Microbial Diversity in the Eukaryotic SAR Clade: Illuminating the Darkness Between Morphology and Molecular Data

Despite their diversity and ecological importance, many areas of the SAR—Stramenopila, Alveolata, and Rhizaria—clade are poorly understood as the majority (90%) of SAR species lack molecular data and only 5% of species are from well-sampled families. Here, we review and summarize the state of knowledge about the three major clades of SAR, describing the diversity within each clade and identifying synapomorphies when possible. We also assess the “dark area” of SAR: the morphologically described species that are missing molecular data. The majority of molecular data for SAR lineages are characterized from marine samples and vertebrate hosts, highlighting the need for additional research effort in areas such as freshwater and terrestrial habitats and “non-vertebrate” hosts. We also describe the paucity of data on the biogeography of SAR species, and point to opportunities to illuminate diversity in this major eukaryotic clade. See also the video abstract above

Marked seasonality and high spatial variation in estuarine ciliates are driven by exchanges between the ‘abundant’ and ‘intermediate’ biospheres

Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/. The file attached is the Published/publisher’s pdf version of the article

Distinct Assemblage of Planktonic Ciliates Dominates Both Photic and Deep Waters on the New England Shelf

Microbes are critical members of marine ecosystems, given their roles as both primary producers and consumers in food webs. Despite their importance, data on biogeographical patterns of microbial eukaryotes are limited. Past studies have generally targeted either all eukaryotes or broad clades like Rhizaria and Alveolata. For this study, we focus more narrowly on oligotrich and choreotrich ciliates (both members of the class Spirotrichea) as these lineages play major roles in marine food webs. We assess distribution patterns of abundant ciliate community members along a 163 km transect off the coast of New England, USA. Over 3 d, we sampled ciliates at 23 stations from shallow waters (depth) to beyond the continental shelf (\u3e800 m). We used a community DNA finger-printing technique, denaturing gradient gel electrophoresis (DGGE), to assess patterns for abundant community members and found 2 overlapping assemblages of ciliates: one common in samples from inshore to offshore (up to 180 km from the coast) and from the surface to 850 m deep; and a second that is generally restricted to offshore waters. The distributions of these 2 assemblages correspond with distance from the coast but not with the environmental factors that we measured, including depth, temperature, degree of stratification, phytoplankton fluorescence and accessory pigment composition (a proxy for phytoplankton composition). The presence of these ciliate assemblages as deep as 850 m suggests they may have a broader impact on marine food webs than just photic zone herbivory

Distribution and Diversity of Oligotrich and Choreotrich Ciliates Assessed by Morphology and DGGE in Temperate Coastal Waters

We assessed the diversity of coastal planktonic ciliates (Oligotrichia and Cho reotrichia, Class: Spirotrichea) in Fishers Island Sound off the coast of Connecticut, USA using a combination of denaturant gradient gel electrophoresis (DGGE) and morphological analyses. To test the hypothesis that ciliate communities followed water masses, we sampled 3 times at a surface drifter (i.e. floating buoy) and twice at intervening times from points 1 km away. By repeating both PCRs and gel electrophoresis under varying conditions, we confirmed that DGGE is an appropriate tool to capture the ciliate community composition, based on the high repeatability of samples. The 2 methods used for assessing ciliate community structure showed similar levels of diversity for tintinnids. However, there was a mismatch in diversity estimates for the aloricate ciliates, especially for the oligotrichs where the estimated diversity was greater by DGGE than by microscopy. This may be attributable to biases in the DGGE (e.g. primer or gene copy number issues) and/or misidentification by morphology. However, the pattern of community structure assessed by cluster analyses is similar for both microscopy and DGGE, suggesting that the mismatch between these methods does not introduce bias in biogeographical analysis. Analyses of both DGGE haplotypes and microscopically observed morphospecies revealed that the ciliate communities were not static within the water mass. Community structure and abundance patterns varied with salinity and currents. These changes could be due to mixing with adjacent estuarine and coastal assemblages, ciliate behavior, and/or other factors that cause assemblages to be dynamic over short (i.e. ultradian) periods

Lack-of P-limitation of phytoplankton and heterotrophic prokaryotes in surface waters of three anticyclonic eddies in the stratified Mediterranean Sea

International audienceWe investigated the identity of the limiting nutrient of the pelagic microbial food web in the Mediter-ranean Sea using nutrient manipulated microcosms during summer 2008. Experiments were carried out with surface waters at the center of anticyclonic eddies in the Western Basin, the Ionian Basin, and the Levantine Basin. In situ, the ratio of N to P was always higher in both dissolved and particulate organic fractions compared to the Redfield ratio , suggesting a relative P-starvation. In each experiment, four different treatments in triplicates (addition of ammo-nium, phosphate, a combination of both, and the unamended control) were employed and chemical and biological parameters monitored throughout a 3-4 day incubation. Temporal changes of turnover time of phosphate and ATP, and alkaline phosphatase activity during the incubation suggested that the phytoplankton and heterotrophic prokaryotes (Hprok) communities were not P-limited at the sites. Furthermore, Correspondence to: T. Tanaka ([email protected]) statistical comparison among treatments at the end of the incubation did not support a hypothesis of P-limitation at the three study sites. In contrast, primary production was consistently limited by N, and Hprok growth was not limited by N nor P in the Western Basin, but N-limited in the Ionian Basin, and N and P co-limited in the Levantine Basin. Our results demonstrated the gap between biogeochemical features (an apparent P-starved status) and biological responses (no apparent P-limitation). We question the general notion that Mediterranean surface waters are limited by P alone during the stratified period

N-limited or N and P co-limited indications in the surface waters of three Mediterranean basins

International audienceThe limiting nutrient for the pelagic microbial food web in the Mediterranean Sea was investigated in the nutrient manipulated microcosms during summer 2008. Surface waters were collected into 12 carboys at a center of anticyclonic eddy at the Western Basin, the Ionian Basin, and the Levantine Basin, respectively. As compared to the Redfield ratio, the ratio of N to P in the collected waters was always smaller in the dissolved inorganic fraction but higher in both dissolved and particulate organic fractions. Four different treatments in triplicates (addition of ammonium, phosphate, a combination of both, and the unamended control) were set up for the carboys. Responses of chemical and biological parameters in these different treatments were measured during the incubation (3-4 days). Temporal changes of turnover time of phosphate and ATP, and alkaline phosphatase activity during the incubation suggested that the phytoplankton and heterotrophic prokaryotes (Hprok) communities were not purely P-limited at any studied stations. Statistical comparison between the treatments for a given parameter measured at the end of the incubation did not find pure P-limitation in any chemical and biological parameters at three study sites. Primary production was consistently limited by N, and Hprok growth was not limited by N nor P in the Western Basin, but N-limited in the Ionian Basin, and N and P co-limited in the Levantine Basin. Our results demonstrated the gap between biogeochemical features and biological responses in terms of the limiting nutrient. We question the general notion that Mediterranean surface waters are limited by P alone during the stratified period

Microbial food webs and metabolic state across oligotrophic waters of the Mediterranean Sea during summer

The abundance and activity of the major members of the heterotrophic microbial community – from viruses to ciliates – were studied along a longitudinal transect across the Mediterranean Sea in the summer of 2008. The Mediterranean Sea is characterized by a west to-east gradient of deepening of DCM (deep chlorophyll maximum) and increasing oligotrophy reflected in gradients of biomass and production. However, within this well documented longitudinal trend, hydrological mesoscale features exist and likely influence microbial dynamics. Here we present data from a W-E transect of 17 stations during the period of summer stratification. Along the transect the production and fate of organic matter was investigated at three selected sites each one located in the centre of an anticyclonic eddy: in the Algero-Provencal Basin (St. A), the Ionian Basin (St. B), and the Levantine Basin (St. C). The 3 geographically distant eddies showed low values of the different heterotrophic compartments of the microbial food web, and except for viruses in site C, all integrated (0–150 m) stocks were higher in reference stations located in the same basin outside the eddies. During our study the 3 eddies showed equilibrium between GPP (Gross Primary Production) and DCR (Dark Community Respiration). Integrated PPp (Particulate Primary Production) values at A, B and C varied from ~140 to ~190 mg C m<sup>−2</sup>

Using APASS and 2GSS for studying variable stars

The AAVSO Photometric All-Sky Survey (APASS) provides calibrated magnitudes in the range 7 < V < 17 for the entire sky, in the BVugriZsY bandpasses. While primarily designed for 0.02 mag calibration, it provides photometry over a many-year baseline, and also has near daily cadence in the standard field regions on the equator. Likewise, the Second Generation Synoptic Survey (2GSS) is a follow-on to APASS, and will provide daily cadence in two passbands for the entire sky