Name: microbial communities in soil and extremes
Uploaded: 2026-03-12T13:57:28.000Z
Duration: 1 min 28 s
Channel: JoVE

K12 Standards

Alabama Course of Study Science

9-12

Environmental Science

Unity and Diversity

9-12.EVS.2.3.b

Introduction to Microbial Ecology

Microbial ecology is the study of microbial diversity and how microorganisms interact within various ecosystems.An ecosystem is a functional unit where microbes interact with both biotic and abiotic factors.In these ecosystems, habitats like leaves, roots, and soil host many microbes. Microbes of the same species form a population.When different populations coexist and interact in a habitat, they form a microbial community.All microorganisms within an ecosystem constitute the microbiota, and the total collection of their genetic material is referred to as the microbiome.Microbial diversity within communities is measured by species richness and relative abundance, both of which are influenced by factors such as nutrient availability and environmental conditions, including temperature, pH, and oxygen levels.For example, nutrient-rich soils support high species richness, with many microbes coexisting at moderate abundances.On the other hand, extreme ecosystems like acidic, iron-rich lakes support low species richness but high abundance of specialized microbes, such as Acidithiobacillus ferrooxidans.

introduction to microbial ecology

Microbial ecology examines the complex web of interactions and diversity among microorganisms within various ecosystems. This field seeks to understand how microbial populations adapt to and influence their environments and how these interactions shape broader ecological processes. Microbes are integral to ecosystem function, participating in nutrient cycling, energy flow, and the maintenance of environmental homeostasis.An ecosystem represents a dynamic interaction between living organisms (biotic components) and their non-living (abiotic) environment. Microorganisms thrive in distinct habitats within these ecosystems, forming populations&#8212;aggregates of the same species residing together at a particular time. When microbial populations from different species coexist and interact, they constitute a microbial community. These communities are not static; they evolve in response to environmental pressures, resource availability, and interspecies interactions.Microbial diversity is characterized by species richness&#8212;the number of species present&#8212;and species abundance&#8212;the relative number of individuals of each species. These parameters are influenced by the ecosystem's physical and chemical properties, including nutrient levels, pH, temperature, and moisture. For instance, in fertile, organic-rich soils, high species richness is observed, with numerous microbial species coexisting at moderate abundance. Such environments provide niches for various metabolic pathways, enabling coexistence through resource partitioning.When a microbial community becomes established within a particular environment, it is known as the microbiota&#8212;though the term is often used for host-associated communities as well. The collective genome of these microorganisms is called the microbiome, which reflects the functional potential of the community. Microbiomes are essential for understanding the metabolic capabilities and ecological roles of microbes in their environments.On the other hand, extreme environments&#8212;such as acidic, iron-rich lakes&#8212;support specialized microbial life. These habitats show low species richness due to harsh conditions but the high abundance of certain extremophiles. For example, Acidithiobacillus ferrooxidans, a chemolithoautotroph, dominates such niches by oxidizing ferrous iron and surviving in low pH conditions, illustrating microbial life's adaptability and ecological specialization in extreme settings.

Microbial ecology examines the complex web of interactions and diversity among microorganisms within various ecosystems. This field seeks to understand ...

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Education

JoVE Core

Microbiology

Unit

Microbial Ecology

KEY TERMS AND CONCEPTS

microbial communities in soil and extremes

Microbial ecology looks at how microorganisms live, interact, and adapt in different ecosystems. It also shows how these tiny organisms help shape nutrient cycling, energy flow, and environmental balance. An ecosystem includes living parts and non-living parts, and microbes respond to both.

Microorganisms can form populations, which are groups of the same species living together at the same time. When populations from different species live and interact in the same place, they form a microbial community. These communities change over time as conditions, resources, and interactions with other species change.

Microbial diversity is often described using species richness and species abundance. Species richness means the number of species present. Species abundance means how many individuals of each species are present. These patterns depend on physical and chemical features such as nutrients, pH, temperature, and moisture.

Rich soils with lots of organic matter can support high species richness. Many different microbial species can live there at moderate abundance. These habitats offer multiple niches, so different metabolic pathways can coexist through resource partitioning.

When a microbial community becomes established in a specific environment, it is called the microbiota. The term is also often used for communities that live in or on a host. The microbiome is the collective genome of these microorganisms, and it helps show the community’s functional potential.

Extreme environments can support fewer species but many specialists. Acidic, iron-rich lakes are one example. In these harsh habitats, low species richness is common, but some extremophiles can become highly abundant. Acidithiobacillus ferrooxidans is one such chemolithoautotroph. It survives low pH by oxidizing ferrous iron, which shows how microbes can specialize for very difficult conditions.

Microbial Communities in Soil and Extremes

microbial-communities-in-soil-and-extremes

Microbial ecology looks at how microorganisms live, interact, and adapt in different ecosystems. It also shows how these tiny organisms help shape nutrient cycling, energy flow, and environmental balance. An ecosystem includes living parts and non-living parts, and microbes respond to both. Microorganisms can form populations, which are groups of the same species living together at the same time. When populations from different species live and interact in the same place, they form a microbial...

ecological niche

Microbial Niches in Ecosystems

Microbial niches describe how microorganisms survive, grow, and interact in an ecosystem. A niche includes how a microbe gets resources, reproduces, and relates to other species in its environment. This idea helps explain microbial community dynamics, biogeography, and ecosystem function. A microorganism’s fundamental niche is the full range of conditions where it could survive, grow, and reproduce. These conditions include both biotic factors, such as living interactions, and abiotic factors,...

methods to assess microbial populations

Measuring Microbes in Samples

Measuring microbes in a sample helps scientists study health, ecology, and industry. Microbial counts can show how many cells are present, how diverse they are, and what they may be doing. To do this, researchers use both culture-based and molecular methods. A viable plate count is a classic culture method for estimating living microbes. The sample is first diluted step by step, then spread on nutrient agar plates. Each viable cell can grow into a visible colony, so the colonies can be counted.

methods to assess microbial communities

Measuring Microbial Diversity and Activity

Microbial communities include bacteria, archaea, and eukaryotic microorganisms. They live in many ecosystems and affect important environmental and biological processes. Scientists study these communities by looking at how many species are present, how many individuals each species has, and how evenly the species are spread out. Species richness is the number of different species in a sample. Species abundance is the relative amount of each species. Species evenness describes how uniformly the...

the winogradsky column

Microbial Layers Inside a Winogradsky Column

A Winogradsky column shows how microbial layers form in a simple, sealed ecosystem. It is a clear model for studying microbial ecology and how different metabolisms interact in sediment over time. The setup uses a transparent glass cylinder. Half of it is filled with sediment mixed with cellulose, such as shredded paper, calcium carbonate, and gypsum. The cellulose provides a carbon source. Calcium carbonate buffers pH, and gypsum supplies sulfate. The rest of the cylinder is filled with pond...

microenvironments

Microbial Niches in Tiny Habitats

Microorganisms live in tiny habitats called microenvironments. These spaces have their own physical and chemical conditions. Oxygen level, pH, temperature, light, and nutrient supply can all differ from the surrounding area. These local conditions strongly affect microbial growth, metabolism, and which species can live there. Microenvironments often have sharp gradients over very small distances. In soil, oxygen may be available at the particle surface but drop off just a few millimeters below.

microbial mats

Microbial Mats and Oxygen Gradients

Microbial mats are layered communities of microbes that grow in response to changes in light, oxygen, and nutrients. These ecosystems are highly organized, and different microorganisms live at different depths. Biofilms are the early stage of this growth and are only a few millimeters thick. Mature microbial mats can grow to centimeter scale and show clear vertical structure. This layered arrangement lets microbes fill separate niches within a very small space. In cyanobacterial mats from hot...

microbial interactions: mutualism

Mutualistic Partnerships in Nature

Mutualistic partnerships in nature show how two or more organisms can benefit from living together. These symbiotic relationships can be obligate, meaning the partners depend on each other, or facultative, meaning the association is helpful but not required. Mutualism helps support many ecosystem functions across land and water. One common example is the partnership between plant roots and mycorrhizal fungi, such as Rhizophagus species. The fungal hyphae grow into the root hairs and epidermis,...

microbial interactions: cooperation

Microbial Cooperation in Soil and Hosts

Microbial cooperation describes helpful interactions between different species. In these partnerships, microbes work together for one or mutual benefit. These interactions can shape ecosystems and evolution. They also play major roles in symbiosis and disease. One clear example involves the Gram-negative bacterium Xenorhabdus nematophila and the parasitic nematode Steinernema carpocapsae. Juvenile nematodes carry the bacteria in the soil and need an insect host to mature. When the nematode...

microbial interactions: predation

How Microbes Hunt and Defend

Microbial predation is a form of interaction in which one microorganism kills and eats another to gain nutrients and energy. It includes both bacterial predators and protozoan predators. This process helps shape microbial communities and affects how nutrients move through the environment. Some bacterial predators attack from the outside, while others enter the prey cell. Epibiotic predators, such as Vampirococcus, attach to the surface of a prey cell and release hydrolytic enzymes. These...

microbial interactions: competition

Microbial Competition and Niche Partitioning

Microbial competition shapes how bacteria and other microbes share space and resources. In shared environments, they compete for nutrients, space, or light. The strength of this competition depends on the environment, including nutrient levels, space limits, and how many microbial species are present. These interactions help determine the structure, function, and resilience of microbial communities. Microbial competition is usually grouped into exploitative competition and interference...

microbial interactions: parasitism

Microbial Parasites and Host Dependence

Microbial parasites depend on a host for nutrients and shelter, and this dependence often harms the host. In parasitism, only the parasite benefits. This is different from mutualism, where both organisms gain from the relationship. Microbial parasites are classified by where they live in or on the host. Ectoparasites stay on the host’s surface, such as the skin or outer tissues, and take in nutrients from outside. Endoparasites live inside the host’s body and invade tissues or organs.

microbe-plant interactions

How Plant Microbes Affect Growth

Plant microbes can help, harm, or simply live alongside their hosts. These microbe-plant interactions shape plant growth, health, and ecosystem function. The plant microbiome includes bacteria, fungi, archaea, protists, and viruses, and these organisms may live on the plant surface, inside plant tissues, or in symbiosis throughout the plant. Some of the most important beneficial partnerships involve mycorrhizal fungi. These fungi form close connections with roots and are grouped as arbuscular...

microbes and the carbon cycle

How Microbes Move Carbon Through Earth

Microbes move carbon through Earth’s major reservoirs and help drive the carbon cycle. Carbon shifts among the biosphere, lithosphere, atmosphere, and hydrosphere, where it supports life and helps regulate climate. It commonly cycles as carbon dioxide (CO2), the oxidized form of carbon, but methane (CH4) and organic compounds also matter. Photosynthetic microbes take in atmospheric CO2 and turn it into organic carbon. Cyanobacteria are especially important because they carry out oxygenic...

microbes and methanogenesis

How Microbes Produce Methane

Methane production in anaerobic ecosystems depends on methanogenic archaea and the microbes that work with them. This process happens where oxygen is absent, such as wetlands, sediments, and animal gastrointestinal tracts. In these anoxic habitats, aerobic respiration cannot run, so microbes use other pathways to break down organic matter. Anaerobic decomposition starts when cellulolytic bacteria, or cellulose-digesting bacteria, hydrolyze dead organic material into simple sugars. Other...

microbes and the nitrogen cycle

Microbial Steps in the Nitrogen Cycle

Microbes drive the nitrogen cycle by changing nitrogen into forms that plants and other organisms can use. This biogeochemical cycle keeps nitrogenous compounds balanced in ecosystems. It also supports plant growth and microbial growth. Nitrogen fixation begins the cycle by converting inert atmospheric nitrogen gas, N2, into ammonia, NH3. This step depends on nitrogenase enzymes. Free-living diazotrophs do this on their own. Aerobic bacteria such as Azotobacter spp. and anaerobic bacteria such...

microbes and the sulfur cycle

Sulfur Cycling Through Microbial Reactions

Sulfur cycling depends on microbial reactions that move sulfur through rocks, water, soil, and the air. In Earth systems, sulfur shifts among inorganic forms such as sulfate, elemental sulfur, and sulfide. These changes happen through both abiotic processes and biological activity in oxic and anoxic environments. Sulfate is the most oxidized form of sulfur. It is stored mainly in rocks, marine sediments, and ocean water, where it acts as a long-term reservoir in the global sulfur cycle. In...

microbes and other elemental cycles

Microbes Driving Iron and Manganese Cycles

Microbes drive iron and manganese cycling in aquatic environments by changing these metals between reduced and oxidized forms. These reactions are especially important along redox gradients, where oxygen levels shift across stratified water layers. The microbes use these metals for energy, growth, and structural needs. In oxygen-rich surface waters, iron is usually present as insoluble ferric iron, Fe(III). Some bacteria release siderophores, which are small organic molecules that bind ferric...

marine microbial ecology

Microbial Life in the Ocean

Marine microbial life is shaped by salinity, low nutrients, and changing oxygen levels. These physical and chemical limits influence which microbes can survive and how they function. They also affect how ocean microbes help drive nutrient and carbon cycling. Small cell size is common in these environments because it gives microbes a larger surface-to-volume ratio. That helps them take up nutrients more efficiently when nutrients are scarce. In estuaries, where salinity changes often,...

deep sea microbial ecology

Deep Sea Microbes and Extreme Conditions

Deep sea microbes live in one of Earth’s harshest environments. The deep ocean is far below the sunlit photic zone, which usually reaches the upper 100 to 200 meters of open water. Below that layer, the bathypelagic and abyssal zones stretch from about 1,000 to 6,000 meters, and hadal trenches go even deeper. This region is dark, cold, and highly pressurized. Temperatures are usually around 2 to 3°C, although hydrothermal vents can be slightly warmer. Pressure rises by about 1 atmosphere for...

freshwater microbial ecology

Microbes in Streams, Lakes, and Rivers

Freshwater microbes live in streams, rivers, lakes, ponds, and marshes, but their communities change with water movement, light, depth, and nutrients. These systems are often grouped into lotic waters, which flow, and lentic waters, which are still or slow-moving. The physical setting shapes where microbes grow and how they get energy. In lentic systems, phytoplankton are the main producers. They make autochthonous organic carbon, which means carbon made within the water body. In lotic...

soil microbial ecology

How Soil Microbes Cycle Nutrients

Soil microbes drive nutrient cycling, organic matter turnover, and ecosystem stability. A gram of soil can contain thousands of bacterial and archaeal taxa, but their shared job is what helps sustain land ecosystems. Their activity changes the way carbon, nitrogen, and other nutrients move through soil. Soil is a patchwork of minerals, organic matter, water, and air. Microbes live in tiny microhabitats shaped by pore size, moisture, oxygen, and nutrients. Sandy soils drain fast and tend to...

key terms and concepts

Explore how microbial communities form in soils and extreme habitats, and learn the difference between populations, microbiota, and microbiomes.

Microbial Communities in Soil and Extremes | JoVE K12

JoVE Core Microbiology provides an engaging introduction to the microbial world and its influence on health, industry, and the environment. This comprehensive collection covers key concepts such as microbial structure, metabolism, genetics, and ecology. It introduces essential laboratory techniques and microscopy methods through visually engaging animations. Corresponding scientist-in-action videos bridge classroom concepts with real-world research and applications.

microbiology

What are Populations and Communities?

Populations are groups of individuals of the same species that inhabit a shared environment. Communities include multiple co-existing, interacting ...

Distribution and Dispersion

Ecology is the study of how organisms interact with their environment and with one another. An important aspect of ecology is understanding where species ...

Life Histories

Constrained by limited energy and resources, organisms must compromise between offspring quantity and parental investment. This trade-off is represented ...

Ecological Niches

All organisms have a position within an ecosystem. The complete set of living and nonliving factors&#x2014;including food resources, climate, and ...

Ecological Succession

Ecological succession is influenced by the processes of facilitation, inhibition, and toleration. Facilitation occurs when early successional species ...

What is an Ecosystem?

Overview

An ecosystem is the interaction between all abiotic and biotic factors in an environment and can be classified as terrestrial or aquatic. ...

3. Construct an explanation of how biotic and abiotic factors affect biodiversity and populations in ecosystems. Examples: Explain how factors such as biomass, reproductive strategies, succession, climate, and geography affect an organism's chances of surviving and reproducing through successive generations.

9-12.EVS.2.3

Keystone Species

Measures of species biodiversity, such as richness (i.e., the number of species present) and evenness (i.e., their relative abundance), describe an ...

What is Biodiversity?

Biodiversity describes the variety of living things at multiple organizational levels: genetic, species and ecosystem diversity. Species diversity ...

Threats to Biodiversity

There have been five major extinction events throughout geological history, resulting in the elimination of biodiversity, followed by a rebound of species ...

analysis-of-earthworm-populations-in-soil

Analysis of Earthworm Populations in Soil

Source: Laboratories of Margaret Workman and Kimberly Frye - Depaul University
Using mustard, Lumbricus terrestris earthworm populations can be sampled ...

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Water Quality Analysis via Indicator Organisms

Source: Laboratories of Dr. Ian Pepper and Dr. Charles Gerba -The University of Arizona
Demonstrating Author: Luisa Ikner
Water quality analysis monitors ...

What is Conservation Biology?

Conservation biology is a scientific field that focuses on the preservation of biodiversity in order to protect ecosystems while meeting the needs of the ...

Measuring Biodiversity

Diverse ecosystems are important for the health of the planet and our survival as humans; it is therefore incredibly important for us to understand and ...

Community Diversity

Populations do not live in isolation; thus, every population interacts with others in certain ways. These interactions give rise to a network of ...

a. Support a claim that biodiversity is a natural resource which fosters ecosystem resilience, including the role of keystone, invasive, native, endemic, and indicator species.

9-12.EVS.2.3.a

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GIS Software, Hardware, and Sources of GIS Data

A Geographic Information System (GIS) combines specialized software and hardware to effectively manage, analyze, and present spatial and related data. GIS ...

Manipulation and Analysis

GIS manipulation and analysis functions are vital for decision-making and planning. These activities range from data retrieval tasks, such as selecting ...

Using GIS to Investigate Urban Forestry

Source: Laboratories of Margaret Workman and Kimberly Frye - Depaul University
Urban forests broadly include urban parks, street trees, landscaped ...

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Using Topographic Maps to Generate Topographic Profiles

Source: Laboratory of Alan Lester - University of Colorado Boulder
Topographic maps are &#34;plan-view&#34; representations of Earth&#39;s ...

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Tree Survey: Point-Centered Quarter Sampling Method

A number of methods are available for sampling forest communities. Point-centered quarter is one such method. It is used to gather information on the ...

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Tree Identification: How To Use a Dichotomous Key

Source: Laboratories of Margaret Workman and Kimberly Frye - Depaul University
A dichotomous key is a tool that identifies items in nature, such as ...

Species Distribution and Biogeography

Simulating Colonization and Extinction on Islands
ExpandForm groups of three. One member of the group will simulate colonization by throwing balls into ...

Freshwater Microbial Ecology

Freshwater systems such as streams, rivers, and lakes exhibit distinct physical and biological characteristics that influence their microbial communities. ...

Soil Microbial Ecology

Soil microbial ecology is defined by highly diverse, spatially structured communities that drive nutrient cycling, organic matter turnover, and overall ...

b. Analyze and interpret data collected through geographic research and field investigations to describe Alabama's biodiversity by region. Examples: Use relief, topographic, and physiographic maps or information on rivers, forests, and watersheds to investigate species distributions and diversity.

Microbial Communities in Soil and Extremes

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