title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=1094 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: Variation of soil nutrients and bacterial community diversity of different land utilization types in Yangtze River Basin, Chongqing Municipality link: https://peerj.com/articles/9386 last-modified: 2020-07-17 description: The diversity and community distribution of soil bacteria in different land use types in Yangtze River Basin, Chongqing Municipality were studied by using Illumina MiSeq analysis methods. Soil physical and chemical properties were determined, and correlation analyses were performed to identify the key factors affecting bacterial numbers and α-diversity in these soils. The results showed that the soil physical and chemical properties of different land use types decrease in the order: mixed forest (M2) > pure forest (P1) > grassland (G3) > bare land (B4). There were significant differences in bacterial diversity and communities of different land use types. The diversity of different land use types showed the same sequence with the soil physical and chemical properties. The abundance and diversity of bacterial in M2 and P1 soils was significantly higher than that in G3 and B4 soils. At phylum level, G3 and B4 soils were rich in only Proteobacteria and Actinobacteria, whereas M2 and P1 soils were rich in Proteobacteria, Actinobacteria and Firmicutes. At genus level, Faecalibacterium and Agathobacter were the most abundant populations in M2 soil and were not found in other soils. Pearson correlation analysis showed that soil moisture content, pH, AN, AP, AK and soil enzyme activity were significantly related to bacterial numbers, diversity and community distribution. creator: Yanlin Li creator: Chunmei Zeng creator: Meijun Long uri: https://doi.org/10.7717/peerj.9386 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Li et al. title: Biodiversity of carapace epibiont diatoms in loggerhead sea turtles (Caretta caretta Linnaeus 1758) in the Aegean Sea Turkish coast link: https://peerj.com/articles/9406 last-modified: 2020-07-17 description: BackgroundThe Aegean Sea coast of Turkey hosts one of the most important nesting grounds for loggerhead sea turtles (Caretta caretta) in the Mediterranean Sea. Previous studies have revealed that the sea turtle carapace provides favourable conditions for various epibiontic organisms. Epibionts occurring on the carapace have been examined from different locations in the oceans.MethodsThis is the first time such a high number (39) of samples collected from nesting turtles during such a long time period (extending from 2011 to 2018) has been used for the study of the diatom component of the microbiome on the turtle carapaces. A total of 33 samples were investigated in terms of light microscopy (LM) and scanning electron microscopy (SEM). Six unprocessed biofilm fragments were subject to SEM observations.ResultsA total of 457 epizoic diatom taxa belonging to 86 genera were identified. Epizoic forms, e.g., Achnanthes spp., Chelonicola spp. or Tripterion spp. (also identified by SEM observations of the undisturbed pieces of the microbiome) dominated in terms of relative abundance, but the highest numbers of taxa were ubiquitously represented by Navicula (79), Nitzschia (45), Amphora (40), Cocconeis (32), Diploneis (25) and Mastogloia (23). Navicula perminuta and Delphineis australis were the most frequent taxa, present in 65% of the samples, both with an average relative abundance of 10%. The results of our study revealed that diatoms are an essential component of the loggerhead sea turtles’ microbiome, in terms of high biodiversity and abundance. Although strict epibionts provide a signature of the turtle microbiome, the carapace as a solid substrate attracts numerous benthic diatom species which are considered opportunistic forms and can be found in the surrounding benthic habitats of the vast ocean littoral space. creator: Aydın Kaleli creator: Ana Car creator: Andrzej Witkowski creator: Marta Krzywda creator: Catherine Riaux-Gobin creator: Cüneyt Nadir Solak creator: Yakup Kaska creator: Izabela Zgłobicka creator: Tomasz Płociński creator: Rafał Wróbel creator: Krzysztof Kurzydłowski uri: https://doi.org/10.7717/peerj.9406 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Kaleli et al. title: An updated genetic marker for detection of Lake Sinai Virus and metagenetic applications link: https://peerj.com/articles/9424 last-modified: 2020-07-17 description: BackgroundLake Sinai Viruses (LSV) are common RNA viruses of honey bees (Apis mellifera) that frequently reach high abundance but are not linked to overt disease. LSVs are genetically heterogeneous and collectively widespread, but despite frequent detection in surveys, the ecological and geographic factors structuring their distribution in A. mellifera are not understood. Even less is known about their distribution in other species. Better understanding of LSV prevalence and ecology have been hampered by high sequence diversity within the LSV clade.MethodsHere we report a new polymerase chain reaction (PCR) assay that is compatible with currently known lineages with minimal primer degeneracy, producing an expected 365 bp amplicon suitable for end-point PCR and metagenetic sequencing. Using the Illumina MiSeq platform, we performed pilot metagenetic assessments of three sample sets, each representing a distinct variable that might structure LSV diversity (geography, tissue, and species).ResultsThe first sample set in our pilot assessment compared cDNA pools from managed A. mellifera hives in California (n = 8) and Maryland (n = 6) that had previously been evaluated for LSV2, confirming that the primers co-amplify divergent lineages in real-world samples. The second sample set included cDNA pools derived from different tissues (thorax vs. abdomen, n = 24 paired samples), collected from managed A. mellifera hives in North Dakota. End-point detection of LSV frequently differed between the two tissue types; LSV metagenetic composition was similar in one pair of sequenced samples but divergent in a second pair. Overall, LSV1 and intermediate lineages were common in these samples whereas variants clustering with LSV2 were rare. The third sample set included cDNA from individual pollinator specimens collected from diverse landscapes in the vicinity of Lincoln, Nebraska. We detected LSV in the bee Halictus ligatus (four of 63 specimens tested, 6.3%) at a similar rate as A. mellifera (nine of 115 specimens, 7.8%), but only one H. ligatus sequencing library yielded sufficient data for compositional analysis. Sequenced samples often contained multiple divergent LSV lineages, including individual specimens. While these studies were exploratory rather than statistically powerful tests of hypotheses, they illustrate the utility of high-throughput sequencing for understanding LSV transmission within and among species. creator: Deborah D. Iwanowicz creator: Judy Y. Wu-Smart creator: Tugce Olgun creator: Autumn H. Smart creator: Clint R.V. Otto creator: Dawn Lopez creator: Jay D. Evans creator: Robert Cornman uri: https://doi.org/10.7717/peerj.9424 license: https://creativecommons.org/publicdomain/zero/1.0/ rights: ©2020 Iwanowicz et al. title: Mesozooplankton grazing minimally impacts phytoplankton abundance during spring in the western North Atlantic link: https://peerj.com/articles/9430 last-modified: 2020-07-17 description: The impacts of grazing by meso- and microzooplankton on phytoplankton primary production (PP) was investigated in the surface layer of the western North Atlantic during spring. Shipboard experiments were performed on a latitudinal transect at three stations that differed in mixed layer depth, temperature, and mesozooplankton taxonomic composition. The mesozooplankton community was numerically dominated by Calanus finmarchicus at the northern and central station, with Calanus hyperboreus also present at the northern station. The southern station was >10 °C warmer than the other stations and had the most diverse mesozooplankton assemblage, dominated by small copepods including Paracalanus spp. Microzooplankton grazing was detected only at the northern station, where it removed 97% of PP. Estimated clearance rates by C. hyperboreus and C. finmarchicus suggested that at in-situ abundance these mesozooplankton were not likely to have a major impact on phytoplankton abundance, unless locally aggregated. Although mesozooplankton grazing impact on total phytoplankton was minimal, these grazers completely removed the numerically scarce > 10 µm particles, altering the particle-size spectrum. At the southern station, grazing by the whole mesozooplankton assemblage resulted in a removal of 14% of PP, and its effect on net phytoplankton growth rate was similar irrespective of ambient light. In contrast, reduction in light availability had an approximately 3-fold greater impact on net phytoplankton growth rate than mesozooplankton grazing pressure. The low mesozooplankton grazing impact across stations suggests limited mesozooplankton-mediated vertical export of phytoplankton production. The constraints provided here on trophic transfer, as well as quantitative estimates of the relative contribution of light and grazer controls of PP and of grazer-induced shifts in particle size spectra, illuminate food web dynamics and aid in parameterizing modeling-frameworks assessing global elemental fluxes and carbon export. creator: Francoise Morison creator: James Joseph Pierson creator: Andreas Oikonomou creator: Susanne Menden-Deuer uri: https://doi.org/10.7717/peerj.9430 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Morison et al. title: The switch from one substance-of-abuse to another: illicit drug substitution behaviors in a sample of high-risk drug users link: https://peerj.com/articles/9461 last-modified: 2020-07-17 description: BackgroundSubstitution can be defined as the consciously motivated choice to use one drug, either licit or illicit, instead of another, due to perceptions of cost, availability, safety, legality, substance characteristics, and substance attributions. Substitution represents a potential risk to drug users, mainly when substitutes are of higher potency and toxicity. This study offers a basic conceptualization of illicit substitution behavior and describes substitution patterns among users of two highly prevalent drugs of abuse—heroin and cannabis.MethodsHere, 592 high-risk drug users undergoing pharmacological and psycho-social treatment were interviewed. Patients were asked questions about current drug use, lifetime substitution, and substitution patterns. Descriptive statistics, chi-square tests of independence, and multinomial logistic regressions were used to identify and test correlates of substitution patterns for heroin and cannabis.ResultsOf the 592 drug users interviewed, 448 subjects (75.7%) reported having substituted their preferred drug for another illicit substance. Interviews yielded a total of 275 substitution events reported by users of cannabis, and 351 substitution events reported by users of heroin. The most frequently reported substitution substances for responders who preferred heroin were illicit non-prescribed “street” methadone (35.9%), followed by oral and transdermal prescription opioids (17.7%). For responders who preferred cannabis, substitution for synthetic cannabinoid receptor agonists (33.5%) followed by alcohol (16.0%) were the most commonly reported. Age at onset–of–use (p < 0.005), population group (p = 0.008), and attending treatment for the first time (p = 0.026) were significantly associated with reported lifetime substitution. Past-year use of stimulants, heroin, hallucinogens, methylenedioxymethamphetamine (MDMA), and novel psychoactive substances were—at the 95% confidence level—also significantly associated with reported lifetime substitution. In multivariate analysis, the odds for methadone substitution among heroin users were significantly affected by age at onset-of-use, type of treatment center, and education. Odds for substitution for synthetic cannabinoid receptor agonists among cannabis users were significantly affected by age, population group, type of treatment center, and education.ConclusionSelf-substitution behavior should be considered by clinicians and policymakers as a common practice among most drugusers. Substitution for street methadone provides evidence for the ongoing diversion of this substance from Opioid Maintenance Treatment Centers, while the prominence of substitution of synthetic cannabinoids among dual-diagnosis patients should be regarded as an ongoing risk to patients that needs to be addressed by clinicians. Analysis of additional substitution patterns should provide further valuable insights into the behavior of drugusers. creator: Barak Shapira creator: Paola Rosca creator: Ronny Berkovitz creator: Igor Gorjaltsan creator: Yehuda Neumark uri: https://doi.org/10.7717/peerj.9461 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Shapira et al. title: Mechanisms behind bottom-up effects: eutrophication increases fecundity by shortening the interspawning interval in stickleback link: https://peerj.com/articles/9521 last-modified: 2020-07-17 description: Anthropogenic eutrophication is altering aquatic environments by promoting primary production. This influences the population dynamics of consumers through bottom-up effects, but the underlying mechanisms and pathways are not always clear. To evaluate and mitigate effects of eutrophication on ecological communities, more research is needed on the underlying factors. Here we show that anthropogenic eutrophication increases population fecundity in the threespine stickleback (Gasterosteus aculeatus) by increasing the number of times females reproduce—lifetime fecundity—rather than instantaneous fecundity. When we exposed females to nutrient-enriched waters with enhanced algal growth, their interspawning interval shortened but the size of their egg clutches, or the size of their eggs, did not change. The shortening of the interspawning interval was probably caused by higher food intake, as algae growth promotes the growth of preferred prey populations. Enhanced female lifetime fecundity could increase offspring production and, hence, influence population dynamics. In support of this, earlier studies show that more offspring are emerging in habitats with denser algae growth. Thus, our results stress the importance of considering lifetime fecundity, in addition to instantaneous fecundity, when investigating the impact of human-induced eutrophication on population processes. At a broader level, our results highlight the importance of following individuals over longer time spans when evaluating the pathways and processes through which environmental changes influence individual fitness and population processes. creator: Anne Saarinen creator: Ulrika Candolin uri: https://doi.org/10.7717/peerj.9521 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Saarinen and Candolin title: Genome-wide identification and expression profiles of ERF subfamily transcription factors in Zea mays link: https://peerj.com/articles/9551 last-modified: 2020-07-17 description: The Ethylene-Response Factor (ERF) subfamily transcription factors (TFs) belong to the APETALA2/Ethylene-Responsive Factor (AP2/ERF) superfamily and play a vital role in plant growth and development. However, identification and analysis of the ERF subfamily genes in maize have not yet been performed at genome-wide level. In this study, a total of 76 ERF subfamily TFs were identified and were found to be unevenly distributed on the maize chromosomes. These maize ERF (ZmERF) TFs were classified into six groups, namely groups B1 to B6, based on phylogenetic analysis. Synteny analysis showed that 50, 54, and 58 of the ZmERF genes were orthologous to those in rice, Brachypodium, and Sorghum, respectively. Cis-element analysis showed that elements related to plant growth and development, hormones, and abiotic stress were identified in the promoter region of ZmERF genes. Expression profiles suggested that ZmERF genes might participate in plant development and in response to salinity and drought stresses. Our findings lay a foundation and provide clues for understanding the biological functions of ERF TFs in maize. creator: Lidong Hao creator: Shubing Shi creator: Haibin Guo creator: Ming Li creator: Pan Hu creator: Yadong Wei creator: Yanfei Feng uri: https://doi.org/10.7717/peerj.9551 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Hao et al. title: Understanding genomic diversity, pan-genome, and evolution of SARS-CoV-2 link: https://peerj.com/articles/9576 last-modified: 2020-07-17 description: Coronovirus disease 2019 (COVID-19) infection, which originated from Wuhan, China, has seized the whole world in its grasp and created a huge pandemic situation before humanity. Since December 2019, genomes of numerous isolates have been sequenced and analyzed for testing confirmation, epidemiology, and evolutionary studies. In the first half of this article, we provide a detailed review of the history and origin of COVID-19, followed by the taxonomy, nomenclature and genome organization of its causative agent Severe Acute Respiratory Syndrome-related Coronavirus-2 (SARS-CoV-2). In the latter half, we analyze subgenus Sarbecovirus (167 SARS-CoV-2, 312 SARS-CoV, and 5 Pangolin CoV) genomes to understand their diversity, origin, and evolution, along with pan-genome analysis of genus Betacoronavirus members. Whole-genome sequence-based phylogeny of subgenus Sarbecovirus genomes reasserted the fact that SARS-CoV-2 strains evolved from their common ancestors putatively residing in bat or pangolin hosts. We predicted a few country-specific patterns of relatedness and identified mutational hotspots with high, medium and low probability based on genome alignment of 167 SARS-CoV-2 strains. A total of 100-nucleotide segment-based homology studies revealed that the majority of the SARS-CoV-2 genome segments are close to Bat CoV, followed by some to Pangolin CoV, and some are unique ones. Open pan-genome of genus Betacoronavirus members indicates the diversity contributed by the novel viruses emerging in this group. Overall, the exploration of the diversity of these isolates, mutational hotspots and pan-genome will shed light on the evolution and pathogenicity of SARS-CoV-2 and help in developing putative methods of diagnosis and treatment. creator: Arohi Parlikar creator: Kishan Kalia creator: Shruti Sinha creator: Sucheta Patnaik creator: Neeraj Sharma creator: Sai Gayatri Vemuri creator: Gaurav Sharma uri: https://doi.org/10.7717/peerj.9576 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Parlikar et al. title: Assessment of biomass potentials of microalgal communities in open pond raceways using mass cultivation link: https://peerj.com/articles/9418 last-modified: 2020-07-16 description: Metagenome studies have provided us with insights into the complex interactions of microorganisms with their environments and hosts. Few studies have focused on microalgae-associated metagenomes, and no study has addressed aquatic microalgae and their bacterial communities in open pond raceways (OPRs). This study explored the possibility of using microalgal biomasses from OPRs for biodiesel and biofertilizer production. The fatty acid profiles of the biomasses and the physical and chemical properties of derived fuels were evaluated. In addition, the phenotype-based environmental adaptation ability of soybean plants was assessed. The growth rate, biomass, and lipid productivity of microalgae were also examined during mass cultivation from April to November 2017. Metagenomics analysis using MiSeq identified ∼127 eukaryotic phylotypes following mass cultivation with (OPR 1) or without (OPR 3) a semitransparent film. Of these, ∼80 phylotypes were found in both OPRs, while 23 and 24 phylotypes were identified in OPRs 1 and 3, respectively. The phylotypes belonged to various genera, such as Desmodesmus, Pseudopediastrum, Tetradesmus, and Chlorella, of which, the dominant microalgal species was Desmodesmus sp. On average, OPRs 1 and 3 produced ∼8.6 and 9.9 g m−2 d−1 (0.307 and 0.309 DW L−1) of total biomass, respectively, of which 14.0 and 13.3 wt% respectively, was lipid content. Fatty acid profiling revealed that total saturated fatty acids (mainly C16:0) of biodiesel obtained from the microalgal biomasses in OPRs 1 and 3 were 34.93% and 32.85%, respectively; total monounsaturated fatty acids (C16:1 and C18:1) were 32.40% and 31.64%, respectively; and polyunsaturated fatty acids (including C18:3) were 32.68% and 35.50%, respectively. Fuel properties determined by empirical equations were within the limits of biodiesel standards ASTM D6751 and EN 14214. Culture solutions with or without microalgal biomasses enhanced the environmental adaptation ability of soybean plants, increasing their seed production. Therefore, microalgal biomass produced through mass cultivation is excellent feedstock for producing high-quality biodiesel and biofertilizer. creator: Seung-Woo Jo creator: Jeong-Mi Do creator: Ho Na creator: Ji Won Hong creator: Il-Sup Kim creator: Ho-Sung Yoon uri: https://doi.org/10.7717/peerj.9418 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Jo et al. title: Subcellular compartmentalization of the plant antioxidant system: an integrated overview link: https://peerj.com/articles/9451 last-modified: 2020-07-16 description: The antioxidant system (AOS) maintains the optimal concentration of reactive oxygen species (ROS) in a cell and protects it against oxidative stress. In plants, the AOS consists of seven main classes of antioxidant enzymes, low-molecular antioxidants (e.g., ascorbate, glutathione, and their oxidized forms) and thioredoxin/glutaredoxin systems which can serve as reducing agents for antioxidant enzymes. The number of genes encoding AOS enzymes varies between classes, and same class enzymes encoded by different gene copies may have different subcellular localizations, functional loads and modes of evolution. These facts hereafter reinforce the complex nature of AOS regulation and functioning. Further studies can describe new trends in the behavior and functioning of systems components, and provide new fundamental knowledge about systems regulation. The system is revealed to have a lot of interactions and interplay pathways between its components at the subcellular level (antioxidants, enzymes, ROS level, and hormonal and transcriptional regulation). These facts should be taken into account in further studies during the AOS modeling by describing the main pathways of generating and utilizing ROS, as well as the associated signaling processes and regulation of the system on cellular and organelle levels, which is a complicated and ambitious task. Another objective for studying the phenomenon of the AOS is related to the influence of cell dynamics and circadian rhythms on it. Therefore, the AOS requires an integrated and multi-level approach to study. We focused this review on the existing scientific background and experimental data used for the systems biology research of the plant AOS. creator: Aleksandr Bobrovskikh creator: Ulyana Zubairova creator: Alexey Kolodkin creator: Alexey Doroshkov uri: https://doi.org/10.7717/peerj.9451 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Bobrovskikh et al.