Dataset Information

Temporal dynamics of eukaryotic microbial diversity at a coastal Pacific site.

ABSTRACT: High-throughput sequencing of ocean biomes has revealed vast eukaryotic microbial diversity, a significant proportion of which remains uncharacterized. Here we use a temporal approach to understanding eukaryotic diversity at the Scripps Pier, La Jolla, California, USA, via high-throughput amplicon sequencing of the 18S rRNA gene, the abundances of both Synechococcus and Synechococcus grazers, and traditional oceanographic parameters. We also exploit our ability to track operational taxonomic units (OTUs) temporally to evaluate the ability of 18S sequence-based OTU assignments to meaningfully reflect ecological dynamics. The eukaryotic community is highly dynamic in terms of both species richness and composition, although proportional representation of higher-order taxa remains fairly consistent over time. Synechococcus abundance fluctuates throughout the year. OTUs unique to dates of Synechococcus blooms and crashes or enriched in Synechococcus addition incubation experiments suggest that the prasinophyte Tetraselmis sp. and Gymnodinium-like dinoflagellates are likely Synechococcus grazers under certain conditions, and may play an important role in their population fluctuations.

SUBMITTER: Nagarkar M

PROVIDER: S-EPMC6092440 | biostudies-literature | 2018 Sep

REPOSITORIES: biostudies-literature

ACCESS DATA

Publications

Temporal dynamics of eukaryotic microbial diversity at a coastal Pacific site.

Nagarkar Maitreyi M Countway Peter D PD Du Yoo Yeong Y Daniels Emy E Poulton Nicole J NJ Palenik Brian B

The ISME journal 20180613 9

High-throughput sequencing of ocean biomes has revealed vast eukaryotic microbial diversity, a significant proportion of which remains uncharacterized. Here we use a temporal approach to understanding eukaryotic diversity at the Scripps Pier, La Jolla, California, USA, via high-throughput amplicon sequencing of the 18S rRNA gene, the abundances of both Synechococcus and Synechococcus grazers, and traditional oceanographic parameters. We also exploit our ability to track operational taxonomic uni ...[more]

PMID: 29899506

Similar Datasets

Project description:BACKGROUND: Migrations allow animals to find food resources, rearing habitats, or mates, but often impose considerable predation risk. Several behavioural strategies may reduce this risk, including faster travel speed and taking routes with shorter total distance. Descriptions of the natural range of variation in migration strategies among individuals and populations is necessary before the ecological consequences of such variation can be established. METHODOLOGY/PRINCIPAL FINDINGS: Movements of tagged juvenile coho, steelhead, sockeye, and Chinook salmon were quantified using a large-scale acoustic tracking array in southern British Columbia, Canada. Smolts from 13 watersheds (49 watershed/species/year combinations) were tagged between 2004-2008 and combined into a mixed-effects model analysis of travel speed. During the downstream migration, steelhead were slower on average than other species, possibly related to freshwater residualization. During the migration through the Strait of Georgia, coho were slower than steelhead and sockeye, likely related to some degree of inshore summer residency. Hatchery-reared smolts were slower than wild smolts during the downstream migration, but after ocean entry, average speeds were similar. In small rivers, downstream travel speed increased with body length, but in the larger Fraser River and during the coastal migration, average speed was independent of body length. Smolts leaving rivers located towards the northern end of the Strait of Georgia ecosystem migrated strictly northwards after ocean entry, but those from rivers towards the southern end displayed split-route migration patterns within populations, with some moving southward. CONCLUSIONS/SIGNIFICANCE: Our results reveal a tremendous diversity of behavioural migration strategies used by juvenile salmon, across species, rearing histories, and habitats, as well as within individual populations. During the downstream migration, factors that had strong effects on travel speeds included species, wild or hatchery-rearing history, watershed size and, in smaller rivers, body length. During the coastal migration, travel speeds were only strongly affected by species differences.

Project description:How microbial communities change over time in response to the environment is poorly understood. Previously a six-year time series of 16S rRNA V6 data from the Western English Channel demonstrated robust seasonal structure within the bacterial community, with diversity negatively correlated with day-length. Here we determine whether metagenomes and metatranscriptomes follow similar patterns. We generated 16S rRNA datasets, metagenomes (1.2 GB) and metatranscriptomes (157 MB) for eight additional time points sampled in 2008, representing three seasons (Winter, Spring, Summer) and including day and night samples. This is the first microbial 'multi-omic' study to combine 16S rRNA amplicon sequencing with metagenomic and metatranscriptomic profiling. Five main conclusions can be drawn from analysis of these data: 1) Archaea follow the same seasonal patterns as Bacteria, but show lower relative diversity; 2) Higher 16S rRNA diversity also reflects a higher diversity of transcripts; 3) Diversity is highest in winter and at night; 4) Community-level changes in 16S-based diversity and metagenomic profiles are better explained by seasonal patterns (with samples closest in time being most similar), while metatranscriptomic profiles are better explained by diel patterns and shifts in particular categories (i.e., functional groups) of genes; 5) Changes in key genes occur among seasons and between day and night (i.e., photosynthesis); but these samples contain large numbers of orphan genes without known homologues and it is these unknown gene sets that appear to contribute most towards defining the differences observed between times. Despite the huge diversity of these microbial communities, there are clear signs of predictable patterns and detectable stability over time. Renewed and intensified efforts are required to reveal fundamental deterministic patterns in the most complex microbial communities. Further, the presence of a substantial proportion of orphan sequences underscores the need to determine the gene products of sequences with currently unknown function.

Dataset Information

Temporal dynamics of eukaryotic microbial diversity at a coastal Pacific site.

Publications

Temporal dynamics of eukaryotic microbial diversity at a coastal Pacific site.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets