Phytobiomes are compositionally nested from the ground up
Plant-associated microbes are critical players in host health, fitness and productivity. Despite microbes’ importance in plants, seeds are mostly sterile, and most plant microbes are recruited from an environmental pool. Surprisingly little is known about the processes that govern how environmental microbes assemble on plants in nature. In this study we examine how bacteria are distributed across plant parts, and how these distributions interact with spatial gradients. We sequenced amplicons of bacteria from the surfaces of six plant parts and adjacent soil of Scaevola taccada, a common beach shrub, along a 60 km transect spanning O’ahu island’s windward coast, as well as within a single intensively-sampled site. Bacteria are more strongly partitioned by plant part as compared with location. Within S. taccada plants, microbial communities are highly nested: soil and rhizosphere communities contain much of the diversity found elsewhere, whereas reproductive parts fall at the bottom of the nestedness hierarchy. Nestedness patterns suggest either that microbes follow a source/sink gradient from the ground up, or else that assembly processes correlate with other traits, such as tissue persistence, that are vertically stratified. Our work shines light on the origins and determinants of plant-associated microbes across plant and landscape scales.
Amend et al. (2019) Phytobiomes are compositionally nested from the ground up. PeerJ 7:e6609 https://doi.org/10.7717/peerj.6609
A metagenomic study of DNA viruses from samples of local varieties of common bean in Kenya
Common bean (Phaseolus vulgaris L.) is the primary source of protein and nutrients in the majority of households in sub-Saharan Africa. However, pests and viral diseases are key drivers in the reduction of bean production. To date, the majority of viruses reported in beans have been RNA viruses. In this study, we carried out a viral metagenomic analysis on virus symptomatic bean plants. Our virus detection pipeline identified three viral fragments of the double-stranded DNA virus Pelargonium vein banding virus (PVBV) (family, Caulimoviridae, genus Badnavirus). This is the first report of the dsDNA virus and specifically PVBV in legumes to our knowledge. In addition two previously reported +ssRNA viruses the bean common mosaic necrosis virus (BCMNVA) (Potyviridae) and aphid lethal paralysis virus (ALPV) (Dicistroviridae) were identified. Bayesian phylogenetic analysis of the Badnavirus (PVBV) using amino acid sequences of the RT/RNA-dependent DNA polymerase region showed the Kenyan sequence (SRF019_MK014483) was closely matched with two Badnavirus viruses: Dracaena mottle virus (DrMV) (YP_610965) and Lucky bamboo bacilliform virus (ABR01170). Phylogenetic analysis of BCMNVA was based on amino acid sequences of the Nib region. The BCMNVA phylogenetic tree resolved two clades identified as clade (I and II). Sequence from this study SRF35_MK014482, clustered within clade I with other Kenyan sequences. Conversely, Bayesian phylogenetic analysis of ALPV was based on nucleotide sequences of the hypothetical protein gene 1 and 2. Three main clades were resolved and identified as clades I–III. The Kenyan sequence from this study (SRF35_MK014481) clustered within clade II, and nested within a sub-clade; comprising of sequences from China and an earlier ALPV sequences from Kenya isolated from maize (MF458892). Our findings support the use of viral metagenomics to reveal the nascent viruses, their viral diversity and evolutionary history of these viruses. The detection of ALPV and PVBV indicate that these viruses have likely been underreported due to the unavailability of diagnostic tools.
Wainaina et al. (2019) A metagenomic study of DNA viruses from samples of local varieties of common bean in Kenya. PeerJ 7:e6465 https://doi.org/10.7717/peerj.6465
Vocal recognition of a nest-predator in black grouse
Corvids count among the important predators of bird nests. They are vocal animals and one can expect that birds threatened by their predation, such as black grouse, are sensitive to and recognize their calls. Within the framework of field studies, we noticed that adult black grouse were alerted by raven calls during periods outside the breeding season. Since black grouse are large, extremely precocial birds, this reaction can hardly be explained by sensitization specifically to the threat of nest predation by ravens. This surprising observation prompted us to study the phenomenon more systematically. According to our knowledge, the response of birds to corvid vocalization has been studied in altricial birds only. We tested whether the black grouse distinguishes and responds specifically to playback calls of the common raven. Black grouse recognized raven calls and were alerted, displaying typical neck stretching, followed by head scanning, and eventual escape. Surprisingly, males tended to react faster and exhibited a longer duration of vigilance behavior compared to females. Although raven calls are recognized by adult black grouse out of the nesting period, they are not directly endangered by the raven. We speculate that the responsiveness of adult grouse to raven calls might be explained as a learned response in juveniles from nesting hens that is then preserved in adults, or by a known association between the raven and the red fox. In that case, calls of the raven would be rather interpreted as a warning signal of probable proximity of the red fox.
Policht et al. (2019) Vocal recognition of a nest-predator in black grouse. PeerJ 7:e6533 https://doi.org/10.7717/peerj.6533
Phylogenetic signal analysis in the basicranium of Ursidae (Carnivora, Mammalia)
Ursidae is a monophyletic group comprised of three subfamilies: Tremarctinae, Ursinae and Ailuropodinae, all of which have a rich geographical distribution. The phylogenetic relationships within the Ursidae group have been underexamined, especially regarding morphological traits such as the basicranium. Importantly, the basicranium is a highly complex region that covers a small portion of the skull, combining both structural and functional aspects that determine its morphology. Phylogenetic hypotheses of the Ursidae (including Tremarctinae) have been made based on morphological characters that considers skull, mandible and teeth features, while specific characters of the auditory region and basicranium have not been taken into account. To do this, we analyse the shape and size macroevolution of the basicranium of Ursidae, testing its morphological disparity in a phylogenetic context, which is quantified by means of the phylogenetic signal. We investigated phylogenetical autocorrelation by shape (depicted by Principal Components Analysis scores from previous published analyses) and basicranium size (depicted by centroid size, CS) using an orthonormal decomposition analysis and Abouheif C mean. The main advantages of these methods are that they rely exclusively on cladogram topology and do not require branch-length estimates. Also, an optimisation of the ancestral nodes was performed using TNT 1.5 software. In relation to the phylogenetic signal, both methods showed similar results: the presence of autocorrelation was detected in PC1 and PC2, while in PC3, PC4 and PC5 and in the size of the basicranium (CS), the absence of autocorrelation occurred. The most significant nodes (where there is autocorrelation) are the basal nodes ‘Ursidae’ and ‘Ursinae-Tremarctinae’. Within this last group, distinctive basicranium morphology is observed, being more conservative in Tremarctinae than in Ursinae. The differences between these subfamilies could be related to historical events involving varying food and environmental preferences. The high phylogenetic signal in the node Tremarctinae probably indicates that the basicranium configuration of these bears was obtained early in their evolutionary history. Finally, our results of the basicranium and skull length ratios indicate that in Tremarctinae, the basicranium size was not determined by phylogeny but instead by other factors, such as adaptive responses to climatic changes and competition with other carnivores.
Arnaudo et al. (2019) Phylogenetic signal analysis in the basicranium of Ursidae (Carnivora, Mammalia). PeerJ 7:e6597 https://doi.org/10.7717/peerj.6597
Predicting electrocardiogram interpretation performance in Advanced Cardiovascular Life Support simulation: comparing knowledge tests and simulation performance among Mexican medical students
Background Simulation plays a key role in assessing performance in Advanced Cardiovascular Life Support (ACLS). Traditional knowledge tests are also important for assessing the cognitive elements of ACLS performance. However, the association between the two has not been established. In this study, we focus on one important element in ACLS—interpretation of electrocardiograms (ECG)—and the potential of knowledge tests to serve as predictors of improvement in ACLS performance. Methods We looked at the correlation between Mexican medical students’ improvement in ECG interpretation performance in ACLS megacode simulations (from the start of the semester to the end of the semester), and their scores on ECG interpretation knowledge tests. Results We found significant improvement in ECG interpretation in ACLS megacode simulation (from pre-semester to post-semester), but this was not predicted by the ECG interpretation knowledge test scores. The correlation was .079 (p = 0.66). Conclusions These results suggest that even cognitive tasks such as ECG interpretation can be expressed and assessed differently in simulation versus traditional knowledge testing.
Smith et al. (2019) Predicting electrocardiogram interpretation performance in Advanced Cardiovascular Life Support simulation: comparing knowledge tests and simulation performance among Mexican medical students. PeerJ 7:e6632 https://doi.org/10.7717/peerj.6632
Genome-wide analysis of the Catalpa bungei caffeic acid O-methyltransferase (COMT) gene family: identification and expression profiles in normal, tension, and opposite wood
Caffeic acid O-methyltransferase (COMT) is an important protein that participates in lignin synthesis and is associated with the ratio of G-/S-type lignin in plants. COMTs are associated with the wood properties of forest trees; however, little known about the COMT family in Catalpa bungei, a valuable timber tree species in China . We performed a comprehensive analysis of COMT genes in the C. bungei genome by describing the gene structure and phylogenetic relationships of each family member using bioinformatics-based methods. A total of 23 putative COMT genes were identified using the conserved domain sequences and amino acid sequences of COMTs from Arabidopsis thaliana and Populus trichocarpa as probes. Phylogenetic analysis showed that 23 CbuCOMTs can be divided into three groups based on their structural characteristics; five conserved domains were found in the COMT family. Promoter analysis indicated that the CbuCOMT promoters included various cis-acting elements related to growth and development. Real-time quantitative polymerase chain reaction (PCR) analysis showed differential expression among CbuCOMTs. CbuCOMT2, 7, 8, 9, 10, 12, 13, 14, 21, and 23 were mainly expressed in xylem. Only CbuCOMT23 was significantly downregulated in tension wood and upregulated in opposite wood compared to normal wood. Our study provides new information about the CbuCOMT gene family and will facilitate functional characterisation in further research.
Lu et al. (2019) Genome-wide analysis of the Catalpa bungei caffeic acid O-methyltransferase (COMT) gene family: identification and expression profiles in normal, tension, and opposite wood. PeerJ 7:e6520 https://doi.org/10.7717/peerj.6520
Identification of four hub genes associated with adrenocortical carcinoma progression by WGCNA
Background Adrenocortical carcinoma (ACC) is a rare and aggressive malignant cancer in the adrenal cortex with poor prognosis. Though previous research has attempted to elucidate the progression of ACC, its molecular mechanism remains poorly understood. Methods Gene transcripts per million (TPM) data were downloaded from the UCSC Xena database, which included ACC (The Cancer Genome Atlas, n = 77) and normal samples (Genotype Tissue Expression, n = 128). We used weighted gene co-expression network analysis to identify gene connections. Overall survival (OS) was determined using the univariate Cox model. A protein–protein interaction (PPI) network was constructed by the search tool for the retrieval of interacting genes. Results To determine the critical genes involved in ACC progression, we obtained 2,953 significantly differentially expressed genes and nine modules. Among them, the blue module demonstrated significant correlation with the “Stage” of ACC. Enrichment analysis revealed that genes in the blue module were mainly enriched in cell division, cell cycle, and DNA replication. Combined with the PPI and co-expression networks, we identified four hub genes (i.e., TOP2A, TTK, CHEK1, and CENPA) that were highly expressed in ACC and negatively correlated with OS. Thus, these identified genes may play important roles in the progression of ACC and serve as potential biomarkers for future diagnosis.
Xia et al. (2019) Identification of four hub genes associated with adrenocortical carcinoma progression by WGCNA. PeerJ 7:e6555 https://doi.org/10.7717/peerj.6555
Acute toxicity and responses of antioxidant systems to dibutyl phthalate in neonate and adult Daphnia magna
Dibutyl phthalate (DBP) poses a severe threat to aquatic ecosystems, introducing hazards to both aquatic species and human health. The ecotoxic effects of DBP on aquatic organisms have not been fully investigated. This study investigates acute toxicity, oxidative damage, and antioxidant enzyme parameters in neonate and adult Daphnia magna exposed to DBP. The obtained results show comparable DBP toxic responses in neonates and adults. The median lethal concentrations (LC50) of DBP in neonates exposed for 24 and 48 h were 3.48 and 2.83 mg/L, respectively. The LC50 of adults for the same DBP exposure durations were 4.92 and 4.31 mg/L, respectively. Increased hydrogen peroxide and malondialdehyde were found in neonates and adults at both 24 and 48 h, while the total antioxidant capacity decreased. Superoxide dismutase activity increased significantly in neonates and adults exposed to 0.5 mg/L DBP, and subsequently diminished at higher DBP concentrations and prolonged exposure. Catalase and glutathione S-transferases activities both decreased markedly in neonates and adults. The changes observed were found to be time and concentration dependent. Overall, these data indicated that the acute toxic effects of DBP exposure on neonates were more pronounced than in adults, and oxidative injury may be the main mechanism of DBP toxicity. These results provide a functional link for lipid peroxidation, antioxidant capacity, and antioxidant enzyme levels in the Daphnia magna response to DBP exposure.
Shen et al. (2019) Acute toxicity and responses of antioxidant systems to dibutyl phthalate in neonate and adult Daphnia magna. PeerJ 7:e6584 https://doi.org/10.7717/peerj.6584
Staphylococcus spp. associated with subclinical bovine mastitis in central and northeast provinces of Thailand
Background Staphylococcus spp. are major cause of bovine mastitis (BM) worldwide leading to economic damage to dairy farms and public health threat. Recently, a newly emerged Staphylococcus argenteus has been found as a human and animal pathogen. Molecular characteristics, virulence and antibiotic resistant phenotypes of bacteria causing BM in Thailand are rare. This study aimed to investigated Staphylococcus spp. associated with subclinical bovine mastitis (SCM) in Thailand. Methods Milk samples were collected from 224 cows of 52 dairy herds in four central and northeast provinces. Total somatic cell counts (SCC) and California mastitis test (CMT) were used to identify SCM cows. Milk samples were cultured for Staphylococcus spp. Coagulase-positive isolates were subjected to pulsed-field gel electrophoresis (PFGE) and multilocus sequence typing (MLST). Organisms suspected as S. argenteus were verified by detecting nonribosomal peptide synthetase gene. All isolates were checked for antibiograms and the presence of various virulence genes. Results From the 224 milk samples of 224 cows, 132 (59%) were positive for SCM by SCC and CMT and 229 staphylococcal isolates were recovered. They were 32 coagulase-positive (24 S. aureus and eight S. argenteus) and 197 coagulase-negative. PFGE of the S. aureus and S. argenteus revealed 11 clusters and a non-typeable pattern. MLST of representatives of the 11 PFGE clusters, three PFGE non-typeable S. aureus isolates from different locations and S. argenteus showed 12 sequence types. The eight S. argenteus isolates belonged to ST1223 (three isolates), ST2250 (two isolates), and ST2793 (two isolates). The antimicrobial tests identified 11 (46%) methicillin-resistant S. aureus and 25 (13%) methicillin-resistant coagulase-negative isolates, while seven S. argenteus were methicillin-susceptible and one isolate was methicillin-resistant. All of the 229 isolates were multiply resistant to other antibiotics. The most prevalent virulence genes of the 24 S. aureus isolates were clfA, coa and spa (X and IgG-binding region) (100%), hla (96%), pvl (96%) and sec (79%). Six S. argenteus isolates carried one enterotoxin gene each and other virulence genes including coa, clfA, hla/hlb, spa, tsst and pvl, indicating their pathogenic potential. Conclusion and perspective This is the first report on the S. argenteus from cow milk samples with SCM. Data on the molecular characteristics, virulence genes and antibiograms of the Staphylococcus spp. obtained from the present study showed a wide spread and increasing trend of methicillin-resistance and multiple resistance to other antibiotics. This suggests that the “One Health” practice should be nurtured, not only at the dairy farm level, but also at the national or even the international levels through cooperation of different sectors (dairy farmers, veterinarians, medical and public health personnel and scientists) in order to effectively combat and control the spread of these pathogens.
Pumipuntu et al. (2019) Staphylococcus spp. associated with subclinical bovine mastitis in central and northeast provinces of Thailand. PeerJ 7:e6587 https://doi.org/10.7717/peerj.6587
Circadian disruption and divergent microbiota acquisition under extended photoperiod regimens in chicken
The gut microbiota is crucial for metabolic homeostasis, immunity, growth and overall health, and it is recognized that early-life microbiota acquisition is a pivotal event for later-life health. Recent studies show that gut microbiota diversity and functional activity are synchronized with the host circadian rhythms in healthy individuals, and circadian disruption elicits dysbiosis in mammalian models. However, no studies have determined the associations between circadian disruption in early life, microbiota colonization, and the consequences for microbiota structure in birds. Chickens, as a major source of protein around the world, are one of the most important agricultural species, and their gut and metabolic health are significant concerns. The poultry industry routinely employs extended photoperiods (>18 h light) as a management tool, and their impacts on the chicken circadian, its role in gut microbiota acquisition in early life (first 3 weeks of life), and consequences for later life microbiota structure remain unknown. In this study, the objectives were to (a) characterize circadian activity under two different light regimes in layer chicken (12/12 h′ Light/Dark (LD) and 23/1 h LD), (b) characterize gut microbiota acquisition and composition in the first 4 weeks of life, (c) determine if gut microbiota oscillate in synchrony with the host circadian rhythm, and (d) to determine if fecal microbiota is representative of cecal microbiota in early life. Expression of clock genes (clock, bmal1, and per2) was assayed, and fecal and cecal microbiotas were characterized using 16S rRNA gene amplicon analyses from birds raised under two photoperiod treatments. Chickens raised under 12/12 LD photoperiods exhibited rhythmic clock gene activity, which was absent in birds raised under the extended (23/1 LD) photoperiod. There was differential microbiota acquisition under different photoperiod regimes in newly hatched chicks. Gut microbiota members showed a similar oscillating pattern as the host, but this association was not as strong as found in mammals. Finally, the fecal microbiota was found to be not representative of cecal microbiota membership and structure in young birds. This is one of the first studies to demonstrate the use of photoperiods to modulate microbiota acquisition in newly hatched chicks, and show their potential as a tool to promote the colonization of beneficial microorganisms.
Hieke et al. (2019) Circadian disruption and divergent microbiota acquisition under extended photoperiod regimens in chicken. PeerJ 7:e6592 https://doi.org/10.7717/peerj.6592