NITROGEN CYCLING AND BACTERIAL DIVERSITY

MUHAMMAD FAHRI.
BRAWIJAYA UNIVERSITY MALANG
2009

Bacteria are essential organisms in the cycling of organic matter in natural environments, but the mechanisms controlling these processes are vaguely known. In addition to quality of the organic matter, availability of elements such as N, P, Fe and S often influences the microbial capacity for degradation of the organic matter. In the present study, we focussed on dissolved organic nitrogen (DON) as a representative type of natural organic matter. The cycling of DON was related to uptake or release of inorganic N and composition of the bacterial communities.
The main working hypothesis has been that the diversity of natural bacterial communities explains the frequent unpredictable variation in cycling of organic and inorganic nitrogen in aquatic environments.

The experimental work has been carried out by PhD Lone Frette as a partial fulfilment for her PhD thesis (Thesis title: Population dynamics in aquatic bacterioplankton, accepted January 2002).

Main conclusion of the experimental work is given in the following manuscripts:
1. Genetic and functional diversity of pelagic, culturable chemoorganotrophic bacteria from marine and estuarine environments
Bacteria from Kattegat (3.5 m depth), Skagerrak (30 and 79 m depth) and Roskilde Fjord were isolated on 10% ZoBell agar. From each locality 30 randomly picked isolates were chosen for identification by 16S rDNA sequencing. The isolates were further characterized with respect to enzymatic potential and growth on different C and N sources
Main results: Although a bacterial community may include a large variation in species composition, only a limited number of species will be numerically dominant at a certain locality at a given time. This is due to a close interplay between bacteria and the environment [link to manuscript abstract]
2. Interactions between protozoan grazing, availability of dissolved nitrogen, and bacterial community composition in experimental model systems

Preliminary experiments demonstrated that some of the bacterial isolates (manuscript above) had a preferential uptake of specific N compounds when grown in pure cultures. This selective uptake of N compounds may lead to different N profiles in the environment, e.g., if non-protein degrading bacteria dominate, this may lead to a higher ambient protein content. To examine whether different bacterial species, each with a different N preference, actually can influence the ambient N composition, four-species microcosms were offered typical, natural N compounds such as amino acids, protein, DNA, urea, nitrate and ammonium. In an additional series of experiments, the effect of bacterial grazing by the ciliate Uronema on the species dynamics was studied.

Main results: The environment (water and bacteria) influences the composition of the bacterial community through both a selective removal (grazing) and a selective growth stimulation (amount of N). However, due to a superfluous bacterial enzyme capacity for utilization of the tested N compounds (all were common N sources in aquatic systems), the bacterial activity in the different microcosms did not lead to major differences in the final ambient N pools. Thus, although natural microbial populations vary, this difference seems not to cause differences in the ambient N pools. Fig. 1 (pdf file): Preliminary graph demonstrating growth of four bacterial species as a function of N source.

In addition, a new, cellulose-degrading species species was identified:

3. Characterisation of Tenacibaculum cellulophagum sp. nov., a cellulose-utilising bacterium isolated from the pelagic of Skagerrak, Denmark
In this work two isolated bacteria within the Cythophaga-Flavobacter-Bacteroides group are described. These bacteria are known to be important in the degradation of polymer compounds. Although they are often isolated from marine surfaces, the present two species were pelagic organisms from Skagerrak.
Analysis of 16S rDNA sequences demonstrated that the two isolated species belonged to the recently described genera Tenacibaculum

AQUATIC FUNGI AS DECOMPOSERS OF ORGANIC MATTER
Fungi are traditionally considered to be dominant in organic matter cycling in terrestrial environments, while bacteria correspondingly are superior in aquatic areas. However, fungi are commonly found in sea and lake water, and their importance in nutrient cycling may be higher than expected.

Most research on aquatic fungi have focussed on either taxonomy and morphology, e.g. of spores, and on degradation of leaves and plant debris. Little is known about their growth physiology and ability to grow on planktonic cell remains such as dead phytoplankton cells.

Presence of fungi in natural waters raise interesting questions such as (1) is occurrence of fungi in water unintended (transport into the water due to wind and rain?) (2) do aquatic fungi form hyphae like terrestrial species and if yes, how do they cope with waves etc.? (3) can the fungi grow on minute surfaces such as dead planktonic algae? and (4) how do the fungi survive in an environments crowed by bacteria that are expected to have a high uptake capacity for organic matter?
In an attempt to answer these questions, an array of preliminary experiments have been conducted.

Experiments
Aquatic fungi were isolated from estuarine and marine environments by spreading a small volume of water onto petri dishes with potato-starch agar. About 10 colonies/species with a acceptable growth potential were reisolated and used for experiments.

Suspensions of the fungi (whirl-mixed hyphae in water) were added to cultures of dead Chlorella sp. algae in natural lake or sea water. After a week the fungal biomass had increased up to 20-fold (based on ergosterol content), while the density of the bacteria only increased slightly. Analysis of the proteolytic, extracellular activity (leu-MCA assay) in the water demonstrated an up to 6-fold higher activity when fungi were present.

These preliminary tests show that aquatic fungi in lake water with a moderate algal biomass can compete with bacteria for degradation of dead algae. This suggests that the organic matter content - at least in eutrophic environments - can support a successful growth of aquatic fungi.

Future?
The research on aquatic fungi is currently on hold due to lack of funding. Any suggestions to future collaboration - and financing - are most welcome!

DECOMPOSER
For the Matches album of the same name, see Decomposer.
The fungi on this tree are decomposers.

Decomposers (or saprotrophs) are organisms that consume dead organisms, and, in doing so, carry out the natural process of decomposition. Like herbivores and predators, decomposers are heterotrophic, meaning that they use organic substrates to get their energy, carbon and nutrients for growth and development. Decomposers use deceased organisms and non-living organic compounds as their food source. The primary decomposers are bacteria and fungi.

1 Importance of decomposers in the ecosystem
2 Bacteria
3 Fungi
4 Decomposers and detritivores
5 References

IMPORTANCE OF DECOMPOSERS IN THE ECOSYSTEM
When a plant or animal dies, it leaves behind nutrients and energy in the organic material that comprised its body. Scavengers and detritivores can feed on the carcasses, but they will inevitably leave behind a considerable amount of unused energy and nutrients. Unused energy and nutrients will be present both in the unconsumed portions (bones, feathers or fur in the case of animals, wood and other indigestable litter in the case of plants) and in the feces of the scavengers and detritivores. Decomposers eat things by breaking down this remaining organic matter by breaking it into pieces. Decomposers eventually convert all organic matter into carbon dioxide (which they respire) and nutrients. This releases raw nutrients (such as nitrogen, phosphorus, and magnesium) in a form usable to plants and algae, which incorporate the chemicals into their own cells. This process resupplies nutrients to the ecosystem, in turn allowing for greater primary production.

Although decomposers are generally located on the bottom of ecosystem diagrams such as food chains, food webs, and energy pyramids, decomposers in the biosphere are crucial to the environment. By breaking down dead material, they provide the nutrients that other organisms need to survive. As decomposers feed on dead organisms, they leave behind nutrients. These nutrients then become part of the soil.

Therefore, more plants can grow and thrive.

Bacteria
Bacteria are the primary decomposers of dead animals (carrion) and are the primary decomposers of dead plant matter (litter) in some ecosystems. In soils, where active fungal hyphae, and bacteria in such ecosystems are much more important in the recycling of nutrients. Bacteria can also be very important in agricultural fields, because tillage usually increases the abundance of bacteria relative to fungi.

Fungi
Fungi are the primary decomposers of litter in many ecosystems. Unlike bacteria, which are unicellular, most saprotrophic fungi grow as a branching network of hyphae. While bacteria are restricted to growing and feeding on the exposed surfaces of organic matter, fungi can use their hyphae to penetrate larger pieces of organic matter. Additionally, only fungi have evolved the enzymes necessary to decompose lignin, a chemically complex substance found in wood. These two factors make fungi the primary decomposers in forests, where litter has high concentrations of lignin and is often in large pieces. Also, if manufactured with other organisms, may grow elsewhere from its chemical pursuit, leaving behind the same type of bacteria left on the plant, tree organism, etc.

DECOMPOSERS AND DETRITIVORES
Some animals, like millipedes and woodlice, are commonly called decomposers, because such animals consume dead organic matter and contribute to the process of decomposition. Scientists, however, refer to such organisms as detritivores. This distinction is made because bacteria and fungi are capable of digesting many complex chemical molecules that animals are incapable of digesting. Additionally, bacteria and fungi digest and decompose organic matter more fully than detritivores, reducing it to inorganic material. For these reasons, bacteria and fungi play a more fundamental role in the processes of decomposition and nutrient recycling than animals. There are a lot of other kinds of decomposers around the world, including slugs and worms.

DETRITIVORE
Earthworms are a good example of soil-dwelling deposit feeders
Detritivores, also known as detritus feeders or saprophages, are heterotrophs that obtain nutrients by consuming detritus (decomposing organic matter). By doing so, they contribute to decomposition and the nutrient cycles.
Detritivores are an important aspect of many ecosystems. They can live on any soil with an organic component, and even live in marine ecosystems where they are termed interchangeably with bottom feeders.

Typical detritivorous animals include millipedes, woodlice, dung flies, many terrestrial worms, burying beetles, some sedentary polychaetes such as amphitrite, terebellids and fiddler crabs.

Many species of bacteria, fungi and protists, unable to ingest discrete lumps of matter, instead live by absorbing and metabolising on a molecular scale. Scavengers are typically not thought to be detritivores, as they generally consume larger quantities of organic matter. Coprovores are also usually treated separately as they exhibit a slightly different feeding behaviour. The eating of wood, whether live or dead, is known as xylophagy.

ECOLOGY
Woodlice can commonly be found eating damp rotting wood
In food webs, detritivores generally play the role of decomposers. Detritivores are often eaten by consumers and therefore commonly play important roles as recyclers in ecosystem energy flow and biogeochemical cycles.

Many detritivores live in mature woodland, though the term can be applied to certain bottom-feeders in wet environments. These organisms play a crucial role in benthic ecosystems, forming essential food chains and participating in the nitrogen cycle.
Fungi, acting as decomposers, are important in today's terrestrial environment. During the Carboniferous period, fungi and bacteria had yet to evolve the capacity to digest lignin, and so large deposits of dead plant tissue accumulated during this period, later becoming the fossil fuels[citation needed].

By feeding on sediments directly to extract the organic component, some detritivores accidentally concentrate toxic pollutants.

SAPROPHYTES
'Saprophyte' (-phyte meaning 'plant') is a botanical term that is now considered obsolete. There are no truly saprotrophic organisms that are embryophytes, and fungi and bacteria are no longer placed in the Plant Kingdom. Plants that were once considered saprophytes, such as non-photosynthetic orchids and monotropes, are now known to be parasites on fungi. These species are now termed myco-heterotrophs.[3][4][5]

DECOMPOSITION
For other uses, see Decomposition (disambiguation). Signs of death
1. Pallor mortis
2. Algor mortis
3. Rigor mortis
4. Livor mortis
5. Decomposition
6. Skeletonization

Decomposition (or spoilage) refers to the process by which tissues of dead organisms break down into simpler forms of matter. Such a breakdown of dead organisms is essential for new growth and development of living organisms because it recycles the finite chemical constituents and frees up the limited physical space in the biome. Bodies of living organisms begin to decompose shortly after death. It is a cascade of processes that go through distinct phases. It may be categorized in two stages by the types of end products. The first stage is limited to the production of vapors. The second stage is characterized by the formation of liquid materials; flesh or plant matter begin to decompose. The science which studies such decomposition generally is called taphonomy from the Greek word taphos - which means grave. Besides the two stages mentioned above, historically the progression of decomposition of the flesh of dead organisms has been viewed also as four phases: (1) fresh (autolysis), (2) bloat (putrefaction), (3) decay (putrefaction and carnivores) and (4) dry (diagenesis).

ANIMAL DECOMPOSITION
Ants cleaning dead snake
Decomposition begins at the moment of death, caused by two factors: autolysis, the breaking down of tissues by the body's own internal chemicals and enzymes and putrefaction, the breakdown of tissues by bacteria. These processes release gases that are the chief source of the unmistakably putrid odor of decaying animal tissue. Most decomposers are bacteria or fungi. Scavengers play an important role in decomposition. If the body is accessible to insects and other animals, they are typically the next agent of decomposition. The most important insects that are typically involved in the process include the flesh-flies (Sarcophagidae) and blow-flies (Calliphoridae). The green-bottle fly seen in the summer is a blowfly. The most important animals that are typically involved in the process include larger scavengers, such as coyotes, dogs, wolves, foxes, rats, and mice. Some of these animals also remove and scatter bones. Then they digest the bones.

PRINCETON ECOLOGY EDUCATION SERVICES
Nature Notes: Recycling Nutrients - The Decomposition Process
Recycling is an excellent stewardship activity since it can reduce the depletion of Earth's natural resources, as well as the number of landfills needed for storing our waste. However, in the natural world, recycling is not an optional event. Every living thing is made up of a variety of elements (e.g., carbon, hydrogen, and nitrogen) that are essential for existence. The total amount of these elements on planet Earth has not changed over millions of years. For example, the amount of water (hydrogen and oxygen elements combined) present today is the same amount that existed when dinosaurs roamed the Earth. If these elements were not recycled, life would cease to exist since nature would rapidly exhaust its supply of these nutrients.
Technically we call the circular movement of elements biogeochemical cycles since these chemicals, over a period of time, move through the living and nonliving environment. The term "nutrient cycle" is really a generalized designation for the different biogeochemical cycles of many different elements. It could, for example, be the water cycle, the oxygen cycle, the carbon cycle, the phosphorus cycle or the nitrogen cycle. When inorganic elements pass through living organisms they often become bound up as complex organic substances (e.g., organic molecules called carbohydrates contain the inorganic elements carbon, hydrogen and oxygen). When organisms die in both terrestrial and aquatic ecosystems, their bodies represent a reservoir of inorganic elements (nutrients). However, nature needs to separate the elements from their bound up state so that they can be recycled. All dead organic matter (dead bodies of all living things, as well as animal feces and shed body parts like snake skin) is called detritus. Some elements are removed from detritus by the leaching action of water. However, most removal occurs from the action of organisms called detritivores (pronounced di try' ti vores) and decomposers.

Detritivores digest the organic matter internally after ingesting it. They speed up decay by shredding the dead matter, thereby increasing the surface area for attack by the decomposers - bacteria and fungi (e.g., mushrooms). Both bacteria and fungi have the capacity to release enzymes that break apart the organic molecules, thereby releasing the inorganic elements into the environment (e.g., soil or water). This process is called decomposition. Some of these elements are then taken inside the bacteria or fungus to provide them with nutrients, as well as energy; those that are not taken in may be absorbed by plants and are eventually passed to herbivores and carnivores in the food chain. Nutrient cycling within an ecosystem is not a perfect process because some nutrients may be lost from the ecosystem as a result of soil erosion.

Detritivores and decomposers play a vital ecological role in assuring the survival of plants, and thus all life, by recycling nutrients back to them. Also, detritivores and decomposers are nature's garbage collectors - insuring that an ecosystem will not suffocate under a mass of dead matter.

Some books erroneously list organisms such as termites and earthworms as decomposers. They loosely use the terms detritivore and decomposer synonymously. This is a mistake. While detritivores increase the surface area for decomposition, they are not true decomposers since they do not convert dead tissue into inorganic elements.
The rate of decomposition is affected by a variety of abiotic (nonliving) factors. For example, decomposition is reduced by low temperature, poor aeration of the soil, a lack of moisture and acidic conditions.

A gardener who composts lawn matter and food remains works to overcome these limitations in order to accelerate decomposition. By creating the proper environment for detritivores and decomposers, the outcome will be nutrient rich matter that will stimulate the growth of plant life. Composting is an excellent stewardship activity, in which students can observe the decomposition process, detritivores and decomposers.

Detritus - Dead organic matter. It includes the dead bodies of all organisms, as well as fecal matter and shed body parts (e.g., snake skin, outer shell of crayfish after it is molted).

Detritivore - Organism that eats detritus. These are important in decomposition, but they are not decomposers. The term scavenger specifically refers to animals that feed on dead animals or their remains.

Decomposer - Organism (bacteria or fungi) that is able to release enzymes outside of its body in order to digest organic matter into inorganic elements.
Decomposition - gradual disintegration of dead organic matter resulting in the release of energy and inorganic elements from their organic state.

REFERENCES
Wetzel, R. G. 2001. Limnology: Lake and River Ecosystems. Academic Press. 3rd. p.700.
Nitrogen in Benthic Food ChainsPDF, Tenore, K.R., SCOPE publication.
Hershey DR. 1999. Myco-heterophytes and parasitic plants in food chains. American Biology Teacher 61:575-578.
Leake JR. 2005. Plants parasitic on fungi: unearthing the fungi in myco-heterotrophs and debunking the ‘saprophytic’ plant myth. The Mycologist 19:113-122.
Werner PG. 2006. Myco-heterotrophs: Hacking the mycorrhizal network. Mycena News 57:1,8.
Beare MH, Parmelee RW, Hendrix PF, Cheng W (1992) Microbial and faunal interactions and effects on litter nitrogen and decomposition in agroecosystems. Ecological Monographs 62: 569-591
Hunt HW, Coleman DC, Ingham ER, Ingham RE, Elliot ET, Moore JC, Rose SL, Reid CPP, Morley CR (1987) "The detrital food web in a shortgrass prairie". Biology and Fertility of Soils 3: 57-68
Smith TM, Smith RL (2006) Elements of Ecology. Sixth edition. Benjamin Cummings, San Francisco, CA.
Swift MJ, Heal OW, Anderson JM (1979) Decomposition in Terrestrial Ecosystems. University of California Press, Berkeley, CA.