Improved quantitative microbiome profiling for environmental antibiotic resistance surveillance

Background Understanding environmental microbiomes and antibiotic resistance (AR) is hindered by over reliance on relative abundance data from next-generation sequencing. Relative data limits our ability to quantify changes in microbiomes and resistomes over space and time because sequencing depth is not considered and makes data less suitable for Quantitative Microbial Risk Assessments (QMRA), critical in quantifying environmental AR exposure and transmission risks. Results Here we combine quantitative microbiome profiling (QMP; parallelization of amplicon sequencing and 16S rRNA qPCR to estimate cell counts) and absolute resistome profiling (based on high-throughput qPCR) to quantify AR along an anthropogenically impacted river. We show QMP overcomes biases caused by relative taxa abundance data and show the benefits of using unified Hill number diversities to describe environmental microbial communities. Our approach overcomes weaknesses in previous methods and shows Hill numbers are better for QMP in diversity characterisation. Conclusions Methods here can be adapted for any microbiome and resistome research question, but especially providing more quantitative data for QMRA and other environmental applications.

Morphological variability and genetic diversity of Aman rice germplasm of Bangladesh cultivated in Mymensingh region

Thirty-one Aman rice germplasm were evaluated to assess their morphological variability and genetic diversity considering ten quantitative and thirty one qualitative traits at the field experimental plot of Bangladesh Institute of Nuclear Agriculture, Mymensingh, following randomized complete block design. The germplasm showed significant differences for all the studied traits. The highest grain yield/plant was recorded in Sentu-16 whereas the lowest was found in Gaindha. The genotypic coefficient of variation (GCV) was lower than those of the corresponding phenotypic coefficient of variation (PCV) for all the traits. High PCV and GCV along with heritability, genetic advance (GA) and GA in percentage of mean were recorded for number of filled grains/panicle and number of unfilled grains/panicle. Grain yield/plant had positively significant correlation with plant height, number of total tillers/hill, number of effective tillers/hill, number of filled grains/panicle and thousand grain weight. Path co-efficient analysis suggested that grain yield/plant had positive direct effect in association with days to fifty percent flowering, number of effective tillers/hill, panicle length, number of filled grains/panicle and thousand grain weight. Principal component analysis revealed that the first three components accounted for 79.57% of cumulative variance. Cluster analyses were revealed that the studied rice germplasm organized into five clusters based on D2 values where maximum inter-cluster distance was observed between cluster II and V. Qualitative characterization by distinctness, uniformity and stability test revealed that a wide range of variation was observed among the genotypes. Therefore, this study would be useful for breeders to choose and identify the revival and preservation of beneficial genes for crop improvement.

Genetic Association and Path Coefficient Analysis for Grain Yield Characters in Elite Rice (Oryza sativa L.) Germplasm

The study was carried out to study the correlation and path coefficient analysis for grain yield characters in 36 rice genotypes including one check for 13 quantitative parameters. The experimental material was carried out during Kharif, 2020, in a randomized block design with three replications obtained from the Department of Genetics and Plant Breeding, SHUATS, Allahabad, U.P., India. Analysis of variance revealed that there is significant variability among the genotypes. Correlation coefficient analysis at genotype level and phenotypic level revealed that plant height, flag leaf length, flag leaf width, number of tillers per hill, number of panicles per hill, number of spikelets per panicle, biological yield, and harvest index, showed positive significant correlation with grain yield per plant. Path coefficient analysis at both genotypic and phenotypic levels revealed that flag leaf length, number of panicles per hill, days to maturity, biological yield, harvest index and test weight had positive direct effect on grain yield per hill. Biological yield per hill (0.8481) exerted high positive direct effect as well as high positive significant association (0.809**) with grain yield per hill thus this character resulted as most essential direct yield character.

Dorsal Skin Microbial Assemblages in Free-ranging Hellbenders, Cryptobranchus Alleganiensis, Associated With Subspecies and Chronic Toe Lesions, but Not With Chytrid Fungal Infection.

BackgroundSkin microbiomes are important components of skin health and have been shown to contribute to immunity in amphibians, especially against the chytrid fungus, Batrachochytrium dendrobatidis (Bd). Hellbenders (Cryptobranchus alleganiensis) are large aquatic amphibians (Order Caudata) native to the eastern United States that have experienced population declines of both the Ozark and eastern subspecies, C. a. bishopi and C. a. alleganiensis, respectively. In addition, ulcerative non-healing toe lesions have become increasingly prevalent in C. a. bishopi, in Arkansas (AR) where populations are now reduced to a single river. To evaluate the potential impacts of both chronic toe lesions and Bd on hellbender health, we compared dorsal skin microbial assemblages based on 16S rRNA gene amplicons between a declining Ozark hellbender population in Arkansas (AR) presenting lesions and a reference, recruiting, lesion-free, population of eastern hellbenders in eastern Tennessee (ETN). We further evaluated effects of mass and life stage across both subspecies, as well as toe lesion severity and Bd infection status within AR, to better understand the associations between microbiomes and disease in a wild salamander.ResultsWe found skin of ETN hellbenders to have greater bacterial alpha diversity compared to AR, with this disparity decreasing as Hill number order increased. Conversely, within AR, animals with more severe lesions had decreased alpha diversity than those with mild lesions, which became more pronounced with increasing Hill number. Further, the average microbial assemblage structure differed between ETN and AR. Specifically, AR communities displayed increased beta diversity compared to those from ETN, which appeared to be linked to toe lesion severity. Neither size class (mass) nor Bd infection status had a significant effect on alpha or beta diversity. Taxonomic analysis revealed ETN to have greater OTU abundance of phylum Cyanobacteria 24.3%) compared to AR (5.9%); whereas AR had increased abundance of Proteobacteria (48.5%), Firmicutes (9.1%), and Synergistetes (1.5%), in comparison to ETN (31.5%, 2.6%, 0.2%, respectively).ConclusionsResults demonstrate that eastern hellbenders of ETN have richer and less dispersed dorsal skin bacterial assemblages compared to Ozark hellbenders of AR. Furthermore, we suggest that increased severity of toe lesions may be linked to systemic changes resulting in skin microbial dysbiosis, independent of Bd infection. Although lesions remain to have an unknown etiology, this study is another step towards understanding skin bacterial microbiomes in hellbenders, and their potential associations with chronic disease.

Enhanced Fuzzy Assessment Methodology to Find Overlapping in Membership Function Using K Ratio to Find the Yield of Rice

Fuzzy expert systems are designed based on fuzzy logic and deal with fuzzy sets. Many fuzzy expert systems have been developed for diagnosis. Fuzzy expert systems are developed using fuzzification interface, enhanced fuzzy assessment methodology, and defuzzification interface. Fuzzification helps to convert crisp values into fuzzy values. By applying the enhanced fuzzy assessment methodology for rice, the yield parameters of rice can be diagnosed with number of tillers per hill, number of grains per panicle, and 1000 grain weight. Pest and disease incidence becomes simple for scientists. Enhanced fuzzy assessment methodology for rice uses triangular membership function with Mamdani's inference and K Ratio. Defuzzification interface is adopted to convert the fuzzy values into crisp values. Performance of the system can be evaluated using the accuracy level. Accuracy is the proportion of the total number of predictions that are correct. The proposed algorithm was implemented using MATLAB fuzzy logic tool box to construct fuzzy expert system for rice.

INDEKS KEANEKARAGAMAN HAYATI IKAN DEMERSAL DI PERAIRAN ARAFURA

Penelitian tentang indeks keanekaragaman hayati ikan demersal telah dilakukan pada periode tahun 2001 sampai dengan 2006 menggunakan sarana kapal riset KM. Mutiara, KM. Bawal Putih I, dan KM. Mandidihang 02. Data spesies ikan demersal dikumpulkan dari hasil pengambilan contoh penangkapan menggunakan alat tangkap jaring pukat dasar dengan metode sapuan area. Pengambilan contoh dilakukan di sub lahan tepian Laut Arafura (sekitar daerah Mappi sampai dengan Dolak) dan sub lahan tengah Laut Arafura (sekitar Kepulauan Aru). Hasil analisis menunjukkan bahwa status kekayaan jenis ikan demersal sampai dengan tahun 2006 memiliki 149 spesies yang tergolong dalam 71 famili. Ikan-ikan yang cenderung memiliki jumlah individu terbanyak adalah kelompok famili ikan petek (Leiognathidae), gerot-gerot (Pomadasyidae), dan gulamah (Scianidae). Tingkat keanekaragaman jenis ikan demersal di perairan Arafura termasuk dalam kategori sedang. Kondisi komunitas bersifat labil dan cenderung mengalami penurunan. Status keanekaragaman hayati sampai dengan tahun 2006 memiliki indeks keanekaragaman jenis Shanon-Wiener (H’) berkisar 2,22 sampai dengan 2,79; indeks kekayaan jenis Margalef (R1 ) berkisar 4,84 sampai dengan 11,23; indeks keragaman Hill number (N1) berkisar 9,2 sampai dengan 16,3 dan indeks kemerataan jenis Pielou (E) berkisar 0,54 sampai dengan 0,56. Study on biodiversity indices of demersal fish was conducted in the period of 2001 until 2006 by using research vessel MV. MUTIARA, MV. BAWAL PUTIH I, and MV. MANDIDIHANG 02. Species data of demersal fish were collected from fishing samples by using bottom trawl with swept area method. Sampling location in the waters shore of Arafura Sea with sub area Mappi to Dolak and middle area of Arafura Sea (around of Aru Island). Result indicates that status of richness species of demersal fish till year 2006 of 149 species belongging to 71 families were recorded. Dominant families were Leiognathidae, Pomadasyidae, and Scianidae. From diversity analysis it also indicates that species diversity index in the Arafura Sea was at mid level. Condition of fish community was likely labile and the trend of it was decreasing. Index of biodiversity up to 2006 Shanon-Wiener (H’) was 2.22 until 2.79; species richness indices of Margalef (R1 ) were 4.84 until 1.23, diversity number Hill (N1) 9.2 until 16.3, and evenness indices of Pielou (E 1) were 0.54 until 0.56.

PERAKITAN TEKNOLOGI PENGELOLAAN HARA SPESIFIK LOKASI PADI SISTEM GOGO RANCAH DI DESA SEMAWUNG KECAMATAN ANDONG KABUPATEN BOYOLALI

<p>ABSTRACT</p><p>Rainfed ricefield, planted at least for one cropping season in a year, depends heavily on rainfall for its water supply. This land generally is low in fertility as indicated by the limited availability of essential plant nutrients in particular nitrogen (N), phosphorus (P), and potassium (K) as well as organic matter. Its productivity is relatively low with a rather erratic precipitation distribution. In order to overcome fertility issue in rainfed land, it is necessary to conduct an integrated nutrient management; one of which is by implementing location specific nutrient management. This study aims to seek the appropriate nutrient management in rainfed paddy field of Semawung village in the sub-district of Andong of Boyolali regency to be provisioned as a technological tool of location specific nutrient management. Research on nutrient management of gogo rancah system-based paddy production was carried out from October 2014 to January 2015. The field experiment was arranged in a Randomized Block Design involving eight treatments and three replications for each treatment. Treatments were combinations of NPK fertilizer, Organofosfat, and straw-based organic fertilizer. Nutrient management using NPK fertilizer and its combination with Organofosfat or organic fertilizer had very significant effect on plant height and number of stem per hill, significantly affected number of panicle per hill, panicle length, and number of fully-filled grain but did not result in difference of fully filled grain percentage and weight of 1000 grains. There was no significant difference between the treatment of 100% of NPK fertilizer and the combination of 75% of NPK fertilizer with straw-based fertilizer regarding these variables: number of stem per hill, number of panicle per hill, panicle length, number of grain per hill, number and percentage of fully-filled grain, weight of 1000 grains, and weight of fresh grain and milled grain yield. Therefore, the latter treatment is feasible as an option of location-specific nutrient management Semawung village.</p>

Estimating and comparing microbial diversity in the presence of sequencing errors

Estimating and comparing microbial diversity are statistically challenging due to limited sampling and possible sequencing errors for low-frequency counts, producing spurious singletons. The inflated singleton count seriously affects statistical analysis and inferences about microbial diversity. Previous statistical approaches to tackle the sequencing errors generally require different parametric assumptions about the sampling model or about the functional form of frequency counts. Different parametric assumptions may lead to drastically different diversity estimates. We focus on nonparametric methods which are universally valid for all parametric assumptions and can be used to compare diversity across communities. We develop here a nonparametric estimator of the true singleton count to replace the spurious singleton count in all methods/approaches. Our estimator of the true singleton count is in terms of the frequency counts of doubletons, tripletons and quadrupletons, provided these three frequency counts are reliable. To quantify microbial alpha diversity for an individual community, we adopt the measure of Hill numbers (effective number of taxa) under a nonparametric framework. Hill numbers, parameterized by an orderqthat determines the measures’ emphasis on rare or common species, include taxa richness (q= 0), Shannon diversity (q= 1, the exponential of Shannon entropy), and Simpson diversity (q= 2, the inverse of Simpson index). A diversity profile which depicts the Hill number as a function of orderqconveys all information contained in a taxa abundance distribution. Based on the estimated singleton count and the original non-singleton frequency counts, two statistical approaches (non-asymptotic and asymptotic) are developed to compare microbial diversity for multiple communities. (1) A non-asymptotic approach refers to the comparison of estimated diversities of standardized samples with a common finite sample size or sample completeness. This approach aims to compare diversity estimates for equally-large or equally-complete samples; it is based on the seamless rarefaction and extrapolation sampling curves of Hill numbers, specifically forq= 0, 1 and 2. (2) An asymptotic approach refers to the comparison of the estimated asymptotic diversity profiles. That is, this approach compares the estimated profiles for complete samples or samples whose size tends to be sufficiently large. It is based on statistical estimation of the true Hill number of any orderq≥ 0. In the two approaches, replacing the spurious singleton count by our estimated count, we can greatly remove the positive biases associated with diversity estimates due to spurious singletons and also make fair comparisons across microbial communities, as illustrated in our simulation results and in applying our method to analyze sequencing data from viral metagenomes.

CHARACTER ASSOCIATION IN F4 GENERATION OF RICE (Oryza sativa L.)

Twenty five rice genotypes were used to study the genetic components, correlation and path coefficients during Aman season of 2011. Thirteen characters were studied to find out the suitable traits for the improvement of rice yield. Among these characters considerable correlation were observed. Correlation values of grain yield per square meter with plant height, number of tillers per hill, number of panicles per hill, panicle length, number of primary branches, number of filled grain per panicle, spikelet sterility (%), 1000 grain weight and days to flowering revealed that selection based on this traits could significantly be improved the grain yield of rice. Number of tillers per hill, number of panicles per hill, panicle length, number of filled grains per panicle, 1000-grain weight exhibited high direct effect coupled with significant positive correlation on grain yield indicating selection on the basis of these traits would enhanced yield potentiality of rice. The residual effect was found 0.179 which indicated that 82.10% of the variability was accounted for 13 yield and yield contributing traits included in the present study. Rest 17.90% variability might be controlled by other yield contributed traits that was not included in the present investigation. So direct selection based on these traits would be effective for improvement of these F4 materials