The microbiome of the pelagic tunicate Dolioletta gegenbauri: a potential link between the grazing and microbial food web

Doliolids often form massive blooms during upwelling conditions in sub-tropical shelves. However, their trophic role, including their nutritious fecal pellets, in pelagic marine food webs remains poorly investigated. In this study, we performed three independent feeding experiments of cultured Dolioletta gegenbauri and used qPCR analysis and 16S rRNA metabarcoding to characterize the microbial community associated with full gut (FG) and empty (EG) doliolids, fresh (FP2Hrs) and senescing (FP24Hrs) fecal pellets, and the surrounding natural seawater (SW). Bacterial abundance (i.e., 16S rRNA gene copies) in EG samples was an order of magnitude lower than in SW and three orders lower than in FP24Hrs. Diversity analyses, based on the 16S rRNA metabarcoding data, supported a richer microbial community in SW, FP2Hrs, FP24Hrs, and FG samples. Furthermore, microbial community structure was determined by sample type, with FG samples appearing more similar to either FP2Hrs or FP24Hrs. These patterns resulted from the higher number of shared ASVs and consequently the contribution of similar major bacterial taxa (e.g., Rhodobacteraceae, Pirellulaceae). These observations support the hypothesis that there are significant ecological and trophic interactions between D. gegenbauri and the ocean microbiome. Predicted gene function recovered many genes related to key processes in the marine environment and supported greater similarity between FP2Hrs, FP24Hrs, and FG samples. These observations suggest that pelagic marine bacteria are utilized by D. gegenbauri to digest captured prey particles, and the subsequent release of fecal pellets supports the rapid proliferation of distinct microbial communities which likely influence key biogeochemical processes in the ocean.

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Assessment of two DNA extraction kits for profiling poultry respiratory microbiota from multiple sample types

10.1101/2020.10.21.348508 ◽

2020 ◽

Author(s):

Michael E.C. Abundo ◽

John M. Ngunjiri ◽

Kara J.M. Taylor ◽

Hana Ji ◽

Amir Ghorbani ◽

...

Keyword(s):

16S Rrna ◽

16S Rrna Gene ◽

Dna Extraction ◽

Extraction Process ◽

Production Performance ◽

Rrna Gene ◽

Sample Type ◽

Alpha And Beta Diversity ◽

Gene Copies ◽

Diversity Metrics

AbstractCharacterization of poultry microbiota is becoming increasingly important due to the growing need for microbiome-based interventions to improve poultry health and production performance. However, the lack of standardized protocols for sampling, sample processing, DNA extraction, sequencing, and bioinformatic analysis can hinder data comparison between studies. Here, we investigated how the DNA extraction process affects microbial community compositions and diversity metrics in different chicken respiratory sample types including choanal and tracheal swabs, nasal cavity and tracheal washes, and lower respiratory lavage. We did a side-by-side comparison of the performances of Qiagen DNeasy blood and tissue (BT) and ZymoBIOMICS DNA Miniprep (ZB) kits. In general, samples extracted with the BT kit yielded higher concentrations of total DNA while those extracted with the ZB kit contained higher numbers of bacterial 16S rRNA gene copies per unit volume. Therefore, the samples were normalized to equal amounts of 16S rRNA gene copies prior to sequencing. For each sample type, all predominant taxa detected in samples extracted with one kit were present in replicate samples extracted with the other kit and did not show significant differences at the class level. Furthermore, between-kit differences in alpha and beta diversity metrics were statistically indistinguishable. Therefore, both kits perform similarly with regard to 16S rRNA gene-based poultry microbiome analysis.

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Assessment of two DNA extraction kits for profiling poultry respiratory microbiota from multiple sample types

PLoS ONE ◽

10.1371/journal.pone.0241732 ◽

2021 ◽

Vol 16 (1) ◽

pp. e0241732

Author(s):

Michael E. C. Abundo ◽

John M. Ngunjiri ◽

Kara J. M. Taylor ◽

Hana Ji ◽

Amir Ghorbani ◽

...

Keyword(s):

16S Rrna ◽

16S Rrna Gene ◽

Dna Extraction ◽

Production Performance ◽

Rrna Gene ◽

Sequence Variant ◽

Sample Type ◽

Alpha And Beta Diversity ◽

Gene Copies ◽

Diversity Metrics

Characterization of poultry microbiota is becoming increasingly important due to the growing need for microbiome-based interventions to improve poultry health and production performance. However, the lack of standardized protocols for sampling, sample processing, DNA extraction, sequencing, and bioinformatic analysis can hinder data comparison between studies. Here, we investigated how the DNA extraction process affects microbial community compositions and diversity metrics in different chicken respiratory sample types including choanal and tracheal swabs, nasal cavity and tracheal washes, and lower respiratory lavage. We did a side-by-side comparison of the performances of Qiagen DNeasy blood and tissue (BT) and ZymoBIOMICS DNA Miniprep (ZB) kits. In general, samples extracted with the BT kit yielded higher concentrations of total DNA while those extracted with the ZB kit contained higher numbers of bacterial 16S rRNA gene copies per unit volume. Therefore, the samples were normalized to equal amounts of 16S rRNA gene copies prior to sequencing. For each sample type, all predominant bacterial taxa detected in samples extracted with one kit were present in replicate samples extracted with the other kit and did not show significant differences at the class level. However, a few differentially abundant shared taxa were observed at family and genus levels. Furthermore, between-kit differences in alpha and beta diversity metrics at the amplicon sequence variant level were statistically indistinguishable. Therefore, both kits perform similarly in terms of 16S rRNA gene-based poultry microbiome analysis for the sample types analyzed in this study.

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Monitoring Abundance and Expression of “Dehalococcoides” Species Chloroethene-Reductive Dehalogenases in a Tetrachloroethene-Dechlorinating Flow Column

Applied and Environmental Microbiology ◽

10.1128/aem.00926-08 ◽

2008 ◽

Vol 74 (18) ◽

pp. 5695-5703 ◽

Cited By ~ 94

Author(s):

Sebastian Behrens ◽

Mohammad F. Azizian ◽

Paul J. McMurdie ◽

Andrew Sabalowsky ◽

Mark E. Dolan ◽

...

Keyword(s):

Microbial Community ◽

16S Rrna ◽

16S Rrna Gene ◽

Reductive Dehalogenation ◽

Gene Copy ◽

Rrna Gene ◽

Reductive Dehalogenase ◽

Gene Copies ◽

Donor And Acceptor ◽

Rdase Genes

ABSTRACT We investigated the distribution and activity of chloroethene-degrading microorganisms and associated functional genes during reductive dehalogenation of tetrachloroethene to ethene in a laboratory continuous-flow column. Using real-time PCR, we quantified “Dehalococcoides” species 16S rRNA and chloroethene-reductive dehalogenase (RDase) genes (pceA, tceA, vcrA, and bvcA) in nucleic acid extracts from different sections of the column. Dehalococcoides 16S rRNA gene copies were highest at the inflow port [(3.6 ± 0.6) × 106 (mean ± standard deviation) per gram soil] where the electron donor and acceptor were introduced into the column. The highest transcript numbers for tceA, vcrA, and bvcA were detected 5 to 10 cm from the column inflow. bvcA was the most highly expressed of all RDase genes and the only vinyl chloride reductase-encoding transcript detectable close to the column outflow. Interestingly, no expression of pceA was detected in the column, despite the presence of the genes in the microbial community throughout the column. By comparing the 16S rRNA gene copy numbers to the sum of all four RDase genes, we found that 50% of the Dehalococcoides population in the first part of the column did not contain either one of the known chloroethene RDase genes. Analysis of 16S rRNA gene clone libraries from both ends of the flow column revealed a microbial community dominated by members of Firmicutes and Actinobacteria. Higher clone sequence diversity was observed near the column outflow. The results presented have implications for our understanding of the ecophysiology of reductively dehalogenating Dehalococcoides spp. and their role in bioremediation of chloroethenes.

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Gastrointestinal Segments Influenced Fermentation End-Products, Microbiota and Microbial Abundances in Goats

10.21203/rs.3.rs-359515/v1 ◽

2021 ◽

Author(s):

Tsegay Gebremariam ◽

Zhiliang Tan

Keyword(s):

Fatty Acids ◽

Microbial Community ◽

16S Rrna ◽

16S Rrna Gene ◽

18S Rrna ◽

18S Rrna Gene ◽

Rrna Gene ◽

Gene Copies ◽

End Products ◽

The Impact

Abstract Purpose: Carbohydrate diets altered fermentation end-products and microbial community in the gastrointestinal tracts (GIT) of goats. Gastrointestinal contents used to determine the impact of carbohydrate feeds on fermentation end-products and microbial community in goats.Methodology: in the study goats were assigned to one of the two treatments corn meal (CM) or Corn gluten (CG) in a randomized block design (400 g/kg DM each). Goats were slaughtered, GIT liquids were used to determine dissolved gasses, fatty acids and microbial community.Results: Goats fed CG increased molar acetate (P < 0.05), lowered butyrate and propionate in the fore and hindgut comparing to those goats received CM. Goats received CM had higher (P < 0.05) dH2 while lowered dH2S in the fore and hindgut than those goats fed with CG treatment. The fore and hindgut had higher (P < 0.01) 16S rRNA gene copies of bacteria, protozoa, methanogens and 18S rRNA gene copies fungi than in the ileum and cecum. Goats fed CG diet had higher (P < 0.05)16S rRNA gene copies of bacteria, protozoa, methanogens, and 18S rRNA gene copies of fungi than those goats fed with CM diet. Conclusion fore and hindguts improved dissolved gasses, fatty acids and microbial community comparing with in the ileum and cecum. Goats fed CM had improved the Methanobacterials order and Methanobrevibacter genus as compared with those goats fed CG. The study suggested that hindgut segments have a reasonable contribution as foregut to methane emissions from goats.

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The diversity of active microbial groups in an activated sludge process treating painting process wastewater

E3S Web of Conferences ◽

10.1051/e3sconf/202014801002 ◽

2020 ◽

Vol 148 ◽

pp. 01002

Author(s):

Herto Dwi Ariesyady ◽

Mentari Rizki Mayanda ◽

Tsukasa Ito

Keyword(s):

Wastewater Treatment ◽

Microbial Community ◽

16S Rrna ◽

16S Rrna Gene ◽

Activated Sludge ◽

Biological Treatment ◽

Rrna Gene ◽

Activated Sludge Process ◽

Painting Process ◽

Process Wastewater

Activated sludge process is one of the wastewater treatment method that is applied for many wastewater types including painting process wastewater of automotive industry. This wastewater is well-known to have high heavy metals concentration which could deteriorate water environment if appropriate performance of the wastewater treatment could not be achieved. In this study, we monitored microbial community diversity in a Painting Biological Treatment (PBT) system. We applied a combination of cultivation and genotypic biological methods based on 16S rRNA gene sequence analysis to identify the diversity of active microbial community. The results showed that active microbes that could grow in this activated sludge system were dominated by Gram-negative bacteria. Based on 16S rRNA gene sequencing analysis, it was revealed that their microbial diversity has close association with Bacterium strain E286, Isosphaera pallida, Lycinibacillus fusiformis, Microbacterium sp., Orchobactrum sp., Pseudomonas guariconensis, Pseudomonas sp. strain MR84, Pseudomonas sp. MC 54, Serpens sp., Stenotrophomonas acidaminiphila, and Xylella fastidiosa with similarity of 86 – 99%. This findings reflects that microbial community in a Painting Biological Treatment (PBT) system using activated sludge process could adapt with xenobiotics in the wastewater and has a wide range of diversity indicating a complex metabolism mechanism in the treatment process.

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Intragenomic and intraspecific heterogeneity in rrs may surpass interspecific variability in a natural population of Veillonella

Microbiology ◽

10.1099/mic.0.038224-0 ◽

2010 ◽

Vol 156 (7) ◽

pp. 2080-2091 ◽

Cited By ~ 28

Author(s):

Anne-Laure Michon ◽

Fabien Aujoulat ◽

Laurent Roudière ◽

Olivier Soulier ◽

Isabelle Zorgniotti ◽

...

Keyword(s):

16S Rrna ◽

16S Rrna Gene ◽

Gene Diversity ◽

Natural Populations ◽

Variable Region ◽

Housekeeping Gene ◽

Single Copy ◽

Population Based ◽

Rrna Gene ◽

Gene Copies

As well as intraspecific heterogeneity, intragenomic heterogeneity between 16S rRNA gene copies has been described for a range of bacteria. Due to the wide use of 16S rRNA gene sequence analysis for taxonomy, identification and metagenomics, evaluating the extent of these heterogeneities in natural populations is an essential prerequisite. We investigated inter- and intragenomic 16S rRNA gene heterogeneity of the variable region V3 in a population of 149 clinical isolates of Veillonella spp. of human origin and in 13 type or reference Veillonella strains using PCR-temporal temperature gel electrophoresis (TTGE). 16S rRNA gene diversity was high in the studied population, as 45 different banding patterns were observed. Intragenomic heterogeneity was demonstrated for 110 (74 %) isolates and 8 (61.5 %) type or reference strains displaying two or three different gene copies. Polymorphic nucleotide positions accounted for 0.5–2.5 % of the sequence and were scattered in helices H16 and H17 of the rRNA molecule. Some of them changed the secondary structure of H17. Phylotaxonomic structure of the population based on the single-copy housekeeping gene rpoB was compared with TTGE patterns. The intragenomic V3 heterogeneity, as well as recombination events between strains or isolates of different rpoB clades, impaired the 16S rRNA-based identification for some Veillonella species. Such approaches should be conducted in other bacterial populations to optimize the interpretation of 16S rRNA gene sequences in taxonomy and/or diversity studies.

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