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

微生物生態学は、微生物の多様性と、さまざまな生態系内で微生物がどのように相互作用するかを研究する学問です。生態系とは、微生物が生物的要因と非生物的要因の両方と相互作用する機能的単位です。これらの生態系では、葉や根、土壌などの生息地に多くの微生物が宿っています。同じ種の微生物が集団を形成します。異なる個体群が共存し、生息地で相互作用すると、微生物群集が形成されます。生態系内のすべての微生物がマイクロバイオータを構成し、その遺伝物質の総集合体はマイクロバイオームと呼ばれます。群集内の微生物多様性は種の豊富さや相対的な個体数によって測定され、これらは栄養素の利用可能性や温度、pH、酸素レベルなどの環境条件に影響されます。例えば、栄養豊富な土壌は種の多様性が高く、多くの微生物が適度な個体数で共存しています。一方、酸性で鉄分を多く含む極端な生態系は、種の豊富さは低いものの、 Acidithiobacillus ferrooxidansのような特殊な微生物の豊富度を支持します。

微生物生態学入門

微生物生態学は、さまざまな生態系内の微生物間の複雑な相互作用と多様性の網を調査します。この分野は、微生物集団がどのように環境に適応し影響を与えるか、そしてこれらの相互作用がより広範な生態学的プロセスをどのように形成するかを理解しようとしています。微生物は生態系の機能に不可欠であり、栄養循環、エネルギーの流れ、環境の恒常性維持に関与しています。生態系とは、生物(生物的要素)とその非生物的(非生物的)環境との動的な相互作用を表します。微生物はこれらの生態系内の異なる生息地で繁栄し、特定の時期に共存する同種の集団を形成します。異なる種の微生物集団が共存し相互作用する場合、それらは微生物群集を形成します。これらのコミュニティは静的ではありません。環境圧力、資源の利用可能性、種間相互作用に応じて進化します。微生物の多様性は、種の豊富さ(存在する種の数)と種の豊富さ(各種の個体数)によって特徴づけられます。これらのパラメータは、栄養素レベル、pH、温度、湿度などの生態系の物理的・化学的特性によって影響を受けます。例えば、肥沃で有機物が豊富な土壌では、多くの微生物種が中程度の個体数で共存し、種の多様性が高いことが観察されます。このような環境は様々な代謝経路のニッチを提供し、資源分割を通じて共存を可能にします。特定の環境内に微生物群集が確立されると、それは微生物叢(microbiota)と呼ばれますが、この用語は宿主に関連する群集にもよく使われます。これらの微生物の集合ゲノムはマイクロバイオームと呼ばれ、コミュニティの機能的可能性を反映しています。マイクロバイオームは、微生物の代謝能力や環境における生態学的役割を理解する上で不可欠です。一方で、酸性で鉄分を多く含む湖のような極端な環境は、特殊な微生物の生命を支えています。これらの生息地は過酷な環境のために種の多様性が低いものの、特定の極限環境微生物の豊富さが見られます。例えば、ケモリソオートトロフィーである アシディオバチルス・フェロオキシダンは、鉄鉄を酸化し低pH条件下で生存することでこれらのニッチを支配しており、微生物生命の適応力と極端な環境での生態学的特化を示しています。

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

微生物学

Unit

ユニット

Microbial Ecology

微生物生態学

KEY TERMS AND CONCEPTS

主要用語と概念

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

introduction to microbial ecology

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

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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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