Barry F. Sherr

Significance of predation by protists in aquatic microbial food webs.

Predation in aquatic microbial food webs is dominated by phagotrophic protists, yet these microorganisms are still understudied compared to bacteria and phytoplankton. In pelagic ecosystems, predaceous protists are ubiquitous, range in size from 2 μm flagellates to >100 μm ciliates and dinoflagellates, and exhibit a wide array of feeding strategies. Their trophic states run the gamut from strictly phagotrophic, to mixotrophic: partly autotrophic and partly phagotrophic, to primarily autotrophic but capable of phagotrophy. Protists are a major source of mortality for both heterotrophic and autotrophic bacteria. They compete with herbivorous meso- and macro-zooplankton for all size classes of phytoplankton. Protist grazing may affect the rate of organic sinking flux from the euphotic zone. Protist excretions are an important source of remineralized nutrients, and of colloidal and dissolved trace metals such as iron, in aquatic systems. Work on predation by protists is being facilitated by methodological advances, e.g., molecular genetic analysis of protistan diversity and application of flow cytometry to study population growth and feeding rates. Examples of new research areas are studies of impact of protistan predation on the community structure of prey assemblages and of chemical communication between predator and prey in microbial food webs.

High bacterial production, uptake and concentrations of dissolved organic matter in the Central Arctic Ocean

Recent studies have indicated that biological activity is higher in the central Arctic Ocean than once thought. To assess the contribution of heterotrophic processes, we examined bacterial production and the uptake of specific components of the dissolved organic matter (DOM) pool during a trans-Arctic expedition. Bacterial production generally covaried with phytoplankton production and bacterial numbers; the highest values of all three parameters were in the more open waters of the Chukchi Sea and they were generally lower at the other stations which were covered by ice. Although bacterial production correlated with phytoplankton production, the ratio of bacterial to phytoplankton production (BP:PP) varied substantially. It was lowest (BP:PP<0.1) at stations with some open water and highest at ice-covered stations, sometimes exceeding 1, depending on how bacterial production was measured. These high BP:PP ratios imply that bacterial respiration and DOM fluxes are large. This bacterial activity could be accounted for by the uptake of dissolved free amino acids (DFAA) and glucose. Uptake of these DOM components was high because of rapid turnover and high concentrations, especially of DFAA. Concentrations of dissolved combined neutral carbohydrates (e.g. polysaccharides) were often also high compared to other environments. These data indicate that heterotrophic bacteria and the rest of the microbial loop are large and active components of the biological community in the Arctic Ocean in spite of perennially low temperatures.

Temporal and spatial variation in stocks of autotrophic and heterotrophic microbes in the upper water column of the central Arctic Ocean

Abstract As part of the SHEBA/JOIS drift experiment, we continually analysed abundance and biomass of autotrophic and heterotrophic microbes in the upper 120xa0m of the water column of the ice-covered Central Arctic Ocean from November 1997 through August 1998. Microbial biomass was concentrated in the upper 60xa0m of the water column. There were low but persistent stocks of heterotrophic and autotrophic microbes during the winter months. Phytoplankton biomass began increasing when winter snow melted from the ice-pack in early June, after which there was a progressive decline of nitrate and silicate in the euphotic zone. We observed three distinct blooms over the summer. The initial bloom consisted of diatoms and phytoflagellates, mainly 2xa0μm-sized Micromonas sp.; the two subsequent blooms were dominated by the flagellated (non-colonial) Phaeocystis sp. The carbon:chlorophyll ratio of the phytoplankton was 31±11. Stocks of bacteria and heterotrophic protists approximately doubled during the growing season, increasing in tandem with increase in phytoplankton biomass. Increase in cell abundances of bacteria and of the phytoflagellate Micromonas over 40–50xa0d periods during the initial bloom period yielded estimates of realised growth rate of 0.025xa0d −1 for bacteria and of 0.11xa0d −1 for Micromonas . Heterotrophic protists included flagellates, ciliates, and dinoflagellates, with biomass divided nearly evenly between nanoplankton (Hnano, 0–20xa0μm) and microplankton (Hmicro, 20–200xa0μm) size classes.

Heterotrophic protists in the Central Arctic Ocean

Distribution, general composition and activity of heterotrophic protists, as well as the distribution of bacteria, were assessed in the upper water column of the central Arctic Ocean during the Arctic Ocean Section, July–September 1994. Bacterial biomass varied from 5 to > 25 mg C 1−1, with the highest values occurring in the Chukchi Sea. Protist biomass was highest (5–107 mg Cl−1) in the upper 50 m of the water column. Higher integrated (0–50 m) protist biomass values (average 910±250 mg C m−2, range 580–1370 mg C m−2) were found in the Chukchi Sea, compared to the central Arctic Ocean (average 480±320 mg C m−2, range 120–1120 mg C m−2). Heterotrophic dinoflagellates were more abundant than ciliates in the >20 μm size class at all stations. In the central Arctic Ocean, the <20 μm size class was numerically composed of dinoflagellates (16%), choanoflagellates (4%) and other flagellates (80%). Choanoflagellates were slightly more abundant in the Chukchi Sea (9% of cell numbers), but were a large component of the flagellate assemblage (55% of cell numbers) at only one station, in the Nansen Basin. Bacterivory estimated via uptake of added fluorescently labeled bacteria ranged from 1·2 × 103 to 46 × 103 bacteria ml−1 day−1; the highest rate was found at the station with a high choanoflagellate abundance. Observation of food vacuole contents showed that all size classes and taxonomic types of protists ingested phytoplankton. Choanoflagellates, and monads as small as 1·5 μm in size, ingested picoplanktonic eukaryotic phytoplankton, which were abundant (103−104 cells ml−1) in the upper 50 m. Larger protists ingested cryptomonads and diatoms, as well as pico-autotrophs. Clearance rates of 10–100 μm sized ciliates and dinoflagellates, based on the uptake of 1–5 μm fluorescent microspheres, were similar to rates reported for herbivorous protists in temperate waters. In terms of ecosystem carbon flow, we infer that phagotrophic protists in the Arctic Ocean are important consumers of phytoplankton and bacteria, and may represent a significant food resource for zooplankton.

Activity and Phylogenetic Diversity of Bacterial Cells with High and Low Nucleic Acid Content and Electron Transport System Activity in an Upwelling Ecosystem

ABSTRACT We evaluated whether bacteria with higher cell-specific nucleic acid content (HNA) or an active electron transport system, i.e., positive for reduction of 5-cyano-2,3-ditolyl tetrazolium chloride (CTC), were responsible for the bulk of bacterioplankton metabolic activity. We also examined whether the phylogenetic diversity of HNA and CTC-positive cells differed from the diversity of Bacteria with low nucleic acid content (LNA). Bacterial assemblages were sampled both in eutrophic shelf waters and in mesotrophic offshore waters in the Oregon coastal upwelling region. Cytometrically sorted HNA, LNA, and CTC-positive cells were assayed for their cell-specific [3H]leucine incorporation rates. Phylogenetic diversity in sorted non-radioactively labeled samples was assayed using denaturing gradient gel electrophoresis (DGGE) of PCR-amplified 16S rRNA genes. Cell-specific rates of leucine incorporation of HNA and CTC-positive cells were on average only slightly greater than the cell-specific rates of LNA cells. HNA cells accounted for most bacterioplankton substrate incorporation due to high abundances, while the low abundances of CTC-positive cells resulted in only a small contribution by these cells to total bacterial activity. The proportion of the total bacterial leucine incorporation attributable to LNA cells was higher in offshore regions than in shelf waters. Sequence data obtained from DGGE bands showed broadly similar phylogenetic diversity across HNA, LNA, and CTC-positive cells, with between-sample and between-region variability in the distribution of phylotypes. Our results suggest that LNA bacteria are not substantially different from HNA bacteria in either cell-specific rates of substrate incorporation or phylogenetic composition and that they can be significant contributors to bacterial metabolism in the sea.

Community respiration/production and bacterial activity in the upper water column of the central Arctic Ocean

Community metabolism (respiration and production) and bacterial activity were assessed in the upper water column of the central Arctic Ocean during the SHEBA/JOIS ice camp experiment, October 1997–September 1998. In the upper 50 m, decrease in integrated dissolved oxygen (DO) stocks over a period of 124 d in mid-winter suggested a respiration rate of B3.3 nM O2 h � 1 and a carbon demand of B4.5 gC m � 2 . Increase in 0–50 m integrated stocks of DO during summer implied a net community production of B20 gC m � 2 . Community respiration rates were directly measured via rate of decrease in DO in whole seawater during 72-h dark incubation experiments. Incubation-based respiration rates were on average 3-fold lower during winter (11.0710.6 nM O2 h � 1 ) compared to summer (35.3724.8 nM O2 h � 1 ). Bacterial heterotrophic activity responded strongly, without noticeable lag, to phytoplankton growth. Rate of leucine incorporation by bacteria (a proxy for protein synthesis and cell growth) increased B10-fold, and the cell-specific rate of leucine incorporation B5-fold, from winter to summer. Rates of production of bacterial biomass in the upper 50 m were, however, low compared to other oceanic regions, averaging 0.5270.47 ngC l � 1 h � 1 during winter and 5.173.1 ngC l � 1 h � 1 during summer. Total carbon demand based on respiration experiments averaged 2.472.3 mgC m � 3 d � 1 in winter and 7.875.5 mgC m � 3 d � 1 in summer. Estimated bacterial carbon demand based on bacterial productivity and an assumed 10% gross growth efficiency was much lower, averaging about 0.1270.12 mgC m � 3 d � 1 in winter and 1.370.7 mgC m � 3 d � 1 in summer. Our estimates of bacterial activity during summer were an order of magnitude less than rates reported from a summer 1994 study in the central Arctic Ocean, implying significant inter-annual variability of microbial processes in this region. r 2003 Elsevier Science Ltd. All rights reserved.

Investigating Microbial Eukaryotic Diversity from a Global Census: Insights from a Comparison of Pyrotag and Full-Length Sequences of 18S rRNA Genes

ABSTRACT Next-generation DNA sequencing (NGS) approaches are rapidly surpassing Sanger sequencing for characterizing the diversity of natural microbial communities. Despite this rapid transition, few comparisons exist between Sanger sequences and the generally much shorter reads of NGS. Operational taxonomic units (OTUs) derived from full-length (Sanger sequencing) and pyrotag (454 sequencing of the V9 hypervariable region) sequences of 18S rRNA genes from 10 global samples were analyzed in order to compare the resulting protistan community structures and species richness. Pyrotag OTUs called at 98% sequence similarity yielded numbers of OTUs that were similar overall to those for full-length sequences when the latter were called at 97% similarity. Singleton OTUs strongly influenced estimates of species richness but not the higher-level taxonomic composition of the community. The pyrotag and full-length sequence data sets had slightly different taxonomic compositions of rhizarians, stramenopiles, cryptophytes, and haptophytes, but the two data sets had similarly high compositions of alveolates. Pyrotag-based OTUs were often derived from sequences that mapped to multiple full-length OTUs at 100% similarity. Thus, pyrotags sequenced from a single hypervariable region might not be appropriate for establishing protistan species-level OTUs. However, nonmetric multidimensional scaling plots constructed with the two data sets yielded similar clusters, indicating that beta diversity analysis results were similar for the Sanger and NGS sequences. Short pyrotag sequences can provide holistic assessments of protistan communities, although care must be taken in interpreting the results. The longer reads (>500 bp) that are now becoming available through NGS should provide powerful tools for assessing the diversity of microbial eukaryotic assemblages.

Composition and biomass of plankton in spring on the Cape Hatteras shelf, with implications for carbon flux

Abstract The Ocean Margins Program, an interdisciplinary study focussed at Cape Hatteras, is evaluating whether this region is a net source or sink for carbon, while concurrently developing a mechanistic understanding of the production, cycling and fate of organic carbon. Preliminary to a large multi-ship field program in 1996–1997, the first of several short cruises surveyed Cape Hatteras in May 1993. High concentrations of chl a occurred across the shelf. Stations and depths at which chl a was highest also showed elevated concentrations of large phytoplankton, predominantly chained diatoms, but also single-celled dinoflagellates and obligately photosynthetic ciliates. These populations occurred in deeper waters, however, and their abundance was poorly correlated with proxies of community photosynthesis. Instead, small phototrophic nanoplankton, abundant in surface waters, were positively correlated with primary production. Carbon budgets indicated that inner shelf waters contained ca 50% more living POC than outer shelf waters. The relative importance of large phytoplankton and grazers decreased with distance offshore, and they were replaced by photosynthetic nanoplankton and microzooplankton. Even greater changes in living POC occurred in the alongshore direction due to the dramatic reductions in diatoms in southern waters. Estimated herbivory was ca 2–4 gC m −2 d −1 . The ratio of heterotrophic : autotrophic POC increased from 38% in northern waters to 137% in southern waters, suggesting that phytoplankton was being converted into consumer carbon as shelf waters advected south. The dominant consumers at most stations were single-celled protozoan zooplankton and small copepods, whose fecal products remain in suspension in energetic shelf environments, suggesting that much of the non-diatomaceous POC was exported as shelf waters exited at Cape Hatteras.

Distribution and relation of total bacteria, active bacteria, bacterivory, and volume of organic detritus in Atlantic continental shelf waters off Cape Hatteras NC, USA

Abstract During the Ocean Margins Program, we obtained data on the abundances of bacterioplankton and heterotrophic flagellates, and on rates of bacterivory, across the mid-Atlantic continental shelf off Cape Hatteras, NC, during four spring and summer cruises from 1993 to 1996. Bacterial and grazing parameters were compared for inner, middle, and outer shelf regions. In 1996, we sampled during two seasons: early spring (March) and mid-summer (July), and in addition determined the fractions of in situ bacterioplankton that had visible nucleoids (NV cells), or that had highly active electron transport systems (ETS), i.e. that were positive for reduction of the fluorogenic formazan compound, 5 cyano-2,3 ditolyl tetrazolium chloride (CTC+ cells), as well as the volumetric concentration of organic detrital particles. Detrital volumes and abundances of bacterioplankton and of heterotrophic flagellates, varied by an order of magnitude, and decreased from inshore to offshore shelf regions. In 1996, bacterial abundances and percentages of CTC+ cells were higher across the shelf during the early spring bloom season (March) compared to the post-bloom season (July). In March 1996, percentages of bacterial cells with visible nucleoids varied between 20% and 70%, but showed little change across the shelf; while fractions of total bacteria with highly active ETS were lower and more variable (1–16% CTC+ cells), and on average were twice as high in the inner shelf region compared to the rest of the shelf. Percentages of CTC+ cells were also higher for particle-associated bacteria. There was a strong positive relationship between percent CTC+ cells and volume of organic detrital particles. However, % CTC+ cells and detrital volume were not consistently related to either bulk particulate organic carbon or chlorophyll. Bacterivory, assessed via rate of ingestion of fluorescently labeled bacteria, could remove 2–9% (4–18% accounting for motile cells) of total bacterial stocks per day. If bacterivores selectively grazed CTC+ bacteria, then bacterivory could result in turnover of CTC+ cells at rates on the order of 0.4–1.4xa0d−1.

Using Inhibitors to Investigate the Involvement of Cell Signaling in Predation by Marine Phagotrophic Protists

ABSTRACT. Phagotrophic protists are major consumers of microbial biomass in aquatic ecosystems. However, biochemical mechanisms underlying prey recognition and phagocytosis by protists are not well understood. We investigated the potential roles of cell signaling mechanisms in chemosensory response to prey, and in capture of prey cells, by a marine ciliate (Uronema sp.) and a heterotrophic dinoflagellate (Oxyrrhis marina). Inhibition of protein kinase signal transduction biomolecules caused a decrease in both chemosensory response and predation. Inhibition of G‐protein coupled receptor signaling pathways significantly decreased chemosensory response but had no effect on prey ingestion. Inhibitor compounds did not appear to affect general cell health, but had a targeted effect. These results support the idea that cell signaling pathways known in other eukaryotic organisms are involved in feeding behavior of free‐living protists.