16S rRNA gene-based characterization of bacteria potentially associated with phosphate and carbonate precipitation from a granular autotrophic nitrogen removal bioreactor

ABSTRACTOne of the fastest growing fisheries in the UK is the king scallop (Pecten maximusL.), also currently rated as the second most valuable fishery. Mass mortality events in scallops have been reported worldwide, often with the causative agent(s) remaining uncharacterized. In May 2013 and 2014, two mass mortality events affecting king scallops were recorded in the Lyme Bay marine protected area (MPA) in Southwest England. Histopathological examination showed gill epithelial tissues infected with intracellular microcolonies (IMCs) of bacteria resemblingRickettsia-like organisms (RLOs), often with bacteria released in vascular spaces. Large colonies were associated with cellular and tissue disruption of the gills. Ultrastructural examination confirmed the intracellular location of these organisms in affected epithelial cells. The 16S rRNA gene sequences of the putative IMCs obtained from infected king scallop gill samples, collected from both mortality events, were identical and had a 99.4% identity to 16S rRNA gene sequences obtained from “CandidatusEndonucleobacter bathymodioli” and 95% withEndozoicomonasspecies.In situhybridization assays using 16S rRNA gene probes confirmed the presence of the sequenced IMC gene in the gill tissues. Additional DNA sequences of the bacterium were obtained using high-throughput (Illumina) sequencing, and bioinformatic analysis identified over 1,000 genes with high similarity to protein sequences fromEndozoicomonasspp. (ranging from 77 to 87% identity). Specific PCR assays were developed and applied to screen for the presence of IMC 16S rRNA gene sequences in king scallop gill tissues collected at the Lyme Bay MPA during 2015 and 2016. There was 100% prevalence of the IMCs in these gill tissues, and the 16S rRNA gene sequences identified were identical to the sequence found during the previous mortality event.IMPORTANCEMolluscan mass mortalities associated with IMCs have been reported worldwide for many years; however, apart from histological and ultrastructural characterization, characterization of the etiological agents is limited. In the present work, we provide detailed molecular characterization of anEndozoicomonas-like organism (ELO) associated with an important commercial scallop species.

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Deep insights into the green nitrogen removal by anammox in four full-scale WWTPs treating landfill leachate based on 16S rRNA gene and transcripts by 16S rRNA high-throughput sequencing

Journal of Cleaner Production ◽

10.1016/j.jclepro.2020.124176 ◽

2020 ◽

Vol 276 ◽

pp. 124176 ◽

Cited By ~ 2

Author(s):

Yuchun Yang ◽

Meng Li ◽

Zhong Hu ◽

Hojae Shim ◽

Jih-Gaw Lin ◽

...

Keyword(s):

16S Rrna ◽

16S Rrna Gene ◽

High Throughput ◽

Nitrogen Removal ◽

Landfill Leachate ◽

High Throughput Sequencing ◽

Full Scale ◽

Rrna Gene

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Phenotypic characterization of Astragalus glycyphyllos symbionts and their phylogeny based on the 16S rDNA sequences and RFLP of 16S rRNA gene

Antonie van Leeuwenhoek ◽

10.1007/s10482-014-0163-y ◽

2014 ◽

Vol 105 (6) ◽

pp. 1033-1048 ◽

Cited By ~ 12

Author(s):

Sebastian Gnat ◽

Magdalena Wójcik ◽

Sylwia Wdowiak-Wróbel ◽

Michał Kalita ◽

Aneta Ptaszyńska ◽

...

Keyword(s):

16S Rrna ◽

16S Rrna Gene ◽

16S Rdna ◽

Phenotypic Characterization ◽

Rrna Gene ◽

Rdna Sequences ◽

16S Rdna Sequences ◽

Astragalus Glycyphyllos Symbionts

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Characterization of the Community Structure of a Dechlorinating Mixed Culture and Comparisons of Gene Expression in Planktonic and Biofloc-Associated “Dehalococcoides” and Methanospirillum Species

Applied and Environmental Microbiology ◽

10.1128/aem.00445-08 ◽

2008 ◽

Vol 74 (21) ◽

pp. 6709-6719 ◽

Cited By ~ 39

Author(s):

Annette R. Rowe ◽

Brendan J. Lazar ◽

Robert M. Morris ◽

Ruth E. Richardson

Keyword(s):

Gene Expression ◽

16S Rrna ◽

16S Rrna Gene ◽

Population Distribution ◽

Enrichment Culture ◽

Expression Profiles ◽

Expression Patterns ◽

Rrna Gene ◽

Hydrogenase Gene

ABSTRACT This study sought to characterize bacterial and archaeal populations in a perchloroethene- and butyrate-fed enrichment culture containing hydrogen-consuming “Dehalococcoides ethenogenes” strain 195 and a Methanospirillum hungatei strain. Phylogenetic characterization of this microbial community was done via 16S rRNA gene clone library and gradient gel electrophoresis analyses. Fluorescence in situ hybridization was used to quantify populations of “Dehalococcoides” and Archaea and to examine the colocalization of these two groups within culture bioflocs. A technique for enrichment of planktonic and biofloc-associated biomass was developed and used to assess differences in population distribution and gene expression patterns following provision of substrate. On a per-milliliter-of-culture basis, most D. ethenogenes genes (the hydrogenase gene hupL; the highly expressed gene for an oxidoreductase of unknown function, fdhA; the RNA polymerase subunit gene rpoB; and the 16S rRNA gene) showed no statistical difference in expression between planktonic and biofloc enrichments at either time point studied (1 to 2 and 6 h postfeeding). Normalization of transcripts to ribosome (16S rRNA) levels supported that planktonic and biofloc-associated D. ethenogenes had similar gene expression profiles, with one notable exception; planktonic D. ethenogenes showed higher expression of tceA relative to biofloc-associated cells at 6 h postfeeding. These trends were compared to those for the hydrogen-consuming methanogen in the culture, M. hungatei. The vast majority of M. hungatei cells, ribosomes (16S rRNA), and transcripts of the hydrogenase gene mvrD and the housekeeping gene rpoE were observed in the biofloc enrichments. This suggests that, unlike the comparable activity of D. ethenogenes from both enrichments, planktonic M. hungatei is responsible for only a small fraction of the hydrogenotrophic methanogenesis in this culture.

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