Books on the topic 'Heterotrophic bacteria'

Symbiosis, where different species live together for prolonged periods, is ubiquitous and extremely important on coral reefs. The most important symbiosis is between corals and the microalgae (zooxanthellae) that live in their cells, without which coral reefs would not exist. This chapter focuses on the diversity of zooxanthellae, the linkage with coral calcification and the nutrition of the symbiosis, particularly the supply of photosynthetically fixed carbon to coral, and the conservation and recycling of essential nutrients (especially nitrogen and phosphorus) by this symbiosis. The acquisition and breakdown of the symbiosis, particularly under thermal stress (i.e. coral bleaching), is described. Other important coral–microbe symbioses involve cyanobacteria, heterotrophic bacteria, viruses, protozoans and endolithic algae and fungi that live in the coral skeleton. Symbioses between sponges and bacteria or algae are also important, as are the iconic associations between fish and various invertebrates (e.g. the sea anemone–anemonefish symbiosis) or other fish species.

Soon after the discovery that bacteria are abundant in natural environments, the question arose as to whether or not they were active. Although the plate count method suggested that they were dormant if not dead, other methods indicated that a large fraction of bacteria and fungi are active, as discussed in this chapter. It goes on to discuss fundamental equations for exponential growth and logistic growth, and it describes phases of growth in batch cultures, continuous cultures, and chemostats. In contrast with measuring growth in laboratory cultures, it is difficult to measure in natural environments for complex communities with co-occurring mortality. Among many methods that have been suggested over the years, the most common one for bacteria is the leucine approach, while for fungi it is the acetate-in ergosterol method. These methods indicate that the growth rate of the bulk community is on the order of days for bacteria in their natural environment. It is faster in aquatic habitats than in soils, and bacteria grow faster than fungi in soils. But bulk rates for bacteria appear to be slower than those for phytoplankton. All of these rates for natural communities are much slower than rates measured for most microbes in the laboratory. Rates in subsurface environments hundreds of meters from light-driven primary production and high organic carbon conditions are even lower. Rates vary greatly among microbial taxa, according to data on 16S rRNA. Copiotrophic bacteria grow much faster than oligotrophic bacteria, but may have low growth rates when conditions turn unfavorable. Some of the factors limiting heterotrophic bacteria and fungi include temperature and inorganic nutrients, but the supply of organic compounds is perhaps most important in most environments.

Nitrogen is required for the biosynthesis of many cellular components and can take on many oxidation states, ranging from −3 to +5. Consequently, nitrogen compounds can act as either electron donors (chemolithotrophy) or electron acceptors (anaerobic respiration). The nitrogen cycle starts with nitrogen fixation, the reduction of nitrogen gas to ammonium. Nitrogen fixation is carried out only by prokaryotes, mainly some cyanobacteria and heterotrophic bacteria. The ammonium resulting from nitrogen fixation is quickly used by many organisms for biosynthesis, being preferred over nitrate as a nitrogen source. It is also oxidized aerobically by chemolithoautotrophic bacteria and archaea during the first step of nitrification. The second step, nitrite oxidation, is carried out by other bacteria not involved in ammonia oxidation, resulting in the formation of nitrate. Some bacteria are capable of carrying out both steps (“comammox”). This nitrate can then be reduced to nitrogen gas or nitrous oxide during denitrification. It can be reduced to ammonium, a process called “dissimilatory nitrate reduction to ammonium.” Nitrogen gas is also released by anaerobic oxidation of ammonium (“anammox”) which is carried out by bacteria in the Planctomycetes phylum. The theoretical contribution of anammox to total nitrogen gas release is 29%, but the actual contribution varies greatly. Another gas in the nitrogen cycle, nitrous oxide, is a greenhouse gas produced by ammonia-oxidizing bacteria and archaea. The available data indicate that the global nitrogen cycle is in balance, with losses from nitrogen gas production equaling gains via nitrogen fixation. But excess nitrogen from fertilizers is contributing to local imbalances and several environmental problems in drinking waters, reservoirs, lakes, and coastal oceans.

Protists are involved in many ecological roles in natural environments, including primary production, herbivory and carnivory, and parasitism. Microbial ecologists have been interested in these single-cell eukaryotes since Antonie van Leeuwenhoek saw them in his stool and scum from his teeth. This chapter focuses on the role of protozoa (purely heterotrophic protists) and other protists in grazing on other microbes. Heterotrophic nanoflagellates, 3–5 microns long, are the most important grazers of bacteria and small phytoplankton in aquatic environments. In soils, flagellates are also important, followed by naked amoebae, testate amoebae, and ciliates. Many of these protists feed on their prey by phagocytosis, in which the prey particle is engulfed into a food vacuole into which digestive enzymes are released. This mechanism of grazing explains many factors affecting grazing rates, such as prey numbers, size, and composition. Ingestion rates increase with prey numbers before reaching a maximum, similar to the Michaelis–Menten equation describing uptake as a function of substrate concentration. Protists generally eat prey that are about ten-fold smaller than they are. In addition to flagellates, ciliates and dinoflagellates are often important predators in the microbial world and are critical links between microbial food chains and larger organisms Many protists are capable of photosynthesis. In some cases, the predator benefits from photosynthesis carried out by engulfed, but undigested photosynthetic prey or its chloroplasts. Although much can be learnt from the morphology of large protists, small protists (<10 μ‎m) often cannot be distinguished by morphology, and as seen several times in this book, many of the most abundant and presumably important protists are difficult to cultivate, necessitating the use of cultivation-independent methods analogous to those developed for prokaryotes. Instead of the 16S rRNA gene used for bacteria and archaea, the 18S rRNA gene is key for protists. Studies of this gene have uncovered high diversity in natural protist communities and, along with sequences of other genes, have upended models of eukaryote evolution. These studies indicate that the eukaryotic Tree of Life consists almost entirely of protists, with higher plants, fungi, and animals as mere branches.