Secondary Saprotrophs

In this functional group, we group species that are not involved in directly digesting soil litter. Primary saprotrophs were characterized by extracellular digestion of litter in the soil, and the absorption of dis solved nutrients through osmotrophy. Secondary saprotrophs are consumers of primary saprotrophs, or of litter partially digested by primary saprotrophs. Several functional groups can be distinguished, based on which type of organisms are ingested, and the mechanisms used for ingestion (Fig. 4.9).


Species that consume prokaryotes are referred to as bacterivorous. They include species from most taxa found in the soil. Ingestion of bacteria does not occur at random. Experiments show that, typically, pro-tists and invertebrates exhibit clear preferences based on bacterial species, dimensions and other criteria. Therefore, even when bacteria are abundant, many bacterivores may not be active or may grow poorly, because preferred bacterial species are absent. Examples of bacteria choice are numerous in the literature, particularly for nematodes and protozoa.


Within the bacteria, many species of Myxobacteria release enzymes that lyse bacterial cell walls. They are the principal bacterivores amongst prokaryotes (Chapter 1). They grow as motile colonies that spread over bacterial colonies and digest them. Myxobacteria enzymes also digest other SOM molecules, which contribute to general decomposition and nutrient release. The role of bacteriophages should be mentioned because these viruses can infect and lyse susceptible bacterial strains and species that become infected. The lysis of bacteria reduces the popula-

litter from 1° production

1° saprotrophs

2° saprotrophs osmotrophy litter from 1° production

1° saprotrophs

2° saprotrophs osmotrophy

Fig. 4.9. Representation of interactions between several functional groups in decomposition. Arrows indicate direction but not quantity of flow.

tion and releases cytoplasm into the soil solution. The abundance and impact of bacteriophages in soil food webs are studied infrequently (Williams and Lanning, 1984; Lipson and Stozky, 1987; Angle, 1994), although they have been studied in aquatic food webs.


Protist consumers of bacteria are the most numerous bacterivores. These include the nanoflagellates (<12 |im long) from several phyla, which are abundant species of protozoa in the soil. Most protozoan species found in the soil are bacterivorous. However, not all consume bacteria exclusively. The smallest species complement growth by osmotrophy on the soil solution, or may be exclusively osmotrophic. Many small ciliates complement their nutrition by obtaining soluble nutrients from the soil solution. For example, Tetrahymena (a freshwater ciliate, that normally feeds on bacteria) can be grown in the laboratory on an axenic medium of sterile, rich solution of soluble nutrients. The small ciliate Coleps and several other genera of small ciliates aggregate about lysed cells and freshly dead or dying microinvertebrates to feed on the cytoplasm. These also ingest bacteria that grow on the lysate. Certain filamentous and saprotrophic fungi supplement their nutrition by bacterivory. This was observed in several ligninolytic species in the genera Agaricus, Coprinus, Lepista and Pleurotus (Barron, 1988). In these examples, saprotrophic enzymes are released from coralloid haustorial hyphae to digest the bacterial colony, and the nutrients are absorbed by osmotrophy.

The mechanism of ingestion of bacteria by protists is phagocytosis. Phagocytosis is stimulated through membrane receptors and mediated by the cytoskeleton, which invaginates the cell membrane to form a food vacuole (or phagosomes). Bacterivorous protists often have an area of the cell membrane which is specialized for capturing bacterial cells, called the oral region or cytostome. The cytostome can be a simple depression on the cell surface, or an elaborate structure with many specialized organelles associated with it. The cytostome can be an invagi-nated gullet, or funnel-shaped structure, as in many Ciliata, Cryptomonad or Euglenid. Capture of bacteria by the cytostome often involves movement of cilia (Fenchel, 1986; Balczon and Pratt, 1996; Boenigck et al., 2001). In the simplest case, one cilium is used to direct bacteria on to the cytostome area, where phagocytosis is initiated. In other cases, one cilium can be used to hold on to soil particles, while the cytostome is held against a surface for phagocytosis of suitable bacteria. The cytostomes of ciliates are more invaginated in many cases and possess many specialized cilia, sometimes in bundles (Lee et al., 2001). The oral cilia direct a current into the cytostome, and phagocytosis occurs inside, at the cytopharynx. Larger ciliates may have an elaborate cytostome, such as many stichotrich families which are common and ubiquitous in the soil.

Phagocytosis by amoeboid species is distinct because most of the cell membrane is sensitive to detection and capture of bacteria. Cell extensions (pseudopods) which explore the immediate environment capture and engulf bacteria. Many soil nanoflagellates can be partially amoeboid in film water, and some can extend filopodia to search their environment. The Sarcomonadea (Cercozoa or amoeboflagellates) in particular are abundant in soils, though understudied. Filopodia can be <1 |im in diameter and extended into narrow spaces to explore and obtain bacteria (Fig. 2.3). Therefore, even if the cell body cannot reach small spaces, the filopodia can. Pseudopods, including filopodia, are strong enough to exert force on soil particles. This is easily observed under the microscope, and causes some movement and repositioning of particles. Lastly, the Mycetozoa (protozoa: Amoebozoa), which includes the slime moulds (Dictyostelia), are abundant bacterivorous soil amoebae. Under suitable conditions, they excyst in large numbers.

Bacterivory and predation by protozoa in general were reviewed previously (Clark, 1969; Griffiths, 1994). Most experiments on feeding preferences of bacterivorous ciliates were carried out with aquatic species (Sherr et al., 1992; Perez-Uz, 1996 and references therein). Bacterial selectivity by soil amoebae was addressed by Singh (1941, 1942). Selectivity of nanoflagellates and other soil protozoa has been addressed more recently. One study (Ronn et al., 2001) compared the growth response of indigenous soil protozoa on two dissimilar species of bacteria, Mycobacterium chlorophenolicum and Pseudomonas chlororaphis. The former did not stimulate grazing in soil microcosms, whereas the Pseudomonas permitted growth of naked amoebae and heterotrophic flagellates. High-resolution video-microscopy has been useful in examining the mechanisms of prey ingestion, digestion and excretion of food vacuoles. These observations on various prey items are useful in determining feeding strategies, prey capture and retention, and optimal foraging (Boenigk and Arndt, 2000). Characteristics of bacterial processing can be used to differentiate between optimal feeding conditions and niche differentiation within microhabitats (Table 4.10). The process can be subdivided into time budgets for different prey items (contact time, processing time, ingestion time, refractory time and handling time) (Fig. 4.10). In some instances, a bacterium or particle that is partially ingested is ejected without food vacuole formation or digestion (Fig. 4.11). Ejection occurs if it is too large, too long or unpalatable. Important parameters that determine growth efficiency on a bacterium include differences in the time allocated to each portion of the time budget. They also include the nutritional and chemical composition of the bacteria (palatability). Actively growing species are often more palatable and selected for. This video-microscopy approach is suitable for modelling bacterivory rates and selectivity by a variety of nanoflagellates (Boenigk et al., 2001) and other ciliates or amoebae.

Table 4.10. Bacterial capture in four nanoflagellates based on video-microscopy.

Cafeteria roenbergensis Bodo saltans Spumella sp. Ochromonas sp.

Cafeteria roenbergensis Bodo saltans Spumella sp. Ochromonas sp.

Cell volume (^m3)

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