Comparative Analysis of Eukaryotic Marine Microbial Assemblages from 18S rRNA Gene and Gene Transcript Clone Libraries by Using Different Methods of Extraction

Koid, Amy E.; Nelson, Karen E.; Mraz, Amy; Heidelberg, Karla B.

doi:10.1128/aem.06941-11

Cited by 41 publications

(26 citation statements)

References 46 publications

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“…For example, are the discordant metagenomic and metaproteomic datasets an accurate representation of the composition and activity within these biofilms (eg less abundant organisms that are more metabolically active)? Or, do the different methods of biomolecule extraction, processing and varying biology introduce unique biases that account for the observed discordance (Morgan et al 2010;Koid et al 2012;Yuan et al 2012;Leary et al 2013). When dealing with complex environmental samples, the experimental, analytical and statistical choices employed heavily influence the biological conclusions drawn in metaproteomic analyses (Dowd 2012) and most often limit them to those proteins that are most abundant or easiest to access (extraction bias), amenable to the biochemistry and biophysics employed (sample processing bias) and have previously been sequenced (sequence bias) and characterized (bioinformatic database bias) (Leary et al 2013).…”

Section: Discussionmentioning

confidence: 99%

Integrated metagenomic and metaproteomic analyses of marine biofilm communities

Leary

Hamdan

et al. 2014

Biofouling

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Metagenomic and metaproteomic analyses were utilized to determine the composition and function of complex air-water interface biofilms sampled from the hulls of two US Navy destroyers. Prokaryotic community analyses using PhyloChip-based 16S rDNA profiling revealed two significantly different and taxonomically rich biofilm communities (6,942 taxa) in which the majority of unique taxa were ascribed to members of the Gammaproteobacteria, Alphaproteobacteria and Clostridia. Although metagenomic sequencing indicated that both biofilms were dominated by prokaryotic sequence reads (> 91%) with the majority of the bacterial reads belonging to the Alphaproteobacteria, the Ship-1 metagenome harbored greater organismal and functional diversity and was comparatively enriched for sequences from Cyanobacteria, Bacteroidetes and macroscopic eukaryotes, whereas the Ship-2 metagenome was enriched for sequences from Proteobacteria and microscopic photosynthetic eukaryotes. Qualitative liquid chromatography-tandem mass spectrometry metaproteome analyses identified 678 unique proteins, revealed little overlap in species and protein composition between the ships and contrasted with the metagenomic data in that ~80% of classified and annotated proteins were of eukaryotic origin and dominated by members of the Bacillariophyta, Cnidaria, Chordata and Arthropoda (data deposited to the ProteomeXchange, identifier PXD000961). Within the shared metaproteome, quantitative (18)O and iTRAQ analyses demonstrated a significantly greater abundance of structural proteins from macroscopic eukaryotes on Ship-1 and diatom photosynthesis proteins on Ship-2. Photosynthetic pigment composition and elemental analyses confirmed that both biofilms were dominated by phototrophic processes. These data begin to provide a better understanding of the complex organismal and biomolecular composition of marine biofilms while highlighting caveats in the interpretation of stand-alone environmental '-omics' datasets.

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Section: Discussionmentioning

confidence: 99%

Integrated metagenomic and metaproteomic analyses of marine biofilm communities

Leary

Hamdan

et al. 2014

Biofouling

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“…However, ciliates are rare in the typical high-oxygen deep-sea samples and when counts are based on morphological criteria (Aristegui et al, 2009). There are considerable biases that lead to overrepresentation of some groups in the analysis of 18S rRNA gene libraries discussed in detail in Koid et al (2012), including multiple genome copies found especially in alveolates (for example, Dinophycea and Ciliophora). Unless the actual cell numbers can be independently verified by direct cell counts using suitable CARD-FISH probes, results of the relative dominance of some eukaryotic groups in deep-sea samples need to be treated with great caution.…”

Section: Colonization Of Particles By Eukaryotic Microbesmentioning

confidence: 99%

Eukaryotic microbes, principally fungi and labyrinthulomycetes, dominate biomass on bathypelagic marine snow

2016

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In the bathypelagic realm of the ocean, the role of marine snow as a carbon and energy source for the deep-sea biota and as a potential hotspot of microbial diversity and activity has not received adequate attention. Here, we collected bathypelagic marine snow by gentle gravity filtration of sea water onto 30 μm filters from~1000 to 3900 m to investigate the relative distribution of eukaryotic microbes. Compared with sediment traps that select for fast-sinking particles, this method collects particles unbiased by settling velocity. While prokaryotes numerically exceeded eukaryotes on marine snow, eukaryotic microbes belonging to two very distant branches of the eukaryote tree, the fungi and the labyrinthulomycetes, dominated overall biomass. Being tolerant to cold temperature and high hydrostatic pressure, these saprotrophic organisms have the potential to significantly contribute to the degradation of organic matter in the deep sea. Our results demonstrate that the community composition on bathypelagic marine snow differs greatly from that in the ambient water leading to wide ecological niche separation between the two environments.

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“…In general, Melosira showed a notable pattern: we exclusively found Melosira OTUs in the rRNA but none in the rDNA libraries, irrespective of the station and ice type. This might be due to a combination of the following factors: (1) DNA concentrations below detection levels (Deangelis & Firestone, 2012), (2) high activity of species with low relative abundances (Baldrian et al, 2012;Angel et al, 2013), (3) fewer gene copy numbers in rDNA libraries and an accompanied underestimation in rDNA libraries due to 'dilution' of the species by high copy number taxa Koid et al, 2012), or (4) methodological biases (Angel et al, 2013) such as the nucleic acid extraction (Kermarrec et al, 2013). Melosira accounts for a high amount of sub-ice biomass (Syvertsen, 1991;Gutt, 1995;Boetius et al, 2013;Fernández-Méndez et al, 2014) and net primary production (Fernández-Méndez et al, 2014), although its occurrence can be very patchy (Gosselin et al, 1997).…”

Section: Phototrophic Community Of Arctic Fyi and Myimentioning

confidence: 99%

rRNA and rDNA based assessment of sea ice protist biodiversity from the central Arctic Ocean

Stecher

Neuhaus

Lange

et al. 2015

European Journal of Phycology

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Sea ice is a large and diverse ecosystem contributing significantly to primary production in ice-covered regions. In the Arctic Ocean, sea ice consists of mixed multi-year ice (MYI), often several metres thick, and thinner first-year ice (FYI). Current global warming is most severe in Arctic regions; as a consequence, summer sea ice cover is decreasing and MYI is disappearing at an alarming rate. Despite its apparent hostility, sea ice is inhabited by a diverse microbial community of bacteria and protists, many of which are photosynthetic. Here we present an assessment of eukaryotic biodiversity in MYI and FYI from the central Arctic Ocean using high-throughput 454 sequencing of 18S rRNA and rDNA amplicons. We compared the rDNA-based 'total' biodiversity with the 'active' biodiversity from rRNA amplicons and found differences between them including an overrepresentation of Ciliophora, Bicosoecida and Bacillariophyceae operational taxonomic units (OTUs) in the active part of the community. Differences between the two libraries are more pronounced at the lower taxonomic level: certain genera, such as Melosira, are more abundant in the rRNA library, indicating activity of these genera. Furthermore, we found that one FYI station showed a higher activity of potential grazers which was probably due to the advanced stage of melt evident by higher ice temperatures and highly porous ice compared with the other stations.

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Comparative Analysis of Eukaryotic Marine Microbial Assemblages from 18S rRNA Gene and Gene Transcript Clone Libraries by Using Different Methods of Extraction

Cited by 41 publications

References 46 publications

Integrated metagenomic and metaproteomic analyses of marine biofilm communities

Integrated metagenomic and metaproteomic analyses of marine biofilm communities

Eukaryotic microbes, principally fungi and labyrinthulomycetes, dominate biomass on bathypelagic marine snow

rRNA and rDNA based assessment of sea ice protist biodiversity from the central Arctic Ocean

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