Percent Relative Abundance Research Articles

Effects of burning and photochemical degradation of Macondo surrogate oil on its composition and toxicity.

Petroleum products in the environment can produce significant toxicity through photochemically driven processes. Burning surface oil and photochemical degradation were two mechanisms for oil removal after the Deepwater Horizon (DWH) oil spill in the Gulf of Mexico. After burning, residual oil remains in the environment and may undergo further weathering, a poorly understood fate. Although photochemistry was a major degradation pathway of the DWH oil, its effect on burned oil residue in the environment is under studied. Here, we ignited Macondo surrogate crude oil and allowed it to burn to exhaustion. Water-accommodated fractions (WAFs) of the burn residue were created in full sunlight to determine the effects of photochemical weathering on the burned oil residue. Our findings show that increased dissolved organic carbon concentrations (DOC) for the light unburned and light burned after sunlight exposure positively correlated to decreased microbial growth and production inhibition (i.e. more toxic) when compared to the dark controls. Optical and molecular analytical techniques were used to identify the classes of compounds contributing to the toxicity in the dark and light burned and dark and light unburned WAFs. After light exposure, the optical composition between the light unburned and light burned differed significantly (p < 0.05), revealing key fluorescence signatures commonly identified as crude oil degradation products. Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS) analysis showed more condensed aromatic, reduced oxygenated compounds present in the light burned than in the light unburned. FT-ICR MS also showed an increase in the percent relative abundance of carboxyl-rich alicyclic molecules (CRAM) like compounds in the light burned compared to light unburned. The increase in CRAM suggests that the composition of the light burned is more photorefractory, i.e., reduced, explaining the residual toxicity observed in microbial activity. Overall, these data indicate burning removes some but not all toxic compounds, leaving behind compounds which retain considerable toxicity. This study shows that burn oil residues are photolabile breaking down further into complex reduced compounds.

2760. Fecal Microbiota Transplantation for Decolonization of Carbapenemase-Producing Enterobacterales

Abstract Background Fecal microbiota transplantation (FMT) can effectively decolonize multidrug-resistant organisms but its efficacy is variable. We evaluated the impact of FMT treatment at eliminating carbapenemase-producing Enterobacterales (CPE) carriage compared to spontaneous decolonization and identified microbial signatures of successful decolonization. Methods Prospective study, with patients colonized with CPE receiving a single dose of FMT via the nasogastric route. CPE-colonized patients who did not meet our inclusion criteria or decided not to participate in the study comprised the control group where spontaneous decolonization was evaluated. Primary endpoint was complete elimination of CPE carriage 2 weeks after FMT. A secondary endpoint for decolonization was set at 3 months post-FMT. Successful decolonization was defined by 2+ consecutive negative rectal swabs as determined by both culture and PCR. Shotgun metagenomic sequencing was performed to assess gut microbiota composition of donors and recipients before and after FMT. Results Twenty patients colonized with CPE were included, 72.5 ± 18.8 years. Median duration of carriage of CPE before FMT was 62.5 days (IQR 48.75-122.5). At 3 months post-FMT, 40% (n=8/20) of patients were successfully decolonized, while 20% (n=4/20) meeting the 2-week primary endpoint. Kaplan-Meier curves between patients in the FMT cohort and those in the control group (n=82) revealed the same rate of decolonization over time (p=0.9). Microbiota composition analyses post-FMT revealed significantly higher bacterial species richness and alpha diversity in responders versus non-responders (Fig1A,B), and specific taxa including Faecalibacterium prausnitzii, Parabacteroides distasonis, Collinsella aerofaciens, Alistipes finegoldii and Blautia_A sp900066335 were associated with response (Fig.2). Furthermore, CPE abundance levels at baseline were significantly higher in non-responders than in responders (Fig.3). Box and whisker plots of the percent relative abundance for the indicated species in samples from patients with CRE clearance on day 14 (teal), and patients without CRE clearance on day 14 (orange). The median (±interquartile range) is plotted for each species in each group. Whiskers extend to the lowest and highest values no greater than 1.5x the interquartile range from the closest hinge. The displayed taxa were significantly altered between patients with and without CRE clearance at day 14 across all samples, with q-values below 0.01 (MaAslin2 log-transformed linear model). Box and whisker plots indicating the cumulative percent relative abundance of CRE species in samples from patients with CRE clearance on day 14 (teal) and patients without CRE clearance on day 14 (orange). The median (±interquartile range) is plotted for each group at the indicated timepoints. Whiskers extend to the lowest and highest values no greater than 1.5x the interquartile range from the closest hinge. Patients with CRE clearance on day 14 have significantly lower CRE relative abundance than patients without CRE clearance on day 14 at baseline and 1 week post-FMT (Wilcoxen Rank-Sum test with FDR adjustment). Conclusion FMT administration led to complete CPE eradication in a subset of colonized patients but did not achieve statistical significance. Response to FMT was not donor-dependent and correlated with the transfer of specific bacteria taxa and CPE colonization levels. Disclosures Andrea Watson, PhD, Vedanta Biosciences: Advisor/Consultant|Vedanta Biosciences: Honoraria Gianluca Galazzo, PhD, Vedanta Biosciences: Advisor/Consultant|Vedanta Biosciences: Honoraria Ed J. Kuijper, Prof. Dr., Vedanta Biosciences: Advisor/Consultant Silvia Caballero, PhD, Vedanta Biosciences: Advisor/Consultant|Vedanta Biosciences: Board Member|Vedanta Biosciences: Ownership Interest

Post-monsoon seasonal variation of prokaryotic diversity in solfataric soil from the North Sikkim hot spring.

The solfataric soil sediments of the hot springs of Sikkim located at Yume Samdung and Lachen valley were studied for deciphering the bacterial diversity. The main aim here is to present a comparative study and generate a baseline data on the post-monsoon seasonal variation for the months of October and December, analyzed through 16S rRNA V3-V4 amplicon sequencing. The results have shown that there is not much variation at phylum level in the month of October in all the three hot springs such as New Yume Samdung (NYS), Old Yume Samdung (OYS), and Tarum (TAR) hot spring. The abundant phyla mainly present were Firmicutes, followed by Proteobacteria, Actinobacteria, and Bacteroidetes. Similarly, in the month of December, Firmicutes, Proteobacteria, Actinobacteria, and Bacteroidetes were prevalent; however, the percent relative abundance of these phyla in the month of December is relatively less. Besides this decrease in percent abundance, it was interestingly seen that relatively more phyla were found contributing towards the bacterial diversity in the month of December. Similar to phylum level, at genus level, there was not much variation seen among various prevalent genera of the three studied hot springs in both months. The major genera prevalent in both months among all the three hot springs were followed by Bacillus, Desulfotomaculum, Lactobacillus, and Paenibacillus. A similar trend was also seen at gene level that relative abundance of various genera was higher in the month of October but more genera were found to be contributing towards bacterial diversity in the month of December. Few distinct genera were found to be more abundant in the month of December such as Rhodopirellula and Blastopirellula. The results may conclude that there is not much variation in the abundance and type of bacterial communities during the post-monsoon season in the month of October and December. However, this may be assumed that there is the accumulation or increase in the bacterial communities during the winter (relatively higher temperature among hot springs) and may favor few mesophilic and more thermophilic communities as well.

Metagenomic community composition and resistome analysis in a full-scale cold climate wastewater treatment plant

BackgroundWastewater treatment plants are an essential part of maintaining the health and safety of the general public. However, they are also an anthropogenic source of antibiotic resistance genes. In this study, we characterized the resistome, the distribution of classes 1–3 integron-integrase genes (intI1, intI2, and intI3) as mobile genetic element biomarkers, and the bacterial and phage community compositions in the North End Sewage Treatment Plant in Winnipeg, Manitoba. Samples were collected from raw sewage, returned activated sludge, final effluent, and dewatered sludge. A total of 28 bacterial and viral metagenomes were sequenced over two seasons, fall and winter. Integron-integrase genes, the 16S rRNA gene, and the coliform beta-glucuronidase gene were also quantified during this time period.ResultsBacterial classes observed above 1% relative abundance in all treatments were Actinobacteria (39.24% ± 0.25%), Beta-proteobacteria (23.99% ± 0.16%), Gamma-proteobacteria (11.06% ± 0.09%), and Alpha-proteobacteria (9.18 ± 0.04%). Families within the Caudovirales order: Siphoviridae (48.69% ± 0.10%), Podoviridae (23.99% ± 0.07%), and Myoviridae (19.94% ± 0.09%) were the dominant phage observed throughout the NESTP. The most abundant bacterial genera (in terms of average percent relative abundance) in influent, returned activated sludge, final effluent, and sludge, respectively, includes Mycobacterium (37.4%, 18.3%, 46.1%, and 7.7%), Acidovorax (8.9%, 10.8%, 5.4%, and 1.3%), and Polaromonas (2.5%, 3.3%, 1.4%, and 0.4%). The most abundant class of antibiotic resistance in bacterial samples was tetracycline resistance (17.86% ± 0.03%) followed by peptide antibiotics (14.24% ± 0.03%), and macrolides (10.63% ± 0.02%). Similarly, the phage samples contained a higher prevalence of macrolide (30.12% ± 0.30%), peptide antibiotic (10.78% ± 0.13%), and tetracycline (8.69% ± 0.11%) resistance. In addition, intI1 was the most abundant integron-integrase gene throughout treatment (1.14 × 104 gene copies/mL) followed by intI3 (4.97 × 103 gene copies/mL) while intI2 abundance remained low (6.4 × 101 gene copies/mL).ConclusionsWastewater treatment successfully reduced the abundance of bacteria, DNA phage and antibiotic resistance genes although many antibiotic resistance genes remained in effluent and biosolids. The presence of integron-integrase genes throughout treatment and in effluent suggests that antibiotic resistance genes could be actively disseminating resistance between both environmental and pathogenic bacteria.

Inhibition of N2 Fixation by N Fertilization of Common Bean (Phaseolus vulgaris L.) Plants Grown on Fields of Farmers in the Eastern Cape of South Africa, Measured Using 15N Natural Abundance and Tissue Ureide Analysis

Inhibition of N2 fixation in N-fertilized common bean (Phaseolus vulgaris L.) plants growing on the fields of farmers in the Eastern Cape of South Africa was measured using 15N natural abundance and tissue ureide analysis. The N-fertilized bean plants revealed greater soil N uptake, higher concentrations of nitrate in organs, low tissue ureide levels, and much lower percent relative ureide-N abundance when compared with unfertilized plants. In contrast, the unfertilized plants showed greater nodule fresh weight, higher N derived from fixation (e.g., 84.6, 90.4, and 97.1% at Lujecweni fields 2, 3, and 4, respectively), increased amount of N-fixed (e.g., 163.3, 161.3, and 140.3 kg ha−1 at Lujecweni fields 2, 3, and 4, respectively), greater ureide concentration in stems and petioles, higher % relative ureide-N abundance, and low soil N uptake. We also found that the percent N derived from fixation (%Ndfa) was very high for some bean plants receiving a double dose of N fertilizer [e.g., Lujecweni field 1 (51.8%) and Tikitiki field 1 (53.3%], and quite high for others receiving a single dose of N fertilizer [e.g., Tikitiki field 2 (50.1%), Mfabantu fields 1 and 2 (45.5 and 79.9%, respectively), and St. Luthberts field 1 (58.9%)]. Though not assessed in this study, it is likely that the rhizobia that effectively nodulated the N-fertilized bean plants and fixed considerable amounts of symbiotic N had constitutive and/or inducible nitrate reductase genes for reducing nitrate in nodules and bacteroids, hence their ability to form root nodules and derived high %Ndfa in bean with added N. While single- and double-dose N fertilizer applications increased plant growth and grain yield compared to unfertilized bean plants, the single-dose N fertilizer application produced much greater grain yield than the double dose. This indicates that farmers should stop using a double dose of N fertilizers on bean production, as it decreases yields and can potentially pollute the environment. This study has however shown that government supply of free N fertilizers to resource-poor farmers in South Africa increased bean yields for food/nutritional security.

Diet composition of Oreochromis niloticus from selected impoundments of different states, with special focus on toxigenic cyanobacteria identified using molecular techniques

The diet of Oreochromis niloticus from hypereutrophic Lake Chivero and oligo-mesotrophic Lake Kariba was studied in 2017, with focus on the consumption of cyanobacteria. Water and fish were sampled to investigate the relationship between water quality and the diet of 131 fish using microscopy methods. Thirty-six fish were sampled in the second sampling phase to determine the presence of toxin producing cyanobacteria in their stomach contents using PCR methods. Lake Chivero had higher conductivity values, phosphates and total phosphorus levels while temperature and transparency were lower than those recorded in Lake Kariba. Lake Kariba recorded significantly higher water temperatures in June, October and December than Lake Chivero (p<0.05). Cyanobacteria, Microcystis spp. and Cylindrospermopsis sp. dominated in Lake Chivero and Lake Kariba water respectively. Lake Chivero fish were 0.491 times more likely to have empty stomachs than fish from Lake Kariba. Microcystis spp. had the highest relative abundance in fish stomach contents for both lakes and months. Percent relative abundance of Microcystis spp. ranged from 96.51% to 100% for fish from Lake Chivero and 46.74% to 100% for Lake Kariba fish. Stomach fullness index and abundance of cyanobacteria in the stomach contents were influenced by water oxygen percent, dissolved oxygen and temperature, transparency and phosphates for fish from Lake Chivero. For Lake Kariba fish, the stomach fullness index and abundance of cyanobacteria were influenced by total phosphorus, temperature, phosphates, transparency and chlorophyll a. Qualitative molecular analysis of the stomach contents showed the presence of potentially toxin producing cyanobacteria, Microcystis spp., in stomachs of fish from both Lake Kariba and Lake Chivero.

Combined Oral Contraceptive Treatment Does Not Alter the Gut Microbiome or Serum Metabolomic Profile in Obese Girls with Polycystic Ovary Syndrome

Abstract Title: Combined Oral Contraceptive Treatment Does Not Alter the Gut Microbiome or Serum Metabolomic Profile in Obese Girls with Polycystic Ovary Syndrome Background: The gut microbiome is altered in obese adolescents with polycystic ovary syndrome (PCOS), and is associated with free testosterone, metabolic markers and insulin resistance. Combined oral contraceptives (OCP) are a primary treatment for PCOS and lower testosterone, but it was unknown if they changed the gut microbiome in obese adolescents with PCOS. Objective: Assess the gut microbiome profile, targeted serum metabolomics, hormonal and metabolic measures in adolescents with PCOS and obesity with and without OCP treatment. Methods: Adolescent girls with PCOS and obesity with and without PCOS were recruited from a tertiary referral hospital and underwent stool and fasting blood collection, an oral glucose tolerance test and MRI for hepatic fat fraction. Fecal bacterial were profiled by high throughput 16S rRNA gene sequencing and fasting serum metabolomics performed with mass spectroscopy. Groups were compared with t-tests and correlations performed. Results: Twenty-nine obese adolescents with PCOS [Untreated N=21, 16±1.2 years, BMI%ile 36.5± 3.0; OCP N=8, 15.5±0.9, BMI%ile 32.5±3.9] participated. OCP therapy had lower free testosterone and higher SHBG (p&amp;lt;0.001). Platelets were significantly higher (p=0.01), along with a trend in elevated CRP (p=0.09) in the OCP group. There was no difference in measures of fasting glucose, insulin or lipids. Measures of insulin resistance including HOMA-IR and Matsuda were also similar. Principle components analysis of the serum metabolome was not different between the groups. Girls treated with OCP had similar stool microbiome α-diversity measures of bacterial evenness (p=0.28), bacterial diversity (p=0.15), and global microbial composition (β-diversity, p=0.56). Further, the percent relative abundance (%RA) of the Firmicutes: Bacteroidetes ratio was similar, as well as the %RA at the phyla, family and genus level. Bacterial α-diversity was negatively associated with serum bile acids and branched chain amino acids. A higher %RA of family Ruminococcaceae was significantly associated with serum conjugated bile acids and HOMA-IR. Conclusion: Despite changes in free testosterone and SHBG, adolescent girls with PCOS treated with OCP had similar clinical and gut microbiome profile compared to the untreated PCOS group. The significant association between bacterial α-diversity, Ruminococcaceae, clinical markers and bile acids suggests a potential role of the gut microbiome in the pathogenesis of metabolic syndrome and PCOS.

Seasonal periphyton response to low-level nutrient exposure in a least disturbed mountain stream, the Buffalo River, Arkansas

Like most streams located in the Ozark Plateaus, the Buffalo River in Arkansas generally has excellent water quality. Water-quality conditions in Big Creek, however, a major tributary of the middle Buffalo River, have been less favorable than that of other Buffalo River tributaries. Concerns regarding the influence of water quality in Big Creek on the Buffalo River magnified in 2013 when a large confined animal feeding operation (CAFO) began operating in the watershed. In response to these concerns, the U.S. Geological Survey compared monthly nutrient concentrations and seasonal periphyton assemblage metrics of a site on Big Creek downstream of the CAFO, two Buffalo River control sites upstream of the confluence with Big Creek, and three Buffalo River test sites downstream of the confluence with Big Creek. In addition to identifying potential nutrient patterns and periphyton responses along a low-level nutrient exposure gradient, the study determined how nutrient contributions from Big Creek (and the CAFO) are affecting ecological conditions and consequent ecosystem services in the Buffalo River. Nutrient and periphyton data exhibited more temporal than spatial variability. Nutrient concentrations were generally highest of all sites at the Big Creek site. Concentrations at the five sites on the Buffalo River were typically low (near laboratory reporting limits), and concentrations at the three test sites rarely exceeded those of the two control sites. An index developed with three ecologically relevant periphyton metrics (oligotrophic taxa and Homoeothrix percent relative abundance and mesotrophic diatoms percent taxa richness) suggested that nutrient uptake at sites downstream of the Big Creek-Buffalo River confluence resulted in subtle shifts in downstream periphyton assemblages. The periphyton index of biological integrity at control sites was slightly and generally more favorable compared to test sites. Even so, when periphyton data were considered in conjunction with both hydrology and water-quality data, the negative consequences of antecedent high flows and associated scouring exceeded the potential positive effects that low-level nutrients had on algal productivity. These findings emphasize the importance of comparing biological and chemical data across extended temporal scales, particularly when working with low-level nutrient gradients.

Dissolved organic matter sources in glacierized watersheds delineated through compositional and carbon isotopic modeling

AbstractClimate change is decreasing watershed glacial coverage throughout Alaska, impacting the biogeochemistry of downstream ecosystems. We collected streamwater fortnightly over the glacial runoff period from three streams of varying watershed glacier coverage (0–49%) and a subglacial outflow to assess how glacier recession impacts the relative contributions of glacier and terrestrial plant derived dissolved organic matter (DOM) inputs to streams. We show an increase in the fraction of old dissolved organic carbon (up to ∼ 3200 yr old radiocarbon age) with increasing glacial meltwater contribution to streamflow. We use a dual isotopic mixing model (δ13C and Δ14C) to quantify the relative contribution of terrestrial and glacial sources to streamwater DOM. The endmember contributions were further compared to DOM molecular compositional data from Fourier‐transform ion cyclotron resonance mass spectrometry to assess whether DOM composition can be linked to streamwater DOM source in watersheds with varying contributions of glacial runoff. This approach revealed the glacial fraction was positively correlated with percent relative abundance of heteroatom‐containing DOM molecular formulae, aliphatics, and peptide‐like formulae, while the terrestrial fraction was positively correlated with condensed aromatics and polyphenolics. These results provide information about how the retreat of mountain glaciers will impact the composition and thus biogeochemical role of DOM delivered to downstream ecosystems. Our findings highlight that combining an isotopic mixing model and ultrahigh resolution mass spectrometry data can provide novel insights into how changes in watershed landcover impact the source and chemical properties of streamwater DOM.

Feasibility of fecal microbiota transplantation via oral gavage to safely alter gut microbiome composition in marmosets.

Disruption of microbial communities within human hosts has been associated with infection, obesity, cognitive decline, cancer risk and frailty, suggesting that microbiome-targeted therapies may be an option for improving healthspan and lifespan. The objectives of this study were to determine the feasibility of delivering fecal microbiota transplants (FMTs) to marmosets via oral gavage and to evaluate if alteration of the gut microbiome post-FMT could be achieved. This was a prospective study of marmosets housed at the Barshop Institute for Longevity and Aging Studies in San Antonio, Texas. Eligible animals included healthy young adult males (age 2-5 years) with no recent medication use. Stool from two donors was combined and administered in 0.5 ml doses to five young recipients once weekly for 3 weeks. Safety outcomes and alterations in the gut microbiome composition via 16S ribosomal RNA sequencing were compared at baseline and monthly up to 6 months post-FMT. Overall, significant differences in the percent relative abundance was seen in FMT recipients at the phylum and family levels from baseline to 1 month and baseline to 6 months post-FMT. In permutational multivariate analysis of variance analyses, treatment status (donor vs. recipient) (p = .056) and time course (p = .019) predicted β diversity (p = .056). The FMT recipients did not experience any negative health outcomes over the course of the treatment. FMT via oral gavage was safe to administer to young adult marmosets. The marmoset microbiome may be altered by FMT; however, progressive changes in the microbiome are strongly driven by the host and its baseline microbiome composition.

Effect of multispecies probiotic on gut microbiota composition in individuals with intestinal constipation: A double-blind, placebo-controlled randomized trial

The aim of this study was to evaluate the effect of a multispecies probiotic on gut microbiota composition and constipation symptoms. A randomized, double-blind, placebo-controlled clinical trial was conducted with 35 individuals with constipation for 30 days. The individuals were randomized into two groups: the control capsule (CC) and the probiotic capsule (PC) groups. Constipation symptoms were evaluated by the ROME IV criteria and by evacuation diaries. Fecal microbiota was analyzed by 16 S rRNA gene sequencing. The majority of participants were women (85.7%). There was a significant reduction in the percent of participants who had incomplete defecation (P=0.034), blockage sensation (P=0.025), and rarely present liquid stools without the aid of laxatives (P=0.046) only within the PC group (but no significant difference between groups). There was a significant increase in the relative abundance percentage of Blautia faecis and Ruminococcus torques in the CC group (P=0.003 and P=0.011, respectively), although there was no significant change in the PC group (P=0.794 and P=0.958, respectively), with a significant difference between groups (P=0.029 and P 0.013, respectively), suggesting that probiotic treatment prevented the increase of percent relative abundance of these two species. These results suggest that multispecies probiotics in capsule form may modulate gut microbiota by reducing the bacteria that are commonly increased in patients with constipation, contributing to the balance of microbiota and, consequently, to the well-being of the individual. Future studies with larger numbers of patients are required.

Obese Adolescents With PCOS Have Altered Biodiversity and Relative Abundance in Gastrointestinal Microbiota.

Alterations in gut microbiota relate to the metabolic syndrome, but have not been examined in at-risk obese youth with polycystic ovary syndrome (PCOS). Compare the composition and diversity of the gut microbiota and associations with metabolic and hormonal measures between 2 groups of female adolescents with equal obesity with or without PCOS. Prospective, case-control cross-sectional study. Tertiary-care center. A total of 58 obese female adolescents (n = 37 with PCOS; 16.1 ± 0.3 years of age; body mass index [BMI] 98.5th percentile) and (n = 21 without PCOS; 14.5 ± 0.4 years of age; BMI 98.7th percentile). Bacterial diversity, percent relative abundance (%RA), and correlations with hormonal and metabolic measures. Participants with PCOS had decreased α-diversity compared with the non-PCOS group (Shannon diversity P = 0.045 and evenness P = 0.0052). β-diversity, reflecting overall microbial composition, differed between groups (P < 0.001). PCOS had higher %RA of phyla Actinobacteria (P = 0.027), lower Bacteroidetes (P = 0.004), and similar Firmicutes and Proteobacteria. PCOS had lower %RA of families Bacteroidaceae (P < 0.001) and Porphyromonadaceae (P = 0.024) and higher Streptococcaceae (P = 0.047). Lower bacterial α-diversity was strongly associated with higher testosterone concentrations. Several individual taxa correlated with testosterone and metabolic measures within PCOS and across the entire cohort. Receiver operative curve analysis showed 6 taxa for which the %RA related to PCOS status and lower Bacteroidaceae conferred a 4.4-fold likelihood ratio for PCOS. Alterations in the gut microbiota exist in obese adolescents with PCOS versus obese adolescents without PCOS and these changes relate to markers of metabolic disease and testosterone. Further work is needed to determine if microbiota changes are reflective of, or influencing, hormonal metabolism.

513 A Survey of Bacterial Microbiome Dysbiosis in Burn ICU Patients

With the advancement of nucleic acid sequencing technologies and bioinformatic power, a boom of the “-omic” era has revolutionized how we understand host microbiome interactions. Dysbiosis of the skin and gut microbiota have correlated with many immune disorders and chronic diseases. These associations are often not universal, making it critical for unique populations to be studied individually. Numerous aspects of the response to burn injury and resulting care can influence normal commensal bacteria on the skin and gut. Healthy volunteers were swabbed in two locations on each forearm for validation of non-invasive skin bacterial sampling techniques, with a subset utilized for bacterial population comparison with burn patient samples. Patients with >10% total body surface area (TBSA) burns were sampled using sterile swabs on the burn wound and a corresponding spared site of the skin, as well as one peri-anal and rectal swab. These four locations were sampled on days 0, 3, 7, 14, and 21 of the patient’s ICU stay or up to discharge. Metadata collected includes demographics, medications, nutrition plan, and progress notes. A next generation 16S amplicon sequencing protocol was utilized in conjunction with bioinformatics performed using Nephele under the QIIME pipeline. Twenty healthy volunteers were recruited for method validation. Four male burn patients were recruited with a mean age of 42 (SD=13.4) years and mean total body surface area (TBSA) burn of 24.1% (SD=8.1). Comparison of healthy volunteer skin swabs (n=18) to burn wound swabs (n=12) found a significant reduction in percent relative abundance of the phylum Actinobacteria (p<0.001) and increase in the order Bacillales (p<0.05), composed of primarily Staphylococcus. Varying abundance of non-culturable bacteria were sequenced. The Shannon Diversity Index was most variable among wound swabs (n=12) (mean [SD]: 4.09 [2.15]). No significant difference between pooled taxa percent abundance for rectal and peri-anal sampling (p=0.297) was observed. Proportions of bacterial phyla that are “normal” colonizers of the skin, such as Actinobacteria and Firmicutes, are perturbed on the burn wound and spared skin sites sampled from the four subjects. The clinical significance of non-culturable bacteria remains unknown. These findings suggest that bacterial dysbiosis occurs on the burn wound following injury and remains perturbed during routine care. Rectal and peri-anal swabs did not significantly differ in taxa relative abundance, indicating that less invasive sampling could be used. Profiling microbial populations immediately post burn and throughout care is the first step in elucidating mechanisms by which bacterial dysbiosis occurs and if this perturbation impacts clinical outcomes.

Rice growth stages and temperature affect the abundance of leafhoppers and plant hoppers

Relative abundance of leaf and plant hoppers species regarding plant growth stages and temperature were studied in the rice variety BINA10 field at the research farm of Patuakhali Science and Technology University (PSTU) during October 2013 to April 2014. The percent relative abundance of leafhoppers was in the rank order of M. dorsalis&gt; C. brevis&gt; N. virescens&gt; N. malayanus&gt; N. cincticeps&gt; N. nigropictus at seedling, early and maximum tillering stages while N. virescens&gt; C. brevis&gt; M. dorsalis&gt; N. nigropictus&gt; N. malayanus&gt; N. cincticeps at reproductive stage. The percent relative abundance of planthoppers was in the rank order of N. nervosa&gt; N. lugens&gt; S. furcifera at seedling and reproductive stages while N. lugens&gt; N. nervosa&gt; S. furcifera at early tillering and N. nervosa&gt; S. furcifera and N. lugens at maximum tillering stages. The abundance of all leafhopper species showed highly negative relationship with temperature. This relationship can be expressed by 81% (R2=0.806) for N. virescens, 80% (R2= 0.801) for N. nigropictus, 65% (R2=0.653) for N. cincticeps, 60% (R2=0.600) for C. brevis and 70% (R2=0.698) for M. dorsalis. Among three planthopper species, population of S. furcifera showed highly negative relationship with temperature and this relationship can be expressed by 71% (R2=0.707). The abundance of N. nervosa showed poor positive relationship with temperature. This relationship can be expressed by 3 % for N. nervosa (R2=0.030). N. lugens showed poor negative relationship with temperature and this relationship can be expressed by 31% (R2=0.310) for N. lugens.SAARC J. Agri., 16(1): 95-104 (2018)

Relative abundance of insect pests and their predators on boro rice

The study was conducted to know the relative abundance of insect pests and their predators on 5 boro rice varieties namely Arize tez, Teea, Sakti, Sathi and BRRI Dhan 28. In Arize Tez variety, short horned grasshopper revealed the highest percent relative abundance (87.25%) at tillering stage and green rice leafhopper was only at panical initiation stage. Among insect predators, wasp showed the highest percent relative abundance (33.33%) both at tillering and panical initiation stages. In Teea variety, the highest percent relative abundance of short horned grasshopper was recorded at tillering (80.21%) and panicle initiation (86.03%) stages while spider and lady bird beetle had 21.05% at tillering stage, wasp (21.05% and 40.00%), damselfly (21.05% and 40.00%) at tillering and panical initiation stages, respectively. In Sakti variety, short horned grasshopper had the highest percent relative abundance (72.54% and 69.05%) at tillering and panicle initiation stages while dragonfly had 30.77% at tillering, wasp had 30.77% and 66.66% at tillering and panicle initiation stages. In Shathi variety, the highest percent relative abundance of short horned grasshopper was recorded at tillering (59.46%) and panicle initiation (52.27%) stages while wasp (41.67%) at panical initiation stage. In variety BRRI dhan 28, the highest percent relative abundance of insect pests was recorded in short horned grasshopper (76.73% and 86.05%) both at tillering and panicle initiation stages while in insect predators, wasp had 40% at tillering and 50% at panicle initiation stages but dragonfly had 50% only at panicle initiation stage.Bangladesh J. Agril. Res. 43(1): 81-88, March 2018

Effect of rangeland rehabilitation on the herbaceous species composition and diversity in Suswa catchment, Narok County, Kenya

IntroductionLand degradation is a serious environmental problem of our time. In Kenya, it is estimated that 30% of the total land mass is severely degraded. Suswa catchment within Narok County is a good example with gullies of over 25 m deep and 30 m wide. In response to the increasing land degradation in the area, the Sustainable Land Management (SLM) project rehabilitated the catchment through establishment of soil and water conservation structures such as cutoff drains, semicircular bunds, and water retention ditches. Despite the various rehabilitation approaches carried out, little research has been done to ascertain their effect on successful vegetation recovery. This coupled with the fact that many restoration approaches have failed in East Africa and Kenya in particular gave drive to the study. The objective of this study was to determine the effects of rangeland rehabilitation on herbaceous species composition and diversity in a severely degraded rangeland.MethodsTo assess the diversity of aboveground herbaceous layer in the rehabilitated and degraded areas along a slope (upper, middle, and lower), line transect and quadrat count methods were used. Within each slope position, three 100-m-long transects were placed across the hill parallel to one another 30 m apart using a tape. The species hit, the closest species to the hit, and hits on bare ground were recorded. Along the same transects, 1-m2 quadrats were placed 25 m apart and aboveground biomass determined by the use of the destructive method. In the determination of species richness, diversity, relative abundance, percentage cover, and species composition, the Shannon-Wiener diversity index was used. Data collected on vegetation attributes was subjected to analysis of variance (ANOVA) using Genstat and Tukey’s HSD post hoc used in means separation where F values were significant.ResultsThe results showed that percent cover (74.67%), aboveground biomass (1459 kg/ha), relative abundance, richness, composition, and diversity of perennial grasses significantly (P ≤ 0.05) increased downslope and were higher in the rehabilitated area than in the degraded area. On the contrary, forbs and annual grasses were significantly (P ≤ 0.05) higher within the degraded area compared to the rehabilitated area and increased upslope.ConclusionsIn general, herbaceous species diversity, species richness, relative abundance, percent composition, biomass production, and percent cover of perennial grasses significantly increased downslope and were higher in the rehabilitated area compared to the degraded area. On the contrary, the same attributes for forbs and annual grasses were higher in the degraded area and increased upslope. The study concluded that effective rangeland rehabilitation has the potential to enhance vegetation regeneration and hence forage productivity.

Evaluation of the reproducibility and repeatability of GCMS retention indices and mass spectra of novel psychoactive substances

Novel psychoactive substances (NPSs) are synthetically derived compounds designed to mimic the effects of other illicit drugs. An endless cycle of NPSs continually reach the drug market due to limitations in drug legislation creating two problems – non-availability of standards and multiple isobars indistinguishable even to high resolution mass spectrometry. Lacking standards, laboratories rely on published gas chromatography-mass spectrometry (GCMS) spectra to postulate compound identification. The ability to make such identifications provides vital investigative data and may help uncover new structural variants. However, central to such identifications is an understanding of how much spectral patterns vary across laboratories; the assumption that variation is minimized through the use of a standard tuning compound (PFTBA) has yet to be rigorously tested and demonstrated. In the present study, the variation of mass spectral fragmentation patterns characterized by percent relative abundance was evaluated using three GCMS instruments and 16 NPS compounds. The variation of retention indices was also studied. Retention indices showed <0.35% variation across all systems; mass spectral data showed much greater variation across all compounds and systems. Tuning frequency was one factor correlated with small variation. A means comparison of ion relative abundance did not clearly identify general patterns. Changes in identification of base ion peak was seen with three compounds. Base peak shifting on a single instrument, i.e. one instrument produced multiple base peak ions over the course of the study, generated a ripple effect, where variation across all relative abundances in the effected spectra increased. However, base peak shifting between instrument, i.e. each instrument produced a single base peak but the ion identity was not necessarily the same, did not produce these ripple effects. Either shifting base peak scenario had the potential to skew compound identification during untargeted analyses, which are common in a forensic drug chemistry setting.

Bacterial community structure and microorganism inactivation following water treatment with ferrate(VI) or chlorine

Drinking water disinfection plays a critical role in protecting humans from waterborne pathogens. Ferrate(VI) (FeVIO42−) has also been proposed as a disinfectant. This is the first study investigating the bacterial microbiomes of ferrate(VI)-treated water compared to chlorinated water. Tested water was collected after sand filtration and before disinfection from a drinking water treatment plant at Jiaxing, Zhejiang Province, China. A culture-independent method utilizing propidium monoazide was used with quantitative polymerase chain reaction and pyrosequencing of 16S rRNA genes to distinguish between the viable and nonviable bacterial populations. The operational taxonomic units and α-diversity indexes of the live bacterial phylotypes in the samples were determined. Viable bacteria remained in all samples following chlorination or ferrate treatment. However, the genera Vibrio, Salmonella, Shigella, Escherichia, Campylobacter, Yersinia, Plesiomonas, Legionella, and Helicobacter, which contain important human pathogens, were not present among the 25 dominant genera seen in these samples. The profiles of the bacteria remaining after treatment with either chlorine or ferrate differed. The ferrate-treated samples showed a reduced percent relative abundance of operational taxonomic units of the class Alphaproteobacteria within the total remaining viable bacteria. The genera Flavobacterium and Duganella were relatively resistant to treatment by either chlorine or ferrate(VI). At the highest doses of chlorine and ferrate(VI), the genus Sphingobium represented a greater percentage of live bacteria in the chlorinated sample than in the ferrate(VI)-treated sample. The results suggest that ferrate(VI) and chlorine could inactivate slightly different sets of bacteria and could have different mechanisms of bacterial inactivation.

Long-term soil alteration in historical charcoal hearths affects Tuber melanosporum mycorrhizal development and environmental conditions for fruiting.

Abandoned charcoal hearths constitute a very particular habitat for spontaneous fruiting of Tuber melanosporum, leading some harvesters to hypothesise that the fungus could benefit from the alterations that these soils underwent. However, ecological mechanisms involved in this relation are not fully elucidated yet. As a first step to understand it, the influence of long-term soil alteration on the symbiotic stage of T. melanosporum and on selected soil properties considered key to fruiting was assessed by conducting a greenhouse bioassay and a field observational study. In the bioassay, percent root colonisation and relative abundance of T. melanosporum were significantly lower in hearth than in control soils. Hearth soils showed significantly lower resistance to penetration, larger temperature fluctuation, reduced plant cover and reduced herbaceous root abundance. The results do not support the hypothesis that soil from historical charcoal hearths currently enhances development of T. melanosporum mycorrhizas. However, whether this is due to increased infectivity of native ectomycorrhizal communities or to worse conditions for development of T. melanosporum mycorrhizas remains unresolved. Native ectomycorrhizal communities in hearths showed altered composition, although not a clear change in infectivity or richness. Direction of change in hearth soil properties is compared to alteration occurring in soils spontaneously producing T. melanosporum. The interest of these changes to improve T. melanosporum fruiting in plantations is discussed.

Ecological status of high altitude medicinal plants and their sustainability: Lingshi, Bhutan.

BackgroundHuman beings use plants for a multitude of purposes of which a prominent one across the globe is for their medicinal values. Medicinal plants serve as one of the major sources of income for high altitude inhabitants in the Himalaya, particularly in countries like Nepal, and Bhutan. People here harvest huge volumes of medicinal plants indiscriminately, risking their sustainability. This paper attempts to identify some of the priority medicinal plant species harvested in the wild and assess their ecological status for their judicious utilization, and to help provide policy guidance for possible domestication and support strategic conservation frameworks.ResultsOut of the 16 priority species identified by the expert group, collectors’ perception on ecological status of the priority species differed from survey findings. Chrysosplenium nudicaule (clumps) ranked as most threatened species followed by Corydalis dubia, and Meconopsis simplicifolia. Onosma hookeri, Corydalis crispa and Delphinium glaciale were some of the species ranked as threatened species followed by Halenia elliptica (not in priority list). Percent relative abundance showed irregular pattern of species distribution. High species evenness was recorded among Nardostachys grandiflora, Chrysosplenium nudicaule, Saussurea gossypiphora and Aconitum orochryseum with average species density of 8 plant m−2. Rhodiola crenulata, and Dactylorhiza hatagirea followed by Meconopsis horridula and Meconopsis simplicifolia were ranked as most threatened species with average species density of 0.4, 0.4, 5.6 and 6.0 plant m−2, respectively. The most abundant (common) species was Onosma hookeri (plant m−2). Species composition and density also differed with vegetation, altitude, slope and its aspects.ConclusionPriority species identified by expert group were found vulnerable and patchy in distribution. Survey results and collectors’ perceptions tally to an extent. Some of the species (Dactylorhiza hatagirea, Rhodiola crenulata, Meconopsis simplicifolia and Meconopsis horridula) were critically low in plant density with less than a plant per m2 while Delphinium glaciale, Fritillaria delavayi and Aconitum orochryseum were confined to narrow altitude range. Collectors were aware that most species identified in priority list are threatened and existing harvesting plan are hardly implemented as it is not pragmatic. Moreover, major chunk of medicinal plants harvested remain unaccounted as illegal harvest and marketing seemed to occur across the borders. Policing and monitoring would continue to be a challenge given the rugged terrain and harsh climate. In-depth study and further monitoring of low density species is suggested to ensure its sustainability through long term strategy development.Electronic supplementary materialThe online version of this article (doi:10.1186/s12898-016-0100-1) contains supplementary material, which is available to authorized users.