ensembleTax: an R package for determinations of ensemble taxonomic assignments of phylogenetically-informative marker gene sequences
Background High-throughput sequencing of phylogenetically informative marker genes is a widely used method to assess the diversity and composition of microbial communities. Taxonomic assignment of sampled marker gene sequences (referred to as amplicon sequence variants, or ASVs) imparts ecological significance to these genetic data. To assign taxonomy to an ASV, a taxonomic assignment algorithm compares the ASV to a collection of reference sequences (a reference database) with known taxonomic affiliations. However, many taxonomic assignment algorithms and reference databases are available, and the optimal algorithm and database for a particular scientific question is often unclear. Here, we present the ensembleTax R package, which provides an efficient framework for integrating taxonomic assignments predicted with any number of taxonomic assignment algorithms and reference databases to determine ensemble taxonomic assignments for ASVs. Methods The ensembleTax R package relies on two core algorithms: taxmapper and assign.ensembleTax. The taxmapper algorithm maps taxonomic assignments derived from one reference database onto the taxonomic nomenclature (a set of taxonomic naming and ranking conventions) of another reference database. The assign.ensembleTax algorithm computes ensemble taxonomic assignments for each ASV in a data set based on any number of taxonomic assignments determined with independent methods. Various parameters allow analysts to prioritize obtaining either more ASVs with more predicted clade names or more robust clade name predictions supported by multiple independent methods in ensemble taxonomic assignments. Results The ensembleTax R package is used to compute two sets of ensemble taxonomic assignments for a collection of protistan ASVs sampled from the coastal ocean. Comparisons of taxonomic assignments predicted by individual methods with those predicted by ensemble methods show that conservative implementations of the ensembleTax package minimize disagreements between taxonomic assignments predicted by individual and ensemble methods, but result in ASVs with fewer ranks assigned taxonomy. Less conservative implementations of the ensembleTax package result in an increased fraction of ASVs classified at all taxonomic ranks, but increase the number of ASVs for which ensemble assignments disagree with those predicted by individual methods. Discussion We discuss how implementation of the ensembleTax R package may be optimized to address specific scientific objectives based on the results of the application of the ensembleTax package to marine protist communities. While further work is required to evaluate the accuracy of ensemble taxonomic assignments relative to taxonomic assignments predicted by individual methods, we also discuss scenarios where ensemble methods are expected to improve the accuracy of taxonomy prediction for ASVs.
Catlett et al. (2021) ensembleTax: an R package for determinations of ensemble taxonomic assignments of phylogenetically-informative marker gene sequences. PeerJ 9:e11865 https://doi.org/10.7717/peerj.11865
How C: N: P stoichiometry in soils and carbon distribution in plants respond to forest age in a Pinus tabuliformis plantation in the mountainous area of eastern Liaoning Province, China
Carbon distribution in plants and ecological stoichiometry in soils are important indicators of element cycling and ecosystem stability. In this study, five forest ages, young forest (YF), middle-aged forest (MAF), near-mature forest (NMF), mature forest (MF), and over-mature forest (OMF) in a Pinus tabuliformis plantation were chosen to illustrate interactions among the C: N: P stoichiometry in soils and carbon distribution in plants, in the mountainous area of eastern Liaoning, China. Carbon content was highest in the leaves of MAF (505.90 g⋅kg−1) and NMF (509.00 g⋅kg−1) and the trunks of YF (503.72 g⋅kg−1), MF (509.73 g⋅kg−1), and OMF (504.90 g⋅kg−1), and was lowest in the branches over the entire life cycle of the aboveground components (335.00 g⋅kg−1). The carbon content of the fine roots decreased with soil layer depth. In YF, MAF, and NMF carbon content of fine roots at 0.5 m was always higher than that of fine roots at 1 m; however, it was the opposite in MF and OMF. The carbon content of the leaves changed with forest age; however, carbon content of branches, trunks and fine roots did not change significantly. Soil total carbon (TC), total nitrogen (TN), total phosphorus (TP), and available phosphorus (AP) content was highest in the OMF. Soil TC, TN and AP content, and TC: TN, TC: TP and TN: TP ratio decreased with increasing soil depth. Soil TC, TN, and TP content had a significant effect on the carbon content of fine roots (p < 0.05). The leaf carbon content and soil element content changed obviously with forest age, and the soil TN, TP and AP increased, which might reduce the carbon content allocation of fine roots.
Wang et al. (2021) How C: N: P stoichiometry in soils and carbon distribution in plants respond to forest age in a Pinus tabuliformis plantation in the mountainous area of eastern Liaoning Province, China. PeerJ 9:e11873 https://doi.org/10.7717/peerj.11873
Inter-ethnic genetic variations and novel variant identification in the partial sequences of CYP2B6 gene in Pakistani population
Background Some single nucleotide polymorphisms (SNPs) in the cytochrome P450 (CYP)2B6 gene lead to decreased enzyme activity and have an impact on drug metabolism. The present study was designed to investigate the patterns of genetic distinction across a hypervariable region of the CYP2B6 gene, known to contain important SNPs, i.e. rs4803419 and rs3745274, among five major ethnic groups of the Pakistani population. Methods Arlequin v3.5.DnaSPv6.12. and network 5 resources were used to analyze population genetic variance in the partial CYP2B6 gene sequences obtained from 104 human samples belonging to Punjabi, Pathan, Sindhi, Seraiki and Baloch ethnicities of Pakistan. The partial CYP2B6 gene region analyzed in the current study is previously known to possess important SNPs. Results The data analyses revealed that genetic variance among samples mainly came from differentiation within the ethnic groups. However, significant genetic variation was also found among the various ethnic groups. The high pairwise Fst genetic distinction was observed between Seraiki and Sindhi ethnic groups (Fst = 0.13392, P-value = 0.026) as well as between Seraiki and Balochi groups (Fst = 0.04303, P-value = −0.0030). However, the degree of genetic distinction was low between Pathan and Punjabi ethnic groups. Some SNPs, including rs3745274 and rs4803419, which are previously shown in strong association with increased plasma Efavirenz level, were found in high frequency. Besides, a novel SNP, which was not found in dbSNP and Ensemble databases, was identified in the Balochi ethnicity. This novel SNP is predicted to affect the CYP2B6 splicing pattern. Conclusion These results may have significant implications in Pakistani ethnicities in the context of drugs metabolized by CYP2B6, especially in Seraiki and Balochi ethnicity. The novel heterogeneous SNP, found in the present study, might lead to altered drug-metabolizing potential of CYP2B6 and, therefore, may be implicated in non-responder phenomenon.
Ahmed et al. (2021) Inter-ethnic genetic variations and novel variant identification in the partial sequences of CYP2B6 gene in Pakistani population. PeerJ 9:e11149 https://doi.org/10.7717/peerj.11149
Phenotypic plasticity and evolution of thermal tolerance in bacteria from temperate and hot spring environments
Phenotypic plasticity allows individuals to respond to the selective forces of a new environment, followed by adaptive evolution. We do not know to what extent phenotypic plasticity allows thermal tolerance evolution in bacteria at the border of their physiological limits. We analyzed growth and reaction norms to temperature of strains of two bacterial lineages, Bacillus cereus sensu lato and Bacillus subtilis sensu lato, that evolved in two contrasting environments, a temperate lagoon (T) and a hot spring (H). Our results showed that despite the co-occurrence of members of both lineages in the two contrasting environments, norms of reactions to temperature exhibited a similar pattern only in strains within the lineages, suggesting fixed phenotypic plasticity. Additionally, strains from the H environment showed only two to three degrees centigrade more heat tolerance than strains from the T environment. Their viability decreased at temperatures above their optimal for growth, particularly for the B. cereus lineage. However, sporulation occurred at all temperatures, consistent with the known cell population heterogeneity that allows the Bacillus to anticipate adversity. We suggest that these mesophilic strains survive in the hot-spring as spores and complete their life cycle of germination and growth during intermittent opportunities of moderate temperatures. The limited evolutionary changes towards an increase in heat tolerance in bacteria should alert us of the negative impact of climate change on all biological cycles in the planet, which at its most basic level depends on microorganisms.
Hurtado-Bautista et al. (2021) Phenotypic plasticity and evolution of thermal tolerance in bacteria from temperate and hot spring environments. PeerJ 9:e11734 https://doi.org/10.7717/peerj.11734
Impacts of heat stress and storm events on the benthic communities of Kenting National Park (Taiwan)
Over the past few decades, extreme events—such as ocean warming, typhoons, and coral bleaching—have been increasing in intensity and frequency, threatening coral reefs from the physiological to ecosystem level. In the present study, the impacts of rising seawater temperatures, typhoons, and coral bleaching events on benthic communities were seasonally assessed over a 21 month-period, using photo-transects at 11 sites in Kenting National Park (KNP), Taiwan. Between August 2015 and April 2017, seven typhoon events were recorded and in situ seawater temperatures in KNP reached a maximum of 31.2 °C, as opposed to an average maximum SST of 28.8 °C (2007–2016). The state and response of benthic communities to these events were interpreted based on the environmental conditions of KNP. The repeated storms lowered the levels of thermal stress during the 2015–2016 El Niño event and may have mitigated its impact on the Taiwanese coral reefs. However, storm-induced local shifts from coral to macro-algae dominance were observed. Storms may mitigate the negative effects of heatwaves, but the mechanical damage induced by the storms may also decrease the structural complexity of reefs and their associated diversity. Eventually, despite reef persistence, the composition and function of remnant communities may profoundly diverge from those in regions with less active storms.
Ribas-Deulofeu et al. (2021) Impacts of heat stress and storm events on the benthic communities of Kenting National Park (Taiwan). PeerJ 9:e11744 https://doi.org/10.7717/peerj.11744
Furongian (Jiangshanian) occurrences of radiodonts in Poland and South China and the fossil record of the Hurdiidae
The Furongian period represents an important gap in the fossil record of most groups of non-biomineralizing organisms, owing to a scarcity of Konservat-Lagerstätten of that age. The most significant of these deposits, the Jiangshanian strata of the Sandu Formation near Guole Township (Guangxi, South China), have yielded a moderately abundant, but taxonomically diverse soft-bodied fossil assemblage, which provides rare insights into the evolution of marine life at that time. In this contribution, we report the first discovery of a radiodont fossil from the Guole Konservat-Lagerstätte. The specimen is an incomplete frontal appendage of a possibly new representative of the family Hurdiidae. It is tentatively interpreted as composed of seven podomeres, six of which bearing laminiform endites. The best preserved of these endites is especially long, and it bears short auxiliary spines that greatly vary in size. This is the second occurrence of hurdiids and more generally radiodonts in the Furongian, the first being the external mould of an oral cone from Jiangshanian strata of the Wiśniówka Sandstone Formation in Poland. Restudy of this Polish specimen confirms that it belongs to a hurdiid radiodont and best compares to Peytoia. The family Hurdiidae includes the oldest (basal Cambrian Epoch 2) and youngest (Early Ordovician, possibly Early Devonian) representatives of the Radiodonta and as such, has the longest stratigraphical range of the group. Yet, hurdiids only became prominent components of marine ecosystems during the middle Cambrian (Miaolingian), and their fossil record in younger strata remains limited.
Zhu et al. (2021) Furongian (Jiangshanian) occurrences of radiodonts in Poland and South China and the fossil record of the Hurdiidae. PeerJ 9:e11800 https://doi.org/10.7717/peerj.11800
LncRNA NEAT1 regulated diabetic retinal epithelial-mesenchymal transition through regulating miR-204/SOX4 axis
Aim Epithelial-mesenchymal transition (EMT) of retinal pigment epithelium (RPE) cells is the key of the development of diabetic retinopathy (DR), and lncRNA NEAT1 could accelerate EMT in diabetic nephropathy. Meanwhile, as a diabetes susceptibility gene, whether sex-determining region Y-related (SRY) high-mobility group box 4 (SOX4) has relationship with lncRNA NEAT1 in DR remains unclear. Methods Firstly, NEAT1, SOX4 and miR-204 were evaluated by qRT-PCR (quantitative reverse-transcriptase PCR) under high glucose condition. Then, cell viability, proliferation, migration and invasion were respectively detected by MTT, BrdU staining, wound healing and transwell assay after NEAT1 knockdown or miR-204 overexpression. Also, the EMT-related proteins were examined by western blot and cell immunofluorescence assay. In order to confirm the relationship between miR-204 and NEAT1 or SOX4, dual luciferase reporter gene assay was conducted. At the same time, the protein levels of SOX4 and EMT-related proteins were investigated by immunohistochemistry in vivo. Results High glucose upregulated NEAT1 and SOX4 and downregulated miR-204 in ARPE19 cells. NEAT1 knockdown or miR-204 overexpression inhibited the proliferation and EMT progression of ARPE19 cells induced by high glucose. NEAT1 was identified as a molecular sponge of miR-204 to increase the level of SOX4. The effect of NEAT1 knockdown on the progression of EMT under high glucose condition in ARPE19 cells could be reversed by miR-204 inhibitor. Also, NEAT1 knockdown inhibited retinal EMT in diabetic mice. Conclusion NEAT1 regulated the development of EMT in DR through miR-204/SOX4 pathway, which could provide reference for clinical prevention and treatment.
Yang et al. (2021) LncRNA NEAT1 regulated diabetic retinal epithelial-mesenchymal transition through regulating miR-204/SOX4 axis. PeerJ 9:e11817 https://doi.org/10.7717/peerj.11817
How fish traits and functional diversity respond to environmental changes and species invasion in the largest river in Southeastern China
Background Freshwater fish populations are facing multiple stressors, including climate change, species invasion, and anthropogenic interference. Temporal studies of fish functional diversity and community assembly rules based on trait-environment relationships provide insights into fish community structure in riverine ecosystems. Methods Fish samples were collected in 2015 in the Min River, the largest freshwater riverine system in Southeastern China. Fish functional diversity was compared with the background investigation in 1979. Changes in functional richness, functional evenness, functional divergence, and functional beta diversity were analyzed. Relationships between functional diversity and environmental factors were modeled by random forest regression. Correlations between fish functional traits and environmental factors were detected by fourth-corner combined with RLQ analysis. Results Functional richness was significantly reduced in 2015 compared with 1979. Functional beta diversity in 2015 was significantly higher than that in 1979, with functional nestedness being the driving component. Reduction of functional richness and domination of functional nestedness is associated with species loss. Trait convergence was the dominant mechanism driving the temporal changes of functional diversity. Precipitation, temperature, species invasion, and human population were the most significant factors driving fish functional diversity. Higher precipitation, higher temperature, and presence of invasive species were significantly associated with higher swimming factor and higher relative eye diameter, while the opposite environmental conditions were significantly associated with higher pectoral fin length and eurytopic water flow preference. Conclusions Environmental filtering is the dominant temporal assembly mechanism shaping fish community structure. This work contributes to the understanding of temporal freshwater fish community assembly and the associations between fish functional structure and local environmental conditions, which will be informative for future freshwater fish conservation.
Lin et al. (2021) How fish traits and functional diversity respond to environmental changes and species invasion in the largest river in Southeastern China. PeerJ 9:e11824 https://doi.org/10.7717/peerj.11824
Assessing the quantitative relationships between the impervious surface area and surface heat island effect during urban expansion
As an important component of underlying urban surfaces, the distribution pattern and density of the impervious surface area (ISA) play an important role in the generation of surface urban heat island (SUHI) effects. However, the quantitative and localized exploration of the ISA’s influence on SUHIs in the process of urban expansion from the perspective of temporal and spatial changes is still not clear. Based on multisource remote sensing data, the SUHI effect of urban expansion is revealed by using geospatial analysis methods such as profile, difference and regression analysis. The results show the following: (1) urban expansion plays a significant role in aggravating SUHIs. Overall, the ISA and land surface temperature (LST) have obvious consistency in terms of spatial distribution patterns. However, local spatial differentiation is significant. The areas with the highest LST were not concentrated in the downtown area with the highest ISA but were scattered in the cultivated land and exposed surface areas under development in the northern part of the city. (2) In general, the ISA can explain the spatial distribution of LST well, there is an obvious positive correlation between them, and the quadratic polynomial function is the best fitting model between them. (3) The density and spatial allocation of ecological elements, such as green space and water bodies, play an important role in alleviating SUHIs. This study found that the urban center with the highest ISA coverage rate has no significant SUHI due to the reasonable allocation of green space and water bodies. The research results can provide a scientific basis for future urban planning and ecological environment construction.
Spatial and Geographic Information Science
Ma et al. (2021) Assessing the quantitative relationships between the impervious surface area and surface heat island effect during urban expansion. PeerJ 9:e11854 https://doi.org/10.7717/peerj.11854
Genome-wide identification of alcohol dehydrogenase (ADH) gene family under waterlogging stress in wheat (Triticum aestivum)
Background Alcohol dehydrogenase (ADH) plays an important role in plant survival under anaerobic conditions. Although some research about ADH in many plants have been carried out, the bioinformatics analysis of the ADH gene family from Triticum aestivum and their response to abiotic stress is unclear. Methods A total of 22 ADH genes were identified from the wheat genome, and these genes could be divided into two subfamilies (subfamily I and subfamily II). All TaADH genes belonged to the Medium-chain ADH subfamily. Sequence alignment analysis showed that all TaADH proteins contained a conservative GroES-like domain and Zinc-binding domain. A total of 64 duplicated gene pairs were found, and the Ka/Ks value of these gene pairs was less than 1, which indicated that these genes were relatively conservative and did not change greatly in the process of duplication. Results The organizational analysis showed that nine TaADH genes were highly expressed in all organs, and the rest of TaADH genes had tissue specificity. Cis-acting element analysis showed that almost all of the TaADH genes contained an anaerobic response element. The expression levels of ADH gene in waterlogging tolerant and waterlogging sensitive wheat seeds were analyzed by quantitative real-time PCR (qRT-PCR). This showed that some key ADH genes were significantly responsive to waterlogging stress at the seed germination stage, and the response of waterlogging tolerant and waterlogging sensitive wheat seeds to waterlogging stress was regulated by different ADH genes. The results may be helpful to further study the function of TaADH genes and to determine the candidate gene for wheat stress resistance breeding.
Shen et al. (2021) Genome-wide identification of alcohol dehydrogenase (ADH) gene family under waterlogging stress in wheat (Triticum aestivum). PeerJ 9:e11861 https://doi.org/10.7717/peerj.11861