The anatomy and phylogenetic position of the erythrosuchid archosauriform Guchengosuchus shiguaiensis from the earliest Middle Triassic of China
Erythrosuchidae is a clade of early archosauriform reptiles, which were apex predators in many late Early and Middle Triassic ecosystems, following the Permo-Triassic mass extinction. Erythrosuchids had a worldwide distribution, with well-preserved fossil material known from South Africa, European Russia, and China. We here redescribe the anatomy and revise the taxonomy of Guchengosuchus shiguaiensis, which is one of the stratigraphically oldest erythrosuchids and is known from a single partial skeleton from the lowermost Middle Triassic (lower Anisian) lower Ermaying Formation of Shaanxi Province, China. We provide a new differential diagnosis for Guchengosuchus shiguaiensis, and identify a series of autapomorphies relating to the morphologies of the skull roof and vertebrae. Incorporating updated anatomical information for Guchengosuchus into the most comprehensive morphological phylogenetic analysis available for early archosauromorphs recovers it as an early branching member of Erythrosuchidae, outside of the clade formed by Garjainia, Erythrosuchus, Chalishevia, and Shansisuchus. Fugusuchus hejiapanensis, from the uppermost Lower Triassic to lower Middle Triassic Heshanggou Formation of China, is recovered as the earliest branching member of Erythrosuchidae.
Butler et al. (2019) The anatomy and phylogenetic position of the erythrosuchid archosauriform Guchengosuchus shiguaiensis from the earliest Middle Triassic of China. PeerJ 7:e6435 https://doi.org/10.7717/peerj.6435
Guanidine thiocyanate solution facilitates sample collection for plant rhizosphere microbiome analysis
The interactions between rhizosphere microorganisms and plants are important for the health and development of crops. Analysis of plant rhizosphere bacterial compositions, particularly of those with resistance to biotic/abiotic stresses, may improve their applications in sustainable agriculture. Large-scale rhizosphere samplings in the field are usually required; however, such samples, cannot be immediately frozen. We found that the storage of samples at room temperature for 2 days leads to a considerable reduction in the operational taxonomic unit (OTU) number and the indices of bacterial alpha-diversity of rhizosphere communities. In this study, in order to overcome these problems, we established a method using guanidine thiocyanate (GTC) solution for the preservation of rhizosphere samples after their collection. This method allowed the maintenance of the samples for at least 1 day at room temperature prior to their cryopreservation and was shown to be compatible with conventional DNA isolation protocols. Illumina sequencing of V3 and V4 hypervariable regions of the 16S rRNA gene was used to assess the feasibility and reliability of this method, and no significant differences were observed in the number of OTUs and in the Chao and Shannon indices between samples stored at −70 °C and those stored in GTC solution. Moreover, the representation of Pseudomonas spp. in samples stored in GTC solution was not significantly different from that in samples stored at −70 °C, as determined by real-time quantitative polymerase chain reaction (p > 0.05). Both types of samples were shown to cluster together according to principal coordinate analysis. Furthermore, GTC solution did not affect the bacterial taxon profiles at different storage periods compared with those observed when storing the samples below −70 °C. Even incubation of thawed samples (frozen at −70 °C) for 15 min at room temperature induced minor changes in the bacterial composition. Taken together, our results demonstrated that GTC solution may provide a reliable alternative for the preservation of rhizosphere samples in the field.
Sun et al. (2019) Guanidine thiocyanate solution facilitates sample collection for plant rhizosphere microbiome analysis. PeerJ 7:e6440 https://doi.org/10.7717/peerj.6440
Breastfeeding in the time of Zika: a systematic literature review
Background The disease Zika is considered as emergent. The infection can be acquired through different routes: a bite from the Aedes mosquito, sexual contact, from mother to child during pregnancy and by blood transfusion. The possibility of Zika transmission through human lactation has been considered. Zika is a disease of great concern for public health because it has been associated with neonatal and postnatal microcephaly, among other birth defects. Objectives To review published evidence of the probable transmission of Zika through human lactation. Data sources Electronic databases: Cochrane Central Register of Controlled Trials, EBSCO, Gale, Science Direct, Scopus, US National Library of Medicine (PubMed) and Web of Science. World Health Organization and Centers for Disease Control and Prevention web pages. Study eligibility criteria To be eligible, studies of any design had to provide primary data of human breast milk as a potential fluid for the transmission of Zika, or primary or secondary follow-up data of infants with at least one previous published study that complied with the first criterion of eligibility. Participants Studies about women with suspected, probable or confirmed Zika during pregnancy, or the postnatal period and beyond. Studies about infants who breastfeed directly from the breast or where fed with the expressed breast milk of the suspected, probable or confirmed women with Zika. Results This study only chose data from research papers; no patients were taken directly by the authors. A total of 1,146 were screened and nine studies were included in the qualitative synthesis, from which a total of 10 cases were identified, with documented follow-up in three of these cases. Through the timing of maternal Zika infection, five cases were classified as prenatal (time before delivery), one as immediate postnatal (period from 0 to 4 days after birth); no cases were classified as medium postnatal (period from 5 days to 8 weeks after birth); two were classified as long postnatal (period from 8 weeks to 6 months after birth) and two as beyond six months after birth. Conclusion Human milk may be considered as a potentially infectious fluid, but we found no currently documented studies of the long-term complications in infants up to 32 months of age, with suspected, probable or confirmed Zika through human lactation, or evidence with respect to the human pathophysiology of the infection acquired through human lactation. In the light of the studies reviewed here, the World Health Organization recommendation of June 29th 2016, remains valid: “the benefits of breastfeeding for the infant and mother outweigh any potential risk of Zika virus transmission through breast milk.”
Sampieri et al. (2019) Breastfeeding in the time of Zika: a systematic literature review. PeerJ 7:e6452 https://doi.org/10.7717/peerj.6452
Impact of agricultural farms on the environment of the Puck Commune: Integrated agriculture calculator—CalcGosPuck
Background Leaching of nutrients from agricultural areas is the main cause of water pollution and eutrophication of the Baltic Sea. A variety of remedial actions to reduce nitrogen and phosphorus losses from agricultural holdings and cultivated fields have been taken in the past. However, knowledge about the risk of nutrient leaching has not yet reached many farmers operating in the water catchment area of the Baltic Sea. Methods The nutrient balance method known as “At the farm gate” involves calculating separate balances for nitrogen (N), phosphorus (P) and potassium (K). After estimating all the components of the nutrient balance, the total balance for NPK is calculated and the data obtained is expressed as the ratio of total change (surplus) to the area of arable land on a farm. In addition, the nutrient usage efficiency on a farm is also calculated. An opinion poll was conducted in 2017 on 3.6% (n = 31) of the farms located in commune of Puck. The total area of the farms including arable and grass land ranged from 5 to 130 ha with an average of 45.82 ha. The arable land was on average 30.79 ha ranging from 4.45 to 130 ha while the grassland averaged 12.77 ha and ranged from 0 to 53 ha. Results The average consumption of mineral fertilizer in the sample population of farms was 114.9 kg N, 9.3 kg P, and 22.9 kg K·ha−1of agricultural land (AL), respectively. N balance in the sample farms being ranged from −23.3 to 254.5 kg N·ha−1AL while nutrient use efficiency ranged from 0.40% to 231.3%. In comparison, P surplus in the sample farms was 5.0 kg P·ha−1AL with the P use efficiency of 0.4–266.5%. Discussion Mean N fertilizer consumption in the tested farms was higher than the average usage across Poland and in the Pomeranian Voivodeship. However, mean consumption of potassium fertilizers was lower than mentioned averages. Mean P fertilizer consumption was higher than in the Pomeranian Voivodeship, but lower compared to the entire country. Generally, on the basis of designated research indicators of farm pressures on water quality, concentrations of total nitrogen and total phosphorus were obtained. CalcGosPuck (an integrated agriculture calculator) will help to raise farmers’ awareness about NPK flow on farm scale and to improve nutrient management.
Dzierzbicka-Glowacka et al. (2019) Impact of agricultural farms on the environment of the Puck Commune: Integrated agriculture calculator—CalcGosPuck. PeerJ 7:e6478 https://doi.org/10.7717/peerj.6478
Hybrid identification for Glycine max and Glycine soja with SSR markers and analysis of salt tolerance
Glycine max cultivars Lee68, Nannong 1138-2, and Nannong 8831 were used as the female parents, and hybrid lines (F5) 4,111, 4,076 (N23674 × BB52), 3,060 (Lee68 × N23227), and 185 (Jackson × BB52) that selected for salt tolerance generation by generation from the cross combination of G. max and G. soja were used as the male parents, 11 (A–K) backcrosses or three-way crosses were designed and 213 single hybrids were harvested. The optimized soybean simple sequence repeat (SSR)–polymerase chain reaction (PCR) system was used to analyze the SSR polymorphism of above parental lines and get the parental co-dominant SSR markers for hybrid identification, and in which 30 true hybrids were gained. The true hybrids (G1, G3, G9, G12, G13, G16) of G cross combination were chosen as the representative for the salt tolerance test, and the results showed that, as exposed to salt stress, the seedlings of G9 line displayed higher salt tolerant coefficient, relative growth rate, and dry matter accumulation, when compared with their female parent Nannong 1138-2, and even performed equally strong salt tolerance as the male parent 3,060. It provides a feasible method of the combination of molecular SSR markers and simple physiological parameters to identify the true hybrids of G. max and G. soja, and to innovate the salt-tolerant soybean germplasms.
Li et al. (2019) Hybrid identification for Glycine max and Glycine soja with SSR markers and analysis of salt tolerance. PeerJ 7:e6483 https://doi.org/10.7717/peerj.6483
Phytochemical content and antioxidant activity in aqueous extracts of Cyclocarya paliurus leaves collected from different populations
Cyclocarya paliurus (Batal) Iljinskaja is a multiple function tree species, but its main utilization is for the harvesting of its leaves as materials for tea production and recently as ingredients for the food industry. In this study aqueous extracts of C. paliurus leaves collected from 21 natural populations were evaluated for their phytochemical content and antioxidant activity. The content of water-soluble polysaccharide, total flavonoid and total polyphenol varied from 66.05 to 153.32 mg/g, 9.01 to 19.65 mg/g and 20.80 to 52.69 mg/g, respectively. Quercetin-3-O-glucuronide, aemferol-3-O-glucuronide and 3-O-caffeoylquinic acid were the major phenolic components in aqueous extracts of C. paliurus leaves. Both redundancy analysis and Pearson's correlation analysis indicated that water-soluble polysaccharide, total polyphenol, total flavonoid, quercetin-3-O-glucuronide, 3-O-caffeoylquinic acid and 4-O-caffeoylquinic acid were significantly correlated with antioxidant activity, but total polyphenol showed the greatest contribution to antioxidant capacity. The antioxidant activity of the 21 populations was classified into six distinct groups based on the squared Euclidean distance. These results would provide a theoretical basis for obtaining the greatest yield of targeted antioxidant phytochemicals of C. paliurus leaves for tea and food ingredient production.
Zhou et al. (2019) Phytochemical content and antioxidant activity in aqueous extracts of Cyclocarya paliurus leaves collected from different populations. PeerJ 7:e6492 https://doi.org/10.7717/peerj.6492
A new testudinoid turtle from the middle to late Eocene of Vietnam
Background Testudinoidea is a major clade of turtles that has colonized different ecological environments across the globe throughout the Tertiary. Aquatic testudinoids have a particularly rich fossil record in the Tertiary of the northern hemisphere, but little is known about the evolutionary history of the group, as the phylogenetic relationships of most fossils have not been established with confidence, in part due to high levels of homoplasy and polymorphism. Methods We here focus on describing a sample of 30 testudinoid shells, belonging to a single population that was collected from lake sediments from the middle to late Eocene (35–39 Ma) Na Duong Formation in Vietnam. The phylogenetic placement of this new material is investigated by integrating it and 11 other species of putative geoemydids from the Eocene and Oligocene to a recently published matrix of geoemydid turtles, that embraces the use of polymorphic characters, and then running a total-evidence analysis. Results The new material is highly polymorphic, but can be inferred with confidence to be a new taxon, Banhxeochelys trani gen. et sp. nov. It shares morphological similarities with other southeastern Asian testudinoids, Isometremys lacuna and Guangdongemys pingi, but is placed phylogenetically at the base of Pan-Testuguria when fossils are included in the analysis, or as a stem geoemydid when other fossils are deactivated from the matrix. The vast majority of other putative fossil geoemydids are placed at the base of Pan-Testuguria as well. Discussion The phylogenetic placement of fossil testudinoids used in the analysis is discussed individually and each species compared to Banhxeochelys trani gen. et sp. nov. The high levels of polymorphism observed in the new taxon is discussed in terms of ontogenetic and random variability. This is the first time that a large sample of fossil testudinoids has its morphological variation described in detail.
Garbin et al. (2019) A new testudinoid turtle from the middle to late Eocene of Vietnam. PeerJ 7:e6280 https://doi.org/10.7717/peerj.6280
Diverse microbial communities hosted by the model carnivorous pitcher plant Sarracenia purpurea: analysis of both bacterial and eukaryotic composition across distinct host plant populations
Background The pitcher plant Sarracenia purpurea supplements nutrient acquisition through carnivory, capturing insect prey which are digested by a food web community of eukaryotes and bacteria. While the food web invertebrates are well studied, and some recent studies have characterized bacteria, detailed genetic analysis of eukaryotic diversity is lacking. This study aimed to compare eukaryotic and bacterial composition and diversity of pitcher communities within and between populations of host plants in nearby but distinct wetland habitats, and to characterize microbial functions across populations and in comparison with another freshwater community. Methods Pitcher fluid was sampled from the two wetlands, Cedarburg and Sapa Bogs, community DNA was extracted, and 16S and 18S rRNA amplicons were sequenced and data processed for community-level comparisons. Results and Conclusions Bacterial diversity in the small pitcher volume rivaled that of larger aquatic communities. Between pitcher plant populations, several bacterial families (Kiloniellaceae, Acetobacteraceae, Xanthobacteraceae, Sanguibacteraceae, Oligoflexaceae, Nitrosomonadaceae, Chromatiaceae, Saprospiraceae) were significantly higher in one population. However, although predicted pitcher bacterial functions were distinct from other freshwater communities, especially for some amino acid metabolism, functions were similar across all the pitchers in the two populations. This suggests some functional redundancy among bacterial taxa, and that functions converge to achieve similar food web processes. The sequencing identified a previously under-appreciated high diversity of ciliates, Acari mites, fungi and flagellates in pitcher communities; the most abundant sequences from eukaryotic taxa were Oligohymenophorea ciliates, millipedes and Ichthyosporea flagellates. Two thirds of taxa were identified as food web inhabitants and less than one third as prey organisms. Although eukaryotic composition was not significantly different between populations, there were different species of core taxonomic groups present in different pitchers—these differences may be driven by wetland habitats providing different populations to colonize new pitchers. Eukaryotic composition was more variable than bacterial composition, and there was a poor relationship between bacterial and eukaryotic composition within individual pitchers, suggesting that colonization by eukaryotes may be more stochastic than for bacteria, and bacterial recruitment to pitchers may involve factors other than prey capture and colonization by eukaryotic food web inhabitants.
Grothjan et al. (2019) Diverse microbial communities hosted by the model carnivorous pitcher plant Sarracenia purpurea: analysis of both bacterial and eukaryotic composition across distinct host plant populations. PeerJ 7:e6392 https://doi.org/10.7717/peerj.6392
Analysis of the genetic diversity and population structure of Salix psammophila based on phenotypic traits and simple sequence repeat markers
Salix psammophila (desert willow) is a shrub endemic to the Kubuqi Desert and the Mu Us Desert, China, that plays an important role in maintaining local ecosystems and can be used as a biomass feedstock for biofuels and bioenergy. However, the lack of information on phenotypic traits and molecular markers for this species limits the study of genetic diversity and population structure. In this study, nine phenotypic traits were analyzed to assess the morphological diversity and variation. The mean coefficient of variation of 17 populations ranged from 18.35% (branch angle (BA)) to 38.52% (leaf area (LA)). Unweighted pair-group method with arithmetic mean analysis of nine phenotypic traits of S. psammophila showed the same results, with the 17 populations clustering into five groups. We selected 491 genets of the 17 populations to analyze genetic diversity and population structure based on simple sequence repeat (SSR) markers. Analysis of molecular variance (AMOVA) revealed that most of the genetic variance (95%) was within populations, whereas only a small portion (5%) was among populations. Moreover, using the animal model with SSR-based relatedness estimated of S. psammophila, we found relatively moderate heritability values for phenotypic traits, suggesting that most of trait variation were caused by environmental or developmental variation. Principal coordinate and phylogenetic analyses based on SSR data revealed that populations P1, P2, P9, P16, and P17 were separated from the others. The results showed that the marginal populations located in the northeastern and southwestern had lower genetic diversity, which may be related to the direction of wind. These results provide a theoretical basis for germplasm management and genetic improvement of desert willow.
Hao et al. (2019) Analysis of the genetic diversity and population structure of Salix psammophila based on phenotypic traits and simple sequence repeat markers. PeerJ 7:e6419 https://doi.org/10.7717/peerj.6419
Mycorrhization of Quercus acutissima with Chinese black truffle significantly altered the host physiology and root-associated microbiomes
Background Our aim was to explore how the ectomycorrhizae of an indigenous tree,Quercus acutissima, with a commercial truffle, Chinese black truffle (Tuber indicum), affects the host plant physiology and shapes the associated microbial communities in the surrounding environment during the early stage of symbiosis. Methods To achieve this, changes in root morphology and microscopic characteristics, plant physiology indices, and the rhizosphere soil properties were investigated when six-month-old ectomycorrhizae were synthesized. Meanwhile, next-generation sequencing technology was used to analyze the bacterial and fungal communities in the root endosphere and rhizosphere soil inoculated with T. indicum or not. Results The results showed that colonization by T. indicum significantly improved the activity of superoxide dismutase in roots but significantly decreased the root activity. The biomass, leaf chlorophyll content and root peroxidase activity did not obviously differ. Ectomycorrhization of Q. acutissima with T. indicum affected the characteristics of the rhizosphere soil, improving the content of organic matter, total nitrogen, total phosphorus and available nitrogen. The bacterial and fungal community composition in the root endosphere and rhizosphere soil was altered by T. indicum colonization, as was the community richness and diversity. The dominant bacteria in all the samples were Proteobacteria and Actinobacteria, and the dominant fungi were Eukaryota_norank, Ascomycota, and Mucoromycota. Some bacterial communities, such as Streptomyces, SM1A02, and Rhizomicrobium were more abundant in the ectomycorrhizae or ectomycorrhizosphere soil. Tuber was the second-most abundant fungal genus, and Fusarium was present at lower amounts in the inoculated samples. Discussion Overall, the symbiotic relationship between Q. acutissima and T. indicum had an obvious effect on host plant physiology, soil properties, and microbial community composition in the root endosphere and rhizosphere soil, which could improve our understanding of the symbiotic relationship between Q. acutissima and T. indicum, and may contribute to the cultivation of truffle.
Zhang et al. (2019) Mycorrhization of Quercus acutissima with Chinese black truffle significantly altered the host physiology and root-associated microbiomes. PeerJ 7:e6421 https://doi.org/10.7717/peerj.6421