Phylogenetic identification and in situ detection of individual microbial cells without cultivation.

Recently developed techniques for estimating bacterial biomass and productivity indicate that bacterial biomass in the sea is related to phytoplankton concentration and that bacteria utilise 10 to 50 % of carbon fixed by photosynthesis. Evidence is presented to suggest that numbers of free bacteria are controlled by nanoplankton~c heterotrophic flagellates which are ubiquitous in the marine water column. The flagellates in turn are preyed upon by microzooplankton. Heterotrophic flagellates and microzooplankton cover the same size range as the phytoplankton, thus providing the means for returning some energy from the 'microbial loop' to the conventional planktonic food chain.

/pdf/the-ecological-role-of-water-column-microbes-in-the-sea-34dv8tiwzr.pdf

The Ecological Role of Water-Column Microbes in the Sea*

Fluorescent oligonucleotide hybridization probes were used to label bacterial cells for analysis by flow cytometry. The probes, complementary to short sequence elements within the 16S rRNA common to phylogenetically coherent assemblages of microorganisms, were labeled with tetramethylrhodamine and hybridized to suspensions of fixed cells. Flow cytometry was used to resolve individual target and nontarget bacteria (1 to 5 microns) via probe-conferred fluorescence. Target cells were quantified in an excess of nontarget cells. The intensity of fluorescence was increased additively by the combined use of two or three fluorescent probes complementary to different regions of the same 16S rRNA. Images

Combination of 16S rRNA-targeted oligonucleotide probes with flow cytometry for analyzing mixed microbial populations.

The evolution of marine microbes over billions of years predicts that the composition of microbial communities should be much greater than the published estimates of a few thousand distinct kinds of microbes per liter of seawater. By adopting a massively parallel tag sequencing strategy, we show that bacterial communities of deep water masses of the North Atlantic and diffuse flow hydrothermal vents are one to two orders of magnitude more complex than previously reported for any microbial environment. A relatively small number of different populations dominate all samples, but thousands of low-abundance populations account for most of the observed phylogenetic diversity. This "rare biosphere" is very ancient and may represent a nearly inexhaustible source of genomic innovation. Members of the rare biosphere are highly divergent from each other and, at different times in earth's history, may have had a profound impact on shaping planetary processes.

/pdf/microbial-diversity-in-the-deep-sea-and-the-underexplored-mh8sm5okzt.pdf

Microbial diversity in the deep sea and the underexplored “rare biosphere”

Beginning with Emlen (1966) and MacArthur and Pianka (1966) and extending through the last ten years, several authors have sought to predict the foraging behavior of animals by means of mathematical models. These models are very similar,in that they all assume that the fitness of a foraging animal is a function of the efficiency of foraging measured in terms of some "currency" (Schoener, 1971) -usually energy- and that natural selection has resulted in animals that forage so as to maximize this fitness. As a result of these similarities, the models have become known as "optimal foraging models"; and the theory that embodies them, "optimal foraging theory." The situations to which optimal foraging theory has been applied, with the exception of a few recent studies, can be divided into the following four categories: (1) choice by an animal of which food types to eat (i.e., optimal diet); (2) choice of which patch type to feed in (i.e., optimal patch choice); (3) optimal allocation of time to different patches; and (4) optimal patterns and speed of movements. In this review we discuss each of these categories separately, dealing with both the theoretical developments and the data that permit tests of the predictions. The review is selective in the sense that we emphasize studies that either develop testable predictions or that attempt to test predictions in a precise quantitative manner. We also discuss what we see to be some of the future developments in the area of optimal foraging theory and how this theory can be related to other areas of biology. Our general conclusion is that the simple models so far formulated are supported are supported reasonably well by available data and that we are optimistic about the value both now and in the future of optimal foraging theory. We argue, however, that these simple models will requre much modification, espicially to deal with situations that either cannot easily be put into one or another of the above four categories or entail currencies more complicated that just energy.

Citation classic - optimal foraging - a selective review of theory and tests

A highly specific and sensitive fluorescing DNA stain, 4′6-diamidino-2-phenylindole (DAPI) was compared with acridine orange (AO) for counting aquatic microflora. Use of DAPI improved visualization and counting of <1-µm bacteria and blue-green algae in seston-rich samples and extended sample storage to at least 24 weeks.

https://aslopubs.onlinelibrary.wiley.com/doi/epdf/10.4319/lo.1980.25.5.0943

The use of DAPI for identifying and counting aquatic microflora1

Bacterivory in eutrophic Lake Oglethorpe, Georgia, was determined by direct observation of tracer particle uptake by all members of the planktonic community. Heterotrophic flagellates dominated grazing at all times, accounting for 49-8 1% of grazing on an areal basis and up to 98% of grazing at some depths. Pigmented (mixotrophic) flagellates were major grazers during winter and spring blooms, when they contributed up to 45% of community grazing on an areal basis and 79% at depths of maximum abundance. In late spring to early summer, rotifers and ciliates were responsible for as much as 25 and 30% of bacterivory at some depths, but averaged 3 and 11% over the year, respectively. Grazing impact of cladoceran crustaceans was generally < 1% of the total. Bacterivory by copepods was not detected. Total bacterial mortality due to grazing ranged from 11 to 162% of bacterial cell production estimated from the incorporation of [3H]thymidine. Use of 0.57-pm microspheres as tracers gave similar estimates ofingestion to fluorescently labeled bacteria in this system. The use of 4% ice-cold glutaraldehyde mixed 1 : 1 with the water sample was found to be equally effective to an acrolein-tannic acid mixture for reducing egestion of particles by protists. We therefore consider our findings to be representative of bacterivory by the planktonic community in this eutrophic system.

https://aslopubs.onlinelibrary.wiley.com/doi/pdf/10.4319/lo.1989.34.4.0673

Seasonal patterns of bacterivory by flagellates, ciliates, rotifers, and cladocerans in a freshwater planktonic community

Protozoa are now being recognized as important members of planktonic food webs. This is due to the inclusion of microbial links in our paradigm of trophic relationships. Heterotrophic microflagellates and ciliates are major grazers of bacteria. They can stimulate production through nutrient recycling and can transform microbial production into larger particles, which are then available for macroconsumers. In this paper we add new groups, the small (< 20 μm) ciliates and myxotrophic flagellates, to the planktonic food web.

Protozoa in Planktonic Food Webs1,2

Abstruct Swimming patterns, fecging behaviors, and ingestion, filtering, assimilation, and respiration rates were measured for Daphnia mugnu in food concentrations from 0 to 10” Chlamydomonas reinhnrdi cells * cm-“, equivalent to O-20 mg C* liter-‘. A Helling type 2 functional response curve or an Ivlev model without a threshold appear to be biologically meaningful descriptions of Daphnia feeding response to different food concentrations. Daphnia has no feeding threshold or reduced filtering activity at low concentrations such as are predicted by optimal foraging models. Above the incipient limiting concentration, constant ingestion rates and an over-collection of food result in increased rejection rates. These behaviors may cause high respiratory rates and reduced net assimilation rates at the highest food concentration. Daphnia does not orient to or alter swimming patterns in response to algal patches.

https://aslopubs.onlinelibrary.wiley.com/doi/pdf/10.4319/lo.1982.27.5.0935

The effect of food concentration on swimming patterns, feeding behavior, ingestion, assimilation, and respiration by Daphnia1

THE potential importance of bacteria in freshwater planktonic food webs is recognised1, but the mechanisms of their incorporation are not fully known. Most planktonic bacteria are not attached to particles and are less than 1 µm (refs 2–4) in size—a range inefficiently filtered by crustacean zooplankton5. Daphnia and Diaptomus feed at lower rates on free living bacteria than on algae6,7. Bacterial food sources have been used with varying degrees of success to culture zooplankton8–11. These variations may be due to the unnatural range of concentrations used and the uncontrolled effects of different culture media, laboratory strains and the degree of accessibility to the zooplankton (because of cell clumping and sedimentation). Ciliate protozoan microzooplankton may be important intermediaries which transform ultrafine organic matter, including bacteria, into a particle size range readily available to crustacean zooplankton. Here we present evidence that ciliates are cropped by crustacean zooplankton in the natural environment. We have also measured feeding, filtering, and assimilation rates of Daphnia magna on both a large and small ciliate in the laboratory and have observed feeding behaviour directly. Dissolved organic carbon, bacteria, ciliate protozoans and crustacean zooplankton may represent a significant pathway of carbon flow in the freshwater plankton.

Karen G. Porter

Papers

The use of DAPI for identifying and counting aquatic microflora1

Seasonal patterns of bacterivory by flagellates, ciliates, rotifers, and cladocerans in a freshwater planktonic community

Protozoa in Planktonic Food Webs1,2

The effect of food concentration on swimming patterns, feeding behavior, ingestion, assimilation, and respiration by Daphnia1

Ciliate protozoans as links in freshwater planktonic food chains