scholarly journals Taxonomic composition of the particle‐attached and free‐living bacterial assemblages in the N orthwest M editerranean S ea analyzed by pyrosequencing of the 16S rRNA

2013 ◽  
Vol 2 (4) ◽  
pp. 541-552 ◽  
Author(s):  
Bibiana G. Crespo ◽  
Thomas Pommier ◽  
Beatriz Fernández‐Gómez ◽  
Carlos Pedrós‐Alió
Keyword(s):  
16S Rrna ◽  
Taxonomic Composition ◽  
Free Living ◽  
Bacterial Assemblages

scholarly journals Opening a next-generation black box: ecological trends for hundreds of species-like taxa uncovered within a single bacterial >99% 16S rRNA operational taxonomic unit

2021 ◽  
Author(s):  
Martin Hahn ◽  
Andrea Huemer ◽  
Alexandra Pitt ◽  
Matthias Hoetzinger
Keyword(s):  
16S Rrna ◽  
Sequence Similarity ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Rrna Gene ◽  
Taxon Richness ◽  
Large Set ◽  
Free Living ◽  
Environmental Distribution ◽  
Living Bacteria

Current knowledge on environmental distribution and taxon richness of free-living bacteria is mainly based on cultivation-independent investigations employing 16S rRNA gene sequencing methods. Yet, 16S rRNA genes are evolutionarily rather conserved, resulting in limited taxonomic and ecological resolutions provided by this marker. We used a faster evolving protein-encoding marker to reveal ecological patterns hidden within a single OTU defined by >99% 16S rRNA sequence similarity. The studied taxon, subcluster PnecC of the genus Polynucleobacter, represents a ubiquitous group of planktonic freshwater bacteria with cosmopolitan distribution, which is very frequently detected by diversity surveys of freshwater systems. Based on genome taxonomy and a large set of genome sequences, a sequence similarity threshold for delineation of species-like taxa could be established. In total, 600 species-like taxa were detected in 99 freshwater habitats scattered across three regions representing a latitudinal range of 3400 km (42°N to 71°N) and a pH gradient of 4.2 to 8.6. Besides the unexpectedly high richness, the increased taxonomic resolution revealed structuring of Polynucleobacter communities by a couple of macroecological trends, which was previously only demonstrated for phylogenetically much broader groups of bacteria. A unexpected pattern was the almost complete compositional separation of Polynucleobacter communities of Ca-rich and Ca-poor habitats, which strongly resembled the vicariance of plant species on silicate and limestone soils. The presented new cultivation-independent approach opened a window to an incredible, previously unseen diversity, and enables investigations aiming on deeper understanding of how environmental conditions shape bacterial communities and drive evolution of free-living bacteria.

scholarly journals Isolation of Oligotrophic Denitrifiers Carrying Previously Uncharacterized Functional Gene Sequences

2010 ◽  
Vol 77 (1) ◽  
pp. 338-342 ◽  
Author(s):  
Satoshi Ishii ◽  
Naoaki Ashida ◽  
Shigeto Otsuka ◽  
Keishi Senoo
Keyword(s):  
16S Rrna ◽  
Single Cell ◽  
Nitrite Reductase ◽  
Cell Isolation ◽  
Taxonomic Composition ◽  
Functional Gene ◽  
Gene Sequences ◽  
Isolation Technique ◽  
Culture Independent ◽  
Single Cell Isolation

ABSTRACTOligotrophic denitrifying bacteria, including those belonging to the generaHerbaspirillum,Azospirillum, andBradyrhizobium, were obtained using a single-cell isolation technique. The taxonomic composition of the denitrifier population was similar to those assessed by previous culture-independent studies. The sequencing of nitrite reductase and N2O reductase genes of these strains revealed previously unknown links between 16S rRNA and the denitrification-functional gene phylogenies. In particular, we identifiedBradyrhizobiumstrains that harbornirSsequences previously detected only in culture-independent studies.

Biodiversity of free-living marine nematodes on the coast of Brazil: a review

Zootaxa ◽  
2010 ◽  
Vol 2568 (1) ◽  
pp. 39 ◽  
Author(s):  
VIRÁG VENEKEY ◽  
VERÔNICA G. FONSECA-GENEVOIS ◽  
PAULO J. P. SANTOS
Keyword(s):  
Sandy Beaches ◽  
Oceanic Islands ◽  
Taxonomic Composition ◽  
Artificial Substrates ◽  
Rocky Shores ◽  
Coastal Habitats ◽  
Free Living ◽  
Generic Composition ◽  
Faunal List ◽  
First Time

The taxonomic richness of the marine Nematoda in coastal habitats of Brazil and similarities in generic composition among them are analysed. A complete faunal list is presented, containing 11 orders, 59 families, 294 genera and 231 species, among which 1 family, 10 genera and 87 species were discovered for the first time in Brazil. Seven habitats were considered (sandy beaches, estuaries, phytal, oceanic islands, beach rocks, salt works and artificial substrates): sandy beaches had the greatest generic richness (241), followed by estuaries (142) and the phytal environment (126). Taxonomic composition was similar to that of other coastal habitats sampled worldwide, with Chromadoridae and Xyalidae the most representative families. The three major habitats (beaches, rocky shores and estuaries), showed statistically significant differences in faunas. Estuaries were the most uniform in composition.

scholarly journals Polynucleobacter cosmopolitanus sp. nov., free-living planktonic bacteria inhabiting freshwater lakes and rivers

2010 ◽  
Vol 60 (1) ◽  
pp. 166-173 ◽  
Author(s):  
Martin W. Hahn ◽  
Elke Lang ◽  
Ulrike Brandt ◽  
Heinrich Lünsdorf ◽  
Qinglong L. Wu ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Novel Species ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
Natural Environments ◽  
The Novel ◽  
Free Living ◽  
Monophyletic Cluster ◽  
Freshwater Habitats

Five heterotrophic, aerobic, catalase- and oxidase-positive, non-motile strains were characterized from freshwater habitats located in Austria, France, Uganda, P. R. China and New Zealand. The strains shared 16S rRNA gene similarities of ≥99.3 %. The novel strains grew on NSY medium over a temperature range of 10–35 °C (two strains also grew at 5 °C and one strain grew at 38 °C) and a NaCl tolerance range of 0.0–0.3 % (four strains grew up to 0.5 % NaCl). The predominant fatty acids were C16 : 0, C18 : 1 ω7c, C12 : 0 3-OH, and summed feature 3 (including C16 : 1 ω7c). The DNA G+C content of strain MWH-MoIso2T was 44.9 mol%. Phylogenetic analysis of 16S rRNA gene sequences demonstrated that the five new strains formed a monophyletic cluster closely related to Polynucleobacter necessarius (96–97 % sequence similarity). This cluster also harboured other isolates as well as environmental sequences which have been obtained from several habitats. Investigations with taxon-specific FISH probes demonstrated that the novel bacteria dwell as free-living, planktonic cells in freshwater systems. Based on the revealed phylogeny and pronounced chemotaxonomic differences to P. necessarius (presence of >7 % C12 : 0 3-OH and absence of C12 : 0 and C12 : 0 2-OH), the new strains are suggested to represent a novel species, for which the name Polynucleobacter cosmopolitanus sp. nov. is proposed. The type strain is MWH-MoIso2T (=DSM 21490T=CIP 109840T=LMG 25212T). The novel species belongs to the minority of described species of free-living bacteria for which both in situ data from their natural environments and culture-based knowledge are available.

scholarly journals Changes in the Community Structure of Under-Ice and Open-Water Microbiomes in Urban Lakes Exposed to Road Salts

2021 ◽  
Vol 12 ◽  
Author(s):  
Isabelle B. Fournier ◽  
Connie Lovejoy ◽  
Warwick F. Vincent
Keyword(s):  
Community Structure ◽  
16S Rrna ◽  
18S Rrna ◽  
Photosynthetic Pigment ◽  
Open Water ◽  
Taxonomic Composition ◽  
Pigment Analysis ◽  
Road Salts ◽  
Rrna Sequencing ◽  
Nitrogen Concentrations

Salinization of freshwater is increasingly observed in regions where chloride de-icing salts are applied to the roads in winter, but little is known about the effects on microbial communities. In this study, we analyzed the planktonic microbiomes of four lakes that differed in degree of urbanization, eutrophication and salinization, from an oligotrophic reference lake with no surrounding roads, to a eutrophic, salinized lake receiving runoff from a highway. We tested the hypothesis that an influence of road salts would be superimposed on the effects of season and trophic status. We evaluated the microbial community structure by 16S rRNA sequencing for Bacteria, and by four methods for eukaryotes: 16S rRNA chloroplast analysis, 18S rRNA sequencing, photosynthetic pigment analysis and microscopy. Consistent with our hypothesis, chloride and total nitrogen concentrations were among the most important statistical factors explaining the differences in taxonomic composition. These factors were positively correlated with the abundance of cryptophytes, haptophytes, and cyanobacteria. Ice-cover was also a major structuring factor, with clear differences between the winter communities and those of the open-water period. Nitrifying and methane oxidizing bacteria were more abundant in winter, suggesting the importance of anaerobic sediment processes and release of reduced compounds into the ice-covered water columns. The four methods for eukaryotic analysis provided complementary information. The 18S rRNA observations were strongly influenced by the presence of ribosome-rich ciliates, but revealed a much higher degree of taxonomic richness and greater separation of lakes, seasonal changes and potential salinity effects than the other methods.

scholarly journals Candidatus Rickettsia colombianensi in ticks from reptiles in Córdoba, Colombia

2020 ◽  
Vol 13 (9) ◽  
pp. 1764-1770
Author(s):  
Jorge Miranda ◽  
Lina Violet-Lozano ◽  
Samia Barrera ◽  
Salim Mattar ◽  
Santiago Monsalve-Buriticá ◽  
...  
Keyword(s):  
16S Rrna ◽  
Public Health Problem ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Rt Pcr ◽  
Free Living ◽  
The Family ◽  
Number Of Microorganisms ◽  
Polymerase Chain ◽  
Sanger Method

Background and Aim: Wildlife animals are reservoirs of a large number of microorganisms pathogenic to humans, and ticks could be responsible for the transmission of these pathogens. Rickettsia spp. are the most prevalent pathogens found in ticks. This study was conducted to detect Rickettsia spp. in ticks collected from free-living and illegally trafficked reptiles from the Department of Córdoba, Colombia. Materials and Methods: During the period from October 2011 to July 2014, ticks belonging to the family Ixodidae were collected, preserved in 96% ethanol, identified using taxonomic keys, and pooled (between 1 and 14 ticks) according to sex, stage, host, and collected place for subsequent DNA extraction. Rickettsia detection was performed using real-time polymerase chain reaction (RT-PCR), followed by conventional PCR to amplify a larger fragment of the gltA and 16S rRNA genes. The amplicons were sequenced using the Sanger method, and the nucleotide sequences were subjected to BLAST analysis to identify homologous sequences in GenBank, after which phylogenetic analysis was performed using the MEGA X software. Results: In total, 21 specimens of nine species of reptiles were sampled, from which 805 Amblyomma dissimile ticks were collected, but only 180 ticks were selected to create 34 groups. The DNA of Rickettsia spp. was detected in 30/34 (88%) groups. The sequences of the gene gltA and 16S rRNA revealed a 100% identity with Candidatus Rickettsia colombianensi (GenBank: KF905456 and GenBank: KF691750). Conclusion: A. dissimile was the only tick found in all the sampled reptiles. The presence of Candidatus Rickettsia colombianensi in reptile ticks could represent a public health problem due to the risk of transmission to humans and the introduction of microorganisms to other geographical areas.

scholarly journals Taxonomic diversity of bacterial assemblage in technosol of the revegetating fly ash dump

2019 ◽  
Vol 2 (3) ◽  
Author(s):  
Natalia B. Naumova ◽  
Ivan P. Belanov ◽  
Tatiana Yu. Alikina
Keyword(s):  
Fly Ash ◽  
16S Rrna ◽  
Thermoelectric Power ◽  
Relative Abundance ◽  
Rrna Genes ◽  
Gene Sequences ◽  
Power Station ◽  
Bacterial Assemblage ◽  
Early Stages ◽  
Bacterial Assemblages

Background. The aim of the study was to assess the composition and structure of bacterial assemblages by estimating 16S rRNA gene sequences diversity in a young Technosol, developing on a revegetating fly ash dump. Location and place of the study. Two soils were chosen for the study in the environs of the thermoelectric power station No.5 in Novosibirsk region: 1) nine years old Technosol (54°59' NL, 83°03' EL), developing on the spontaneously revegetating fly ash dump, and 2) Phaeozem under undisturbed white birch forest (55°00' NL, 83°04' EL). Soils were sampled from the 0-5 cm layer as three individual replicates each. Materials and methods. The total DNA extracted from soil samples was used as a matrix for PCR amplification using V-3-V4 primers for 16S rRNA genes. The obtained amplicons were sequenced on Illumina MiSeq platform in the Genomics Core Facility of the Institute of Chemical Biology and Fundamental Medicine SB RAS (Novosibirsk, Russia). Descriptive statistics and principal components analysis were used to analyze and present the data. Results. Overall 4887 different operational taxonomic units (OTUs) were found at the 97% similarity level; the OTUs were ascribed to 306 genera, 212 families, 123 orders, 84 classes and 32 phyla of bacteria domain. At the phylum level bacterial assemblages in both soils were dominated by Proteobacteria, Acidobacteria and Actinobacteria, showing rather similar outline of the phyla relative abundance, confirming the direction of pedogenesis towards Phaeozem. Higher abundance of Chloroflexi a physiologically diverse phyla with aerobic and anaerobic thermophiles, anoxigenic phototrophs and anaerobes, able to respire organic halides, in the young Technosol complies with harsh edaphic conditions there. Although the relative abundance of Rhizobiales, Actinomycetales and unclassified Acidobacteria_Gp6 and Acidobacteria_Gp3 was found to be 1.5–2.4 times higher in the undisturbed Phaeozem, they also were predominating in the Technosol samples. The α-biodiversity indices, pertaining mostly to species/OTUs richness, i.e. Chao-1, OTUs number, Margalef, Fisher’s alpha, were higher in Phaeozem, whereas evenness and equitability were higher in Technosol. Both soils demonstrated similar Shanno indices, which were rather high (6.3). Conclusions. Nine years of spontaneous revegetation on the terminated fly ash dump of the thermoelectric power station resulted in the development of the Technosol, containing quite rich and diverse bacterial assemblage, which was rather close in structure at the phylum taxonomic level to the adjacent undisturbed Phaeozem. Overall the early stages of pedogenesis were dominated by specific bacterial assemblage (Chloroflexi, Xanthomonadales, Geobacter, Aciditerrimonas, Iamiaceae and some others), performing weathering of the pedogenic substrate, i.e. fly ash. The present of nitrificators (Nitrospira), denitrificators денитрификаторов (Reyranella) together with diazotrophs (Bradyrhizobium, Rhizobiales) dominance evidences the establishment of the entire network of nitrogen transformation process already at the early stages of revegetation of the fly ash dump. Large percentage (17%) of Bacteria, the information about which ribosomal gene sequences is most likely absent in the respective data bases necessitates more detailed research into the soil microbiome on fly ash dumps.

scholarly journals Inference based PICRUSt accuracy varies across sample types and functional categories

2019 ◽  
Author(s):  
Shan Sun ◽  
Roshonda B. Jones ◽  
Anthony A. Fodor
Keyword(s):  
16S Rrna ◽  
Gene Prediction ◽  
Amplicon Sequencing ◽  
Taxonomic Composition ◽  
Inference Models ◽  
16S Rrna Amplicon Sequencing ◽  
Gene Profiles ◽  
Metagenome Sequencing ◽  
The Cost ◽  
Functional Profiles

AbstractBackgroundDespite recent decreases in the cost of sequencing, shotgun metagenome sequencing remains more expensive compared with 16S rRNA amplicon sequencing. Methods have been developed to predict the functional profiles of microbial communities based on their taxonomic composition, and PICRUSt is the most widely used of these techniques. In this study, we evaluated the performance of PICRUSt by comparing the significance of the differential abundance of functional gene profiles predicted with PICRUSt to those from shotgun metagenome sequencing across different environments.ResultsWe selected 7 datasets of human, non-human animal and environmental (soil) samples that have publicly available 16S rRNA and shotgun metagenome sequences. As we would expect based on previous literature, strong Spearman correlations were observed between gene compositions predicted with PICRUSt and measured with shotgun metagenome sequencing. However, these strong correlations were preserved even when the sample labels were shuffled. This suggests that simple correlation coefficient is a highly unreliable measure for the performance of algorithms like PICRUSt. As an alternative, we compared the performance of PICRUSt predicted genes to metagenome genes in inference models associated with metadata within each dataset. With this method, we found reasonable performance for human datasets, with PICRUSt performing better for inference on genes related to “house-keeping” functions. However, the performance of PICRUSt degraded sharply outside of human datasets when used for inference.ConclusionWe conclude that the utility of PICRUSt for inference with the default database is likely limited outside of human samples and that development of tools for gene prediction specific to different non-human and environmental samples is warranted.

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