16S rRNA gene metabarcoding and TEM reveals different ecological strategies within the genus Neogloboquadrina (planktonic foraminifer)

@article{Bird201816SRG,
  title={16S rRNA gene metabarcoding and TEM reveals different ecological strategies within the genus Neogloboquadrina (planktonic foraminifer)},
  author={Clare Bird and Kate F. Darling and Ann D Russell and Jennifer Fehrenbacher and Catherine V. Davis and Andrew Free and Bryne T. Ngwenya},
  journal={PLoS ONE},
  year={2018},
  volume={13}
}
Uncovering the complexities of trophic and metabolic interactions among microorganisms is essential for the understanding of marine biogeochemical cycling and modelling climate-driven ecosystem shifts. High-throughput DNA sequencing methods provide valuable tools for examining these complex interactions, although this remains challenging, as many microorganisms are difficult to isolate, identify and culture. We use two species of planktonic foraminifera from the climatically susceptible… 
Metabarcoding Insights Into the Trophic Behavior and Identity of Intertidal Benthic Foraminifera
TLDR
The application of metabarcoding is proposed as a tool for the elucidation of the in situ feeding behavior of benthic foraminifera, while also allowing the correct taxonomic assignment of the feeder, using the V9 region of the 18S (small subunit; SSU) rRNA gene.
Enrichment of intracellular sulphur cycle –associated bacteria in intertidal benthic foraminifera revealed by 16S and aprA gene analysis
TLDR
The detection of sulphur-cycle related bacterial genes in this study suggests a putative role for these bacteria in the metabolism of the foraminiferal host and future investigation into environmental conditions under which transcription of S-cycle genes are activated would enable assessment of their role and the potential foraminIFeral/endobiont contribution to the sulphur -cycle.
Single-cell metabarcoding reveals biotic interactions of the Arctic calcifier Neogloboquadrina pachyderma with the eukaryotic pelagic community
TLDR
The strong but taxonomically non-specific association with algae, existing irrespective of depth and occurring in specimens collected far below the photic zone indicates that opportunistically grazed diatom-fuelled marine aggregates likely represent the main interaction substrate of N. pachyderma.
Single-cell metabarcoding reveals biotic interactions of the Arctic calcifier Neogloboquadrina pachyderma with the eukaryotic pelagic community
TLDR
The strong but taxonomically non-specific association with algae, existing irrespective of depth and occurring in specimens collected far below the photic zone indicates that opportunistically grazed diatom-fuelled marine aggregates likely represent the main interaction substrate of N. pachyderma.
Exploring the composition, variation and interactions of unicellular organisms in the marine benthic community with DNA metabarcoding
TLDR
DNA metabarcoding can provide a comprehensive tool for the investigation of life strategies and ecology of even unicellular organisms, such as the foraminifera, and is demonstrated to have a potential for applications in biomonitoring and environmental assessment.
Symbiont arrangement and metabolism can explain high δ13C in Eocene planktonic foraminifera
An important question in climate modeling is whether carbon cycling is fundamentally different in warm versus cold climate states. A key line of evidence regarding this question comes from the
Seawater pH reconstruction using boron isotopes in multiple planktonic foraminifera species with different depth habitats and their potential to constrain pH and pCO2 gradients
Abstract. Boron isotope systematics of planktonic foraminifera from core-top sediments and culture experiments have been studied to investigate the sensitivity of δ11B of calcite tests to seawater
Characterizing photosymbiosis in modern planktonic foraminifera
Abstract. Photosymbiosis has played a key role in the diversification of foraminifera and their carbonate production through geologic history. However, identification of photosymbiosis in extinct
Characterizing photosymbiosis in modern planktonic foraminifera
TLDR
The objectively quantified photosymbiotic characteristics have been used to design a metric of photoymbiosis, which allows the studied species to be classified along a gradient of photosynthetic activity, providing a framework for future ecological and physiological investigations of planktonic foraminifera.
Current practice in plankton metabarcoding: optimization and error management
TLDR
Synthesis of multiple plankton metabarcoding evaluations shows that high-quality data for qualitative and some semiquantitative goals can be achieved by implementing three checkpoints: first, rigorous protocol optimization; second, error minimization; and third, downstream analysis that considers potentially remaining biases.
...
1
2
3
4
...

References

SHOWING 1-10 OF 128 REFERENCES
PhytoREF: a reference database of the plastidial 16S rRNA gene of photosynthetic eukaryotes with curated taxonomy
TLDR
The PhytoREF database is built that contains 6490 plastidial 16S rDNA reference sequences that originate from a large diversity of eukaryotes representing all known major photosynthetic lineages and mainly focuses on marine microalgae, but sequences from land plants and freshwater taxa were also included to broaden the applicability of Phy toREF to different aquatic and terrestrial habitats.
Cyanobacterial endobionts within a major marine planktonic calcifier ( Globigerina bulloides , Foraminifera) revealed by 16S rRNA metabarcoding
TLDR
The possibility of bacterial symbiosis in Globigerina bulloides, a palaeoceanographically important, planktonic foraminifer, is investigated and it is suggested that Synechococcus is an endobiont of G. bulloide type IId, which is the first report of a bacterial endobionst in the planktoned foraminifa.
The genetic diversity of planktic foraminifera and the global distribution of ribosomal RNA genotypes
TLDR
An overview of the genetic and biogeographic data available to date for the planktic foraminifera is provided and global biogeographies highlighting the distribution of genetic types in the eight planktics foraminiferal morphospecies for which detailed molecular evidence is available are presented.
Unveiling in situ interactions between marine protists and bacteria through single cell sequencing
TLDR
The power of single cell sequencing to untangle ecological interactions between uncultured protists and prokaryotes is demonstrated and suggests a discovery of novel symbionts associated with Cercozoa and Chrysophyta cells.
srDna‐based taxonomic affinities of algal symbionts from a planktonic foraminifer and a solitary radiolarian
TLDR
The nuclear small subunit ribosomal DNA (srDNA) isolated from the symbionts of the spinose planktonic foraminiferan Globigerinella siphonifera d'Orbigny and a solitary radiolarian were analyzed in order to determine the identity of these symbIONts, confirming the first confirmed case of a symbiotic prymnesiophyte.
Phylogenetic diversity of aggregate‐attached vs. free‐living marine bacterial assemblages
TLDR
The data indicate that specific bacterial populations, different from those which predominate in free-living bacterioplankton, develop on marine phytodetrital aggregates.
Every base matters: assessing small subunit rRNA primers for marine microbiomes with mock communities, time series and global field samples.
TLDR
It is shown that beyond in silico predictions, testing with mock communities and field samples is important in primer selection, and a single mismatch can strongly bias amplification, but even perfectly matched primers can exhibit preferential amplification.
Marine bacterial, archaeal and protistan association networks reveal ecological linkages
TLDR
The analysis revealed a progression of microbial communities through time, and also a group of unknown eukaryotes that were highly correlated with dinoflagellates, indicating possible symbioses or parasitism, and a network generated from these statistical correlations provides new insights into the natural history of microbes.
Minor revision to V4 region SSU rRNA 806R gene primer greatly increases detection of SAR11 bacterioplankton
TLDR
It is demonstrated that a minor adjustment to the 806R primer will greatly increase detec- tion of the globally abundant SAR11 clade in marine and lake environments, and enable inclusion of this important bacterial lineage in experimental and environmental-based studies.
Metabarcoding and metabolome analyses of copepod grazing reveal feeding preference and linkage to metabolite classes in dynamic microbial plankton communities
In order to characterize copepod feeding in relation to microbial plankton community dynamics, we combined metabarcoding and metabolome analyses during a 22‐day seawater mesocosm experiment. Nutrient
...
1
2
3
4
5
...