Name: measuring microbial diversity and activity
Uploaded: 2026-03-12T13:57:42.000Z
Duration: 1 min 19 s
Channel: JoVE

微生物群集とは、共有された生息地内で共存し相互作用する細菌、古細菌、微生物真核生物のコンソーシアムです。微生物群集の構造は、しばしばリッチネス、相対的な存在ごと、均一性で記述されます。サンプルにおいて、リッチネスは検出された分類群の数であり、相対個体数は各分類群の割合を定量化します。均等性とは、個体が分類群全体に均一に分布していることを示します。現在、培養に依存しない分子アプローチが微生物群集のプロファイリングに用いられています。メタゲノミクスは土壌などの環境サンプルからDNAを研究し、主に微生物群集の構成をプロファイリングするために用いられます。メタトランスクリプトミクスはmRNA発現の評価を可能にし、酵素生成や油分分解などの活性微生物機能のスナップショットを提供します。メタプロテオミクスとメタボロミクスは環境中のタンパク質や代謝物を特定し、微生物が栄養分解や生地球化学的循環などのプロセスにどのように関与するかを明らかにします。

微生物群集を評価する方法

Methods to Assess Microbial Communities

細菌、古細菌、真核生物を含む微生物群落は多様な生態系に生息し、環境や生物学的プロセスにおいて重要な役割を果たしています。その多様性は主に3つのパラメータで定義されます: 種の豊富さ (異なる種の数)、 種の個体 数(各種の相対的な数量)、 そして種の均一 さ(個々の種がさまざまな場所でどれだけ均一に分布しているか)です。これらの要因が合わさって、群集の構造と生態学的バランスを形成します。<h3>微生物多様性の定量化</h3>微生物の多様性を評価するために、科学者は数学的指標を用います。 シャノン指数 は富裕度と均一さの両方を考慮し、値が高いほど多様性とバランスが高まります。 シンプソン指数 は、サンプルからランダムに選ばれた2つの個体が同一種に属する確率を測定します。シンプソン値が低いことは、種の優位性が減少したため多様性が高いことを示唆しています。これらの指標は、コミュニティの健康と生態系の安定性を評価するのに役立ちます。<h3>文化に基づく方法と文化に依存しない方法</h3>微生物群集は、培養 依存 的な方法で調べることができ、これは実験室での培養に依存しています。しかし、多くの微生物は標準条件下では培養不可であるため、このアプローチは制限されています。対照的に、 培養に依存し ない技術は環境サンプルから直接微生物を分析し、微生物の多様性と機能をより包括的に評価することを可能にします。<h3>分子的アプローチによるコミュニティ評価</h3><ul><li>メタゲノミクス:この技術は環境サンプルからゲノムDNAを配列決定します。微生物分類群を特定し、培養不可能な希少生物を含む群集の遺伝的可能性を明らかにします。</li><li>メタトランスクリプトミクス:この方法はmRNAを配列し、どの遺伝子が積極的に転写されているかを特定します。これは、コミュニティ内で進行中の代謝活動の機能的なスナップショットを提供します。</li><li>メタプロテオミクス:このアプローチは環境サンプル中のすべてのタンパク質を解析します。どのタンパク質が合成されているかを明らかにし、活発な代謝経路や生理学的プロセスに関する洞察を提供します。</li><li>メタボロミクス:この技術は微生物活動の最終産物である小分子代謝物をプロファイリングします。これらの代謝物は生理状態や微生物間相互作用を反映し、栄養循環や環境ストレス反応などのプロセスを説明するのに役立ちます。</li></ul>これらの方法は利用可能なツールのごく一部に過ぎません。多様な技術を統合することで、微生物の多様性、機能、生態系の複雑さの理解が深まります。

Microbial communities, comprising bacteria, archaea, and eukaryotic microorganisms, inhabit diverse ecosystems and play crucial roles in environmental and ...

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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

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 individuals are distributed among species. Together, these measures help show the structure and ecological balance of a microbial community.

Researchers also use diversity indices to quantify microbial communities. The Shannon index includes both richness and evenness, and higher values show greater diversity and balance. The Simpson index measures the chance that two randomly chosen individuals belong to the same species. Lower Simpson values indicate higher diversity because no single species dominates as much.

Microbial communities can be studied with culture-based methods or with culture-independent methods. Culture-based methods depend on growing microbes in the lab. This approach has limits because many microbes cannot be cultured under standard conditions. Culture-independent methods examine microbes directly from environmental samples and can give a broader view of diversity and function.

Several molecular methods are used in culture-independent analysis. Metagenomics sequences genomic DNA from environmental samples to identify microbial taxa and reveal the genetic potential of the community, including rare or unculturable organisms. Metatranscriptomics sequences mRNA to show which genes are actively being transcribed, so it gives a snapshot of ongoing metabolic activity.

Other methods add more detail about community function. Metaproteomics analyzes all proteins in a sample and shows which proteins are being made. This helps reveal active metabolic pathways and physiological processes. Metabolomics profiles small-molecule metabolites, which are the end-products of microbial activity. These metabolites can reflect physiological state, microbial interactions, nutrient cycling, and responses to environmental stress.

Together, these tools give scientists a fuller picture of microbial diversity and ecosystem complexity. Using more than one method can improve understanding of both who is there and what they are doing in the community.

Measuring Microbial Diversity and Activity

measuring-microbial-diversity-and-activity

introduction to microbial ecology

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

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

Learn how scientists assess microbial communities using richness, evenness, Shannon and Simpson indices, plus metagenomics, transcriptomics, proteomics, and metabolomics.

Measuring Microbial Diversity and Activity | 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

Measuring Microbial Diversity and Activity

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