Microorganisms & Nutrient Cycling

A microbiome is the community of bacteria, archaea, fungi and viruses living in a defined habitat, together with their genes. Sequencing technology has shown these communities are far larger and more important than once thought.

The human microbiome

Trillions of microorganisms live on the skin, in the mouth and airways, and above all in the large intestine. The gut microbiome:

• digests fibre that human enzymes cannot break down, releasing short-chain fatty acids the gut lining uses for energy
• synthesises vitamin K and several B vitamins
• competes with pathogens for space and nutrients, and trains the immune system
• influences metabolism, weight and even mood through the gut-brain axis

Diet, antibiotics, stress and birth method shape it. Broad-spectrum antibiotics can wipe out helpful species and allow Clostridioides difficile to take over; faecal microbiota transplant can restore a healthy community. Fibre-rich foods and fermented foods support diversity, and low diversity is linked to obesity, allergy and inflammatory bowel disease.

The soil microbiome

A teaspoon of healthy soil holds billions of microorganisms. They decompose dead material and return nutrients, drive the nitrogen cycle through nitrogen fixation, nitrification and denitrification, and form mycorrhizal partnerships in which fungi extend a plant's root system in exchange for sugars. Microbial products bind soil particles into crumbs, improving structure, drainage and carbon storage.

Ploughing, monoculture, pesticide use and compaction reduce soil microbial diversity, which lowers fertility and increases the need for artificial fertiliser. Crop rotation, cover crops, reduced tillage and adding organic matter rebuild it. Soil microbes are also the source of most antibiotics in use today.

A growth curve plots cell numbers against time and has four phases: lag (cells adapt and make enzymes), log (exponential growth while nutrients are plentiful), stationary (growth rate equals death rate as nutrients run low and waste builds up) and decline (deaths exceed new cells).

Why the phase matters

Primary metabolites such as ethanol, lactic acid and enzymes are produced during the log phase, because they are made as part of normal growth. Secondary metabolites such as penicillin are produced mainly in the stationary phase, when growth has slowed. Knowing which product is wanted tells the operator when to harvest and how long to run the fermenter.

Controlling the fermenter

A bioreactor keeps conditions at the optimum so the culture stays productive: temperature control by a water jacket, pH adjusted automatically, sterile air supplied for aerobic processes, and a stirrer to keep cells, oxygen and nutrients evenly distributed. Everything is sterilised first so no competing microbe uses the nutrients or spoils the product. Probes monitor pH, oxygen, temperature and cell density throughout.

Batch versus continuous culture

In batch culture the fermenter is filled, run through the full curve, harvested and cleaned. It suits secondary metabolites and makes contamination easy to contain. In continuous culture nutrients are added and product removed at a steady rate, holding the population in the log phase indefinitely. This gives a much higher output for primary metabolites, but any contamination ruins the whole run.

Yield can be improved further by selecting or genetically modifying high-producing strains, optimising the nutrient medium, and immobilising the cells so they can be reused and the product stays uncontaminated.