Seasonal analysis of protistan community structure and diversity at the USC Microbial Observatory (San Pedro Channel, North Pacific Ocean)

Abstract

The structure and genetic diversity of marine protistan assemblages were investigated in the upper 500 m of the water column at a Pacific Ocean time-series station off the coast of Southern California. Deoxyribonucleic acid sequence-based microbial eukaryote diversity was examined in January, April, July, and October of 2001 at four depths (5 m, chlorophyll maximum [CM], 150 m, and 500 m). A total of 2956 partial 18S ribosomal ribonucleic acid gene sequences yielded representatives from most of the major eukaryotic lineages. Notable among the taxonomic groups were recently described lineages of stramenopiles, alveolates, and euglenozoa. A large number of polycystine and acantharean sequences were observed at depth. Pairwise sequence analysis was performed to establish operational taxonomic units (OTUs) that were then used to estimate the unsampled protistan diversity by parametric and nonparametric techniques. A total of 2246 protistan sequences grouped into 377 distinct OTUs, with remaining sequences attributed to metazoa. Protistan richness estimates ranged from , 600 to 1500 OTUs when all depths and seasons were combined into a single data set. Seasonal and depth-related trends in the observed protistan diversity were apparent from comparisons of univariate and multivariate analyses. Cluster analysis combined with nonmetric multidimensional scaling and analysis of similarity testing identified distinct protistan assemblages at the shallowest depths (5 m and CM) for each season, which were significantly different (p , 0.03) from assemblages at the two deepest depths (150 and 500 m) where seasonal changes in the protistan assemblage were not apparent.

The metatranscriptome of a deep-sea hydrothermal plume is dominated by water column methanotrophs and lithotrophs

“…Archaeal OTUs that dominated the metatranscriptome were MGI and II archaea (Figure 1). Abundant eukaryotic OTUs were most similar to a variety of groups, including Copepoda, Ciliophora, Cnidaria and Amoebozoa ( Figure 1), which are common in marine environments (Caron et al, 2009;Countway et al, 2010;Sauvadet et al, 2010). Many eukaryotic SSU rRNA transcripts displayed sequence similarities below 95% ID to reference sequences, suggesting an abundance of novel microbial eukaroyotes.…”

Small-scale temporal and spatial variations in protistan community composition at the San Pedro Ocean Time-series station off the coast of southern California

“…A wide diversity of taxa was observed among the less common OTUs in the present study (not included in Tables S1 & S2). Previous studies using cloning and sequencing for the identification of components of the protistan community at the SPOT station have revealed a large number of alveolates and stramenopiles as well as a number of chlorophytes and haptophytes in surface waters (Countway et al 2010, Schnetzer et al 2011. D. Y.…”

“…One is the San Pedro Ocean Timeseries (SPOT) station, where protistan communities have been collected since 2000 as a component of the University of Southern California (USC) Microbial Observatory project (2000 to 2012) and the Dimensions of Biodiversity program (2012 to present). This extensive collection of data has provided insights into the monthly-to-interannual changes in protistan community composition as well as the vertical structure of this assemblage (Countway et al 2010, Schnetzer et al 2011, Steele et al 2011.…”

“…Chlorophyll samples were extracted in 7 ml of 100% acetone for 24 h and analyzed on a TD-700 fluorometer (Turner Designs) before and after acidification (Strickland & Parsons 1972). Samples for DNA analysis were prefiltered through 80 µm mesh by gravity to remove most metazoa, in accordance with other protistan DNA samples collected and processed from the SPOT station (Countway et al 2010, Schnetzer et al 2011. Prefiltered water (2 l) was then filtered onto a GF/F filter (47 mm, Whatman) by vacuum filtration (<10 mm Hg).…”

Temporal variability and coherence of euphotic zone bacterial communities over a decade in the Southern California Bight

“…Prior research at the San Pedro Ocean Time-series (SPOT) has focused on determining the temporal variability of bacterial, archaeal and protistan taxa and the development of ecological networks that link these communities (Countway and Caron, 2006;Fuhrman et al, 2006;Beman et al, 2010;Countway et al, 2010;Beman et al, 2011;Steele et al, 2011). Here, we assessed inter-annual, seasonal and monthly variability and resilience of bacterial communities in the surface water and deep chlorophyll maximum (DCM), as revealed by Automated Ribosomal Intergenic Spacer Analysis (ARISA), over a full decade.…”