Deep sequencing uncovers protistan plankton diversity in the Portuguese Ria Formosa solar saltern ponds

Filker, Sabine; Gimmler, Anna; Dunthorn, Micah; Mahé, Frédéric; Stoeck, Thorsten

doi:10.1007/s00792-014-0713-2

Cited by 44 publications

(61 citation statements)

References 81 publications

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“…Extremophile Hartmannellidae amoebozoans have been previously detected in hypersaline ponds (Filker et al. ). The green algae Scenedesmus is commonly observed in wastewater and is currently under study for its potential use in its bioremediation (Durvasula et al.…”

Section: Discussionmentioning

confidence: 99%

Next‐Generation Sequencing Assessment of Eukaryotic Diversity in Oil Sands Tailings Ponds Sediments and Surface Water

Aguilar

Richardson

Tan

et al. 2016

J Eukaryotic Microbiology

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Tailings ponds in the Athabasca oil sands (Canada) contain fluid wastes, generated by the extraction of bitumen from oil sands ores. Although the autochthonous prokaryotic communities have been relatively well characterized, almost nothing is known about microbial eukaryotes living in the anoxic soft sediments of tailings ponds or in the thin oxic layer of water that covers them. We carried out the first next-generation sequencing study of microbial eukaryotic diversity in oil sands tailings ponds. In metagenomes prepared from tailings sediment and surface water, we detected very low numbers of sequences encoding eukaryotic small subunit ribosomal RNA representing seven major taxonomic groups of protists. We also produced and analysed three amplicon-based 18S rRNA libraries prepared from sediment samples. These revealed a more diverse set of taxa, 169 different OTUs encompassing up to eleven higher order groups of eukaryotes, according to detailed classification using homology searching and phylogenetic methods. The 10 most abundant OTUs accounted for > 90% of the total of reads, vs. large numbers of rare OTUs (< 1% abundance). Despite the anoxic and hydrocarbon-enriched nature of the environment, the tailings ponds harbour complex communities of microbial eukaryotes indicating that these organisms should be taken into account when studying the microbiology of the oil sands.

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Section: Discussionmentioning

confidence: 99%

Next‐Generation Sequencing Assessment of Eukaryotic Diversity in Oil Sands Tailings Ponds Sediments and Surface Water

Aguilar

Richardson

Tan

et al. 2016

J Eukaryotic Microbiology

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“…Some ciliates are also found in such a high salinity environments. Filker et al (2015) reported a negative relationship between salinity (40-380 PSU) and OTU richness that appears to be related with a lower OTU richness in ANtCoast1.…”

Section: Community Structure Of Bipolar Regionsmentioning

confidence: 92%

Patchy-distributed ciliate (Protozoa) diversity of eight polar communities as determined by 454 amplicon pyrosequencing

Jung

Park

Yang

et al. 2015

Animal Cells and Systems

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To determine ciliate diversity and community structure in the polar ecosystem efficiently, we applied the pyrosequencing technique to the polar samples. To select the appropriate sequencing depth using a ciliate-specific primer, we evaluated different pyrosequencing depths, ranging 4149-112,306 reads. At a 3% distance cutoff for clustering, 750 operational taxonomic units (OTUs) were identified, and 332 were composed of a single read (singletons). The singletons showed a 1.8-fold increase in OTU richness, although their beta diversity showed no significant changes. The ratio of singletons in each sequencing depth was sharply decreased after reaching the sequencing depth of approximately 10,000 reads, and the singletons did not completely disappear even at 73,435 qualified reads. The data set without singletons showed saturated trends in rarefaction curves. In addition, we built a normalized data set without the singletons (1227 reads × eight samples). Among the samples, one brackish water having a broad range of salinity (3-23 PSU) at the Arctic coast presented the highest OTU richness (103), while a temporal pool at the Antarctic coast with a high salinity of 53.4 PSU, showed a relatively lower OTUs (8). Each normalized sample showed a distinct community structure. Interestingly, a freshwater lake on King George Island shared relatively higher OTUs with salt-water samples (72.1%), suggesting a higher inter-relationship with closely located coastal water environment.

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“…Since its introduction, Swarm v1 has been used in a variety of datasets Filker et al, 2015;Lima-Mendez et al, 2015;Mahé et al, 2015;Oikonomou et al, 2015). However, since the breaking phase was written in Python, it lacked scalability and was cumbersome to use.…”

Section: Introductionmentioning

confidence: 99%

Swarm v2: highly-scalable and high-resolution amplicon clustering

Mahé

Rognes

Quince

et al. 2015

Preprint

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114

149

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Previously we presented Swarm v1, a novel and open source amplicon clustering program that produced fine-scale molecular operational taxonomic units (OTUs), free of arbitrary global clustering thresholds and input-order dependency. Swarm v1 worked with an initial phase that used iterative single-linkage with a local clustering threshold (d), followed by a phase that used the internal abundance structures of clusters to break chained OTUs. Here we present Swarm v2 that has two important novel features: 1) a new algorithm for d = 1 that allows the computation time of the program to scale linearly with increasing amounts of data; and 2) the new fastidious option that reduces under-grouping by grafting low abundant OTUs (e.g., singletons and doubletons) onto larger ones. Swarm v2 also directly integrates the clustering and breaking phases, dereplicates sequencing reads with d = 0, outputs OTU representatives in fasta format, and plots individual OTUs as two-dimensional networks.

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Deep sequencing uncovers protistan plankton diversity in the Portuguese Ria Formosa solar saltern ponds

Cited by 44 publications

References 81 publications

Next‐Generation Sequencing Assessment of Eukaryotic Diversity in Oil Sands Tailings Ponds Sediments and Surface Water

Next‐Generation Sequencing Assessment of Eukaryotic Diversity in Oil Sands Tailings Ponds Sediments and Surface Water

Patchy-distributed ciliate (Protozoa) diversity of eight polar communities as determined by 454 amplicon pyrosequencing

Swarm v2: highly-scalable and high-resolution amplicon clustering

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