Organic soil amendments using vermicomposts under inoculation of N2-fixing bacteria for sustainable rice production
Organic and biological fertilizers are considered as a very important source of plant nutrients. A field experiment was conducted during 2017−2018 in paddy soil to investigate the effect of vermicomposting of cattle manure mixture with Azolla and rice straw on soil microbial activity, nutrient uptake, and grain yield under inoculation of N2-fixing bacteria. Experimental factors consisted of organic amendments at six levels (vermicomposts prepared from manure (VM); manure + rice straw (VRM); manure + Azolla mixture (VAM); manure + rice straw + Azolla mixture (VRAM); raw manure without vermicomposting (M), and a control) and N2-fixing bacteria at three levels (Azotobacter chroococcum, Azospirillum brasilence, and non−inoculation). The results showed that, vermicompost treatments compared to control and raw manure significantly increased the number and biomass−C of soil microorganisms, urease activity, number of tillers hill−1, phosphorus (P) and potassium (K) uptake, and grain and protein yield. Inoculation of plants with N2-fixing bacteria, especially Azotobacter increased the efficiency of organic amendments, so that the maximum urease activity, soil microbial activity, P and N uptake, and grain yield (4,667 (2017) and 5,081 (2018) kg/h) were observed in vermicompost treatments containing Azolla (VAM and VRAM) under inoculation with Azotobacter. The results of the study suggested that, using an organic source along with inoculation with appropriate N2-fixing bacteria for vermicompost has a great effect on enzyme activity, soil biology, nutrient uptake and grain yield has a synergistic interaction on agronomic traits under flooded conditions. Therefore, this nutrient method can be used as one of the nutrient management strategies in the sustainable rice production.
Ghadimi et al. (2021) Organic soil amendments using vermicomposts under inoculation of N2-fixing bacteria for sustainable rice production. PeerJ 9:e10833 https://doi.org/10.7717/peerj.10833
Weak spatial-genetic structure in a native invasive, the southern pine beetle (Dendroctonus frontalis), across the eastern United States
The southern pine beetle, Dendroctonus frontalis, is a native pest of pine trees that has recently expanded its range into the northeastern United States. Understanding its colonization, dispersal, and connectivity will be critical for mitigating negative economic and ecological impacts in the newly invaded areas. Characterization of spatial-genetic structure can contribute to this; however, previous studies have reached different conclusions about regional population genetic structure, with one study reporting a weak east-west pattern, and the most recent reporting an absence of structure. Here we systematically assessed several explanations for the absence of spatial-genetic structure. To do this, we developed nine new microsatellite markers and combined them with an existing 24-locus data matrix for the same individuals. We then reanalyzed this full dataset alongside datasets in which certain loci were omitted with the goal of creating more favorable signal to noise ratios. We also partitioned the data based on the sex of D. frontalis individuals, and then employed a broad suite of genotypic clustering and isolation-by-distance (IBD) analyses. We found that neither inadequate information content in the molecular marker set, nor unfavorable signal-to-noise ratio, nor insensitivity of the analytical approaches could explain the absence of structure. Regardless of dataset composition, there was little evidence for clusters (i.e., distinct geo-genetic groups) or clines (i.e., gradients of increasing allele frequency differences over larger geographic distances), with one exception: significant IBD was repeatedly detected using an individual-based measure of relatedness whenever datasets included males (but not for female-only datasets). This is strongly indicative of broad-scale female-biased dispersal, which has not previously been reported for D. frontalis, in part owing to logistical limitations of direct approaches (e.g., capture-mark-recapture). Weak spatial-genetic structure suggests long-distance connectivity and that gene flow is high, but additional research is needed to understand range expansion and outbreak dynamics in this species using alternate approaches.
Garrick et al. (2021) Weak spatial-genetic structure in a native invasive, the southern pine beetle (Dendroctonus frontalis), across the eastern United States. PeerJ 9:e11947 https://doi.org/10.7717/peerj.11947
Genomic analysis of early transmissibility assessment of the D614G mutant strain of SARS-CoV-2 in travelers returning to Taiwan from the United States of America
Background There is a global pandemic of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Information on viral genomics is crucial for understanding global dispersion and for providing insight into viral pathogenicity and transmission. Here, we characterized the SARS-CoV-2 genomes isolated from five travelers who returned to Taiwan from the United States of America (USA) between March and April 2020. Methods Haplotype network analysis was performed using genome-wide single-nucleotide variations to trace potential infection routes. To determine the genetic variations and evolutionary trajectory of the isolates, the genomes of isolates were compared to those of global virus strains from GISAID. Pharyngeal specimens were confirmed to be SARS-CoV-2-positive by RT-PCR. Direct whole-genome sequencing was performed, and viral assemblies were subsequently uploaded to GISAID. Comparative genome sequence and single-nucleotide variation analyses were performed. Results The D614G mutation was identified in imported cases, which separated into two clusters related to viruses originally detected in the USA. Our findings highlight the risk of spreading SARS-CoV-2 variants through air travel and the need for continued genomic tracing for the epidemiological investigation and surveillance of SARS-CoV-2 using viral genomic data. Conclusions Continuous genomic surveillance is warranted to trace virus circulation and evolution in different global settings during future outbreaks.
Jian et al. (2021) Genomic analysis of early transmissibility assessment of the D614G mutant strain of SARS-CoV-2 in travelers returning to Taiwan from the United States of America. PeerJ 9:e11991 https://doi.org/10.7717/peerj.11991
The spleen bacteriome of wild rodents and shrews from Marigat, Baringo County, Kenya
Background There is a global increase in reports of emerging diseases, some of which have emerged as spillover events from wild animals. The spleen is a major phagocytic organ and can therefore be probed for systemic microbiome. This study assessed bacterial diversity in the spleen of wild caught small mammals so as to evaluate their utility as surveillance tools for monitoring bacteria in an ecosystem shared with humans. Methods Fifty-four small mammals (rodents and shrews) were trapped from different sites in Marigat, Baringo County, Kenya. To characterize their bacteriome, DNA was extracted from their spleens and the V3–V4 regions of the 16S rRNA amplified and then sequenced on Illumina MiSeq. A non-target control sample was used to track laboratory contaminants. Sequence data was analyzed with Mothur v1.35, and taxomy determined using the SILVA database. The Shannon diversity index was used to estimate bacterial diversity in each animal and then aggregated to genus level before computing the means. Animal species within the rodents and shrews were identified by amplification of mitochondrial cytochrome b (cytb) gene followed by Sanger sequencing. CLC workbench was used to assemble the cytb gene sequences, after which their phylogenetic placements were determined by querying them against the GenBank nucleotide database. Results cytb gene sequences were generated for 49/54 mammalian samples: 38 rodents (Rodentia) and 11 shrews (Eulipotyphyla). Within the order Rodentia, 21 Acomys, eight Mastomys, six Arvicanthis and three Rattus were identified. In the order Eulipotyphyla, 11 Crucidura were identified. Bacteria characterization revealed 17 phyla that grouped into 182 genera. Of the phyla, Proteobacteria was the most abundant (67.9%). Other phyla included Actinobacteria (16.5%), Firmicutes (5.5%), Chlamydiae (3.8%), Chloroflexi (2.6%) and Bacteroidetes (1.3%) among others. Of the potentially pathogenic bacteria, Bartonella was the most abundant (45.6%), followed by Anaplasma (8.0%), Methylobacterium (3.5%), Delftia (3.8%), Coxiella (2.6%), Bradyrhizobium (1.6%) and Acinetobacter (1.1%). Other less abundant (<1%) and potentially pathogenic included Ehrlichia, Rickettsia, Leptospira, Borrelia, Brucella, Chlamydia and Streptococcus. By Shannon diversity index, Acomys spleens carried more diverse bacteria (mean Shannon diversity index of 2.86, p = 0.008) compared to 1.77 for Crocidura, 1.44 for Rattus, 1.40 for Arvicathis and 0.60 for Mastomys. Conclusion This study examined systemic bacteria that are filtered by the spleen and the findings underscore the utility of 16S rRNA deep sequencing in characterizing complex microbiota that are potentially relevant to one health issues. An inherent problem with the V3-V4 region of 16S rRNA is the inability to classify bacteria reliably beyond the genera. Future studies should utilize the newer long read methods of 16S rRNA analysis that can delimit the species composition.
Liyai et al. (2021) The spleen bacteriome of wild rodents and shrews from Marigat, Baringo County, Kenya. PeerJ 9:e12067 https://doi.org/10.7717/peerj.12067
Hemin attenuates response of primary rat adipocytes to adrenergic stimulation
Hemin is an activator of heme oxygenase-1 (HO-1), an enzyme catalyzing heme degradation. Up-regulation of HO-1 is observed in response to various pathological conditions. Moreover, pharmacological activation of HO-1 is associated with numerous beneficial effects in the organism. Hemin was shown to exert, among other, anti-diabetic and anti-obesity properties. These effects are strongly linked with adipose tissue. However, the direct influence of hemin on metabolism of the fat cells have not been explored. The present study aimed to determine the short-term effects of hemin on metabolism of the primary rat adipocytes. We focused on processes directly related to lipid accumulation, such as lipogenesis and lipolysis. For this purpose, the isolated cells were subjected for 2 h to 40 µM hemin, and effects of this compound on insulin-stimulated glucose conversion to lipids, lactate release, lipolysis induced by various stimuli, and also on the antilipolytic action of insulin were determined. It was shown that hemin did not affect insulin-induced lipogenesis and lactate release. However, hemin significantly decreased lipolysis stimulated by epinephrine. The inhibitory effect of hemin on epinephrine-induced lipolysis was not abolished in the presence of SnMP, an inhibitor of HO-1, which suggests hemin action irrespective of this enzyme. Similar inhibitory effects on epinephrine-induced lipolysis were observed in the presence of 3 and 12 mM glucose. Moreover, hemin was shown to reduce epinephrine-induced lipolysis also when glucose was replaced by alanine or by succinate. Apart from changes in epinephrine action, it was found that the lipolytic response of the adipocytes to isoproterenol was also diminished by hemin. However, hemin failed to affect lipolysis stimulated by dibutyryl-cAMP (a direct activator of protein kinase A), forskolin (an activator of adenylate cyclase), and also by DPCPX (an adenosine A1 receptor antagonist). Additionally, epinephrine-induced lipolysis was shown to be decreased by insulin, and this effect was deepened in the presence of hemin. These results indicate that short-term exposure of the adipocytes to hemin does not affect processes related to glucose metabolism, such as lipogenesis and lactate release. However, hemin was found to decrease the lipolytic response to adrenergic stimulation, which is associated with reduced lipid release from adipocytes. Moreover, our results indicate that hemin is also capable of diminishing the exaggerated lipolysis, which occurs in the presence of supraphysiological concentrations of glucose.
Szkudelski et al. (2021) Hemin attenuates response of primary rat adipocytes to adrenergic stimulation. PeerJ 9:e12092 https://doi.org/10.7717/peerj.12092
Species diversity and community structure of crustacean zooplankton in the highland small waterbodies in Northwest Yunnan, China
Small waterbodies are a unique aquatic ecosystem with an increasing recognition for their important role in maintaining regional biodiversity and delivering ecosystem services. However, small waterbodies in Northwest Yunnan, one of the most concerned global biodiversity hot-spots, remain largely unknown. Here, we investigated the community structure of crustacean zooplankton and their relationships with limnological, morphometric and spatial variables in the highland small waterbodies in Northwest Yunnan in both the dry (October 2015) and rainy (June 2016) seasons. A total of 38 species of crustacean zooplankton were identified in our study, which is significantly higher than many other reported waterbodies in the Yunnan–Guizhou plateau as well as in the Yangtze River basin. This suggests that the highland small waterbodies are critical in maintaining regional zooplankton diversity in Northwest Yunnan. Meanwhile, we found limnological variables could explain most variation of crustacean zooplankton community, comparing to the morphometric and spatial variables in both the rainy and dry seasons. Our study revealed the diversity and community structure of crustacean zooplankton in the highland small waterbodies in Northwest Yunnan and highlighted the importance of small waterbodies in maintaining regional biodiversity.
Chen et al. (2021) Species diversity and community structure of crustacean zooplankton in the highland small waterbodies in Northwest Yunnan, China. PeerJ 9:e12103 https://doi.org/10.7717/peerj.12103
Extending density surface models to include multiple and double-observer survey data
Spatial models of density and abundance are widely used in both ecological research (e.g., to study habitat use) and wildlife management (e.g., for population monitoring and environmental impact assessment). Increasingly, modellers are tasked with integrating data from multiple sources, collected via different observation processes. Distance sampling is an efficient and widely used survey and analysis technique. Within this framework, observation processes are modelled via detection functions. We seek to take multiple data sources and fit them in a single spatial model. Density surface models (DSMs) are a two-stage approach: first accounting for detectability via distance sampling methods, then modelling distribution via a generalized additive model. However, current software and theory does not address the issue of multiple data sources. We extend the DSM approach to accommodate data from multiple surveys, collected via conventional distance sampling, double-observer distance sampling (used to account for incomplete detection at zero distance) and strip transects. Variance propagation ensures that uncertainty is correctly accounted for in final estimates of abundance. Methods described here are implemented in the dsm R package. We briefly analyse two datasets to illustrate these new developments. Our new methodology enables data from multiple distance sampling surveys of different types to be treated in a single spatial model, enabling more robust abundance estimation, potentially over wider geographical or temporal domains.
Miller et al. (2021) Extending density surface models to include multiple and double-observer survey data. PeerJ 9:e12113 https://doi.org/10.7717/peerj.12113
Level of anxiety among healthcare providers during COVID-19 pandemic in Saudi Arabia: cross-sectional study
Background The burden of the spread of the COVID-19 pandemic has impacted widely on the healthcare providers physically and mentally. Many healthcare providers are exposed to psychological stressors due to their high risk of contracting the virus. Aims This study aimed to measure the level of anxiety among healthcare providers during the COVID-19 pandemic in Saudi Arabia. In addition, this study aimed to measure the level of anxiety based on demographic characteristics. Method A cross-sectional survey was employed to recruit a convenience sample of healthcare providers. A pencil and paper self-administered questionnaires were used to collect data from demographic and generalized anxiety disorder GAD-7 data. However, this study received written informed consent from participants of the study. In addition, the study was approved by the Institutional Review Board at Dr. Sulaiman Al Habib Medical Group (IRB Log No. RC20.06.88-03). Results A total of 650 participants were recruited, results of GAD-7 showed that 43.5%, 28.9% and 27.5% of healthcare providers in Saudi Arabia experienced mild, moderate and severe anxiety, respectively, during the COVID-19 pandemic. Results indicated that age, health specialty, nationality, and sleeping disorders before COVID-19 were associated with anxiety levels. Conclusion The generalized anxiety among healthcare providers in Saudi Arabia was mild. Older healthcare providers were found to have a higher level of anxiety compared to other participating healthcare providers. Several factors may contribute to a higher level of anxiety including age, socioeconomic status, marital status, having chronic conditions, and sleeping disorder before the COVID-19 pandemic. To further understand the level of anxiety among healthcare providers during the COVID-19 pandemic in Saudi Arabia, longitudinal and mixed-method research is needed.
Al Mutair et al. (2021) Level of anxiety among healthcare providers during COVID-19 pandemic in Saudi Arabia: cross-sectional study. PeerJ 9:e12119 https://doi.org/10.7717/peerj.12119
Revisiting food-sourced vitamins for consumer diet and health needs: a perspective review, from vitamin classification, metabolic functions, absorption, utilization, to balancing nutritional requirements
The significant attention gained by food-sourced vitamins has provided insights into numerous current researches; for instance, the potential reversal of epigenetic age using a diet and lifestyle intervention, the balance between food and dietary supplements in the general population, the role of diet and food intake in age-related macular degeneration, and the association of dietary supplement use, nutrient intake and mortality among adults. As relevant literature about food-sourced vitamin increases, continuous synthesis is warranted. To supplement existing information, this perspective review discussed food-sourced vitamins for consumer diet and health needs, scoping from vitamin absorption, metabolic functions, utilization, to balancing nutritional requirements. Relevant literatures were identified through a search of databases like Google Scholar, Web of Science, the Interscience Online Library, ScienceDirect, and PubMed. We demonstrated that vitamins whether from plant- and animal-based sources are prerequisites for the metabolic functions of the human body. The fat- and water-soluble classification of vitamins remains consistent with their respective absorption and dissolution potentials, underpinned by numerous physiological functions. Vitamins, largely absorbed in the small intestine, have their bioavailability dependent on the food composition, its associated interactions, as well as alignment with their metabolic functions, which involves antioxidants, coenzymes, electron acceptor/donor, and hormones. Moreover, vitamin deficiencies, in every form, pose a serious threat to human health. Vitamin toxicities remain rare, but can still occur mainly from supplementation, although it appears much less in water-soluble vitamins of which some excesses get readily removed by the human body, different from the fat-soluble ones that are stored in tissues and organs. Besides discussions of absorption, transport, and cellular uptake of vitamins, this perspective review also included approaches to meeting vitamin requirements and therapeutic strategies against micronutrient deficiency and COVID-19. We have also attempted on how to strike the balance between food-sourced vitamins and dietary supplements.
Ofoedu et al. (2021) Revisiting food-sourced vitamins for consumer diet and health needs: a perspective review, from vitamin classification, metabolic functions, absorption, utilization, to balancing nutritional requirements. PeerJ 9:e11940 https://doi.org/10.7717/peerj.11940
Antimicrobial resistance among Enterobacteriaceae, Staphylococcus aureus, and Pseudomonas spp. isolates from clinical specimens from a hospital in Nairobi, Kenya
Background Antimicrobial resistance among pathogens of public health importance is an emerging problem in sub-Saharan Africa. Unfortunately, published information on the burden and patterns of antimicrobial resistance (AMR) in this region is sparse. There is evidence that the burden and patterns of AMR vary by geography and facility. Knowledge of local epidemiology of AMR is thus important for guiding clinical decisions and mitigation strategies. Therefore, the objective of this study was to determine the burden and predictors of AMR and multidrug resistance (MDR) among bacterial pathogens isolated from specimens submitted to the diagnostic laboratory of a hospital in Nairobi, Kenya. Methods This retrospective study used laboratory records of 1,217 clinical specimens submitted for bacterial culture and sensitivity testing at the diagnostic laboratory of The Karen Hospital in Nairobi, Kenya between 2012 and 2016. Records from specimens positive for Enterobacteriaceae, Staphylococcus aureus, or Pseudomonas spp. isolates were included for analysis. Firth logistic models, which minimize small sample bias, were used to investigate determinants of AMR and MDR of the isolates. Results A total of 222 specimens had bacterial growth. Most Enterobacteriaceae isolates were resistant to commonly used drugs such as penicillin/β-lactamase inhibitor combinations (91.2%) and folate pathway inhibitors (83.7%). Resistance to extended-spectrum cephalosporins was also high (52.9%). Levels of AMR and MDR for Enterobacteriaceae were 88.5% and 51%, respectively. Among S. aureus isolates, 57.1% were AMR, while 16.7% were MDR. As many as 42.1% of the Pseudomonas spp. isolates were aminoglycoside-resistant and 15% were fluoroquinolone-resistant, but none exhibited resistance to antipseudomonal carbapenems. Half of Pseudomonas spp. isolates were AMR but none were MDR. Significant predictors of MDR among Enterobacteriaceae were organism species (p = 0.002) and patient gender (p = 0.024). Conclusions The high levels of extended-spectrum cephalosporin resistance and MDR among Enterobacteriaceae isolates are concerning. However, the relatively low levels of MDR S. aureus, and an absence of carbapenem resistance among Pseudomonas isolates, suggests that last-line drugs are still effective against S. aureus and Pseudomonas infections. These findings are relevant for guiding evidence-based treatment decisions as well as surveillance efforts and directions for future research, and contribute to the sparse literature on AMR in sub-Saharan Africa.
Lord et al. (2021) Antimicrobial resistance among Enterobacteriaceae, Staphylococcus aureus, and Pseudomonas spp. isolates from clinical specimens from a hospital in Nairobi, Kenya. PeerJ 9:e11958 https://doi.org/10.7717/peerj.11958