title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=669 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: Evaluation of colonization and mutualistic endophytic symbiosis of Escherichia coli with tomato and Bermuda grass seedlings link: https://peerj.com/articles/13879 last-modified: 2022-08-10 description: Escherichia coli is generally considered a bacterium associated with animal microbiomes. However, we present evidence that E. coli may also mutualistically colonize roots of plant species, even to the extent that it may become endophytic in plants. In this study we used GFP tagged E. coli to observe its colonization and effects on tomato (Solanum lycopersicum) and Bermuda grass (Cynodon dactylon) seedling development and growth. Inoculation with the bacterium significantly improved root development of both seedlings tested. Treatment also increased the photosynthetic pigments in Bermuda grass seedlings. However, effects on shoot length in both seedlings were not significant. This bacterium was found to produce indole acetic acid (IAA) up to 8.68 ± 0.43 µg ml−1 in the broth medium amended with tryptophan. Effects on seedling root growth could, in part, be explained by IAA production. Bacteria successfully colonized the root surfaces and interiors of both seedlings. Tagged bacteria expressing the GFP were observed in the vascular tissues of Bermuda grass seedling roots. Seedlings with bacteria showed greater survival and were healthier than seedlings without bacteria, indicating that E. coli set up a successful mutualistic symbiosis with seedlings. E. coli is not commonly considered to be a plant endophyte but is more generally considered to be a crop contaminant. In this study we show that E. coli may also be an endophyte in plant tissues. creator: Satish K. Verma creator: Qiang Chen creator: James Francis White uri: https://doi.org/10.7717/peerj.13879 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Verma et al. title: Accuracy of anthropometric indicators of obesity to identify high blood pressure in adolescents—systematic review link: https://peerj.com/articles/13590 last-modified: 2022-08-09 description: BackgroundAnthropometric indicators of obesity have been associated with blood pressure in adolescents. However, the accuracy of anthropometric indicators of obesity for screening for high blood pressure (HBP) in adolescents is not known. Thus, the aim of the present study was to summarize the set of evidence regarding the predictive ability of anthropometric indicators of obesity to identify HBP in adolescents.MethodsSearches were performed in five databases: MEDLINE, Web of Knowledge, Scopus, Scientific Electronic online (SciELO) and SportDiscus. The inclusion criteria for studies were: adolescents aged 10–19 years or mean age included in this range, observational and intervention studies, studies that proposed cutoff points for anthropometric indicators of obesity, and studies in English, Portuguese and Spanish. The methodological quality of studies was assessed using the QUADAS-2 instrument.ResultsTen studies met the inclusion criteria and had their information summarized. Based on the information described in these studies, the anthropometric indicators body mass index (BMI), waist circumference (WC), waist-to-height-ratio (WHtR), triceps skinfold thickness, body adiposity index, C index, body mass, waist-to-arm span ratio, arm fat area, average arm perimeter, fat percentage and arm span were likely to be used in high blood pressure (HBP) screening among adolescents. However, only one study showed acceptable values (moderate to high precision) in relation to the accuracy measurements of described cutoffs.ConclusionCaution is suggested in the use of anthropometric indicators of obesity for HBP screening in adolescents, in which a greater number of studies with accurate diagnostic tools are necessary. creator: Leandro Lima Borges creator: Tiago Rodrigues de Lima creator: Diego Augusto Santos Silva uri: https://doi.org/10.7717/peerj.13590 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Lima Borges et al. title: Deep evaluation of the evolutionary history of the Heat Shock Factor (HSF) gene family and its expansion pattern in seed plants link: https://peerj.com/articles/13603 last-modified: 2022-08-09 description: Heat shock factor (HSF) genes are essential in some of the basic developmental pathways in plants. Despite extensive studies on the structure, functional diversification, and evolution of HSF genes, their divergence history and gene duplication pattern remain unknown. To further illustrate the probable divergence patterns in these subfamilies, we analyzed the evolutionary history of HSF genes using phylogenetic reconstruction and genomic syntenic analyses, taking advantage of the increased sampling of genomic data from pteridophytes, gymnosperms and basal angiosperms. We identified a novel clade that includes HSFA2, HSFA6, HSFA7, and HSFA9 with a complex relationship, which is very likely due to orthologous or paralogous genes retained after frequent gene duplication events. We hypothesized that HSFA9 derives from HSFA2 through gene duplication in eudicots at the ancestral state, and then expanded in a lineage-specific way. Our findings indicate that HSFB3 and HSFB5 emerged before the divergence of ancestral angiosperms, but were lost in the most recent common ancestors of monocots. We also presumed that HSFC2 derives from HSFC1 in ancestral monocots. This work proposes that during the radiation of flowering plants, an era during which there was a differentiation of angiosperms, the size of the HSF gene family was also being adjusted with considerable sub- or neo-functionalization. The independent evolution of HSFs in eudicots and monocots, including lineage-specific gene duplication, gave rise to a new gene in ancestral eudicots and monocots, and lineage-specific gene loss in ancestral monocots. Our analyses provide essential insights for studying the evolutionary history of this multigene family. creator: Yiying Liao creator: Zhiming Liu creator: Andrew W. Gichira creator: Min Yang creator: Ruth Wambui Mbichi creator: Linping Meng creator: Tao Wan uri: https://doi.org/10.7717/peerj.13603 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Liao et al. title: Spatio-temporal distribution of ostracod species in saline inland lakes (Mansfeld lake area; Central Germany) link: https://peerj.com/articles/13668 last-modified: 2022-08-09 description: Ostracods are a diverse group of microcrustaceans with a ubiquitous distribution in a wide array of aquatic habitats and are common constituents of lake sediments. Inferences on the temporal-spatial distribution of ostracod species is a prerequisite for reconstructions of palaeoenvironmental conditions. This requires a precise knowledge not only about ecological preferences and specific life histories, but also the understanding how (local) ecological parameters affect ostracod species assemblages (abundance and composition). Generally, these studies are rare and often characterized by an insufficient differentiation of living specimens from the total amount of valves of the modern population leading to uncertainties in species occurrences and diversity data. Modern ostracod populations were sampled from 12 water bodies within a relatively small study area (Mansfeld lake area, Central Germany). Physico-chemical parameters (temperature, oxygen content, conductivity, pH) were measured in situ and the uppermost 2 cm of sediment were collected in different seasons (April, June, September). Relative abundances of ostracods (living and dead), differentiated for adults and juveniles, were used for statistical analyses (Spearman‘s rank correlation, Canonical correspondence analysis, Cluster analyses, Fisher’s α), to investigate relationships between species distribution and environmental factors as well as to identify habitat similarities and ostracod species assemblages. In total, 27 ostracod species (20 living species) were identified. Majority of them are considered as very common (cosmopolitan) freshwater species. Only two species are usually known from brackish water (Cytheromorpha fuscata and Cyprideis torosa). This is the first confirmation of living C. torosa in German inland waters. The relative abundances of ostracods show strong fluctuations during the study period and differences in composition of the ostracod species assemblages between and within the water bodies. There are also strong differences between bio- and taphocoenoses. The measured physico-chemical parameters which are usually considered as most important drivers on ostracod species distribution do not contribute to explain the observed temporal-spatial distribution of the ostracod species. Differences in taphocoenoses show, that taphonomic processes can be very local and the sampling site, as well as the sampling time, is crucial. Biodiversity of ostracods is biased by sampling time, the variability of the ostracod assemblages between sampling month and the relationship between abundance of valves and living ostracods is not straightforward. Therefore, without precise knowledge of the ecological requirements of a species at a local scale, uncertainties may exist for the palaeoecological indication of a species. creator: Marlene Hoehle creator: Claudia Wrozyna uri: https://doi.org/10.7717/peerj.13668 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Hoehle and Wrozyna title: Genome-wide characterization and expression analysis of bHLH gene family in physic nut (Jatropha curcas L.) link: https://peerj.com/articles/13786 last-modified: 2022-08-09 description: The basic helix loop helix (bHLH) transcription factor perform essential roles in plant development and abiotic stress. Here, a total of 122 bHLH family members were identified from the physic nut (Jatropha curcas L.) genomic database. Chromosomal localization results showed that 120 members were located on 11 chromosomes. The phylogenetic tree manifested that the JcbHLHs could be grouped into 28 subfamilies. Syntenic analysis showed that there were 10 bHLH collinear genes among the physic nut, Arabidopsis thaliana and Oryza sativa. These genes, except JcbHLH84, were highly expressed in various tissues of the physic nut, implying a key role in plant development. Gene expression profiles showed that ten genes (especially JcbHLH33, JcbHLH45 and JcbHLH55) correspond to both salinity and drought stresses; while eight genes only respond to salinity and another eight genes only respond to drought stress. Moreover, the protein interaction network revealed that the JcbHLHs are involved in growth, development and stress signal transduction pathways. These discoveries will help to excavate several key genes may involve in salt or drought stresses and seed development, elucidate the complex transcriptional regulation mechanism of JcbHLH genes and provide the theoretical basis for stress response and genetic improvement of physic nut. creator: Lin Zhang creator: Wei Chen creator: Rongrong Liu creator: Ben Shi creator: Youju Shu creator: Haoyu Zhang uri: https://doi.org/10.7717/peerj.13786 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Zhang et al. title: The use of synthetic agonists of quorum sensing N- acyl homoserine lactone pathway improves the bioleaching ability in Acidithiobacillus and Pseudomonas bacteria link: https://peerj.com/articles/13801 last-modified: 2022-08-09 description: Metal solubilization from discarded electrical material and electronic devices (e-waste) using the bioleaching capabilities of bacterial cells is highly effective. However, gaps in understanding about the microbiological processes involved in the bioleaching reaction leads to less efficient metal solubilization in large-scale e-waste processing. In this study, bacterial species belonging to the genera Acidithiobacillus and Pseudomonas were used to leach copper and gold from discarded printed circuit boards (PCB). Through modulation of the cell-to-cell communication system in these bacteria, phenotypic traits directly involved in the bioleaching reaction were regulated in order to improve the metal solubilization. Addition of the long chain synthetic autoinducer molecule N-acyl homoserine lactone (AHL) of the quorum sensing pathway to the bioleaching reaction resulted in a significant enhancement of metal extraction from PCB. Factors such as: cell attachment to PCB, biofilm formation and hydrogen cyanide (HCN) production were regulated by the quorum sensing system and could be directly related to the improvement of metal bioleaching. Bioleaching reactions using bacterial quorum sensing modulation could represent a valuable tool in overcoming limitations at the industrial level imposed by microbiological traits that lead to inefficient metal bioleaching from e-waste. creator: Juan Carlos Caicedo creator: Sonia Villamizar creator: Giampaolo Orlandoni uri: https://doi.org/10.7717/peerj.13801 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Caicedo et al. title: Arbuscular mycorrhizal fungi enhanced the growth, phosphorus uptake and Pht expression of olive (Olea europaea L.) plantlets link: https://peerj.com/articles/13813 last-modified: 2022-08-09 description: Olive (Olea europaea L.) is a highly mycotrophic species that has been introduced and cultivated in China for half a century. The arbuscular mycorrhizal fungi (AMF) is extremely valuable as a kind of biofertilizer to promote the health and vigor of olive plants. However, it is still unclear how native AMF impact growth and mineral nutrients, especially phosphorus absorption in the area where olive trees were introduced in China. In the present study, through a pot experiment, the effects of native AMF on the growth, phosphorus uptake and expression levels of four phosphate transporter genes (Pht) of olive plantlets were characterized. We found that (1) typical AMF colonization was observed within the roots of inoculated olive plantlets, and the growth of plantlets was significantly promoted; (2) some indigenous consortia (AMF1 and AMF2) notably promoted the absorption of phosphorus, fertilizers significantly increased the foliar content of nitrogen, and both AMF inoculation and fertilization had no significant effect on the uptake of potassium; and (3) AMF inoculation enhanced the expression of phosphate transporter genes in inoculated olive roots. This work demonstrates the effectiveness of native AMF on the cultivation of robust olive plantlets and highlights the role of AMF in increasing phosphorus uptake. There is great potential in using native AMF consortia as inoculants for the production of healthy and robust olive plantlets. creator: Tao Wu creator: Li Pan creator: Isaac Zipori creator: Jihua Mao creator: Rongbo Li creator: Yongpeng Li creator: Yongjie Li creator: Yuebo Jing creator: Haiyun Chen uri: https://doi.org/10.7717/peerj.13813 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Wu et al. title: Association between lung function impairment with urinary heavy metals in a community in Klang Valley, Malaysia link: https://peerj.com/articles/13845 last-modified: 2022-08-09 description: Lung function status can be directly or indirectly affected by exposure to pollutants in the environment. Urinary heavy metals may be an indirect indicator of lung function impairment that leads to various diseases such as chronic obstructive pulmonary disease (COPD). This study aimed to explore the prevalence of lung function impairment as well as its association with urinary heavy metal levels and other influencing factors among the community in Klang Valley, Malaysia. Urinary sampling was done during various community events in the housing areas of Klang Valley between March and October 2019. Only respondents who consented would undergo a lung function test. Urine samples were obtained and sent for Inductively Coupled Plasma Mass Spectrometry (ICP-MS) analysis for heavy metal cadmium (Cd) and lead (Pb) concentration. Of the 200 recruited respondents, 52% were male and their ages ranged from 18 years old to 74 years old with a mean age of 38.4 ± 14.05 years. Urinary samples show high urinary Cd level in 12% of the respondents (n = 24) whereas none recorded a high urinary Pb level. There was a positive correlation between the levels of urinary Cd and urinary Pb (r = 0.303; p = 0.001). Furthermore, a negative correlation was detected between urinary Cd level and forced vital capacity (FVC) (r =  − 0.202, p = 0.004), force expiratory volume at the first second (FEV1) (r =  − 0.225, p = 0.001), and also force expiratory flow between 25–75% of FVC (FEF 25–75%) (r =  − 0.187, p = 0.008). However, urinary Pb did not show any correlation with lung function parameters. Multiple linear regression analysis showed that urinary Cd had a significant negative effect on FVC (p = 0.025) and FEV1 (p = 0.004) based on the predicted value. Additionally, other factors such as education level (p = 0.013) also influenced lung function. However, no interaction was detected between heavy metals or other factors. In short, there was a significant negative linear relationship between urinary Cd and lung function, whereas urinary Pb was not associated with lung function. Beside acting as a biomarker for cadmium exposure level, urinary Cd may also be applied as indirect biomarker for asymptomatic chronic lung function deterioration among the healthy population. creator: Ammar Amsyar Abdul Haddi creator: Mohd Hasni Ja’afar creator: Halim Ismail uri: https://doi.org/10.7717/peerj.13845 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Abdul Haddi et al. title: Application of plasma metabolome for monitoring the effect of rivaroxaban in patients with nonvalvular atrial fibrillation link: https://peerj.com/articles/13853 last-modified: 2022-08-09 description: Rivaroxaban, an oral factor Xa inhibitor, has been used to treating a series of thromboembolic disorders in clinical practice. Measurement of the anticoagulant effect of rivaroxaban is important to avoid serious bleeding events, thus ensuring the safety and efficacy of drug administration. Metabolomics could help to predict differences in the responses among patients by profiling metabolites in biosamples. In this study, plasma metabolomes before and 3 hours after rivaroxaban intake in 150 nonvalvular atrial fibrillation (NVAF) patients and 100 age/gender-matched controls were analyzed by liquid chromatography coupled with mass spectrometry (LC–MS/MS). When compared with controls, a total of thirteen plasma metabolites were differentially expressed in the NVAF patients. Pathway analysis revealed that purine and lipid metabolism were dysregulated. A panel of three metabolites (17a-ethynylestradiol, tryptophyl-glutamate and adenosine) showed good predictive ability to distinguish nonvalvular atrial fibrillation with an area under the receiver operating characteristic curve (AUC) of 1 for the discovery phase and 1 for validation. Under rivaroxaban treatment, a total of seven metabolites changed, the lipid and glycosylphosphatidylinositol biosynthesis pathways were altered and the panel consisting of avocadene, prenyl glucoside and phosphatidylethanolamine showed predictive ability with an AUC of 0.86 for the discovery dataset and 0.82 for the validation. The study showed that plasma metabolomic analyses hold the potential to differentiate nonvalvular atrial fibrillation and can help to monitor the effect of rivaroxaban anticoagulation. creator: Mindi Zhao creator: Xiaoyan Liu creator: Xiaoxiao Bu creator: Yao Li creator: Meng Wang creator: Bo Zhang creator: Wei Sun creator: Chuanbao Li uri: https://doi.org/10.7717/peerj.13853 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Zhao et al. title: Full-length 16S rRNA amplicon sequencing reveals the variation of epibiotic microbiota associated with two shrimp species of Alvinocarididae: possibly co-determined by environmental heterogeneity and specific recognition of hosts link: https://peerj.com/articles/13758 last-modified: 2022-08-08 description: Shrimps of the family Alvinocarididae, endemic species to deep sea chemosynthetic ecosystems, harbor epibiotic microbes on gills which probably play important roles in the survival of the shrimps. Among them, Alvinocaris longirostris and Shinkaicaris leurokolos occupy different ecological niches within the same hydrothermal vent in Okinawa Trough, and A. longirostris also exists in a methane seep of the South China Sea. In this study, full-length 16S rRNA sequences of the gill associated bacteria of two alvinocaridid species from different chemosynthetically ecological niches were first captured by single-molecule real-time sequencing. Totally, 120,792 optimized circular consensus sequences with ∼1,450 bp in length were obtained and clustered into 578 operational taxonomic units. Alpha diversity analysis showed seep A. longirostris had the highest species richness and evenness (average Chao1 = 213.68, Shannon = 3.39). Beta diversity analysis revealed that all samples were clearly divided into three groups, and microbial community of A. longirostris from seep and vent were more related than the other comparisons. By permutational multivariate analysis of variance, the most significant community compositional variance was detected between seep A. longirostris and vent S. leurokolos (R2 = 0.731, P = 0.001). The taxon tags were further classified into 21 phyla, 40 classes, 89 orders, 124 families and 135 genera. Overall, the microbial communities were dominated by Campylobacteria and Gammaproteobacteria. Alphaproteobacteria, Bacteroidia, Verrucomicrobiae, Bacilli and other minor groups were also detected at lower abundance. Taxonomic groups recovered from the vent S. leurokolos samples were only dominated by Sulfurovaceae (94.06%). In comparison, gill-associated microbiota of vent A. longirostris consisted of more diverse sulfur-oxidizing bacteria, including Sulfurovaceae (69.21%), Thiotrichaceae (6.77%) and a putative novel Gammaproteobacteria group (14.37%), while in seep A. longirostris, Gammaproteobacteria un-group (44.01%) constituted the major component, following the methane-oxidizing bacteria Methylomonadaceae (19.38%), and Sulfurovaceae (18.66%). Therefore, the gill associated bacteria composition and abundance of alvinocaridid shrimps are closely related to the habitat heterogeneity and the selection of microbiota by the host. However, the interaction between these alvinocaridid shrimps and the epibiotic communities requires further study based on metagenome sequencing and fluorescence in situ hybridization. creator: Min Hui creator: Aiyang Wang creator: Jiao Cheng creator: Zhongli Sha uri: https://doi.org/10.7717/peerj.13758 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Hui et al.