scholarly journals Coalescence of bacterial groups originating from urban runoffs and artificial infiltration systems among aquifer microbiomes

2020 ◽  
Vol 24 (9) ◽  
pp. 4257-4273
Author(s):  
Yannick Colin ◽  
Rayan Bouchali ◽  
Laurence Marjolet ◽  
Romain Marti ◽  
Florian Vautrin ◽  
...  
Keyword(s):  
16S Rrna ◽  
Microbial Communities ◽  
Dna Sequences ◽  
Meta Analysis ◽  
Bacterial Species ◽  
Rrna Gene ◽  
Stormwater Infiltration ◽  
Bacterial Groups ◽  
Sequence Types ◽  
Hydrocarbon Degraders

Abstract. The invasion of aquifer microbial communities by aboveground microorganisms, a phenomenon known as community coalescence, is likely to be exacerbated in groundwaters fed by stormwater infiltration systems (SISs). Here, the incidence of this increased connectivity with upslope soils and impermeabilized surfaces was assessed through a meta-analysis of 16S rRNA gene libraries. Specifically, DNA sequences encoding 16S rRNA V5-V6 regions from free-living and attached aquifer bacteria (i.e., water and biofilm samples) were analysed upstream and downstream of a SIS and compared with those from bacterial communities from watershed runoffs and surface sediments from the SIS detention and infiltration basins. Significant bacterial transfers were inferred by the SourceTracker Bayesian approach, with 23 % to 57 % of the aquifer bacterial biofilms being composed of taxa from aboveground sediments and urban runoffs. Sediments from the detention basin were found more significant contributors of taxa involved in the buildup of these biofilms than soils from the infiltration basin. Inferred taxa among the coalesced biofilm community were predicted to be high in hydrocarbon degraders such as Sphingobium and Nocardia. The 16S rRNA-based bacterial community structure of the downstream-SIS aquifer waters showed lower coalescence with aboveground taxa (8 % to 38 %) than those of biofilms and higher numbers of taxa predicted to be involved in the N and S cycles. A DNA marker named tpm enabled the tracking of bacterial species from 24 genera including Pseudomonas, Aeromonas and Xanthomonas, among these communities. Several tpm sequence types were found to be shared between the aboveground and aquifer samples. Reads related to Pseudomonas were allocated to 50 species, of which 16 were found in the aquifer samples. Several of these aquifer species were found to be involved in denitrification but also hydrocarbon degradation (P. aeruginosa, P. putida and P. fluorescens). Some tpm sequence types allocated to P. umsongensis and P. chengduensis were found to be enriched among the tpm-harbouring bacteria, respectively, of the aquifer biofilms and waters. Reads related to Aeromonas were allocated to 11 species, but only those from A. caviae were recovered aboveground and in the aquifer samples. Some tpm sequence types of the X. axonopodis phytopathogen  were recorded in higher proportions among the tpm-harbouring bacteria of the aquifer waters than in the aboveground samples. A significant coalescence of microbial communities from an urban watershed with those of an aquifer was thus observed, and recent aquifer biofilms were found to be significantly colonized by runoff-opportunistic taxa able to use urban C sources from aboveground compartments.

scholarly journals Coalescence of bacterial groups originating from urban runoffs and artificial infiltration systems among aquifer microbiomes

2020 ◽  
Author(s):  
Yannick Colin ◽  
Rayan Bouchali ◽  
Laurence Marjolet ◽  
Romain Marti ◽  
Florian Vautrin ◽  
...  
Keyword(s):  
Microbial Communities ◽  
Meta Analysis ◽  
Bacterial Species ◽  
Rrna Gene ◽  
Urban Watershed ◽  
Gene Libraries ◽  
Micro Organisms ◽  
Stormwater Infiltration ◽  
Bacterial Groups ◽  
Hydrocarbon Degraders

Abstract. The invasion of aquifer microbial communities by aboveground micro-organisms, a phenomenon known as community coalescence, is likely to be exacerbated in groundwaters fed by stormwater infiltration systems (SIS). Here, the incidence of this increased connectivity with upslope soils and impermeabilized surfaces was assessed through a meta-analysis of 16S rRNA gene libraries. Specifically, free-living and attached aquifer bacteria (i.e., water and biofilm samples) were characterized upstream and downstream a SIS, and compared with bacterial communities from watershed runoffs, detention and infiltration basins. A significant bacterial transfer was observed, with aquifer bacterial biofilms being largely made up of taxa occurring in aboveground sediments and urban runoffs (44 to 67 % of the total reads). This coalesced biofilm community was rich in hydrocarbon degraders such as Sphingobium and Nocardia. The bacterial community of the downstream SIS aquifer waters showed similar coalescence with aboveground taxa (26.7–66.5 %) but a higher number of taxa involved in the N- and S-cycles was observed. A DNA marker named tpm enabled a tracking of bacterial species from 24 genera including the Pseudomonas, Aeromonas and Xanthomonas among these communities. Reads related to the Pseudomonas were allocated to 50 species, of which 16 were found in the aquifer samples. P. umsongensis and P. chengduensis were inferred to be in higher proportions among the tpm-harboring bacteria, respectively, of the aquifer biofilms, and waters. Several of these aquifer species were found involved in denitrification but also hydrocarbon degradation (P. aeruginosa, P. putida, and P. fluorescens). Reads related to Aeromonas were allocated to 11 species but only those from A. caviae were recovered in the aquifer samples. DNA imprints allocated to the X. axonopodis phytopathogen were recorded in higher proportions among the tpm-harboring bacteria of the aquifer waters than aboveground samples. A coalescence of microbial communities from an urban watershed with those of an aquifer was thus observed, and recent aquifer biofilms were found dominated by runoff opportunistic taxa able to use urban C-sources from aboveground compartments.

scholarly journals Characterization of vaginal microbial communities in adult healthy women using cultivation-independent methods

Microbiology ◽  
2004 ◽  
Vol 150 (8) ◽  
pp. 2565-2573 ◽  
Author(s):  
Xia Zhou ◽  
Stephen J. Bent ◽  
Maria G. Schneider ◽  
Catherine C. Davis ◽  
Mohammed R. Islam ◽  
...  
Keyword(s):  
Microbial Community ◽  
16S Rrna ◽  
Dna Sequences ◽  
Phylogenetic Analyses ◽  
Bacterial Species ◽  
Pcr Amplification ◽  
Single Species ◽  
Rrna Gene ◽  
Caucasian Women ◽  
Tract Infections

The normal microbial flora of the vagina plays an important role in preventing genital and urinary tract infections in women. Thus an accurate understanding of the composition and ecology of the ecosystem is important to understanding the aetiology of these diseases. Common wisdom is that lactobacilli dominate the normal vaginal microflora of post-pubertal women. However, this conclusion is based on methods that require cultivation of microbial populations; an approach that is known to yield a biased and incomplete assessment of microbial community structure. In this study cultivation-independent methods were used to analyse samples collected from the mid-vagina of five normal healthy Caucasian women between the ages of 28 and 44. Total microbial community DNA was isolated following resuspension of microbial cells from vaginal swabs. To identify the constituent numerically dominant populations in each community 16S rRNA gene libraries were prepared following PCR amplification using the 8f and 926r primers. From each library, the DNA sequences of approximately 200 16S rRNA clones were determined and subjected to phylogenetic analyses. The diversity and kinds of organisms that comprise the vaginal microbial community varied among women. Species of Lactobacillus appeared to dominate the communities in four of the five women. However, the community of one woman was dominated by Atopobium sp., whereas a second woman had appreciable numbers of Megasphaera sp., Atopobium sp. and Leptotrichia sp., none of which have previously been shown to be common members of the vaginal ecosystem. Of the women whose communities were dominated by lactobacilli, there were two distinct clusters, each of which consisted of a single species. One class consisted of two women with genetically divergent clones that were related to Lactobacillus crispatus, whereas the second group of two women had clones of Lactobacillus iners that were highly related to a single phylotype. These surprising results suggest that culture-independent methods can provide new insights into the diversity of bacterial species found in the human vagina, and this information could prove to be pivotal in understanding risk factors for various infectious diseases.

scholarly journals The structured diversity of specialized gut symbionts of the New World army ants

2016 ◽  
Author(s):  
Piotr Łukasik ◽  
Justin A. Newton ◽  
Jon G. Sanders ◽  
Yi Hu ◽  
Corrie S. Moreau ◽  
...  
Keyword(s):  
16S Rrna ◽  
Microbial Communities ◽  
New World ◽  
Bacterial Species ◽  
Amplicon Sequencing ◽  
Rrna Gene ◽  
Bacterial Strains ◽  
Army Ants ◽  
Army Ant ◽  
Species Specific

Symbiotic bacteria play important roles in the biology of their arthropod hosts. Yet the microbiota of many diverse and influential groups remain understudied, resulting in a paucity of information on the fidelities and histories of these associations. Motivated by prior findings from a smaller scale, 16S rRNA-based study, we conducted a broad phylogenetic and geographical survey of microbial communities in the ecologically dominant New World army ants (Formicidae: Dorylinae). Amplicon sequencing of the 16S rRNA gene across 28 species spanning the five New World genera showed that the microbial communities of army ants consist of very few common and abundant bacterial species. The two most abundant microbes, referred to as Unclassified Firmicutes and Unclassified Entomoplasmatales, appear to be specialized army ant associates that dominate microbial communities in the gut lumen of three host genera, Eciton, Labidus and Nomamyrmex. Both are present in other army ant genera, including those from the Old World, suggesting that army ant symbioses date back to the Cretaceous. Extensive sequencing of bacterial protein-coding genes revealed multiple strains of these symbionts co-existing within colonies, but seldom within the same individual ant. Bacterial strains formed multiple host species-specific lineages on phylogenies, which often grouped strains from distant geographic locations. These patterns deviate from those seen in other social insects, and raise intriguing questions about the influence of army ant colony swarm-founding and within-colony genetic diversity on strain co-existence, and the effects of hosting a diverse suite of symbiont strains on colony ecology.

scholarly journals Metagenomic 16s rRNA investigation of microbial communities in the Black Sea estuaries in South-West of Ukraine.

2016 ◽  
Vol 63 (2) ◽  
Author(s):  
Oleksandra Bobrova ◽  
Jon Bent Kristoffersen ◽  
Anastasis Oulas ◽  
Volodymyr Ivanytsia
Keyword(s):  
16S Rrna ◽  
Microbial Communities ◽  
16S Rdna ◽  
Black Sea ◽  
Complex Analysis ◽  
Bacterial Species ◽  
Variable Region ◽  
Illumina Miseq ◽  
The Black Sea ◽  
Rrna Gene

The Black Sea estuaries represent interfaces of the sea and river environments. Microorganisms that inhabit estuarine water play an integral role in all biochemical processes that occur there and form unique ecosystems. There are many estuaries located in the Southern-Western part of Ukraine and some of them are already separated from the sea. The aim of this research was to determine the composition of microbial communities in the Khadzhibey, Dniester and Sukhyi estuaries by metagenomic 16S rDNA analysis. This study is the first complex analysis of estuarine microbiota based on isolation of total DNA from a biome that was further subjected to sequencing. DNA was extracted from water samples and sequenced on the Illumina Miseq platform using primers to the V4 variable region of the 16S rRNA gene. Computer analysis of the obtained raw sequences was done with QIIME (Quantitative Insights Into Microbial Ecology) software. As the outcome, 57970 nucleotide sequences were retrieved. Bioinformatic analysis of bacterial community in the studied samples demonstrated a high taxonomic diversity of Prokaryotes at above genus level. It was shown that majority of 16S rDNA bacterial sequences detected in the estuarine samples belonged to phyla Cyanobacteria, Proteobacteria, Bacteroidetes, Actinobacteria, Verrucomicrobia, Planctomycetes. The Khadhzibey estuary was dominated by the Proteobacteria phylum, while Dniester and Sukhyi estuaries were characterized by dominance of Cyanobacteria. The differences in bacterial populations between the Khadzhibey, Dniester and Sukhyi estuaries were demonstrated through the Beta-diversity analysis. It showed that the Khadzhibey estuary's microbial community significantly varies from the Sukhyi and Dniester estuaries. The majority of identified bacterial species is known as typical inhabitants of marine environments, however, for 2.5% of microbial population members in the studied estuaries no relatives were determined.

scholarly journals Vaginal Microbiota of Women with Frequent Vulvovaginal Candidiasis

2009 ◽  
Vol 77 (9) ◽  
pp. 4130-4135 ◽  
Author(s):  
Xia Zhou ◽  
Rachel Westman ◽  
Roxana Hickey ◽  
Melanie A. Hansmann ◽  
Colleen Kennedy ◽  
...  
Keyword(s):  
16S Rrna ◽  
Microbial Communities ◽  
Bacterial Communities ◽  
Bacterial Species ◽  
Vulvovaginal Candidiasis ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Rrna Gene ◽  
16S Rrna Gene Sequences ◽  
Novel Bacteria

ABSTRACT Vulvovaginal candidiasis (VVC) is an insidious infection that afflicts a large proportion of women of all ages, and 5 to 8% of affected women experience recurrent VVC (RVVC). The aim of this study was to explore the possible importance of vaginal bacterial communities in reducing the risk of RVVC. The species composition and diversity of microbial communities were evaluated for 42 women with and without frequent VVC based on profiles of terminal restriction fragment polymorphisms of 16S rRNA genes and phylogenetic analysis of cloned 16S rRNA gene sequences from the numerically dominant microbial populations. The data showed that there were no significant differences between the vaginal microbial communities of women in the two groups (likelihood score, 5.948; bootstrap P value, 0.26). Moreover, no novel bacteria were found in the communities of women with frequent VVC. The vaginal communities of most women in both groups (38/42; 90%) were dominated by species of Lactobacillus. The results of this study failed to provide evidence for the existence of altered or unusual vaginal bacterial communities in women who have frequent VVC compared to women who do not have frequent VVC. The findings suggest that commensal vaginal bacterial species may not be able to prevent VVC.

scholarly journals Impact of Substratum Surface on Microbial Community Structure and Treatment Performance in Biological Aerated Filters

2013 ◽  
Vol 80 (1) ◽  
pp. 177-183 ◽  
Author(s):  
Lavane Kim ◽  
Eulyn Pagaling ◽  
Yi Y. Zuo ◽  
Tao Yan
Keyword(s):  
Microbial Community ◽  
Microbial Communities ◽  
Bacterial Species ◽  
Community Analysis ◽  
Microbial Community Analysis ◽  
Rrna Gene ◽  
Content Type ◽  
Property Change ◽  
And Control ◽  
Start Ups

ABSTRACTThe impact of substratum surface property change on biofilm community structure was investigated using laboratory biological aerated filter (BAF) reactors and molecular microbial community analysis. Two substratum surfaces that differed in surface properties were created via surface coating and used to develop biofilms in test (modified surface) and control (original surface) BAF reactors. Microbial community analysis by 16S rRNA gene-based PCR-denaturing gradient gel electrophoresis (DGGE) showed that the surface property change consistently resulted in distinct profiles of microbial populations during replicate reactor start-ups. Pyrosequencing of the bar-coded 16S rRNA gene amplicons surveyed more than 90% of the microbial diversity in the microbial communities and identified 72 unique bacterial species within 19 bacterial orders. Among the 19 orders of bacteria detected,BurkholderialesandRhodocyclalesof theBetaproteobacteriaclass were numerically dominant and accounted for 90.5 to 97.4% of the sequence reads, and their relative abundances in the test and control BAF reactors were different in consistent patterns during the two reactor start-ups. Three of the five dominant bacterial species also showed consistent relative abundance changes between the test and control BAF reactors. The different biofilm microbial communities led to different treatment efficiencies, with consistently higher total organic carbon (TOC) removal in the test reactor than in the control reactor. Further understanding of how surface properties affect biofilm microbial communities and functional performance would enable the rational design of new generations of substrata for the improvement of biofilm-based biological treatment processes.

scholarly journals Phylogenetic Diversity and Molecular Detection of Bacteria in Gull Feces

2008 ◽  
Vol 74 (13) ◽  
pp. 3969-3976 ◽  
Author(s):  
Jingrang Lu ◽  
Jorge W. Santo Domingo ◽  
Regina Lamendella ◽  
Thomas Edge ◽  
Stephen Hill
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Phylogenetic Diversity ◽  
Bacterial Species ◽  
Rrna Gene ◽  
Fecal Dna ◽  
Environmental Waters ◽  
Potential Risks ◽  
Species Specific ◽  
Gut Microbial Community

ABSTRACT In spite of increasing public health concerns about the potential risks associated with swimming in waters contaminated with waterfowl feces, little is known about the composition of the gut microbial community of aquatic birds. To address this, a gull 16S rRNA gene clone library was developed and analyzed to determine the identities of fecal bacteria. Analysis of 282 16S rRNA gene clones demonstrated that the gull gut bacterial community is mostly composed of populations closely related to Bacilli (37%), Clostridia (17%), Gammaproteobacteria (11%), and Bacteriodetes (1%). Interestingly, a considerable number of sequences (i.e., 26%) were closely related to Catellicoccus marimammalium, a gram-positive, catalase-negative bacterium. To determine the occurrence of C. marimammalium in waterfowl, species-specific 16S rRNA gene PCR and real-time assays were developed and used to test fecal DNA extracts from different bird (n = 13) and mammal (n = 26) species. The results showed that both assays were specific to gull fecal DNA and that C. marimammalium was present in gull fecal samples collected from the five locations in North America (California, Georgia, Ohio, Wisconsin, and Toronto, Canada) tested. Additionally, 48 DNA extracts from waters collected from six sites in southern California, Great Lakes in Michigan, Lake Erie in Ohio, and Lake Ontario in Canada presumed to be impacted with gull feces were positive by the C. marimammalium assay. Due to the widespread presence of this species in gulls and environmental waters contaminated with gull feces, targeting this bacterial species might be useful for detecting gull fecal contamination in waterfowl-impacted waters.

scholarly journals 16S rRNA Long-Read Sequencing of the Granulation Tissue from Nonsmokers and Smokers-Severe Chronic Periodontitis Patients

2018 ◽  
Vol 2018 ◽  
pp. 1-10 ◽  
Author(s):  
Rebecca Chowdhry ◽  
Neetu Singh ◽  
Dinesh Kumar Sahu ◽  
Ratnesh Kumar Tripathi ◽  
Archana Mishra ◽  
...  
Keyword(s):  
16S Rrna ◽  
Granulation Tissue ◽  
Ketone Bodies ◽  
Bacterial Species ◽  
Rrna Gene ◽  
Differential Abundance ◽  
Streptobacillus Moniliformis ◽  
Increased Risk ◽  
Long Read ◽  
Significant Enrichment

Smoking has been associated with increased risk of periodontitis. The aim of the present study was to compare the periodontal disease severity among smokers and nonsmokers which may help in better understanding of predisposition to this chronic inflammation mediated diseases. We selected deep-seated infected granulation tissue removed during periodontal flap surgery procedures for identification and differential abundance of residential bacterial species among smokers and nonsmokers through long-read sequencing technology targeting full-length 16S rRNA gene. A total of 8 phyla were identified among which Firmicutes and Bacteroidetes were most dominating. Differential abundance analysis of OTUs through PICRUST showed significant (p>0.05) abundance of Phyla-Fusobacteria (Streptobacillus moniliformis); Phyla-Firmicutes (Streptococcus equi), and Phyla Proteobacteria (Enhydrobacter aerosaccus) in nonsmokers compared to smokers. The differential abundance of oral metagenomes in smokers showed significant enrichment of host genes modulating pathways involving primary immunodeficiency, citrate cycle, streptomycin biosynthesis, vitamin B6 metabolism, butanoate metabolism, glycine, serine, and threonine metabolism pathways. While thiamine metabolism, amino acid metabolism, homologous recombination, epithelial cell signaling, aminoacyl-tRNA biosynthesis, phosphonate/phosphinate metabolism, polycyclic aromatic hydrocarbon degradation, synthesis and degradation of ketone bodies, translation factors, Ascorbate and aldarate metabolism, and DNA replication pathways were significantly enriched in nonsmokers, modulation of these pathways in oral cavities due to differential enrichment of metagenomes in smokers may lead to an increased susceptibility to infections and/or higher formation of DNA adducts, which may increase the risk of carcinogenesis.

scholarly journals Microbial Diversity Profiling of Gut Microbiota of Macropus giganteus Using Three Hypervariable Regions of the Bacterial 16S rRNA

2021 ◽  
Vol 9 (8) ◽  
pp. 1721
Author(s):  
Christian O’Dea ◽  
Roger Huerlimann ◽  
Nicole Masters ◽  
Anna Kuballa ◽  
Cameron Veal ◽  
...  
Keyword(s):  
16S Rrna ◽  
Gut Microbiota ◽  
Microbial Diversity ◽  
Surface Waters ◽  
Bacterial Species ◽  
Rrna Gene ◽  
Faecal Contamination ◽  
Hypervariable Regions ◽  
Geographical Regions ◽  
V3 Region

Animal faecal contamination of surface waters poses a human health risk, as they may contain pathogenic bacteria or viruses. Of the numerous animal species residing along surface waterways in Australia, macropod species are a top contributor to wild animals’ faecal pollution load. We characterised the gut microbiota of 30 native Australian Eastern Grey Kangaroos from six geographical regions (five kangaroos from each region) within South East Queensland in order to establish their bacterial diversity and identify potential novel species-specific bacteria for the rapid detection of faecal contamination of surface waters by these animals. Using three hypervariable regions (HVRs) of the 16S rRNA gene (i.e., V1–V3, V3–V4, and V5–V6), for their effectiveness in delineating the gut microbial diversity, faecal samples from each region were pooled and microbial genomic DNA was extracted, sequenced, and analysed. Results indicated that V1-V3 yielded a higher taxa richness due to its larger target region (~480 bp); however, higher levels of unassigned taxa were observed using the V1-V3 region. In contrast, the V3–V4 HVR (~569 bp) attained a higher likelihood of a taxonomic hit identity to the bacterial species level, with a 5-fold decrease in unassigned taxa. There were distinct dissimilarities in beta diversity between the regions, with the V1-V3 region displaying the highest number of unique taxa (n = 42), followed by V3–V4 (n = 11) and V5–V6 (n = 8). Variations in the gut microbial diversity profiles of kangaroos from different regions were also observed, which indicates that environmental factors may impact the microbial development and, thus, the composition of the gut microbiome of these animals.

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