dewlap revisited: do predation pressure, sexual selection, and species recognition shape among-population signal diversity?. PeerJ 6:e4722 https://doi.org/10.7717/peerj.4722
Seasonal migrations, body temperature fluctuations, and infection dynamics in adult amphibians
Risks of parasitism vary over time, with infection prevalence often fluctuating with seasonal changes in the annual cycle. Identifying the biological mechanisms underlying seasonality in infection can enable better prediction and prevention of future infection peaks. Obtaining longitudinal data on individual infections and traits across seasons throughout the annual cycle is perhaps the most effective means of achieving this aim, yet few studies have obtained such information for wildlife. Here, we tracked spiny common toads (Bufo spinosus) within and across annual cycles to assess seasonal variation in movement, body temperatures and infection from the fungal parasite, Batrachochytrium dendrobatidis (Bd). Across annual cycles, toads did not consistently sustain infections but instead gained and lost infections from year to year. Radio-tracking showed that infected toads lose infections during post-breeding migrations, and no toads contracted infection following migration, which may be one explanation for the inter-annual variability in Bd infections. We also found pronounced seasonal variation in toad body temperatures. Body temperatures approached 0 °C during winter hibernation but remained largely within the thermal tolerance range of Bd. These findings provide direct documentation of migratory recovery (i.e., loss of infection during migration) and escape in a wild population. The body temperature reductions that we observed during hibernation warrant further consideration into the role that this period plays in seasonal Bd dynamics.
Daversa et al. (2018) Seasonal migrations, body temperature fluctuations, and infection dynamics in adult amphibians. PeerJ 6:e4698 https://doi.org/10.7717/peerj.4698
Fine grained compositional analysis of Port Everglades Inlet microbiome using high throughput DNA sequencing
Background Similar to natural rivers, manmade inlets connect inland runoff to the ocean. Port Everglades Inlet (PEI) is a busy cargo and cruise ship port in South Florida, which can act as a source of pollution to surrounding beaches and offshore coral reefs. Understanding the composition and fluctuations of bacterioplankton communities (“microbiomes”) in major port inlets is important due to potential impacts on surrounding environments. We hypothesize seasonal microbial fluctuations, which were profiled by high throughput 16S rRNA amplicon sequencing and analysis. Methods & Results Surface water samples were collected every week for one year. A total of four samples per month, two from each sampling location, were used for statistical analysis creating a high sampling frequency and finer sampling scale than previous inlet microbiome studies. We observed significant differences in community alpha diversity between months and seasons. Analysis of composition of microbiomes (ANCOM) tests were run in QIIME 2 at genus level taxonomic classification to determine which genera were differentially abundant between seasons and months. Beta diversity results yielded significant differences in PEI community composition in regard to month, season, water temperature, and salinity. Analysis of potentially pathogenic genera showed presence of Staphylococcus and Streptococcus. However, statistical analysis indicated that these organisms were not present in significantly high abundances throughout the year or between seasons. Discussion Significant differences in alpha diversity were observed when comparing microbial communities with respect to time. This observation stems from the high community evenness and low community richness in August. This indicates that only a few organisms dominated the community during this month. August had lower than average rainfall levels for a wet season, which may have contributed to less runoff, and fewer bacterial groups introduced into the port surface waters. Bacterioplankton beta diversity differed significantly by month, season, water temperature, and salinity. The 2013–2014 dry season (October–April), was warmer and wetter than historical averages. This may have driven significant differences in beta diversity. Increased nitrogen and phosphorous concentrations were observed in these dry season months, possibly creating favorable bacterial growth conditions. Potentially pathogenic genera were present in the PEI. However their relatively low, non-significant abundance levels highlight their relatively low risk for public health concerns. This study represents the first to sample a large port at this sampling scale and sequencing depth. These data can help establish the inlet microbial community baseline and supplement the vital monitoring of local marine and recreational environments, all the more poignant in context of local reef disease outbreaks and worldwide coral reef collapse in wake of a harsh 2014–16 El Niño event.
O’Connell et al. (2018) Fine grained compositional analysis of Port Everglades Inlet microbiome using high throughput DNA sequencing. PeerJ 6:e4671 https://doi.org/10.7717/peerj.4671
Uncovering the hidden players in Lepidoptera biology: the heritable microbial endosymbionts
The Lepidoptera is one of the most widespread and recognisable insect orders. Due to their remarkable diversity, economic and ecological importance, moths and butterflies have been studied extensively over the last 200 years. More recently, the relationship between Lepidoptera and their heritable microbial endosymbionts has received increasing attention. Heritable endosymbionts reside within the host’s body and are often, but not exclusively, inherited through the female line. Advancements in molecular genetics have revealed that host-associated microbes are both extremely prevalent among arthropods and highly diverse. Furthermore, heritable endosymbionts have been repeatedly demonstrated to play an integral role in many aspects of host biology, particularly host reproduction. Here, we review the major findings of research of heritable microbial endosymbionts of butterflies and moths. We promote the Lepidoptera as important models in the study of reproductive manipulations employed by heritable endosymbionts, with the mechanisms underlying male-killing and feminisation currently being elucidated in moths and butterflies. We also reveal that the vast majority of research undertaken of Lepidopteran endosymbionts concerns Wolbachia. While this highly prevalent bacterium is undoubtedly important, studies should move towards investigating the presence of other, and interacting endosymbionts, and we discuss the merits of examining the microbiome of Lepidoptera to this end. We finally consider the importance of understanding the influence of endosymbionts under global environmental change and when planning conservation management of endangered Lepidoptera species.
Duplouy et al. (2018) Uncovering the hidden players in Lepidoptera biology: the heritable microbial endosymbionts. PeerJ 6:e4629 https://doi.org/10.7717/peerj.4629
Sponge community of the western Black Sea shallow water caves: diversity and spatial distribution
Marine caves possess unique biocoenotic and ecological characteristics. Sessile benthic species such as sponges associated with cave habitats typically show a marked zonation from the cave entrance towards the end of the cave. We describe three semi-submerged karstic caves of 50 to 83 m length and 936 to 2,291 m3 volume from the poorly explored cavernicolous fauna of North-East Bulgaria. We surveyed sponge diversity and spatial variability. Eight demosponge species were identified based on morphological and molecular data, of which six are known from the adjacent open sea waters of the Black Sea. Two species, Protosuberites denhartogi van Soest & de Kluijver, 2003 and Halichondria bowerbanki Burton, 1930, are reported from the Black Sea for the first time. The spatial sponge distribution inside the caves is in general similar, but shows some differences in species composition and distribution depending on cave relief and hydrodynamics. The species composition of sponges of Bulgarian caves is found to be different from Crimean caves. An updated checklist of the Black Sea sponges is provided.
Ereskovsky et al. (2018) Sponge community of the western Black Sea shallow water caves: diversity and spatial distribution. PeerJ 6:e4596 https://doi.org/10.7717/peerj.4596
Screening of polyhydroxyalkanoate-producing bacteria and PhaC-encoding genes in two hypersaline microbial mats from Guerrero Negro, Baja California Sur, Mexico
Hypersaline microbial mats develop through seasonal and diel fluctuations, as well as under several physicochemical variables. Hence, resident microorganisms commonly employ strategies such as the synthesis of polyhydroxyalkanoates (PHAs) in order to resist changing and stressful conditions. However, the knowledge of bacterial PHA production in hypersaline microbial mats has been limited to date, particularly in regard to medium-chain length PHAs (mcl-PHAs), which have biotechnological applications due to their plastic properties. The aim of this study was to obtain evidence for PHA production in two hypersaline microbial mats of Guerrero Negro, Mexico by searching for PHA granules and PHA synthase genes in isolated bacterial strains and environmental samples. Six PHA-producing strains were identified by 16S rRNA gene sequencing; three of them corresponded to a Halomonas sp. In addition, Paracoccus sp., Planomicrobium sp. and Staphylococcus sp. were also identified as PHA producers. Presumptive PHA granules and PHA synthases genes were detected in both sampling sites. Moreover, phylogenetic analysis showed that most of the phylotypes were distantly related to putative PhaC synthases class I sequences belonging to members of the classes Alphaproteobacteria and Gammaproteobacteria distributed within eight families, with higher abundances corresponding mainly to Rhodobacteraceae and Rhodospirillaceae. This analysis also showed that PhaC synthases class II sequences were closely related to those of Pseudomonas putida, suggesting the presence of this group, which is probably involved in the production of mcl-PHA in the mats. According to our state of knowledge, this study reports for the first time the occurrence of phaC and phaC1 sequences in hypersaline microbial mats, suggesting that these ecosystems may be a novel source for the isolation of short- and medium-chain length PHA producers.
Martínez-Gutiérrez et al. (2018) Screening of polyhydroxyalkanoate-producing bacteria and PhaC-encoding genes in two hypersaline microbial mats from Guerrero Negro, Baja California Sur, Mexico. PeerJ 6:e4780 https://doi.org/10.7717/peerj.4780
Effects of nettle slurry (Urtica dioica L.) used as foliar fertilizer on potato (Solanum tuberosum L.) yield and plant growth
Organic agriculture is becoming increasingly important, and many natural products are now available for organic farmers to manage and improve their crops. Several ethnobotanical studies have indicated that the use of nettle slurry as fertilizer in organic farming for horticultural crops is spreading. Sometimes, however, the consequences of using these natural products have been poorly evaluated, and there is very little scientific evidence for the effects of using these slurries. In this study, we aimed to analyze the possible effect of nettle slurry on potato yields produced by organic farming. To achieve this main objective, we assessed the effect of nettle slurry on potato yields, plant size and growth parameters, chlorophyll content, and the presence of pests and diseases. Different slurry doses were assessed in 36 plots and nine variables were measured during the crop cycle. Under these field experimental conditions, nettle slurry (including one treatment with Urtica in combination with Equisetum) had no significant effects on yield, chlorophyll content, or the presence of pests and diseases in organic potato crops. The highest chlorophyll content was found in the double dose treatment, but the difference was not significant. This result, together with a small improvement in plant height with the double dose treatment, might indicate very slight crop enhancement which, under our experimental conditions, was not enough to improve yield. The Urtica and Equisetum slurry chemical analyses showed very low levels of nitrogen, phosphorus, and potassium.
Garmendia et al. (2018) Effects of nettle slurry (Urtica dioica L.) used as foliar fertilizer on potato (Solanum tuberosum L.) yield and plant growth. PeerJ 6:e4729 https://doi.org/10.7717/peerj.4729
Crystallization and structure analysis of the core motif of the Pks13 acyltransferase domain from Mycobacterium tuberculosis
Type I polyketide synthase 13 (Pks13) is involved in the final step of the biosynthesis of mycolic acid in Mycobacterium tuberculosis. Recent articles have reported that Pks13 is an essential enzyme in the mycolic acid biosynthesis pathway, and it has been deeply studied as a drug target in Tuberculosis. We report a high-resolution structure of the acyltransferase (AT) domain of Pks13 at 2.59 Å resolution. Structural comparison with the full-length AT domain (PDB code, 3TZW, and 3TZZ) reveals a different orientation of the C-terminal helix and rearrangement of some conserved residues.
Yu et al. (2018) Crystallization and structure analysis of the core motif of the Pks13 acyltransferase domain from Mycobacterium tuberculosis. PeerJ 6:e4728 https://doi.org/10.7717/peerj.4728
A survey of the views and capabilities of community pharmacists in Western Australia regarding the rescheduling of selected oral antibiotics in a framework of pharmacist prescribing
Background Antibiotic misuse in the community contributes to antimicrobial resistance. One way to address this may be by better utilizing community pharmacists’ skills in antibiotic prescribing. The aims of this study were to examine the level of support for “down-scheduling” selected antibiotics and to evaluate factors determining the appropriateness of community pharmacist prescribing for a limited range of infections, including their decision to refer to a doctor. Methods Self-administered questionnaires, including graded case vignette scenarios simulating real practice, were sent to Western Australian community pharmacists. In addition to descriptive statistics and chi-square testing, a General Estimating Equation (GEE) was used to identify factors associated with appropriateness of therapy and the decision to refer, for each of the seven vignettes. Results Of the 240 pharmacists surveyed, 90 (37.5%) responded, yielding 630 responses to seven different case vignettes. There was more than 60% respondent support for expanded prescribing (rescheduling) of commonly prescribed antibiotics. Overall 426/630 (67.6%) chose to treat the patient while the remaining 204/630 (32.4%) referred the patient to a doctor. Of those electing to treat, 380/426 (89.2%) opted to use oral antibiotics, with 293/380 (77.2%) treating with an appropriate selection and regimen. The GEE model indicated that pharmacists were more likely to prescribe inappropriately for conditions such as otitis media (p = 0.0060) and urinary tract infection in pregnancy (p < 0.0001) compared to more complex conditions. Over 80% of all pharmacists would refer the patient to a doctor following no improvement within 3 days, or within 24 h in the case of community acquired pneumonia. It was more common for younger pharmacists to refer the patient to a doctor (p = 0.0165). Discussion This study adds further insight into community pharmacy/pharmacist characteristics associated with appropriateness of oral antibiotic selection and the decision to refer to doctors. These findings require consideration in designing pharmacist over-the-counter prescribing models for oral antibiotics.
Sinkala et al. (2018) A survey of the views and capabilities of community pharmacists in Western Australia regarding the rescheduling of selected oral antibiotics in a framework of pharmacist prescribing. PeerJ 6:e4726 https://doi.org/10.7717/peerj.4726