Environmental Microbiology 101: Microbial Habitats

Welcome to the AppliedMicrobio blog! This post is the first in a series that will introduce some basic concepts in environmental microbiology. I hope to leave you with a better understanding of the microorganisms in the world around us and how their habitats shape their lives.

Microorganisms are often associated with human disease, and many people think of them as harmful organisms. As a microbiologist, this makes me sad, because there is so much more to microbes than just making people sick! Our bodies are covered with microorganisms that, rather than harm us, actually protect our health. The human skin, mouth, and digestive system each host their own unique microbial communities. But even these represent only a fraction of the microbes on earth.

There are microbial populations in oceans, lakes, and rivers. Microbes are found in soils, on plants, and within plant tissues. Even the air around us hosts a diverse microbial community. Environmental microbes are key drivers of nutrient cycling, transforming waste materials back into simple compounds. Microbes fix carbon and nitrogen from the atmosphere, adding organic material to the ecosystem and serving as the base of the food chain. In the 21st century, they have also taken on a role in processing human-caused pollution in the environment.

These microorganisms are as varied as the habitats in which they dwell. But despite their differences, almost all microbes are controlled by a few simple factors.

Habitat needs of microorganisms

On a fundamental level, microorganisms have many of the same needs as macroorganisms, those we can see without the aid of a microscope. Just like animals and plants, microbes want to grow and reproduce, and they need water, food, and space to do it. The specific moisture, temperature, and nutrient needs of a microorganism determine what habitats can support its growth.

Water: Because so many cellular processes require water, microbial life is heavily influenced by available moisture. Ecosystem pH is also important, and a pH outside the typical range limits which organisms can live in an environment.

Temperature: Enzymes, the proteins that carry out many key roles in cells, can only function within a certain temperature range. In lower temperatures, enzymes work slower and microbial growth is limited. In higher temperatures, the enzymes can denature, or permanently lose their shape, and stop functioning entirely.

Nutrient availability: microorganisms need carbon, nitrogen, oxygen, and a wide array of other nutrients in quantities that vary by species. There are two broad categories of nutrient use in microbes. Copiotrophs thrive in environments where nutrients are plentiful and readily available. Oligotrophs prefer environments with lower nutrient availability. They have developed specialized features, such as increased quantities of transport proteins to bring nutrients into the cell.

While most organisms thrive in habitats with moderate conditions, there are exceptions to every rule. Microbes known as extremophiles can live and thrive under extreme conditions. Psychrophiles are bacteria that survive in extreme cold environments like the icy permafrost layer, while thermophiles thrive in the heat. There are acidophiles, acid-loving bacteria, living in the geysers of Yellowstone at a pH of 1.0, which would melt flesh off a macroorgnisms's bones. And in the deepest regions of the ocean, piezophiles thrive in pressures greater than 1000 atmospheres. By necessity, many of these organisms are polyextremophiles, meaning they are tolerant of several types of extreme conditions. The Yellowstone geyser bacteria, for example, can tolerate both high acidity and high heat.

As evidenced by the existence of extremophiles, microorganisms have evolved to live practically everywhere on the planet. Two of the most well-studied microbial habitats are water and soil.

Aquatic Habitats

Aquatic habitats are typically low-nutrient environments with thriving microbial communities whose populations are controlled by oxygen and organic matter availability. Producers in the ecosystem make organic matter via photosynthesis and create oxygen as a byproduct, while consumers use organic matter and oxygen for growth, maintaining the balance. When too much organic matter is added, like when nutrient pollution from agriculture runs off into waterways, the consumer populations expand rapidly, using up all the oxygen in the area and creating a dead zone where oxygen is depleted to below livable levels.

The most common bacterial groups in aquatic ecosystems are Proteobacteria, Actinobacteria, Bacteroidetes, Cyanobacteria, and Verrucomicrobia. Dominant archaeal groups are Euryarchaeota, Chrenarchaeota, and Thaumarchaeota.

In freshwater environments, the balance between these organisms varies seasonally. During the warm summer months, the upper layers of the water column heat up along a gradient, while the lower layers remain cool. There is little movement or mixing between layers and distinct communities exist within each. As temperatures drop and the upper layers cool, the water column begins to mix, bringing nutrients and oxygen to lower layers and allowing the microbial community to mingle until spring, when the water column gradually heats up and the layers re-form.

Ocean ecosystems are extremely low in nutrients, so the constraints observed in freshwater ecosystems are magnified. Microbial diversity and total microbial population are both lower. Key organisms in the open ocean include the genus Prochlorococcus, responsible for much of the primary productivity, and Pelagibacter, one of the most abundant organisms on the planet and a major consumer of dissolved organic matter. When these microbes are consumed by larger organisms, they add the organic carbon to the marine food chain.

Soil Habitats

Soils are made up of small particles of sand, silt, and clay held together in aggregates by microbial biofilms. Tiny pores within the aggregates hold water, and that water acts as a habitat for microorganisms. Microbes can also live on the particulate surface.

Soil environments are typically highly heterogeneous, or well-mixed, with particles and aggregates of varying size throughout. There may be a large aggregate with plentiful nutrients and a bustling microbial population only an inch away from a barren zone with few nutrients or microbes. These microhabitats scattered throughout the soil support populations with different species composition and function. The most common microbial phyla in soil systems are Proteobacteria, Acidobacteria, Bacteroidetes, and Actinobacteria, with smaller numbers of Firmicutes and Verrucomicrobia. Archaea groups include Thaumarchaeota and Euryarchaeota. Despite similarities across soils at the phylum level, the genus- and species-level composition of the communities is unique to each soil environment. For this reason, it can be hard to define a "core" set of key soil microbes.

Nitrogen, phosphorus, and potassium are important limiting nutrients in many soil systems. Oxygen can be limiting or plentiful depending on the soil's structure and environmental conditions. In loose, porous soils, oxygen moves freely between particulates and diffuses easily into pore water. In compacted or water-logged soils, oxygen may become depleted in some regions of the soil matrix, creating dead zones similar to those in the oceans, though on a much smaller scale.

Plants are another important factor in shaping the soil microbial community. The area directly around plant roots is called the rhizosphere, and it has up to 100 times as many microbes as bare soil with no plants. Rhizosphere microbes engage in significant nutrient exchange with plants at the surface of their roots. There are even some microbial groups that live within roots. These bacteria, of the genera Rhizobia and Frankia, produce nitrogen for the plants in exchange for the protection offered by the root habitat.

Even within the well-studied water and soil ecosystems, many microorganisms remain a mystery. Only about 1% of the microbes on earth can be grown in a lab for study. The rest depend on the complex conditions in the water or soil, conditions that are impossible to fully replicate in a lab, for survival. In other words, most microbes simply can't grow alone, which I think is kind of sweet. It certainly mirrors the interconnected ecosystems of macro organisms. This issue limited our understanding of microbes for many years, until DNA sequencing technologies led to a leap in our ability to study communities.

Genomic methods expand our microbial knowledge

For most of its time as a field, microbial ecology has been limited by the 1% rule. We could culture a few microbes from a particular habitat and use what we learned to make inferences about the identity and function of other members of the community. Fortunately, this all changed with the introduction of 16S rRNA sequencing and other molecular biology techniques.

16S sequencing allows us to determine the exact identity of microorganisms in a habitat. The technique determines the sequence of a region of the 16S gene, which is possessed by all bacteria, and compares the sequence to an extensive database to identify the organism.

Thanks to many years of building up a global database, microbiologists can now identify the microbes in environmental habitats and infer potential function. This can be done indirectly, with knowledge of what functions have been previously associated with what microorganisms. Or the genes themselves can be identified with whole-genome sequencing, which determines the sequence of not just the 16S gene, but all of the genes from all microbes in a habitat. We can even determine which of those genes are being actively used to make proteins with a method called transcriptomics. Genomic techniques have helped environmental microbiology to develop into a robust field working to understand how the microbes around us work together to survive and thrive.

I hope you enjoyed learning about microorganisms in some of earth's best-studied habitats! In the coming weeks, I will dive deeper into some of the topics introduced above. I will also discuss the ways we can apply environmental microbiology concepts to address environmental challenges! Wondering how you can harness the power of microbes to address your environmental science questions? Reach out to AppliedMicrobio today!

References

Kirchman, D. L. 2012. Processes in Microbial Ecology. Oxford, United Kingdom: Oxford University Press.

Madigan, M. T., K. S. Bender, D. H. Buckley, W. M. Sattley and D. A. Stahl. 2017. Brock Biology of Microorganisms. New York, USA: Pearson.