{"id":14060,"date":"2018-08-01T19:00:56","date_gmt":"2018-08-01T17:00:56","guid":{"rendered":"https:\/\/news.embl.de\/?p=14060"},"modified":"2024-09-30T22:37:50","modified_gmt":"2024-09-30T20:37:50","slug":"understanding-soil-through-its-microbiome","status":"publish","type":"post","link":"https:\/\/www.embl.org\/news\/science\/understanding-soil-through-its-microbiome\/","title":{"rendered":"Understanding soil through its microbiome"},"content":{"rendered":"\n

Soil is full of life, essential for nutrient cycling and carbon storage. To better understand how it functions, an international research team led by EMBL and the University of Tartu (Estonia) conducted the first global study of bacteria and fungi in soil. Their results show that bacteria and fungi are in constant competition for nutrients and produce an arsenal of antibiotics to gain an advantage over one another. The study can also help predict the impact of climate change on soil, and help us make better use of natural soil components in agriculture. Nature <\/em>publishes the results on 1 August 2018.<\/p>\n\n\n\n

Research on the soil microbiome requires scientists to get their hands dirty. Over the course of five years, 58.000 soil samples were collected from 1450 sites all over the world (40 subsamples per site), that were carefully selected to be unaffected by human activities such as agriculture. First authors Mohamad Bahram (University of Tartu) and Falk Hildebrand (EMBL), together with a large team of collaborators, set up this massive project, gathered samples, and analysed the 14.2 terabyte dataset. Of the 1450 sites sampled, 189 were selected for in-depth analysis, covering the world\u2019s most important biomes, from tropical forests to tundra, on all continents.<\/p>\n\n\n\n

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The 189 selected sample sites spread over 5 continents. IMAGE: Bahram\/Hildebrand\/EMBL<\/em><\/figcaption><\/figure>\n\n\n\n

Global microbial war in soil<\/h2>\n\n\n\n

Only half <\/em>a percent of the millions of genes found in this study overlapped with existing data from gut and ocean microbiomes. \u201cThe amount of unknown genes is overwhelming, but the ones we can<\/em> interpret clearly point to a global war between bacteria and fungi in soil,\u201d says Peer Bork<\/a>, EMBL group leader and corresponding author of the paper.<\/p>\n\n\n\n

Overall, the bacterial diversity in soil is lower if there are relatively more fungi. The team also found a strong link between the number of antibiotic resistance genes in bacteria and the amount of fungi, especially those with potential for antibiotics production such as Penicillium. Falk Hildebrand<\/a>: \u201cThis pattern could well be explained by the fact that fungi produce antibiotics in warfare with bacteria, and only bacteria with adequate antibiotic resistance genes can survive this.\u201d<\/p>\n\n\n\n

\u201cThe antagonism between fungi and bacteria influences the overall diversity of bacterial communities and determines their genetic repertoire of antibiotic resistance\u201d, says  Mohamad Bahram. This information can be used to predict the spread of genes that lead to antibiotic resistance in different ecosystems, and via what routes they may reach human pathogens. It could also help predict and pinpoint locations with high levels of natural antibiotics producers.<\/p>\n\n\n\n

Regional differences<\/h2>\n\n\n\n

The team also found regional differences in the distribution of bacteria and fungi. Bacteria are everywhere, with the highest genetic diversity in temperate zones with a moderate climate. Environmental factors such as temperature are most decisive in their relative abundance: they often prefer hot and wet locations. Fungi are usually more prevalent in colder and dryer climates like the tundra. They also tend to be more geographically restricted, with differences in populations between continents. This implies that the relative contributions of bacteria and fungi to nutrient cycling are different around the world, and that global climate change may affect their composition and function differently.<\/p>\n\n\n\n

Effects of human activity<\/h2>\n\n\n\n

When comparing data from the unspoiled soil sites with data from locations affected by humans, such as farmland or garden lawns, the ratios between bacteria, fungi and antibiotics were completely different. According to the scientists, this shift in the natural balance \u2013 that probably evolved over most of the earth\u2019s history \u2013 shows the effect of human activities on the soil microbiome, with unknown consequences so far. However, a better understanding of the interactions between fungi and bacteria in soil could help to reduce the usage of soil fertilizer in agriculture, as one could give beneficial microorganisms a better chance at survival in their natural environment.<\/p>\n\n\n\n

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Das Mikrobiom als Schl\u00fcssel zum Verst\u00e4ndnis des Bodens<\/h2>\n\n\n\n

Zwischen Pilzen und Bakterien in der Erde herrscht ein permanenter Wettkampf, wie die erste weltweite Untersuchung der Bodengenomik aufzeigt<\/h3>\n\n\n\n

Der Boden steckt voller Leben, was entscheidend f\u00fcr den globalen N\u00e4hrstoffkreislauf und die Kohlenstoffanreicherung ist. Um die Prozesse innerhalb des Bodens besser zu verstehen, f\u00fchrte ein internationales Forschungsteam unter Leitung des EMBL und der Universit\u00e4t Tartu (Estland) die erste weltweite Untersuchung von Bakterien und Pilzen durch. Diese Daten zeigten, dass Bakterien und Pilze in st\u00e4ndigem Wettbewerb um N\u00e4hrstoffe stehen. Unter anderem werden mikrobiell produzierte Antibiotika benutzt, um sich einen Vorteil gegen\u00fcber den konkurrierenden St\u00e4mmen zu verschaffen. Diese Untersuchung kann dazu beitragen, nat\u00fcrliche vorkommende Mikroben besser in der Landwirtschaft zu nutzen und die Auswirkungen des Klimawandels auf die Erdmikrosph\u00e4re genauer vorherzusagen. Das Fachmagazin Nature<\/em> ver\u00f6ffentlicht die Ergebnisse am 01 August.<\/p>\n\n\n\n

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IMAGE: Hildebrand\/Krolik in collaboration with Campbell Medical Illustration\/EMBL<\/figcaption><\/figure>\n\n\n\n

Bei der Erforschung des Bodenmikrobioms m\u00fcssen sich die Wissenschaftler die H\u00e4nde schmutzig machen. \u00dcber f\u00fcnf Jahre hinweg entnahmen sie 58.000 Bodenproben an 1.450 Standorten auf der ganzen Welt (40 Teilproben pro Standort); die Standorte wurden danach ausgew\u00e4hlt, ob sie von menschlichen Aktivit\u00e4ten wie der Landwirtschaft unbeeinflusst waren. Mohamad Bahram (Universit\u00e4t Tartu) und Falk Hildebrand (EMBL) haben dieses gigantische Projekt zusammen mit einem gro\u00dfen Team von Kooperationspartnern ins Leben gerufen. Sie haben Proben gesammelt und den 14,2 Terabyte gro\u00dfen Datensatz bioinformatisch ausgewertet, und sich dabei auf 189 \/ 1.450 Bodenproben f\u00fcr eine detaillierte Analyse konzentriert (siehe Abbildung 1), welche die wichtigsten Biome der Welt, von Tropenw\u00e4ldern bis zur Tundra, auf allen Kontinenten umfasst.<\/p>\n\n\n\n

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Abbildung 1. Um die globale mikrobielle Zusammensetzung besser zu bestimmen, wurden 189 Proben von unber\u00fchrten Habitaten auf f\u00fcnf Kontinenten ausgewertet. IMAGE: Bahram\/Hildebrand\/EMBL<\/figcaption><\/figure>\n\n\n\n\n\n\n\n

Globaler Kampf der Mikroben um Ressourcen<\/h2>\n\n\n\n

W\u00e4hrend die Studie viele Millionen Gene der Mirkoben analysierte, \u00fcberlappte lediglich ein halbes Prozent dieser mit Genen in den internationalen Datenbanken auf. \u201eDie schiere Menge bisher unbekannter Gene ist \u00fcberw\u00e4ltigend, aber diejenigen, die wir interpretieren k\u00f6nnen, weisen eindeutig auf einen globalen Krieg zwischen Bodenbakterien und -pilzen hin”, sagt Peer Bork, EMBL-Gruppenleiter und Korrespondenzautor des Artikels.<\/p>\n\n\n\n

Wie die Forscher entdeckten, kommen weniger Bakterien im Boden vor, wenn mehr Pilze vorhanden sind. Das Team stellte einen starken Zusammenhang zwischen der Anzahl von bakteriellen Antibiotikaresistenzgenen in Bakterien und der Menge von Pilzen fest. Insbesondere trifft dies in der Gegenwart von Pilzen zu, die zur Bildung von Antibiotika in der Lage sind, wie etwa Penicillium. \u201eDieses Muster\u201c, so Falk Hildebrand, \u201ek\u00f6nnte dadurch erkl\u00e4rt werden, dass Pilze im Kampf um mehr Ressourcen Antibiotika produzieren, wodurch nur Bakterien mit den entsprechenden Antibiotikaresistenzgenen \u00fcberleben und so den Pilzen einen Vorteil verschafft.”<\/p>\n\n\n\n

Der Antagonismus zwischen Pilzen und Bakterien beeinflusst die Vielfalt bakterieller Gemeinschaften und bestimmt deren genetisches Repertoire an Antibiotikaresistenzen. Dieses Verst\u00e4ndnis kann zur Vorhersage genutzt werden, wie sich Antibiotikaresistenzgene verbreiten und \u00fcber welche Wege sie menschliche Krankheitserreger erreichen. Au\u00dferdem k\u00f6nnen sie genutzt werden, um Orte mit einem hohen Anteil an nat\u00fcrlichen Antibiotikaproduzenten vorherzusagen. Das ist wichtig, um neue Antibiotika zu finden.<\/p>\n\n\n\n

Regionale Unterschiede<\/h2>\n\n\n\n

Das Team stellte \u00fcberdies regionale Unterschiede in der Verteilung von Bakterien und Pilzen fest. Bodenbakterien finden sich \u00fcberall; die gr\u00f6\u00dfte genetische Vielfalt erreichen sie jedoch in gem\u00e4\u00dfigten Klimazonen. Ausschlaggebend f\u00fcr ihre relative H\u00e4ufigkeit sind Umweltfaktoren wie die Temperatur: sie bevorzugen oft warme und feuchte Standorte. Pilze hingegen kommen h\u00e4ufiger in k\u00fchlen und trockenen Klimazonen wie der Tundra vor. Au\u00dferdem sind sie oft st\u00e4rker geografisch beschr\u00e4nkt, das hei\u00dft es bestehen h\u00e4ufiger Populationsunterschiede zwischen den Kontinenten. Daraus folgt, dass die relativen Beitr\u00e4ge von Bakterien und Pilzen zum N\u00e4hrstoffkreislauf weltweit unterschiedlich sind, sodass der globale Klimawandel sich unterschiedlich auf ihre Zusammensetzung und Funktion auswirken k\u00f6nnte.<\/p>\n\n\n\n

Auswirkungen menschlicher Aktivit\u00e4t<\/h2>\n\n\n\n

Vergleicht man die Daten der unber\u00fchrten Bodenstandorte mit den Daten der vom Menschen beeinflussten Orte wie z.B. Ackerland oder Gartenrasen, f\u00e4llt auf, dass v\u00f6llig unterschiedliche Verh\u00e4ltnisse zwischen Bakterien, Pilzen und Antibiotikaresistenzen bestehen. Diese Verschiebung des nat\u00fcrlichen Gleichgewichts \u2013 das sich vermutlich \u00fcber weite Teile der Erdgeschichte evolviert hat \u2013 zeigt, nach Ansicht der Wissenschaftler, die Auswirkungen menschlicher Aktivit\u00e4ten auf das Bodenmikrobiom, mit bisher unbekannten Folgen. Ein besseres Verst\u00e4ndnis der Wechselwirkungen zwischen Pilzen und Bakterien im Boden k\u00f6nnte jedoch dazu beitragen, den Einsatz von Bodend\u00fcnger in der Landwirtschaft zu reduzieren. N\u00fctzlichen Mikroorganismen w\u00fcrde dadurch eine h\u00f6here \u00dcberlebenschance in ihrer nat\u00fcrlichen Umgebung verschafft.<\/p>\n\n\n\n

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Entender el suelo a trav\u00e9s de su microbioma<\/h2>\n\n\n\n

Primer estudio mundial de gen\u00f3mica del suelo revela una batalla entre hongos y bacterias<\/h3>\n\n\n\n

El suelo est\u00e1 repleto de vida, es esencial para el ciclo de los nutrientes y el almacenamiento de carbono. Para comprender a\u00fan mejor c\u00f3mo funciona, un equipo internacional de investigadores, liderados por el Laboratorio Europeo de Biolog\u00eda Molecular (EMBL, por sus siglas en ingl\u00e9s) y la Universidad de Tartu (Estonia), han llevado a cabo el primer estudio de hongos y bacterias en el suelo. Los resultados revelan que hongos y bacterias compiten constantemente por adquirir nutrientes y producen un arsenal de antibi\u00f3ticos para obtener ventajas los unos sobre los otros. El estudio puede contribuir a predecir el impacto del cambio clim\u00e1tico en el suelo y ayudarnos a darle un mejor uso a los componentes naturales del suelo en la agricultura. La revista Nature<\/em> publica los resultados el 1 de agosto de 2018.<\/p>\n\n\n\n

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IMAGE: Hildebrand\/Krolik in collaboration with Campbell Medical Illustration\/EMBL<\/figcaption><\/figure>\n\n\n\n

Para estudiar el microbioma del suelo, los cient\u00edficos deben ensuciarse las manos. En el transcurso de cinco a\u00f1os, se reunieron 58 000 muestras de suelo provenientes de 1 450 sitios en todo el mundo (40 submuestras por sitio), seleccionando cuidadosamente lugares no afectadas por actividades humanas como la agricultura. Los autores principales, Mohamad Bahram (Universidad de Tartu) y Falk Hildebrand (EMBL), junto a un gran grupo de colaboradores, pusieron en marcha el proyecto, reunieron las muestras y analizaron el volumen de datos de 14,2 terabytes. De los 1 450 sitios muestreados, se seleccionaron 189 para realizar un an\u00e1lisis en profundidad, abarcando los biomas m\u00e1s importantes del mundo, desde selvas tropicales hasta la tundra, en todos los continentes.<\/p>\n\n\n\n

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Figura 1. Los 189 sitios se distribuyen en los cinco continentes. IMAGE: Bahram\/Hildebrand\/EMBL<\/figcaption><\/figure>\n\n\n\n

Batalla microbiana global<\/h2>\n\n\n\n

Tan solo medio punto porcentual de los millones de genes encontrados en este estudio coincide con informaci\u00f3n existente proveniente de microbiomas humanos u oce\u00e1nicos. \u00abLa cantidad de genes desconocidos es asombrosa, pero aquellos que podemos interpretar se\u00f1alan indudablemente que se est\u00e1 librando una batalla global entre los hongos y las bacterias del suelo\u00bb, comenta Peer Bork, l\u00edder del grupo de EMBL y autor para correspondencia del estudio.<\/p>\n\n\n\n

En general, la diversidad bacteriana del suelo es menor si la proporci\u00f3n de hongos es mayor. El equipo identific\u00f3, adem\u00e1s, un estrecho v\u00ednculo entre el n\u00famero de genes de resistencia a los antibi\u00f3ticos que poseen las bacterias y la cantidad de hongos, en especial aquellos con potencial para producir antibi\u00f3ticos tales como el g\u00e9nero de hongo Penicillium. Falk Hildebrand: \u00abEste patr\u00f3n podr\u00eda explicarse teniendo en cuenta que los hongos producen antibi\u00f3ticos para combatir a las bacterias, y solo aquellas que posean genes de resistencia a los antibi\u00f3ticos pueden sobrevivir\u00bb.<\/p>\n\n\n\n

El conflicto entre los hongos y las bacterias incide sobre la diversidad total de comunidades bacterianas y determina el repertorio gen\u00e9tico de resistencia a los antibi\u00f3ticos. Esta informaci\u00f3n puede utilizarse para predecir la proliferaci\u00f3n de genes que originen una resistencia a los antibi\u00f3ticos en diferentes ecosistemas y el medio por el cual podr\u00edan llegar a los agentes pat\u00f3genos humanos. Adem\u00e1s, podr\u00eda ayudar a predecir e identificar regiones con una marcada presencia de productores naturales de antibi\u00f3ticos.<\/p>\n\n\n\n

Diferencias regionales<\/h2>\n\n\n\n

El equipo tambi\u00e9n encontr\u00f3 diferencias regionales en la distribuci\u00f3n de bacterias y hongos. Las bacterias se encuentran presentes en todos lados, y presentan la m\u00e1s alta diversidad gen\u00e9tica en zonas templadas con clima moderado. Factores ambientales tales como la temperatura determinan en forma decisiva su abundancia: generalmente prefieren sitios calurosos y h\u00famedos. Los hongos suelen abundar en climas m\u00e1s fr\u00edos y secos como la tundra. Tambi\u00e9n tienden a estar m\u00e1s limitados geogr\u00e1ficamente \u2014las poblaciones var\u00edan seg\u00fan el continente. Esto significa que las contribuciones relativas de bacterias y hongos al ciclo de nutrientes var\u00edan en todo el mundo, y que el cambio clim\u00e1tico global podr\u00eda afectar su composici\u00f3n y funcionamiento de diferente modo.<\/p>\n\n\n\n

Efectos de la actividad humana<\/h2>\n\n\n\n

Al comparar informaci\u00f3n de sitios con suelos v\u00edrgenes con informaci\u00f3n proveniente de sitios intervenidos por humanos, como granjas o jardines, la proporci\u00f3n de bacterias, hongos y antibi\u00f3ticos revel\u00f3 ser completamente distinta. Seg\u00fan los cient\u00edficos, esta alteraci\u00f3n en el equilibrio natural (que probablemente ha evolucionado durante gran parte de la historia de la Tierra), denota el efecto de las actividades humanas en el microbioma del suelo, cuyas consecuencias son a\u00fan desconocidas. Sin embargo, comprender en mayor profundidad las interacciones entre los hongos y las bacterias en el suelo podr\u00eda ayudar a reducir el uso de fertilizantes en agricultura y as\u00ed darles a los microorganismos beneficiosos la posibilidad de sobrevivir en su ambiente natural.<\/p>\n","protected":false},"excerpt":{"rendered":"

First global survey of soil genomics reveals a war between fungi and bacteria<\/p>\n","protected":false},"author":58,"featured_media":14061,"comment_status":"closed","ping_status":"closed","sticky":false,"template":"","format":"standard","meta":{"_acf_changed":false,"footnotes":""},"categories":[2,17591],"tags":[683,584,494,580,87,365,684,681,88,233,1748,680],"embl_taxonomy":[],"class_list":["post-14060","post","type-post","status-publish","format-standard","has-post-thumbnail","hentry","category-science","category-science-technology","tag-agriculture","tag-antibiotic","tag-antibiotic-resistance","tag-bacteria","tag-biodiversity","tag-bork","tag-environment","tag-fungi","tag-metagenomics","tag-microbiome","tag-press-release","tag-soil"],"acf":{"article_intro":"

First global survey of soil genomics reveals a war between fungi and bacteria<\/p>\n","related_links":[{"link_description":"","link_url":""},{"link_description":"","link_url":""}],"article_sources":[{"source_description":"

Bahram, M., Hildebrand, F., et al<\/em>. Structure and function of the global topsoil microbiome. Nature<\/em>, published online 1 August 2018. DOI: 10.1038\/s41586-018-0386-6<\/p>\n","source_link_url":"http:\/\/dx.doi.org\/10.1038\/s41586-018-0386-6"}],"vf_locked":false,"featured":false,"color":"#007B53","show_featured_image":false,"in_this_article":false,"youtube_url":"","mp4_url":"","video_caption":"","translations":[{"translation_language":"German","translation_anchor":"#de"},{"translation_language":"Spanish","translation_anchor":"#es"}],"press_contact":"EMBL Generic","field_target_display":"embl","field_article_language":{"value":"english","label":"English"},"source_article":false,"article_translations":false,"languages":""},"embl_taxonomy_terms":[],"yoast_head":"\nUnderstanding soil through its microbiome | EMBL<\/title>\n<meta name=\"description\" content=\"EMBL scientists conduct the first global survey of soil genomics, and reveal a war between fungi and bacteria.\" \/>\n<meta name=\"robots\" content=\"index, follow, max-snippet:-1, max-image-preview:large, max-video-preview:-1\" \/>\n<link rel=\"canonical\" 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