Protistan microbial observatory in the Cariaco Basin, Caribbean. II. Habitat specialization

Orsi, William D.; Edgcomb, Virginia P.; Jeon, Sunok; Leslin, Chesley; Bunge, John; Taylor, Gordon T.; Varela, Ramón; Epstein, Slava S.

doi:10.1038/ismej.2011.7

Cited by 76 publications

(133 citation statements)

References 81 publications

(136 reference statements)

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“…Nevertheless, there are, as yet, no universally accepted guidelines to this cut-off value, which ranges from 90 to 99 % (e.g. Stoeck et al 2007;Caron et al 2009;Marande et al 2009;Schnetzer et al 2011;Edgcomb et al 2011;Orsi et al 2011). In our study, we used a modified approach with a highly stringent clustering cut-off value of 99 %.…”

Section: Cut-off Values and Data Analysismentioning

confidence: 99%

“…Caron et al 2009). Indeed, previous studies have explored different cut-off levels ranging from 90 to 100 % (Stoeck et al 2007;Edgcomb et al 2011;Orsi et al 2011;Hadziavdic et al 2014), which is necessary for any new primer set used to amplify a fragment of the 18S rRNA gene. However, to our knowledge, this is the first study using the hierarchical rank approach with environmental DNA data.…”

Section: Cut-off Values and Data Analysismentioning

confidence: 99%

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The influence of vent systems on pelagic eukaryotic micro-organism composition in the Nordic Seas

et al. 2014

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Deep-sea hydrothermal vents and cold seeps are biological hot spots with chemolithotrophic bacterial production sustaining both benthic and pelagic organisms. Although efforts have been made to understand the diversity and function of the bacterial composition of these systems, first-level consumers, pelagic single cell heterotrophic organisms, which represent an important link between bacterial production and higher trophic levels, remain un-described in hydrothermal vents and seeps of the Nordic Seas. Here, we used a molecular biodiversity assay to investigate the impact of water masses and hydrothermal vents on the eukaryotic micro-organisms surrounding two vents systems, Jan Mayen Vent Field and Loki's Castle, and one cold seep, Håkon Mosby Mud Volcano. The assay generated a total of 482 operational taxonomic units (OTUs) based on a 99 % cut-off value, and the OTUs were grouped according to taxonomic rank. Data analysis using hierarchical clustering and non-metric multidimensional scaling with class as taxonomic entries suggested that water masses followed by depth was the dominant effect on eukaryotic micro-organism diversity. However, in one of the vent systems, Loki's Castle, the community was different compared to the reference station. Our data suggest that while the total production of vent systems is higher than the surrounding waters, the biodiversity of eukaryotic micro-organisms is more influenced by both water masses and depth.

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Section: Cut-off Values and Data Analysismentioning

confidence: 99%

Section: Cut-off Values and Data Analysismentioning

confidence: 99%

The influence of vent systems on pelagic eukaryotic micro-organism composition in the Nordic Seas

et al. 2014

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“…For example, vertically-migrating crustacean, zooplankton, chaetognaths and even fish can seek temporary refuge from predation in low-oxygen regions of OMZs (Wishner et al, 1998(Wishner et al, , 2013Escribano et al, 2009). In addition, diverse communities of phagotrophic and parasitic protists are described from oxygen-depleted and anoxic water columns, many of which exhibit complex relationships with prokaryotes (Lin et al, 2007;Edgcomb et al, 2011;Orsi et al, 2011Orsi et al, , 2012Wright et al, 2012).…”

Section: Introductionmentioning

confidence: 99%

A Review of Protist Grazing Below the Photic Zone Emphasizing Studies of Oxygen-Depleted Water Columns and Recent Applications of In situ Approaches

et al. 2017

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Little is still known of the impacts of protist grazing on bacterioplankton communities in the dark ocean. Furthermore, the accuracy of assessments of in situ microbial activities, including protist grazing, can be affected by sampling artifacts introduced during sample retrieval and downstream manipulations. Potential artifacts may be increased when working with deep-sea samples or samples from chemically unique water columns such as oxygen minimum zones (OMZs). OMZs are oxygen-depleted regions in the ocean, where oxygen concentrations can drop to <20 µM. These regions are typically located near eastern boundary upwelling systems and currently occur in waters occupying below about 8% of total ocean surface area, representing ∼1% of the ocean's volume. OMZs have a profound impact not only on the distribution of marine Metazoa, but also on the composition and activities of microbial communities at the base of marine food webs. Here we present an overview of current knowledge of protist phagotrophy below the photic zone, emphasizing studies of oxygen-depleted waters and presenting results of the first attempt to implement new technology for conducting these incubation studies completely in situ (the Microbial Sampling-Submersible Incubation Device, MS-SID). We performed 24-h incubation experiments in the Eastern Tropical South Pacific (ETSP) OMZ. This preliminary study shows that up to 28% of bacterial biomass may be consumed by protists in waters where oxygen concentrations were down to ∼4.8 µM and up to 13% at a station with nitrite accumulation where oxygen concentrations were undetectable. Results also show that shipboard measurements of grazing rates were lower than rates measured from the same water using the MS-SID, suggesting that in situ experiments help to minimize artifacts that may be introduced when conducting incubation studies using waters collected from below the photic zone, particularly from oxygen-depleted regions of the water column.

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“…MAST groups were not monophyletic, but formed independent lineages among basal heterotrophic stramenopiles. Twelve MAST groups were first defined (Massana et al, 2004), and seven more were proposed later (Zuendorf et al, 2006;Orsi et al, 2011). Also, a parallel classification was proposed soon after the first study (Richards and Bass, 2005).…”

Section: Introductionmentioning

confidence: 99%

Exploring the uncultured microeukaryote majority in the oceans: reevaluation of ribogroups within stramenopiles

Massana¹,

Campo²,

Sieracki³

et al. 2013

The ISME Journal

158

175

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Molecular surveys in planktonic marine systems have unveiled a large novel diversity of small protists. A large part of this diversity belongs to basal heterotrophic stramenopiles and is distributed in a set of polyphyletic ribogroups (described from rDNA sequences) collectively named as MAST (MArine STramenopiles). In the few groups investigated, MAST cells are globally distributed and abundant bacterial grazers, therefore having a putatively large impact on marine ecosystem functioning. The main aim of this study is to reevaluate the MAST ribogroups described so far and to determine whether additional groups can be found. For this purpose, we used traditional and state-of-the-art molecular tools, combining 18S rDNA sequences from publicly available clone libraries, single amplified genomes (SAGs) of planktonic protists, and a pyrosequencing survey from coastal waters and sediments. Our analysis indicated a final set of 18 MAST groups plus 5 new ribogroups within Ochrophyta (named as MOCH). The MAST ribogroups were then analyzed in more detail. Seven were typical of anoxic systems and one of oxic sediments. The rest were clearly members of oxic marine picoplankton. We characterized the genetic diversity within each MAST group and defined subclades for the more diverse (46 subclades in 8 groups). The analyses of sequences within subclades revealed further ecological specializations. Our data provide a renovated framework for phylogenetic classification of the numerous MAST ribogroups and support the notion of a tight link between phylogeny and ecological distribution. These diverse and largely uncultured protists are widespread and ecologically relevant members of marine microbial assemblages.

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Protistan microbial observatory in the Cariaco Basin, Caribbean. II. Habitat specialization

Cited by 76 publications

References 81 publications

The influence of vent systems on pelagic eukaryotic micro-organism composition in the Nordic Seas

The influence of vent systems on pelagic eukaryotic micro-organism composition in the Nordic Seas

A Review of Protist Grazing Below the Photic Zone Emphasizing Studies of Oxygen-Depleted Water Columns and Recent Applications of In situ Approaches

Exploring the uncultured microeukaryote majority in the oceans: reevaluation of ribogroups within stramenopiles

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