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

I. the origin of species by means of natural selection

We review the biogeography of microorganisms in light of the biogeography of macroorganisms A large body of research supports the idea that free-living microbial taxa exhibit biogeographic patterns Current evidence confirms that, as proposed by the Baas-Becking hypothesis, 'the environment selects' and is, in part, responsible for spatial variation in microbial diversity However, recent studies also dispute the idea that 'everything is everywhere' We also consider how the processes that generate and maintain biogeographic patterns in macroorganisms could operate in the microbial world

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Microbial biogeography : putting microorganisms on the map

Fatty acids and alcohols are key intermediates in the methanogenic degradation of organic matter, e.g., in anaerobic sewage sludge digestors or freshwater lake sediments. They are produced by classical fermenting bacteria for disposal of electrons derived in simultaneous substrate oxidations. Methanogenic bacteria can degrade primarily only one-carbon compounds. Therefore, acetate, propionate, ethanol, and their higher homologs have to be fermented further to one-carbon compounds. These fermentations are called secondary or syntrophic fermentations. They are endergonic processes under standard conditions and depend on intimate coupling with methanogenesis. The energetic situation of the prokaryotes cooperating in these processes is problematic: the free energy available in the reactions for total conversion of substrate to methane attributes to each partner amounts of energy in the range of the minimum biochemically convertible energy, i.e., 20 to 25 kJ per mol per reaction. This amount corresponds to one-third of an ATP unit and is equivalent to the energy required for a monovalent ion to cross the charged cytoplasmic membrane. Recent studies have revealed that syntrophically fermenting bacteria synthesize ATP by substrate-level phosphorylation and reinvest part of the ATP-bound energy into reversed electron transport processes, to release the electrons at a redox level accessible by the partner bacteria and to balance their energy budget. These findings allow us to understand the energy economy of these bacteria on the basis of concepts derived from the bioenergetics of other microorganisms.

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Energetics of syntrophic cooperation in methanogenic degradation.

Soil microorganisms as controllers of atmospheric trace gases (H2, CO, CH4, OCS, N2O, and NO).

Published estimates of protozoan respiratory rates are reviewed with the object of clarifying their value in ecological studies. The data show a surprisingly large variance when similarly sized cells or individual species are compared. This is attributed to the range of physiological states in the cells concerned. The concept of basal metabolism has little meaning in protozoa. During balanced growth, energy metabolism is nearly linearly proportional to the growth rate constant; at the initiation of starvation, metabolic rate rapidly declines. Motility requires an insignificant fraction of the energy budget of protozoans. For growing cells, metabolic rate is approximately proportional to weight0.75 and the data fall nearly exactly on a curve extrapolated from that describing the respiration rates of poikilotherm metazoans as a function of body weight. It is conceivable that protozoan species exist with lower maximum potential growth and metabolic rates than those predicted from cell volume and the equations derived from the available data. However, the lack of information concerning the state of the cells studied prevents verification of this idea. Laboratory measurements of protozoan respiratory rates have no predictive value for protozoa in nature other than delimiting a potential range. For small protozoans, this range may, on an individual basis, represent a factor of 50.

Respiration rates in heterotrophic, free-living protozoa.

We have quantified the bacteria, heterotrophic nanoplankton (HNAN), and other microorganisms in 108 lakes, ponds, rivers, and bogs worldwide. These water bodies span the range of biological productivities in freshwater. Numbers of HNAN and bacteria are correlated over four orders of magnitude in each (3 x 10(2) to 4 x 10(6) ml-1 and 3 x 10(5) to 1 x 10(9) ml-1, respectively) and both increase with the productivity of the water body. Most HNAN are small (2-5-mu-m), colorless, flagellated protists. They grow at about the same rate as bacteria (mu = 0.01-0.02 h-1) and are capable of consuming the entire bacterial production. We suggest that bacterial abundances are regulated by substrate supply and HNAN grazing pressure. Ciliates and other grazing microzooplankton probably limit HNAN abundance, especially in the more productive water bodies. The structure and function of microbial food webs in freshwater environments may thus be similar to those suggested for marine systems.

https://aslopubs.onlinelibrary.wiley.com/doi/pdf/10.4319/lo.1991.36.1.0139

Protozoan control of bacterial abundances in freshwater.

The purpose of this article is to pull together various elements from current knowledge regarding the natural history of free-living protozoa in fresh waters. We define their functional role, set the likely limits of ‘biodiversity’, and explore how the two may be related. Protozoa are unicellular, phagotrophic organisms, and 16 phyla of protists contain free-living freshwater protozoan species. They are the most important grazers of microbes in aquatic environments and the only grazers of any importance in anoxic habitats. In sediments, ciliates are usually the dominant protozoans. Benthic ciliate biomass accounts for slightly less than 10% of total benthic invertebrate biomass, but ciliate production may equal or even exceed invertebrate production. Freshwater protozoan species are probably ubiquitous, although many may persist locally for long periods in a cryptic state – as ‘potential’ rather than ‘active’ biodiversity. As protozoa are among the largest and most complex of micro-organisms, it follows that bacteria and all other smaller, more numerous microbes are also ubiquitous. The number of protozoan species recorded in local surveys (232) is about 10% of the estimated global species richness (2390). The 'seedbank’ of protozoan (and microbial) species ensures that local microbial diversity is never so impoverished that it cannot play its full part in ecosystem functions such as carbon fixation and nutrient cycling.

Freshwater protozoa: biodiversity and ecological function

On the abundance and distribution of protozoa and their food in a productive freshwater pond.

For more than 200 years, ciliated protozoa have been identified and allocated Species names largely on the basis of the rich morphological variety they present. We have examined the species richness of all free-living ciliate genera, described historical trends in the descriptions of new species, and estimated the number of species currently known. We have quantified the value of taxonomic revisions, and conclude that the number of known, extant free-living species is close to 3000. We have investigated the concept of "species" and the meaning of "biodiversity" in relation to ciliates, and conclude that the bilogical species concept is neither appropriate nor practicable. Insofar as ciliate morphology is closely correlated with the function of the organism in nature, the morphospecies concept is as valid as any, and probably more pragmatic than any other. Thus, when speaking of "species diversity," or the "biodiversity" of ciliates, we refer to diversity of form and function. The majority of ciliate speci...

B. J. Finlay

Papers

Respiration rates in heterotrophic, free-living protozoa.

Protozoan control of bacterial abundances in freshwater.

Freshwater protozoa: biodiversity and ecological function

On the abundance and distribution of protozoa and their food in a productive freshwater pond.

Biodiversity at the microbial level: The number of free-living ciliates in the biosphere