Description: Submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy at the Massachusetts Institute of Technology and the Woods Hole Oceanographic Institution June 1984

Description: The distribution and feeding behavior of bacterivorous micro flagellates (2-20 μm protozoa) and their ingestion by copepods were examined in an attempt to assess the importance of these protozoa as a trophic link between planktonic bacteria and zooplankton. The abundance of microflagellates relative to other picoplankton (0.2-2.0 μm) and nanoplankton (2-20 μm) populations in water samples in the North Atlantic and in Lake Ontario and on macroaggregates in the North Atlantic was determined using direct microscopical and culture estimation techniques. Seasonal, vertical and geographical changes in the density of microflagellates were generally not greater than one order of magnitude. Microscopical counts of heterotrophic nanoplankton (presumably microflagellates) typically ranged from a few hundred to a few thousand m1-1 for a variety of planktonic environments. They constituted approximately 1/3 to 1/2 of the nanoplankton in the euphotic zone and dominated the nanoplankton in the aphotic zone. Most Probable Number (MPN) estimation of the density of bacterivorous protozoa indicated that microflagellates were, on average, an order of magnitude more abundant than bacterivorous ciliates and amoebae. MPN and direct microscopical counts of microflagellates differed by as much as 104. This discrepancy was smaller in eutrophic environments (e.g. Continental Shelf and Lake Ontario) and on macroscopic detrital aggregates. All microbial populations enumerated were highly concentrated on macroscopic detrital aggregates relative to their abundance in the water surrounding the aggregates. Enrichment factors (the ratio of abundance of a population on a macroaggregate to its abundance in the surrounding water) increased along a eutrophic-to-oligotrophic gradient because of the combined effects of an increased abundance of microorganisms on macroaggregates in oligotrophic environments and a decreased abundance in the surrounding water in these same environments. Average enrichment factors for direct microscopical counts of heterotrophic nanoplankton (range = 17-114) were not as large as enrichment factors observed for MPN estimates of the number of bacterivorous microflagellates (range = 273-18400). Microflagellates numerically dominated the bacterivorous protozoa cultured from macroaggregates by one to two orders of magnitude, but ciliates and amoebae were also highly enriched on macroaggregates. Microenvironments are therefore a potentially important aspect for the ecology of planktonic microorganisms. Observations on the microbial colonization of mucus sloughed by ctenophores and discarded appendicularian houses suggest that these materials may be important sources of macroaggregates. Batch and continuous culture experiments were conducted with clonal cultures of microflagellates to test their ability to grow on various types and densities of bacteria. The doubling time of Monas sp. 1 ranged from 43 hr (when fed the cyanobacterium Synechococcus Strain WH 8101) to 6.9 hr (when fed the heterotrophic bacterium Serratia marinorubra). Cell yields (i.e. the conversion of bacterial biomass into protozoan biomass) of Monas sp. 1 fed two species of heterotrophic bacteria were greater than yields for the microflagellate fed two species chroococcoid cyanobacteria (range = 7-68%). Cell yields of two other species of microflagellates (Monas sp. 2 and Cryptobia maris) were 48% and 61%, respectively, on the bacterium Pseudomonas halodurans. Microflagellates grew in continuous culture at concentrations of bacteria which were lower than bacterial densities required for the growth of ciliates as shown by other investigations. Therefore, microflagellates appear to be well-adapted for grazing bacterioplankton. Microflagellates were also investigated for their ability to graze bacteria attached to particles. Bodo nanorensis and Rhynchomonas nasuta both showed a marked ability to graze attached bacteria and a limited ability to graze unattached cells. These results suggest that microflagellates may also be important consumers of bacteria attached to particles in the plankton and may explain the highly elevated densities of microflagellates on macroaggregates. Grazing experiments performed with the copepod Acartia tonsa indicated that heterotrophic microflagellates were ingested by the copepods at rates comparable to the ingestion of phytoplankton of similar size. The presence of heterotrophic microflagellates did not depress filtration rates of the copepods, and one species (Cryptobia maris) appeared to be selectively grazed. Survival of A. tonsa on a diet of heterotrophic microflagellates was similar to survival on a diet of phytoplankton and was significantly longer than survival of starved Controls or copepods fed only bacteria. Due to their ability to grow at in-situ densities of planktonic bacteria, their relatively high cell yields, and their acceptability as food for zooplankton, it is concluded that bacterivorous microflagellates may constitute an important trophic link between bacteria and zooplankton. This link may provide a mechanism whereby organic material and energy from the detrital food chain can be returned to the classical phytoplankton-copepod-fish food chain.

Description: This research was supported by National Science Foundation grants OCE80-2444l and OCE82-l4928 and Ocean Industry Program grant 4473 awarded to Dr. Laurence P. Madin, NSF Doctoral Dissertation grant OCE8l-l299l, the Woods Hole Oceanographic Institution Education Program and the Wood Hole Oceanographic Institution Biology Department.

Description: © The Author(s), 2014. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in PLoS Biology 12 (2014): e1001889, doi:10.1371/journal.pbio.1001889.

Description: Microbial ecology is plagued by problems of an abstract nature. Cell sizes are so small and population sizes so large that both are virtually incomprehensible. Niches are so far from our everyday experience as to make their very definition elusive. Organisms that may be abundant and critical to our survival are little understood, seldom described and/or cultured, and sometimes yet to be even seen. One way to confront these problems is to use data of an even more abstract nature: molecular sequence data. Massive environmental nucleic acid sequencing, such as metagenomics or metatranscriptomics, promises functional analysis of microbial communities as a whole, without prior knowledge of which organisms are in the environment or exactly how they are interacting. But sequence-based ecological studies nearly always use a comparative approach, and that requires relevant reference sequences, which are an extremely limited resource when it comes to microbial eukaryotes. In practice, this means sequence databases need to be populated with enormous quantities of data for which we have some certainties about the source. Most important is the taxonomic identity of the organism from which a sequence is derived and as much functional identification of the encoded proteins as possible. In an ideal world, such information would be available as a large set of complete, well-curated, and annotated genomes for all the major organisms from the environment in question. Reality substantially diverges from this ideal, but at least for bacterial molecular ecology, there is a database consisting of thousands of complete genomes from a wide range of taxa, supplemented by a phylogeny-driven approach to diversifying genomics. For eukaryotes, the number of available genomes is far, far fewer, and we have relied much more heavily on random growth of sequence databases, raising the question as to whether this is fit for purpose.

Description: This project was funded by the Gordon and Betty Moore Foundation (GBMF; Grants GBMF2637 and GBMF3111) to the National Center for Genome Resources (NCGR) and the National Center for Marine Algae and Microbiota (NCMA).