Microbes in Bodies and Ecosystems

Dig up a soybean plant and you can find small round bumps on its roots, and if you cut one open, an active one is often pink inside. Those bumps are packed with bacteria that turn nitrogen from the air into a form the plant can use.

Your own gut also holds trillions of bacteria, and some of them help break down your food. Yet most of us learn the word “bacteria” next to the word “germs.” So which is it: are bacteria and viruses enemies, or are they partners that life depends on?

Explore: switch microbes off in an ecosystem

The simulation shows a simple ecosystem: a field with soybeans, a stream with fallen leaves, a deer, a person and some ocean water. You can switch off one group of microbes at a time: decomposers, nitrogen fixers, gut bacteria, pathogens, or viruses that infect bacteria. Bars show how much matter is moving along each path and how large each population is, using numbers meant only for comparison.

Switch off one group of microbes

None (all microbes working) Decomposers Nitrogen fixers Gut bacteria Pathogens Viruses that infect bacteria

Time after switching off: step 4 of 4 (relative steps, not days or years)

Reset

In this sketch: every bar starts at 100 (relative units, not a measurement) and one group is off at a time. Steps are not days or years. Only the soybean 47 comes from the lesson; every other direction and size is a display assumption, not to scale.

Rule to keep: microbes keep matter moving and shape populations, and whether a microbe helps or harms depends on which microbe it is and where it lives.

Try this.

1. Before you switch off the decomposers, predict what will happen to the pile of dead leaves and to the nutrients in the soil. Then test it.
2. Switch off the nitrogen fixers. Predict which population changes first, the soybeans or the deer that eat plants.
3. Switch off the pathogens. Predict whether the deer population grows without limit or levels off. Watch what happens to the plants.
4. Switch off the viruses in the ocean water. Predict what happens to the number of bacteria and to the nutrients dissolved in the water.

Explain: microbes that keep matter moving

Breaking down the dead

A decomposer is an organism that breaks down dead plants, animals and wastes and returns their nutrients to the soil or water. Bacteria and fungi do most of this work. In an Ohio stream study, both bacteria and fungi grew on fallen maple and oak leaves. These microbes release enzymes that break the large molecules in leaves into smaller ones. Without decomposers, dead matter would pile up and its nutrients would stay locked inside it.

Feeding plants nitrogen

Living things use nitrogen to build proteins and DNA. The air is mostly nitrogen gas, but plants and animals cannot use it in that form. Nitrogen fixation is the change of nitrogen gas from the air into a form living things can use. Only some bacteria and archaea (another group of microbes) can do it.

In soybeans, peanuts and other legumes, these bacteria live inside a nodule, a small swelling on a root that holds nitrogen-fixing bacteria. The bacteria turn nitrogen gas into ammonium, which the plant uses. The plant sends the bacteria energy-rich food made by photosynthesis. A partnership in which both species benefit is called mutualism.

nitrogen gas from the air → bacteria in root nodules → ammonium the plant can use → plant proteins and DNA

When a soybean plant dies, decomposers break down its roots and stems, and some of that fixed nitrogen returns to the soil. You can read more about the whole cycle in Matter Cycles.

Explain: partners in your body, and pathogens

Your gut microbiome

The microbiome is the community of microbes that live in or on a body. In 2016 Ron Sender, Shai Fuchs and Ron Milo estimated that a reference adult man weighing 70 kg carries about 38 trillion bacterial cells and about 30 trillion human cells. Most of those bacteria live in the large intestine.

Your body cannot digest some parts of plant food, called fiber. Gut bacteria break fiber down by fermentation, a process that breaks down food molecules without oxygen. Fermentation of fiber makes small acids that your body can absorb and use as a source of energy. Diet matters to these partners. In a 2016 study, mice carrying a set of human gut bacteria and fed a low-fiber diet had gut bacteria that began feeding on the protective mucus that lines the gut.

Foods and medicines

People have used bacteria for a very long time. Yogurt forms when two kinds of bacteria ferment the sugar in milk and release lactic acid, which thickens the milk and makes it sour. In 1979, researchers reported that E. coli carrying lab-made genes for human insulin made the two parts of insulin, showing that bacteria can be used to make human medicines. More on this comes in Engineering Genes.

Pathogens

A pathogen is a microbe or virus that causes disease in its host, the living thing it lives in or on. Pathogens attack all kinds of hosts:

Host	Pathogen	What it does
Grapevine	the bacterium Xylella fastidiosa	causes Pierce’s disease, which blocks the vine’s water-carrying tubes
Cattle	the bacterium Mycobacterium bovis	causes bovine tuberculosis
Humans	the bacterium Helicobacter pylori	causes inflammation of the stomach lining
Birds and humans	West Nile virus, spread by mosquitoes	causes illness, sometimes severe

How we prevent and treat these diseases is the subject of Germs, Vaccines and Antibiotics.

The same bacterium can be a partner in one place and a problem in another. E. coli usually lives quietly in the large intestine, but some strains cause illness when they get into food or water.

Explain: viruses and diseases reshape ecosystems

A bacteriophage (phage for short) is a virus that infects bacteria. Ocean water holds enormous numbers of phages and other viruses. When a virus bursts its host cell, the cell’s contents spill into the water. Researchers estimate that in surface waters viruses kill a large share of the ocean’s bacteria and archaea every day, though the estimates are rough and vary from place to place.

What happens to those spilled contents? In a lab model ecosystem, Jakob Haaber and Mathias Middelboe let a virus infect an ocean alga called Phaeocystis. Bacteria then broke down the dead algae. The water gained about 148 micrograms of nitrogen and 7 micrograms of phosphorus per liter that other living things could use.

Viruses can also affect biodiversity, the variety of living things in a place. A virus usually infects only certain kinds of bacteria. When one kind becomes very common, its viruses can spread faster and cut it back, which may leave room for other kinds. A 2019 experiment on coastal water found that when viruses switched from lying hidden inside bacteria to bursting them, the bacterial community became more diverse.

On land, disease can reshape whole landscapes. In the Serengeti in East Africa, the virus disease rinderpest disappeared in the 1960s. Wildebeest numbers then rose, they ate more grass, fewer fires burned, and more trees grew.

Elaborate: how much nitrogen do nodules add?

Year	Sampling date	Soybean type	Total nitrogen above ground (kg N/ha)	Nitrogen from fixation (kg N/ha)
2006	13 Sept	Nodulating	282	195
2006	13 Sept	Non-nodulating	150	not applicable
2007	12 Sept	Nodulating	144	95.0
2007	12 Sept	Non-nodulating	67.6	not applicable
2008	23 Sept	Nodulating	148	90.3
2008	23 Sept	Non-nodulating	61.6	not applicable

These are means from a field trial by Snapp, Wilke, Gentry and Zoellner, published in 2017, at the Kellogg Biological Station in Hickory Corners, Michigan. Both soybean types were Williams 82 plants, nearly identical except that one cannot form nodules. Each value is a mean over several farming systems, for one growing season. A hectare is an area of 10,000 square meters, about one and a half soccer fields. “Nitrogen from fixation” was estimated with nitrogen isotopes, so it is not the same as the difference between the two rows.

1. In 2006, how much more nitrogen did nodulating plants hold than non-nodulating plants? Write it as a percentage of the non-nodulating value.
2. Which year had the most nitrogen from fixation? Was the gap between the two soybean types the same every year?
3. Find the mean nitrogen from fixation over the three years.

Design problem

Plan an investigation to test whether adding nodule bacteria helps soybeans grow in nitrogen-poor soil. Name your variables, your control, what you keep the same, how many plants you use, and how you keep it safe.

One way to do it

• Question: does adding nodule bacteria increase soybean growth in soil low in nitrogen?
• Independent variable: nodule bacteria added (a garden-store legume inoculant made for soybeans) or not added.
• Dependent variables: dry plant mass after six weeks, the number of nodules per plant, and how many split nodules are pink inside.
• Control: pots of the same sterile, nitrogen-poor potting mix with no inoculant. Sterile mix matters, because ordinary soil may already hold nodule bacteria.
• Constants: the same seed batch, pot size, amount of soil, water, light and temperature. Add no nitrogen fertilizer to either group.
• Sample size and trials: at least 10 pots per group, with pots mixed together on the shelf so neither group gets the better light. Find the mean for each group. Repeat the whole test if you can.
• Safety: wear gloves when handling the inoculant and soil, follow the product label, and wash your hands afterwards.
• What results would mean: if the inoculated plants have more nodules and a higher mean mass, that supports a benefit from the bacteria in these conditions. If both groups match, the bacteria may not have formed nodules, so check the roots.

Evaluate: check your thinking

The pink bumps on a soybean root are nodules where bacteria turn nitrogen from the air into a form the plant uses, in exchange for food from the plant. Bacteria in your gut ferment fiber, and decomposers recycle dead matter. Some bacteria and viruses cause disease, and even they shape ecosystems, so whether a microbe helps or harms depends on which microbe it is and where it lives.

Science practices you used: predicting and testing in a model ecosystem, reading a data table and calculating a difference, a percentage and a mean, planning a fair test with a control and many plants, and naming the limits of one study’s data.