Exploring nutrient limitation for polyhydroxyalkanoates synthesis by newly isolated strains of Aeromonas sp. using biodiesel-derived glycerol as a substrate
Aeromonas spp. strains isolated from activated sludge in a municipal wastewater treatment plant were found to be able to synthesize polyhydroxyalkanoates (PHA) utilizing pure and crude glycerol. The 16S rRNA gene sequence of the isolates exhibited similarity to Aeromonas hydrophila, A. aquatica, and A. salmonicida. Our results confirmed that the adequate supply of nitrogen and phosphorus during culture in 250-ml shake flasks did not stimulate the synthesis of PHAs. The results indicate that the PHA content of cells was higher under a phosphorus-limiting environment compared to nitrogen starvation. In the two-stage cultivation using glucose (in the first step) and crude glycerol from biodiesel industry (in the second step) as a component of the growth medium, the analyzed strains grew to 3.06 g/l of cell dry weight containing up to 22% of PHAs. Furthermore, during the same culture strategy up to 42% of PHAs were extracted, when in the second step of the process, Aeromonas sp. AC_03 was grown on pure glycerol under phosphorus limitation. The purified biopolymer was confirmed to be polyhydroxybutyrate. Aeromonas sp. AC_02 was also capable to accumulate the poly(3-hydroxybutyrate-co-3-hydroxyvalerate) copolymer when pure glycerol was added as a substrate under nitrogen-deficiency one-step bioprocess. Our results confirm that due to the biopolymer productivity, newly isolated strains could be exploited for obtaining valuable biopolymers using wastes generated from biodiesel industry.
Możejko-Ciesielska et al. (2018) Exploring nutrient limitation for polyhydroxyalkanoates synthesis by newly isolated strains of Aeromonas sp. using biodiesel-derived glycerol as a substrate. PeerJ 6:e5838 https://doi.org/10.7717/peerj.5838
Phosphate sorption and desorption by two contrasting volcanic soils of equatorial Africa
Volcanic soils cover 1% of the Earth’s surface but support 10% of the world’s population. They are among the most fertile soils in the world, due to their excellent physical properties and richness in available nutrients. The major limiting factor for plant growth in volcanic soils is phosphate fixation, which is mainly attributable to active species of aluminium and iron. The sorption and desorption of phosphate is studied on the surface horizons of two African agricultural soils, a silandic Andosol (Rwanda) and a vitric Andosol (São Tomé and Principe). Both soils are slightly acid. The silandic Andosol is rich in active aluminium forms, while the vitric Andosol has high amounts of crystalline iron and aluminium oxides. Sorption isotherms were determined by equilibrating at 293K soil samples with phosphate solutions of concentrations between 0 and 100 mg P L−1 in NaNO3; phosphate was determined by visible spectrophotometry in the equilibrium solution. To study desorption, the soil samples from the sorption experiment were equilibrated with 0.02 M NaNO3. The isotherms were adjusted to mathematical models. In almost all the concentration range, the adsorption of phosphate by the silandic Andosol was greater than 90% of the amount added, being lower in the vitric Andosol but always higher than 65%. The high sorption by the silandic Andosol is attributed to its richness in non-crystalline Fe and Al, while in the vitric Andosol crystalline iron species seem to play a relevant role in the adsorption. The sorption isotherms of both soils fitted to the Temkin model, the adjustment to the Langmuir or Freundlich models being unsatisfactory; throughout the range studied, the sorption increases with increasing phosphorus concentration, a maximum sorption is not predictable (as occurs when the sorption is adjusted to the Langmuir model). For an added P concentration of 100 mg L−1 (3.2 mmol L−1), the sorption is 47.7 µmol P g−1 in the silandic Andosol and 41.6 µmol P g−1 in the vitric Andosol. The desorption is low and the comparison of the sorption and desorption isotherms reveals a pronounced hysteresis, that is, the irreversibility of the sorption. The high phosphate sorption and its irreversibility are comparable to those published for other volcanic soils with high contents of allophane, active aluminium and free iron. The strong phosphate adsorption is a serious limiting factor for plant growth, which requires a careful management of phosphorus fertilization.
© 2018 Gonzalez-Rodriguez and Fernandez-Marcos
Gonzalez-Rodriguez et al. (2018) Phosphate sorption and desorption by two contrasting volcanic soils of equatorial Africa. PeerJ 6:e5820 https://doi.org/10.7717/peerj.5820
©2018 Gonzalez-Rodriguez and Fernandez-Marcos
Proteorhodopsins dominate the expression of phototrophic mechanisms in seasonal and dynamic marine picoplankton communities
The most abundant and ubiquitous microbes in the surface ocean use light as an energy source, capturing it via complex chlorophyll-based photosystems or simple retinal-based rhodopsins. Studies in various ocean regimes compared the abundance of these mechanisms, but few investigated their expression. Here we present the first full seasonal study of abundance and expression of light-harvesting mechanisms (proteorhodopsin, PR; aerobic anoxygenic photosynthesis, AAnP; and oxygenic photosynthesis, PSI) from deep-sequenced metagenomes and metatranscriptomes of marine picoplankton (<1 µm) at three coastal stations of the San Pedro Channel in the Pacific Ocean. We show that, regardless of season or sampling location, the most common phototrophic mechanism in metagenomes of this dynamic region was PR (present in 65–104% of the genomes as estimated by single-copy recA), followed by PSI (5–104%) and AAnP (5–32%). Furthermore, the normalized expression (RNA to DNA ratio) of PR genes was higher than that of oxygenic photosynthesis (average ± standard deviation 26.2 ± 8.4 vs. 11 ± 9.7), and the expression of the AAnP marker gene was significantly lower than both mechanisms (0.013 ± 0.02). We demonstrate that PR expression was dominated by the SAR11-cluster year-round, followed by other Alphaproteobacteria, unknown-environmental clusters and Gammaproteobacteria. This highly dynamic system further allowed us to identify a trend for PR spectral tuning, in which blue-absorbing PR genes dominate in areas with low chlorophyll-a concentrations (<0.25 µgL−1). This suggests that PR phototrophy is not an accessory function but instead a central mechanism that can regulate photoheterotrophic population dynamics.
Sieradzki et al. (2018) Proteorhodopsins dominate the expression of phototrophic mechanisms in seasonal and dynamic marine picoplankton communities. PeerJ 6:e5798 https://doi.org/10.7717/peerj.5798
Creating functional groups of marine fish from categorical traits
Background Functional groups serve two important functions in ecology: they allow for simplification of ecosystem models and can aid in understanding diversity. Despite their important applications, there has not been a universally accepted method of how to define them. A common approach is to cluster species on a set of traits, validated through visual confirmation of resulting groups based primarily on expert opinion. The goal of this research is to determine a suitable procedure for creating and evaluating functional groups that arise from clustering nominal traits. Methods To do so, we produced a species by trait matrix of 22 traits from 116 fish species from Tasman Bay and Golden Bay, New Zealand. Data collected from photographs and published literature were predominantly nominal, and a small number of continuous traits were discretized. Some data were missing, so the benefit of imputing data was assessed using four approaches on data with known missing values. Hierarchical clustering is utilised to search for underlying data structure in the data that may represent functional groups. Within this clustering paradigm there are a number of distance matrices and linkage methods available, several combinations of which we test. The resulting clusters are evaluated using internal metrics developed specifically for nominal clustering. This revealed the choice of number of clusters, distance matrix and linkage method greatly affected the overall within- and between- cluster variability. We visualise the clustering in two dimensions and the stability of clusters is assessed through bootstrapping. Results Missing data imputation showed up to 90% accuracy using polytomous imputation, so was used to impute the real missing data. A division of the species information into three functional groups was the most separated, compact and stable result. Increasing the number of clusters increased the inconsistency of group membership, and selection of the appropriate distance matrix and linkage method improved the fit. Discussion We show that the commonly used methodologies used for the creation of functional groups are fraught with subjectivity, ultimately causing significant variation in the composition of resulting groups. Depending on the research goal dictates the appropriate strategy for selecting number of groups, distance matrix and clustering algorithm combination.
Ladds et al. (2018) Creating functional groups of marine fish from categorical traits. PeerJ 6:e5795 https://doi.org/10.7717/peerj.5795
Epidemiological and genetic characteristics of swine pseudorabies virus in mainland China between 2012 and 2017
The outbreak of pseudorabies (PR) in many Bartha-K61 vaccinated farms in China in late 2011 has seriously damaged the pig industry of one of the largest producers of pork products in the world. To understand the epidemiological characteristics of the pseudorabies virus (PRV) strains currently prevalent in China, a total of 16,256 samples collected from pig farms suspected of PRV infection in 27 Provinces of China between 2012 and 2017 were evaluated for detection of PRV. Since the extensive use of gE-deleted PRV vaccine in China, the PRV-gE was applied for determining wild-type virus infection by PCR. Of the 16,256 samples detected, approximately 1,345 samples were positive for the detection of PRV-gE, yielding an average positive rate of 8.27%. The positive rates of PRV detection from 2012 to 2017 were 11.92% (153/1284), 12.19% (225/1846), 6.70% (169/2523), 11.10% (269/2424), 5.57% (147/2640), and 6.90% (382/5539), respectively. To understand the genetic characteristics of the PRV strains currently circulating, 25 PRV strains isolated from those PRV-gE positive samples were selected for further investigation. Phylogenetic analysis based on gB, gC, and gE showed that PRV strains prevalent in China had a remarkably distinct evolutionary relationship with PRVs from other countries, which might explain the observation that Bartha-K61 vaccine was unable to provide full protection against emergent strains. Sequence alignments identified many amino acid changes within the gB, gC, and gE proteins of the PRVs circulating in China after the outbreak compared to those from other countries or those prevalent in China before the outbreak; those changes also might affect the protective efficacy of previously used vaccines in China, as well as being associated in part with the increased virulence of the current PRV epidemic strains in China.
Sun et al. (2018) Epidemiological and genetic characteristics of swine pseudorabies virus in mainland China between 2012 and 2017. PeerJ 6:e5785 https://doi.org/10.7717/peerj.5785
Non-sutural basicranium-derived cells undergo a unique mineralization pathway via a cartilage intermediate in vitro
The basicranium serves as a key interface in the mammalian skull, interacting with the calvarium, facial skeleton and vertebral column. Despite its critical function, little is known about basicranial bone formation, particularly on a cellular level. The goal of this study was therefore to cultivate a better understanding of basicranial development by isolating and characterizing the osteogenic potential of cells from the neonatal murine cranial base. Osteoblast-like basicranial cells were isolated, seeded in multicellular aggregates (designated micromasses), and cultured in osteogenic medium in the presence or absence of bone morphogenetic protein-6 (BMP6). A minimal osteogenic response was observed in control osteogenic medium, while BMP6 treatment induced a chondrogenic response followed by up-regulation of osteogenic markers and extensive mineralization. This response appears to be distinct from prior analyses of the calvarium and long bones, as basicranial cells did not mineralize under standard osteogenic conditions, but rather required BMP6 to stimulate mineralization, which occurred via an endochondral-like process. These findings suggest that this site may be unique compared to other cranial elements as well as the limb skeleton, and we propose that the distinct characteristics of these cells may be a function of the distinct properties of the basicranium: endochondral ossification, dual embryology, and complex loading environment.
Weiss-Bilka et al. (2018) Non-sutural basicranium-derived cells undergo a unique mineralization pathway via a cartilage intermediate in vitro. PeerJ 6:e5757 https://doi.org/10.7717/peerj.5757
The effectiveness of Payments for Ecosystem Services at delivering improvements in water quality: lessons for experiments at the landscape scale
Background Randomised Control Trials (RCTs) are used in impact evaluation in a range of fields. However, despite calls for their greater use in environmental management, their use to evaluate landscape scale interventions remains rare. Payments for Ecosystem Services (PES) incentivise land users to manage land to provide environmental benefits. We present the first RCT evaluation of a PES program aiming to improve water quality. Watershared is a program which incentivises landowners to avoid deforestation and exclude cattle from riparian forests. Using this unusual landscape-scale experiment we explore the efficacy of Watershared at improving water quality, and draw lessons for future RCT evaluations of landscape-scale environmental management interventions. Methods One hundred and twenty-nine communities in the Bolivian Andes were randomly allocated to treatment (offered Watershared agreements) or control (not offered agreements) following baseline data collection (including Escherichia coli contamination in most communities) in 2010. We collected end-line data in 2015. Using our end-line data, we explored the extent to which variables associated with the intervention (e.g. cattle exclusion, absence of faeces) predict water quality locally. We then investigated the efficacy of the intervention at improving water quality at the landscape scale using the RCT. This analysis was done in two ways; for the subset of communities for which we have both baseline and end-line data from identical locations we used difference-in-differences (matching on baseline water quality), for all sites we compared control and treatment at end-line controlling for selected predictors of water quality. Results The presence of cattle faeces in water adversely affected water quality suggesting excluding cattle has a positive impact on water quality locally. However, both the matched difference-in-differences analysis and the comparison between treatment and control communities at end-line suggested Watershared was not effective at reducing E. coli contamination at the landscape scale. Uptake of Watershared agreements was very low and the most important land from a water quality perspective (land around water intakes) was seldom enrolled. Discussion Although excluding cattle may have a positive local impact on water quality, higher uptake and better targeting would be required to achieve a significant impact on the quality of water consumed in the communities. Although RCTs potentially have an important role to play in building the evidence base for approaches such as PES, they are far from straightforward to implement. In this case, the randomised trial was not central to concluding that Watershared had not produced a landscape scale impact. We suggest that this RCT provides valuable lessons for future use of randomised experiments to evaluate landscape-scale environmental management interventions.
Pynegar et al. (2018) The effectiveness of Payments for Ecosystem Services at delivering improvements in water quality: lessons for experiments at the landscape scale. PeerJ 6:e5753 https://doi.org/10.7717/peerj.5753
Surgical antibiotic prophylaxis use and infection prevalence in non-cosmetic breast surgery procedures at a tertiary hospital in Western Australia—a retrospective study
Background Surgical site infections (SSIs) are a common complication following breast surgery procedures, despite being considered a clean surgery. The prevalence of SSIs can be minimised with the appropriate use of antibiotic prophylaxis as outlined in the Australian Therapeutic Guidelines (eTG). The aims of this study were to evaluate adherence to the eTG for antibiotic prophylaxis in breast surgery procedures at a Western Australian teaching hospital following an update of the guidelines in 2014 and examine the impact of prophylactic antibiotics on SSI incidence and length of hospital stay. Method A retrospective cross-sectional study which reviewed medical records from a random sample of 250 patients selected from 973 patients who underwent breast surgical procedures between February 2015 and March 2017. Results Overall adherence to current eTG occurred in 49.2% (123/250) of operations. Pre-operative and post-operative antibiotics were prescribed in 98.4% (246/250) and 11.2% (28/250) operations respectively. Adherence rates to three specific elements of the eTG (drug prescribed, drug dosage and timing of administration) were 91.6% (229/250), 53.6% (134/250) and 86.4% (216/250) respectively. For the 14.4% (36/250) patients with relevant drug allergies, there was zero adherence to the eTG. Overall recorded SSI prevalence was low at 5.2% (13/250). The mean length of stay in patients (2.3 ± 1.7 days) was not influenced by level of eTG adherence (p = 0.131) or SSIs (p = 0.306). Conclusion These data demonstrate a significant improvement in overall adherence to the eTG from 13.3% to 49.2% (p = < 0.001). The level of detected SSIs in this study was low. Further improvement is necessary with respect to prescribing appropriate antibiotic dosages and for those with allergies.
Lavers et al. (2018) Surgical antibiotic prophylaxis use and infection prevalence in non-cosmetic breast surgery procedures at a tertiary hospital in Western Australia—a retrospective study. PeerJ 6:e5724 https://doi.org/10.7717/peerj.5724
Molecular characterization of the giant freshwater prawn (Macrobrachium rosenbergii) beta-actin gene promoter
Constitutive promoters are important tools for gene function studies and transgenesis. The Beta-actin (actb1) gene promoter has been isolated from many species but remains to be cloned from the giant freshwater prawn (Macrobrachium rosenbergii). In this study, we cloned and characterized the Mractb1 gene promoter. Two alternative promoters were identified for the Mractb1 gene, which direct the generation of two transcripts with different 5′ untranslated regions. Three CpG islands were predicted in the upstream sequence, which are intimately related to transcription initiation and promoter activity. In addition to the CCAAT-box and the CArG-box, molecular dissection of the flanking sequence revealed the existence of one negative and two positive elements in the upstream region and the first intron. Finally, the Mractb1 promoter demonstrated comparative activity to the carp (Cyprinus carpio) actb1 promoter. Our investigations provide a valuable genetic tool for gene function studies and shed light on the regulation of the Mractb1 gene.
Yan et al. (2018) Molecular characterization of the giant freshwater prawn (Macrobrachium rosenbergii) beta-actin gene promoter. PeerJ 6:e5701 https://doi.org/10.7717/peerj.5701
The influence of Neanderthal alleles on cytotoxic response
Various studies have shown that people of Eurasian origin contain traces of DNA inherited from interbreeding with Neanderthals. Recent studies have demonstrated that these Neanderthal variants influence a range of clinically important traits and diseases. Thus, understanding the genetic factors responsible for the variability in individual response to drug or chemical exposure is a key goal of pharmacogenomics and toxicogenomics, as dose responses are clinically and epidemiologically important traits. It is well established that ethnic and racial differences are important in dose response traits, but to our knowledge the influence of Neanderthal ancestry on response to xenobiotics is unknown. Towards this aim, we examined if Neanderthal ancestry plays a role in cytotoxic response to anti-cancer drugs and toxic environmental chemicals. We identified common Neanderthal variants in lymphoblastoid cell lines (LCLs) derived from the globally diverse 1000 Genomes Project and Caucasian cell lines from the Children’s Hospital of Oakland Research Institute. We analyzed the effects of these Neanderthal alleles on cytotoxic response to 29 anti-cancer drugs and 179 environmental chemicals at varying concentrations using genome-wide data. We identified and replicated single nucleotide polymorphisms (SNPs) from these association results, including a SNP in the SNORD-113 cluster. Our results also show that the Neanderthal alleles cumulatively lead to increased sensitivity to both the anti-cancer drugs and the environmental chemicals. Our results demonstrate the influence of Neanderthal ancestry-informative markers on cytotoxic response. These results could be important in identifying biomarkers for personalized medicine or in dissecting the underlying etiology of dose response traits.
Akhtari et al. (2018) The influence of Neanderthal alleles on cytotoxic response. PeerJ 6:e5691 https://doi.org/10.7717/peerj.5691