Name: how scientists identify bacteria and fungi
Uploaded: 2019-01-29T11:04:46.000Z
Duration: 5 min 6 s
Channel: JoVE

K12 Standards

Louisiana Student Standards for Science

High School

Life Sciences

ecosystems-interactions-energy-and-dynamics

Ecosystems: Interactions, Energy And Dynamics

HS-LS2-7

Microbial and Fungal Diversity

Les micro-organismes sont définis comme des formes de vie trop petites pour être vues à l’œil nu. Mais bien que nous ne les voyions généralement pas, les microbes sont partout, faisant de bonnes choses comme aider notre digestion ou faire des yaourts et du vin, à des choses moins bonnes comme provoquer des infections ou des maladies. 
En parlant d’infections, en 1928, Alexander Fleming est rentré de vacances dans son laboratoire et a remarqué une étrange contamination fongique sur l’une de ses plaques de culture bactérienne. Il est intéressant de noter que les colonies bactériennes situées immédiatement autour de la contamination avaient été détruites. Cette observation a conduit à de nombreuses recherches plus approfondies, qui ont finalement abouti au développement de la pénicilline et d’autres antibiotiques qui pourraient traiter les infections bactériennes. Pourtant, bien qu’ils puissent vivre côte à côte dans le monde microscopique, nous savons, en étudiant leurs formes et leurs phylogénies, que les bactéries et les champignons sont des organismes très différents et diversifiés. Passons brièvement en revue certaines des caractéristiques déterminantes de ces deux grands groupes. 
Les bactéries sont des procaryotes unicellulaires, ce qui signifie qu’elles sont des organismes unicellulaires sans noyau. Toutes les bactéries ont une paroi cellulaire, mais sa composition et son épaisseur varient. Les bactéries à Gram positif ont une paroi cellulaire avec une épaisse couche de peptidoglycane, qui retient facilement les molécules de violet cristallin lors de la coloration de Gram. Cependant, les bactéries Gram négatif ont une paroi cellulaire mince entourée d’une membrane lipopolysaccharidique externe, et elles ne retiennent que la contre-couleur, la safranine de couleur rouge. La coloration de Gram permet également d’observer les formes bactériennes. Les bactéries rondes sont appelées cocci. Les bactéries en forme de bâtonnet sont appelées bacilles. Et les bactéries en forme de spirale sont appelées spirille. De plus, les colonies bactériennes peuvent également être caractérisées à l’œil nu, en utilisant des traits tels que la couleur, la forme et la taille de la colonie. 
Jetons maintenant un coup d'œil aux champignons. Contrairement aux bactéries, les champignons sont eucaryotes, et leurs cellules ont donc des organites liés à une membrane et un noyau. Ils sont généralement classés en groupes en fonction de leurs stratégies de reproduction. Par exemple, les ascomycètes, ou champignons à sac, qui comprennent les morilles, le penicillium et les truffes, ont des fructifications appelées ascocarpes. Les morilles sont remplies de ces structures. Si nous les regardons de plus près, ils contiennent de nombreuses structures plus petites appelées asques, qui à leur tour contiennent de nombreuses ascospores formées lors de la reproduction sexuée. Cependant, les Ascomycètes se reproduisent souvent de manière asexuée par bourgeonnement. Le deuxième grand groupe de champignons que nous examinerons est celui des Basidiomycota, ou champignons de club. La plupart des champignons comestibles et vénéneux de la forêt sont en fait des structures reproductrices des Basidiomycètes. Dans ce groupe, ce que nous appellerions le chapeau de champignon est techniquement connu sous le nom de basidiocarpe. Chez les champignons à branchies, les branchies sous le basidiocarpe sont tapissées de minuscules structures appelées basides, et celles-ci produisent des basidiospores, des spores reproductrices microscopiques, pendant la reproduction sexuée. Ces spores sont généralement déboursées par le vent, comme de nombreuses graines de plantes. Ici, nous avons examiné plusieurs grands groupes de bactéries et de champignons, ainsi que les caractéristiques qui les définissent de manière très simplifiée. Cependant, en raison du grand nombre d’espèces microbiennes, plus d’un billion selon de nombreuses estimations, les scientifiques les identifient et les regroupent souvent à l’aide de méthodes supplémentaires, y compris l’examen de leur ADN. 
Dans ce laboratoire, vous identifierez différentes espèces de bactéries à l’aide de la coloration de Gram et examinerez les caractéristiques des colonies. Vous examinerez également les espèces de champignons pour identifier leurs structures reproductives.

diversité microbienne et fongique

Les bactéries et les champignons sont deux groupes d’organismes très divers qui peuvent avoir des effets bénéfiques ou néfastes importants sur la santé humaine. Pour cette raison, il est important de comprendre et de distinguer les espèces individuelles de ces groupes. Comme vous vous en souviendrez, les taxonomistes biologiques regroupent les organismes en fonction de leur parenté phylogénétique. Les trois domaines de la vie, les bactéries, les archées et les eucaryotes, séparent la vie en trois groupes distincts. Alors que toutes les bactéries relèvent du domaine des bactéries, les champignons se trouvent dans le domaine des eucaryotes (règne des champignons). En plus des archées, le domaine des bactéries comprend exclusivement des procaryotes unicellulaires, ce qui signifie que leurs cellules sont dépourvues à la fois d’une membrane nucléaire et d’organites liés à la membrane. En revanche, les champignons du domaine Eucaryota ont des organites délimités par une membrane et comprennent des organismes unicellulaires et multicellulaires.
<h4>Bactéries</h4>
Les bactéries se trouvent presque partout sur Terre et sont très adaptées aux environnements dans lesquels elles se développent. En conséquence, ce domaine comprend une quantité stupéfiante de diversité. L’impact de ces organismes sur la santé humaine est tout aussi divers. Par exemple, des espèces comme Streptococcus thermophilus peuvent être utilisées pour produire des aliments fermentés comme le yogourt, tandis que les spores de la bactérie Bacillus anthracis sont responsables de la maladie potentiellement mortelle de l’anthrax.
Pour aider à l’identification d’un tel organisme, les microbiologistes ont mis au point une myriade de tests pour caractériser à la fois des cellules individuelles et des colonies entières de bactéries1. L’une des méthodes les plus courantes pour identifier les bactéries est la coloration de Gram. Ce test utilise des colorants colorés pour déterminer la composition de la paroi cellulaire de la bactérie. Les bactéries à Gram positif, qui portent une paroi cellulaire épaisse composée d’une protéine appelée peptidoglycane, conservent un colorant appelé violet cristallin et apparaissent donc violettes. En revanche, les bactéries à Gram négatif ont une paroi cellulaire plus mince sans peptidoglycane et ne conservent pas le violet cristallin. Au lieu de cela, ces cellules apparaissent roses en raison d’une contre-coloration appelée safranine. L’utilisation de la coloration de Gram sert souvent d’étape préliminaire à l’identification d’une espèce bactérienne. Une classification plus poussée nécessite l’identification de caractéristiques supplémentaires. Cela peut inclure la forme de bactéries individuelles, qui peuvent être soit des cocci (ronds), soit des spirillum (spirale) ou des bacilles (en forme de bâtonnet). De plus, la couleur, la forme, l’éclat, la texture et même l’odeur des colonies bactériennes peuvent être utilisés pour distinguer les espèces.
<h4>Mycètes</h4>
Les champignons du domaine Eucaryota sont également très diversifiés sur le plan écologique et peuvent varier en taille de la levure microscopique au plus grand organisme sur terre, le champignon du miel (Armillaria ostoyae). Tous les champignons sont hétérotrophes, ce qui signifie qu’ils doivent obtenir leur nourriture de l’environnement. Ces organismes présentent également une diversité dans leurs activités spécifiques, leurs niches et leurs effets potentiels sur la santé humaine. Par exemple, certains champignons sont consommés ou utilisés pour produire de la nourriture par l’homme, tandis que d’autres peuvent provoquer des infections graves, voire mortelles2.
Au sein du règne des champignons, il existe deux divisions taxonomiques distinctes basées sur la stratégie de reproduction de l’espèce. Tout d’abord, les Ascomycètes, connus sous le nom de champignons à sac, ont une structure reproductrice appelée asque. Ensemble, de nombreux asques forment l’ascocarpe, ou « fructification » des champignons. Ces champignons peuvent se reproduire sexuellement ou asexuellement par bourgeonnement. Les ascomycètes se composent de certaines espèces économiquement importantes comme la levure utilisée dans le brassage de la bière et la cuisson du pain, et certaines espèces populaires en cuisine, comme les morilles et les truffes. Le deuxième groupe, Basidiomycota, comprend des organismes communément appelés « champignons massues » en raison de la présence d’une grande structure reproductrice en forme de massue appelée basidium. Contrairement aux Ascomycota, la plupart des Basidomucota se reproduisent exclusivement par reproduction sexuée. Cela se produit lorsque deux mycéliums haploïdes se rejoignent pour former un basidiocarpe. Sur un champignon de Paris, il s’agit de la structure du chapeau. Sur la face inférieure du basidiocarpe, des structures reproductrices appelées branchies bordées de structures appelées basides produisent des noyaux haploïdes qui finissent par former des basidiospores. Les basidiospores sont ensuite dispersées par le vent. Cette division taxonomique comprend de nombreux champignons de Paris couramment consommés, ainsi que des champignons soufflés sauvages.
<h4>Importance de la microbiologie</h4>
Dans l’ensemble, il est clair que les diverses fonctions et propriétés des micro-organismes rendent leur identification extrêmement importante pour la santé et le bien-être humains. Alors qu’un grand nombre d’espèces de champignons et de bactéries ont été identifiées à ce jour, on estime que des millions d’autres doivent encore être identifiées et classifiées. De plus, les disciplines humaines qui explorent les champignons et les bactéries sont aussi diverses que les organismes eux-mêmes et continueront sans aucun doute à se développer. L’importance des micro-organismes dans les domaines médicaux est plus répandue que jamais, car les espèces de bactéries infectieuses multirésistantes aux antibiotiques menacent la santé humaine. La compréhension de la structure et des caractéristiques biologiques des espèces infectieuses et non infectieuses fournit des informations clés nécessaires à la création de nouveaux traitements antibiotiques et de stratégies préventives3-4.
La microbiologie est également essentielle pour l’industrie alimentaire. De nombreux produits, y compris le yogourt, le fromage, le kombucha, le pain et l’alcool, sont fabriqués à partir de catégories ou d’espèces spécifiques de microbes. Dans le même temps, les scientifiques de l’alimentation se concentrent sur l’ingénierie de composés chimiques et de conservateurs qui réduiront la croissance de microbes indésirables sur les aliments. Dans tous ces processus, il est nécessaire de comprendre comment les microbes survivent, se reproduisent et affectent leur environnement.
<h4>Références </h4>
<ol class="références">
	<li>Hiroshi Asakura, Holger Brueggemann, Sou-ichi Makino et Yoshiko Sugita-Konishi, « Approches moléculaires pour la classification des agents pathogènes microbiens d’importance pour la santé publique », BioMed Research International, vol. 2014, ID de l’article 725801, 2 pages, 2014. https://doi.org/10.1155/2014/725801.</li>
	<li>Treseder, K. K. et J. T. Lennon (2015). « Traits fongiques qui déterminent la dynamique de l’écosystème sur terre. » Microbiol Mol Biol Rev 79(2) : 243-262.</li>
	<li>Arvanitis, M. et E. Mylonakis (2015). « Les interactions fongiques-bactériennes et leur pertinence pour la santé. » Microbiol cellulaire 17(10) : 1442-1446.</li>
	<li>Aarestrup, F. M., et al. (2008). « Résistance des bactéries de la chaîne alimentaire : épidémiologie et stratégies de contrôle. » Expert Rev Anti Infect Ther 6(5) : 733-750.</li>
</ol>

Diversité microbienne et fongique

Les bactéries et les champignons sont deux groupes d’organismes très divers qui peuvent avoir des effets bénéfiques ou néfastes importants sur la santé humaine. Pour ce ...

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how scientists identify bacteria and fungi

Bacteria and fungi are highly diverse organisms, and scientists identify them by looking at their structure, growth, and role in health. Some species help people, while others can cause disease, so learning how to tell them apart matters in biology and medicine.

Biological taxonomists group organisms by evolutionary relatedness. Life is divided into three domains: Bacteria, Archaea, and Eukaryota. Bacteria belong to the domain Bacteria, which includes single-celled prokaryotes. Prokaryotic cells lack a nuclear membrane and membrane-bound organelles. Fungi belong to the domain Eukaryota, in Kingdom Fungi. They have membrane-bound organelles and can be either unicellular or multicellular.

Bacteria live almost everywhere on Earth, and their diversity is very large. This group includes helpful species such as Streptococcus thermophilus, which is used to make fermented foods like yogurt. It also includes harmful species such as Bacillus anthracis, whose spores cause anthrax. Microbiologists use several tests to identify bacteria. One common test is Gram staining, which uses colored dyes to show cell wall structure.

Gram-positive bacteria have a thick cell wall made of peptidoglycan, so they retain crystal violet and appear purple. Gram-negative bacteria have a thinner cell wall without peptidoglycan, so they do not keep crystal violet. Instead, they take up safranin and appear pink. Gram staining is often a first step in bacterial identification. Scientists then look at other traits, including cell shape. Cocci are round, spirillum are spiral, and bacilli are rod-shaped. Colony color, shape, sheen, texture, and even smell can also help distinguish species.

Fungi are also diverse and can range from microscopic yeast to the honey fungus, Armillaria ostoyae, which is the largest organism on Earth. Fungi are heterotrophic, which means they must get food from their environment. Some fungi are used in food production or are eaten by people, while others can cause severe or even deadly infections.

Within Kingdom Fungi, two major divisions are based on reproduction. Ascomycota are the sac fungi. They have a reproductive structure called an ascus, and many asci form an ascocarp, or fruiting body. These fungi can reproduce sexually or asexually by budding. This group includes yeast used in brewing beer and baking bread, as well as edible fungi like morels and truffles.

Basidiomycota are commonly called club fungi because they have a club-shaped basidium. Most Basidiomycota reproduce sexually. Two haploid mycelia join to form a basidiocarp, which is the cap of a button mushroom. On the underside, gills lined with basidia produce haploid nuclei that later form basidiospores. Wind spreads these spores. This group includes many button mushrooms and wild puff mushrooms.

Studying microbes is important for human health and for food production. Millions of species may still need to be identified and classified, and microbiology continues to grow as a field. This work is especially important now because multi-antibiotic-resistant bacteria can threaten human health. Knowing microbial structure and biology helps scientists develop new antibiotics and prevention strategies. Microbiology also supports the food industry, where microbes are used to make yogurt, cheese, kombucha, bread, and alcohol, while other compounds and preservatives are designed to limit unwanted microbial growth.

How Scientists Identify Bacteria and Fungi

how-scientists-identify-bacteria-and-fungi

natural selection

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microbial and fungal diversity

Bacteria and fungi are highly diverse organisms, and scientists identify them by looking at their structure, growth, and role in health. Some species help people, while others can cause disease, so learning how to tell them apart matters in biology and medicine. Biological taxonomists group organisms by evolutionary relatedness. Life is divided into three domains: Bacteria, Archaea, and Eukaryota. Bacteria belong to the domain Bacteria, which includes single-celled prokaryotes. Prokaryotic...

evolution

Learn how bacteria and fungi are classified, stained, and identified, plus why microbes matter in health, medicine, and food production.

How Scientists Identify Bacteria and Fungi | JoVE K12

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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. ...

Trophic Levels

All organisms in an ecosystem occupy a trophic level in the food chain. The lowest level consists of primary producers, which synthesize their food from ...

Primary Production

The total amount of energy acquired by primary producers in an ecosystem is called gross primary production (GPP). However, of this energy, producers use ...

Production Efficiency

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Trophic Efficiency

Trophic level transfer efficiency (TLTE) is a measure of the total energy transfer from one trophic level to the next. Due to extensive energy loss as ...

Life Histories

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

Energy Budgets and Reproductive Strategies

Organisms must balance energy intake with the energy required for growth, maintenance, and reproduction. These trade-offs result in a variety of ...

Population Growth

Population size is dynamic, increasing with birth rates and immigration, and decreasing with death rates and emigration. In ideal conditions with ...

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 ...

Keystone Species

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Symbiosis

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Competition

When organisms require the same limited resources within an environment, they may have to compete for them. Competition is a net-negative interaction. ...

Predator-Prey Interactions

Predators consume prey for energy. Predators that acquire prey and prey that avoid predation both increase their chances of survival and reproduction ...

Ecological Disturbance

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What is Biodiversity?

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Threats to Biodiversity

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Biodiversity and Human Values

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The Anatomy of Chloroplasts

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Photosystems

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Conservation of Small Populations

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The Photochemical Reaction Center

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What is Weather?

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The Antenna Complex

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Use mathematical and/or computational representations to support explanations of factors that affect carrying capacity, biodiversity and populations of ecosystems at different scales. Emphasis is on quantitative analysis and comparison of the relationships among interdependent factors including boundaries, resources, climate and competition. Examples of mathematical comparisons could include graphs, charts, histograms, or population changes gathered from simulations or historical data sets.

HS-LS2-1

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The Carbon Cycle

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Use mathematical representations to support claims for the cycling of matter and flow of energy among organisms in an ecosystem. Emphasis is on using a mathematical model of stored energy in biomass to describe the transfer of energy from one trophic level to another and that matter and energy are conserved as matter cycles and energy flows through ecosystems. Emphasis is on atoms and molecules such as carbon, oxygen, hydrogen and nitrogen being conserved as they move through an ecosystem.

HS-LS2-4

What are Populations and Communities?

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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 ...

Evaluate the claims, evidence and reasoning that the complex interactions in ecosystems maintain relatively consistent numbers and types of organisms in stable conditions, but changing conditions may result in a new ecosystem. Examples of changes in ecosystem conditions could include modest biological or physical changes, such as moderate hunting or a seasonal flood and extreme changes, such as volcanic eruption or sea level rise. Emphasis should be on describing drivers of ecosystem stability and change, not on the organismal mechanisms of responses and interactions.

HS-LS2-6

How Scientists Identify Bacteria and Fungi

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