scholarly journals Soil bacterial community structures in relation to different oil palm management practices

2020 ◽  
Vol 7 (1) ◽  
Author(s):  
Dirk Berkelmann ◽  
Dominik Schneider ◽  
Nina Hennings ◽  
Anja Meryandini ◽  
Rolf Daniel
Keyword(s):  
Community Composition ◽  
Oil Palm ◽  
Beta Diversity ◽  
Management Practices ◽  
Community Level ◽  
Geochemical Data ◽  
Rrna Gene ◽  
Dna And Rna ◽  
Soil Bacterial ◽  
16 S Rrna

AbstractWe provide soil bacterial 16 S rRNA gene amplicon and geochemical data derived from an oil palm plantation management experiment. The experimental design covered two different intensities of fertilizer application and weeding practices. We sampled the topsoil of 80 plots in total and extracted DNA and RNA. 16 S rRNA gene-derived and transcript-derived amplicons were generated and sequenced to analyse community composition and beta-diversity. One year after establishing the experiment, statistically significant differences of bacterial diversity or community composition between different treatments at entire (DNA-derived) and active (RNA-derived) community level were not detected. The dominant taxa belonged to Acidobacteriota and Actinobacteriota and were more abundant in the active community compared to the entire community. Similarly, the abundant genera Candidatus Solibacter and Haliangium were more abundant at active community level. Furthermore, clustering corresponding to the different sampling site locations was detected. Beta-diversity did not change among the treatments at DNA and RNA level. This dataset is of interest for related studies on the effect of altered management practices on soilborne communities.

scholarly journals Structural and Functional Shift in Soil Bacterial Community in Response to Long-Term Compost Amendment in Paddy Field

2021 ◽  
Vol 11 (5) ◽  
pp. 2183
Author(s):  
Sookjin Kim ◽  
Sandipan Samaddar ◽  
Poulami Chatterjee ◽  
Aritra Roy Choudhury ◽  
Jeongyun Choi ◽  
...  
Keyword(s):  
Community Composition ◽  
Management Practices ◽  
Agricultural Soils ◽  
Growth Promotion ◽  
Microbial Community Composition ◽  
Rrna Gene ◽  
Soil Bacterial Diversity ◽  
Compost Amendment ◽  
Soil Bacterial

Microbial community composition and diversity of agricultural soils primarily depend on management practices. The application of compost on agricultural fields is known to increase soil fertility, which can also help to enhance agricultural productivity. The effects of long-term application of compost along with nitrogen (N), phosphorus (P), and potassium (K) (+Compost) on soil bacterial diversity and community profiles were assessed by amplicon sequencing targeting the 16S rRNA gene of bacteria and compared with those on soils that received only NPK but not compost (−Compost). Ordination plot showed treatments to cluster differently, implying changes in community composition, which were validated with taxonomical data showing Firmicutes, Actinobacteria, and their related classes to be significantly higher in +Compost than in −Compost soils. The predicted abundance of functional genes related to plant growth promotion, development, and decomposition was significantly higher in compost-amended soil than in soils without compost. The results are of particular importance as they provide insights into designing management practices to promote agricultural sustainability.

scholarly journals Analysis of Structure and Composition of Bacterial Core Communities in Mature Drinking Water Biofilms and Bulk Water of a Citywide Network in Germany

2012 ◽  
Vol 78 (10) ◽  
pp. 3530-3538 ◽  
Author(s):  
Karsten Henne ◽  
Leila Kahlisch ◽  
Ingrid Brettar ◽  
Manfred G. Höfle
Keyword(s):  
Drinking Water ◽  
16S Rrna ◽  
Community Composition ◽  
Bulk Water ◽  
Rrna Gene ◽  
Content Type ◽  
Support Materials ◽  
Dna And Rna ◽  
Candidate Division ◽  
The City

ABSTRACTThe bacterial core communities of bulk water and corresponding biofilms of a more than 20-year-old drinking water network were compared using 16S rRNA single-strand confirmation polymorphism (SSCP) fingerprints based on extracted DNA and RNA. The structure and composition of the bacterial core community in the bulk water was highly similar (>70%) across the city of Braunschweig, Germany, whereas all biofilm samples contained a unique community with no overlapping phylotypes from bulk water. Biofilm samples consisted mainly ofAlphaproteobacteria(26% of all phylotypes),Gammaproteobacteria(11%), candidate division TM6 (11%),Chlamydiales(9%), andBetaproteobacteria(9%). The bulk water community consisted primarily ofBacteroidetes(25%),Betaproteobacteria(20%),Actinobacteria(16%), andAlphaproteobacteria(11%). All biofilm communities showed higher relative abundances of single phylotypes and a reduced richness compared to bulk water. Only biofilm communities sampled at nearby sampling points showed similar communities irrespective of support materials. In all of our bulk water studies, the community composition determined from 16S rRNA was completely different from the 16S rRNA gene-based community composition, whereas in biofilms both molecular fractions resulted in community compositions that were similar to each other. We hypothesize that a higher fraction of active bacterial phylotypes and a better protection from oxidative stress in drinking water biofilms are responsible for this higher similarity.

scholarly journals Vaginal bacterial community composition and concentrations of estradiol at the time of artificial insemination in Brangus heifers

2020 ◽  
Vol 98 (6) ◽  
Author(s):  
Riley D Messman ◽  
Zully E Contreras-Correa ◽  
Henry A Paz ◽  
George Perry ◽  
Caleb O Lemley
Keyword(s):  
Bacterial Community ◽  
Community Composition ◽  
Artificial Insemination ◽  
Beta Diversity ◽  
Bacterial Community Composition ◽  
Alpha Diversity ◽  
Species Level ◽  
Rrna Gene ◽  
Microbial Composition ◽  
Vaginal Tract

Abstract The knowledge surrounding the bovine vaginal microbiota and its implications on fertility and reproductive traits remains incomplete. The objective of the current study was to characterize the bovine vaginal bacterial community and estradiol concentrations at the time of artificial insemination (AI). Brangus heifers (n = 78) underwent a 7-d Co-Synch + controlled internal drug release estrus synchronization protocol. At AI, a double-guarded uterine culture swab was used to sample the anterior vaginal tract. Immediately after swabbing the vaginal tract, blood samples were collected by coccygeal venipuncture to determine concentrations of estradiol. Heifers were retrospectively classified as pregnant (n = 29) vs. nonpregnant (n = 49) between 41 and 57 d post-AI. Additionally, heifers were classified into low (1.1 to 2.5 pg/mL; n = 21), medium (2.6 to 6.7 pg/mL; n = 30), and high (7.2 to 17.6 pg/mL; n = 27) concentration of estradiol. The vaginal bacterial community composition was determined through sequencing of the V4 region from the 16S rRNA gene using the Illumina Miseq platform. Alpha diversity was compared via ANOVA and beta diversity was compared via PERMANOVA. There were no differences in the Shannon diversity index (alpha diversity; P = 0.336) or Bray–Curtis dissimilarity (beta diversity; P = 0.744) of pregnant vs. nonpregnant heifers. Overall, bacterial community composition in heifers with high, medium, or low concentrations of estradiol did not differ (P = 0.512). While no overall compositional differences were observed, species-level differences were present within pregnancy status and estradiol concentration groups. The implications of these species-level differences are unknown, but these differences could alter the vaginal environment thereby influencing fertility and vaginal health. Therefore, species-level changes could provide better insight rather than overall microbial composition in relation to an animal’s reproductive health.

scholarly journals 246 Effect of increasing levels of dietary starch on equine cecal microbiota

2020 ◽  
Vol 98 (Supplement_3) ◽  
pp. 21-21
Author(s):  
Michael Y Halpin ◽  
James Drouillard ◽  
Teresa Douthit ◽  
Qinghong Ran ◽  
Barry J Bradford ◽  
...  
Keyword(s):  
Beta Diversity ◽  
Random Effect ◽  
Pcr Amplification ◽  
Illumina Miseq ◽  
Rrna Gene ◽  
Alpha And Beta Diversity ◽  
Cecal Microbiota ◽  
Dietary Starch ◽  
16 S Rrna

Abstract An experiment was conducted with 6 cecally cannulated horses (524 ± 65.5 kg BW) to evaluate effects of increasing dietary starch on equine cecal microbiota. Starch was supplied via corn pellets and was increased by 0.5 g starch/kg BW/meal every 7 d until horses received 3.5 g starch/kg BW/meal. Throughout the experiment, Smooth Bromegrass hay and water were offered ad libitum. Meals were fed every 6 h, starting at 0600 h. On d 7 of each period, cecal digesta was collected every 2 h for 12 h. Within period, cecal samples for each horse were pooled and DNA was extracted for PCR amplification of the 16 S rRNA gene (V3 and V4 regions) and sequencing via Illumina MiSeq. Alpha and beta diversity were measured. Data were analyzed as a randomized complete block with fixed effect of starch level and random effect of horse (SAS version 9.4). If a horse presented with colic, it was removed from the experiment. Parameters when feeding 1.5 g starch/kg BW/meal were compared between horses which completed the trial and those removed using covariate of 0 g starch/kg BW/meal. Feeding 1.5 g starch/kg BW/meal elicited the greatest changes in microbiota, indicated by reduced (P ≤ 0.02) operational taxonomical units and Faith phylogenetic diversity and different (P ≤ 0.017) beta diversity compared to all other treatments. Across treatments, Firmicutes was the most abundant phyla, followed by Bacteroidetes. Feeding 1.5 g starch/kg BW/meal led to lowest (P ≤ 0.0342) relative abundance (RA) of Prevotella, Treponema, Phascolarctobacterium, and [Prevotella]. Horses that persisted throughout the experiment had reduced (P = 0.0163) RA of Ruminococcus and greater RA of Phascolarctobacterium (P = 0.0057) when consuming 1.5 g starch/kg BW/meal compared to those removed. This is the first report describing effects of gradually increasing dietary starch on equine cecal microbiota in vivo.

scholarly journals Impact of enzymatic digestion on bacterial community composition in CF airway samples

PeerJ ◽  
2017 ◽  
Vol 5 ◽  
pp. e3362 ◽  
Author(s):  
Kayla M. Williamson ◽  
Brandie D. Wagner ◽  
Charles E. Robertson ◽  
Emily J. Johnson ◽  
Edith T. Zemanick ◽  
...  
Keyword(s):  
Bacterial Community ◽  
Dna Extraction ◽  
Community Composition ◽  
Bacterial Communities ◽  
Beta Diversity ◽  
Diversity Index ◽  
Bacterial Community Composition ◽  
Microbial Community Composition ◽  
Enzymatic Digestion ◽  
Rrna Gene

BackgroundPrevious studies have demonstrated the importance of DNA extraction methods for molecular detection ofStaphylococcus,an important bacterial group in cystic fibrosis (CF). We sought to evaluate the effect of enzymatic digestion (EnzD) prior to DNA extraction on bacterial communities identified in sputum and oropharyngeal swab (OP) samples from patients with CF.MethodsDNA from 81 samples (39 sputum and 42 OP) collected from 63 patients with CF was extracted in duplicate with and without EnzD. Bacterial communities were determined by rRNA gene sequencing, and measures of alpha and beta diversity were calculated. Principal Coordinate Analysis (PCoA) was used to assess differences at the community level and Wilcoxon Signed Rank tests were used to compare relative abundance (RA) of individual genera for paired samples with and without EnzD.ResultsShannon Diversity Index (alpha-diversity) decreased in sputum and OP samples with the use of EnzD. Larger shifts in community composition were observed for OP samples (beta-diversity, measured by Morisita-Horn), whereas less change in communities was observed for sputum samples. The use of EnzD with OP swabs resulted in significant increase in RA for the generaGemella(p < 0.01),Streptococcus(p < 0.01), andRothia(p < 0.01).Staphylococcus(p < 0.01) was the only genus with a significant increase in RA from sputum, whereas the following genera decreased in RA with EnzD:Veillonella(p < 0.01),Granulicatella(p < 0.01),Prevotella(p < 0.01), andGemella(p = 0.02). In OP samples, higher RA of Gram-positive taxa was associated with larger changes in microbial community composition.DiscussionWe show that the application of EnzD to CF airway samples, particularly OP swabs, results in differences in microbial communities detected by sequencing. Use of EnzD can result in large changes in bacterial community composition, and is particularly useful for detection ofStaphylococcusin CF OP samples. The enhanced identification ofStaphylococcus aureusis a strong indication to utilize EnzD in studies that use OP swabs to monitor CF airway communities.

scholarly journals A method for simultaneous measurement of soil bacterial abundances and community composition via 16S rRNA gene sequencing

2016 ◽  
Vol 96 ◽  
pp. 145-151 ◽  
Author(s):  
Wenke Smets ◽  
Jonathan W. Leff ◽  
Mark A. Bradford ◽  
Rebecca L. McCulley ◽  
Sarah Lebeer ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Community Composition ◽  
Simultaneous Measurement ◽  
Gene Sequencing ◽  
16S Rrna Gene Sequencing ◽  
Rrna Gene ◽  
Soil Bacterial ◽  
Rrna Gene Sequencing

scholarly journals Evaluation of the gut microbiome in association with biological signatures of inflammation in murine polytrauma and shock

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Sandra A. Appiah ◽  
Christine L. Foxx ◽  
Dominik Langgartner ◽  
Annette Palmer ◽  
Cristian A. Zambrano ◽  
...  
Keyword(s):  
Gut Microbiota ◽  
Community Composition ◽  
Gut Microbiome ◽  
Beta Diversity ◽  
Microbial Community Composition ◽  
Alpha Diversity ◽  
Global Changes ◽  
Rrna Gene ◽  
Alpha And Beta Diversity ◽  
Increased Risk

AbstractSevere injuries are frequently accompanied by hemorrhagic shock and harbor an increased risk for complications. Local or systemic inflammation after trauma/hemorrhage may lead to a leaky intestinal epithelial barrier and subsequent translocation of gut microbiota, potentially worsening outcomes. To evaluate the extent with which trauma affects the gut microbiota composition, we performed a post hoc analysis of a murine model of polytrauma and hemorrhage. Four hours after injury, organs and plasma samples were collected, and the diversity and composition of the cecal microbiome were evaluated using 16S rRNA gene sequencing. Although cecal microbial alpha diversity and microbial community composition were not found to be different between experimental groups, norepinephrine support in shock animals resulted in increased alpha diversity, as indicated by higher numbers of distinct microbial features. We observed that the concentrations of proinflammatory mediators in plasma and intestinal tissue were associated with measures of microbial alpha and beta diversity and the presence of specific microbial drivers of inflammation, suggesting that the composition of the gut microbiome at the time of trauma, or shortly after trauma exposure, may play an important role in determining physiological outcomes. In conclusion, we found associations between measures of gut microbial alpha and beta diversity and the severity of systemic and local gut inflammation. Furthermore, our data suggest that four hours following injury is too early for development of global changes in the alpha diversity or community composition of the intestinal microbiome. Future investigations with increased temporal-spatial resolution are needed in order to fully elucidate the effects of trauma and shock on the gut microbiome, biological signatures of inflammation, and proximal and distal outcomes.

scholarly journals Colonic Mucosa-associated Mycobiota in Individuals With Normal Colons

2021 ◽  
Author(s):  
Themistoklis Kourkoumpetis ◽  
Kristi L. Hoffman ◽  
Yuna Kim ◽  
David Y. Graham ◽  
Donna L. White ◽  
...  
Keyword(s):  
Community Composition ◽  
Large Intestine ◽  
Relative Abundance ◽  
Beta Diversity ◽  
Colonic Mucosa ◽  
Alpha Diversity ◽  
Common Species ◽  
Rrna Gene ◽  
Fungal Community Composition ◽  
Colon And Rectum

Abstract To characterize the spatial variation of the mucosa-associated adherent mycobiota along the large intestine in individuals with a normal-colon, we performed eukaryotic rRNA operon’s internal transcribed spacer-2 sequencing to profile fungal community composition and structure in 70 mucosal biopsies taken from the cecum, ascending, transverse, descending colon, and rectum of 14 polyp-free individuals. The bacteriome of these samples was previously characterized by sequencing the V4 region of the 16S rRNA gene. We identified 64 amplicon sequence variants (ASVs) with the relative abundance no less than 0.05% from these colonic mucosa samples. Each individual has a unique community composition of the gut mycobiome (P = 0.001 for beta diversity). Alpha-diversity and beta-diversity did not differ significantly across the colon segments. The most common phyla (relative abundance) were Ascomycota (45.4%) and Basidiomycota (45.3%). The most common genera were Malassezia (28.2%) and Candida (13.4%). Malassezia was found in 13 of 14 individuals. Other fungi genera were sporadically found in the large intestine. The most common species were Malassezia restricta (22.7%), Candida albicans (11.9%), Malasseziales sp. (8.80%), unclassified fungi (7.80%), and Penicillium paneum (5.70%). Malasseziaceae was co-abundant with Enterobacteriaceae and co-exclusive with Barnesiellaceae, Rikenellaceae, and Acidaminococcaceae. Malassezia was widely colonized whereas other fungal genera were sporadically colonized in the large intestine. The physiologic and pathogenic functions of fungi in human gastrointestinal tract including Malasseziaceae that may interact with several bacterial families remain to be fully elucidated.

scholarly journals The bacterial community composition and its environmental drivers in the rivers around eutrophic Chaohu Lake, China

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Keqiang Shao ◽  
Xin Yao ◽  
Zhaoshi Wu ◽  
Xingyu Jiang ◽  
Yang Hu ◽  
...  
Keyword(s):  
Bacterial Community ◽  
Community Composition ◽  
Bacterial Communities ◽  
Bacterial Community Composition ◽  
Cyanobacterial Blooms ◽  
Environmental Drivers ◽  
Chaohu Lake ◽  
Rrna Gene ◽  
Functional Profiles ◽  
16 S Rrna

Abstract Background Bacterial community play a key role in environmental and ecological processes in river ecosystems. Rivers are used as receiving body for treated and untreated urban wastewaters that brings high loads of sewage and excrement bacteria. However, little is known about the bacterial community structure and functional files in the rivers around the eutrophic Chaohu Lake, the fifth largest freshwater lake in China, has been subjected to severe eutrophication and cyanobacterial blooms over the past few decades. Therefore, understanding the taxonomic and functional compositions of bacterial communities in the river will contribute to understanding aquatic microbial ecology. The main aims were to (1) examine the structure of bacterial communities and functional profiles in this system; (2) find the environmental factors of bacterial community variations. Results We studied 88 sites at rivers in the Chaohu Lake basin, and determined bacterial communities using Illumina Miseq sequencing of the 16 S rRNA gene, and predicted functional profiles using PICRUSt2. A total of 3,390,497 bacterial 16 S rRNA gene sequences were obtained, representing 17 phyla, and 424 genera; The dominant phyla present in all samples were Bacteroidetes (1.4-82.50 %), followed by Proteobacteria (12.6–97.30 %), Actinobacteria (0.1–17.20 %). Flavobacterium was the most numerous genera, and accounted for 0.12–80.34 % of assigned 16 S reads, followed by Acinetobacter (0.33–49.28 %). Other dominant bacterial genera including Massilia (0.06–25.40 %), Psychrobacter (0-36.23 %), Chryseobacterium (0.01–22.86 %), Brevundimonas (0.01–12.82 %), Pseudomonas (0-59.73 %), Duganella (0.08–23.37 %), Unidentified Micrococcaceae (0-8.49 %). The functional profiles of the bacterial populations indicated an relation with many human diseases, including infectious diseases. Overall results, using the β diversity measures, coupled with heatmap and RDA showed that there were spatial variations in the bacterial community composition at river sites, and Chemical oxygen demand (CODMn) and (NH4+ )were the dominant environmental drivers affecting the bacterial community variance. Conclusions The high proportion of the opportunistic pathogens (Acinetobacter, Massilia, Brevundimonas) indicated that the discharge of sewage without adequate treatment into the rivers around Chaohu Lake. We propose that these bacteria could be more effective bioindicators for long-term sewage monitoring in eutrophic lakes.

scholarly journals Data analysis workflow for the detection of canine vector-borne pathogens using 16 S rRNA Next-Generation Sequencing

2021 ◽  
Vol 17 (1) ◽  
Author(s):  
Elton J. R. Vasconcelos ◽  
Chayan Roy ◽  
Joseph A. Geiger ◽  
Kristina M. Oney ◽  
Melody Koo ◽  
...  
Keyword(s):  
Veterinary Medicine ◽  
Next Generation Sequencing ◽  
Complete Analysis ◽  
Molecular Diagnostic ◽  
Rrna Gene ◽  
Spotted Fever Group ◽  
Next Generation ◽  
Vector Borne ◽  
16 S Rrna ◽  
Generation Sequencing

Abstract Background Vector-borne diseases (VBDs) impact both human and veterinary medicine and pose special public health challenges. The main bacterial vector-borne pathogens (VBPs) of importance in veterinary medicine include Anaplasma spp., Bartonella spp., Ehrlichia spp., and Spotted Fever Group Rickettsia. Taxon-targeted PCR assays are the current gold standard for VBP diagnostics but limitations on the detection of genetically diverse organisms support a novel approach for broader detection of VBPs. We present a methodology for genetic characterization of VBPs using Next-Generation Sequencing (NGS) and computational approaches. A major advantage of NGS is the ability to detect multiple organisms present in the same clinical sample in an unsupervised (i.e. non-targeted) and semi-quantitative way. The Standard Operating Procedure (SOP) presented here combines industry-standard microbiome analysis tools with our ad-hoc bioinformatic scripts to form a complete analysis pipeline accessible to veterinary scientists and freely available for download and use at https://github.com/eltonjrv/microbiome.westernu/tree/SOP. Results We tested and validated our SOP by mimicking single, double, and triple infections in genomic canine DNA using serial dilutions of plasmids containing the entire 16 S rRNA gene sequence of (A) phagocytophilum, (B) v. berkhoffii, and E. canis. NGS with broad-range 16 S rRNA primers followed by our bioinformatics SOP was capable of detecting these pathogens in biological replicates of different dilutions. These results illustrate the ability of NGS to detect and genetically characterize multi-infections with different amounts of pathogens in a single sample. Conclusions Bloodborne microbiomics & metagenomics approaches may help expand the molecular diagnostic toolbox in veterinary and human medicine. In this paper, we present both in vitro and in silico detailed protocols that can be combined into a single workflow that may provide a significant improvement in VBP diagnostics and also facilitate future applications of microbiome research in veterinary medicine.

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