{"id":42189,"date":"2026-02-02T11:00:29","date_gmt":"2026-02-02T10:00:29","guid":{"rendered":"https:\/\/resoilfoundation.org\/?p=42189"},"modified":"2026-01-29T18:34:19","modified_gmt":"2026-01-29T17:34:19","slug":"usa-microbiome-dna-soil","status":"publish","type":"post","link":"https:\/\/resoilfoundation.org\/en\/innovation-technology\/usa-microbiome-dna-soil\/","title":{"rendered":"US soil microbiome under investigation by researchers"},"content":{"rendered":"<h2>A group of researchers led by Johns Hopkins University is exploring the US microbiome by collecting soil samples from urban and rural locations to identify genetic connections between the environment and microorganisms<\/h2>\n<p style=\"text-align: center;\">by Matteo Cavallito<\/p>\n<p>Soil, <strong>microbiome <\/strong>performs several functions that are crucial for plants and the ecosystem. However, the variety of microorganisms involved is still largely unknown, due to the challenge of monitoring and exploring such a vast environment. Nevertheless, some projects now promise to bring new knowledge. Among these is the work of geneticists at <strong>Johns Hopkins University<\/strong> who, in collaboration with external researchers and students, have embarked on a particularly ambitious project: cataloging the <strong>soil microbiome in the United States<\/strong>. The survey, described in an <a href=\"https:\/\/www.nature.com\/articles\/s41588-025-02442-5\" target=\"_blank\" rel=\"noopener\">article<\/a> published in the journal Nature Genetics, has already led to the discovery of over a thousand new strains of bacteria and microbes that had never been identified before.<\/p>\n<div class='avia-iframe-wrap'>\n<blockquote class=\"wp-embedded-content\" data-secret=\"txp84FQFBH\"><p><a href=\"https:\/\/resoilfoundation.org\/en\/articles\/genetics-plants-microbes-soil\/\">Plant genetics influences the presence of beneficial microbes in the soil<\/a><\/p><\/blockquote>\n<p><iframe loading=\"lazy\" class=\"wp-embedded-content\" sandbox=\"allow-scripts\" security=\"restricted\" style=\"position: absolute; visibility: hidden;\" title=\"&#8220;Plant genetics influences the presence of beneficial microbes in the soil&#8221; &#8212; Re Soil Foundation\" src=\"https:\/\/resoilfoundation.org\/en\/articles\/genetics-plants-microbes-soil\/embed\/#?secret=XFFEp6SyVq#?secret=txp84FQFBH\" data-secret=\"txp84FQFBH\" width=\"600\" height=\"338\" frameborder=\"0\" marginwidth=\"0\" marginheight=\"0\" scrolling=\"no\"><\/iframe><\/div>\n<h5>Microscopic dark matter<\/h5>\n<p>\u201cThe soil is the most biologically active environment on the planet, yet we\u2019ve sampled only a tiny fraction of the life that lives inside it,\u201d said <strong>Michael Schatz<\/strong>, co-author of the study, in a <a href=\"https:\/\/engineering.jhu.edu\/news\/science-army-mobilizes-to-map-u-s-soil-microbiome\/\" target=\"_blank\" rel=\"noopener\">statement <\/a>released by Johns Hopkins. This is a reference to the so-called \u201cmicrobial dark matter,\u201d the world of soil microorganisms that <strong>is still almost entirely unknown today<\/strong>. This world, the authors continue, includes more than half of all existing species, including nematodes, plants, fungi, bacteria, archaea, and other microbial species.<\/p>\n<p>Sixteen years ago, in 2010, an organization called the MetaSUB Consortium launched a groundbreaking study to map and study the microbes present in New York City subway stations. This initiative, which later evolved into a global project, inspired today&#8217;s study. It is being carried out by another consortium, BioDiversity and Informatics for Genomics Scholars (<a href=\"https:\/\/biodigs.org\/\" target=\"_blank\" rel=\"noopener\">BioDIGS<\/a>), which operates at <strong>around 40 sites in the US<\/strong>, collecting soil samples from urban and rural locations in search of genetic relationships and recurring patterns linking soil, the environment, and human health.<\/p>\n<div class='avia-iframe-wrap'>\n<blockquote class=\"wp-embedded-content\" data-secret=\"wNaMyvgJl8\"><p><a href=\"https:\/\/resoilfoundation.org\/en\/articles\/edna-soil-secret\/\">eDNA discloses the secrets of soil and helps us to protect it<\/a><\/p><\/blockquote>\n<p><iframe loading=\"lazy\" class=\"wp-embedded-content\" sandbox=\"allow-scripts\" security=\"restricted\" style=\"position: absolute; visibility: hidden;\" title=\"&#8220;eDNA discloses the secrets of soil and helps us to protect it&#8221; &#8212; Re Soil Foundation\" src=\"https:\/\/resoilfoundation.org\/en\/articles\/edna-soil-secret\/embed\/#?secret=umt9zjiPDg#?secret=wNaMyvgJl8\" data-secret=\"wNaMyvgJl8\" width=\"600\" height=\"338\" frameborder=\"0\" marginwidth=\"0\" marginheight=\"0\" scrolling=\"no\"><\/iframe><\/div>\n<h5>DNA analysis proves crucial<\/h5>\n<p>Microbiome studies have long been based on genetic analysis. Several years ago, researchers at <strong>Toyohashi University of Technology<\/strong> in Japan&#8217;s Aichi Prefecture <a href=\"https:\/\/resoilfoundation.org\/en\/innovation-technology\/japan-study-nematodes\/\" target=\"_blank\" rel=\"noopener\">began monitoring<\/a> <strong>nematodes<\/strong>, <a href=\"https:\/\/journals.plos.org\/plosone\/article?id=10.1371\/journal.pone.0249571\" target=\"_blank\" rel=\"noopener\">small organisms<\/a> that feed on bacteria and fungi, using a technique known as <strong>DNA barcoding<\/strong>, which allows a <a href=\"https:\/\/en.wikipedia.org\/wiki\/DNA_barcoding\" target=\"_blank\" rel=\"noopener\">reference nucleotide sequence<\/a> to be associated with different species to distinguish them from one another.<\/p>\n<blockquote><p>The authors point out that the US project has been made possible by other <strong>recent advances<\/strong> in <strong>DNA<\/strong> sequencing technology, starting with long-read sequencing.<\/p><\/blockquote>\n<p>This technology, in other words, is capable of reading <a href=\"https:\/\/en.wikipedia.org\/wiki\/Third-generation_sequencing\" target=\"_blank\" rel=\"noopener\">very large fragments<\/a> of genetic material\u201410-100,000 bases compared to the few hundred guaranteed by previous-generation techniques\u2014in a single action. With the support of this technology, the collection of samples from a wide variety of soils across the country should provide the material needed for a more accurate analysis of microbes genomes.<\/p>\n<div class='avia-iframe-wrap'>\n<blockquote class=\"wp-embedded-content\" data-secret=\"jNLm5tRIfD\"><p><a href=\"https:\/\/resoilfoundation.org\/en\/articles\/ai-plants-mutant-bacteria\/\">AI helps plants track down mutant bacteria<\/a><\/p><\/blockquote>\n<p><iframe loading=\"lazy\" class=\"wp-embedded-content\" sandbox=\"allow-scripts\" security=\"restricted\" style=\"position: absolute; visibility: hidden;\" title=\"&#8220;AI helps plants track down mutant bacteria&#8221; &#8212; Re Soil Foundation\" src=\"https:\/\/resoilfoundation.org\/en\/articles\/ai-plants-mutant-bacteria\/embed\/#?secret=Vfg5x648sq#?secret=jNLm5tRIfD\" data-secret=\"jNLm5tRIfD\" width=\"600\" height=\"338\" frameborder=\"0\" marginwidth=\"0\" marginheight=\"0\" scrolling=\"no\"><\/iframe><\/div>\n<h5>In Europe, the first national monitoring of the microbiome<\/h5>\n<p>Among the latest studies on soil microorganisms, the <a href=\"https:\/\/resoilfoundation.org\/en\/environment\/denmark-mapped-soil-microbiome\/\" target=\"_blank\" rel=\"noopener\">work<\/a> carried out by the <strong>University of Aalborg<\/strong> in Denmark, in collaboration with the <strong>University of Vienna<\/strong>, stands out in particular. The <a href=\"https:\/\/www.nature.com\/articles\/s41586-025-09794-2\" target=\"_blank\" rel=\"noopener\">study<\/a>, published in the journal Nature, examined over 10,000 soil samples to paint a picture of the country&#8217;s different environmental contexts and the microbes that inhabit them. This is the first mapping of a soil microbiome ever carried out at the national level.<\/p>\n<p>The survey, based on <strong>10,683<\/strong> <a href=\"https:\/\/en.wikipedia.org\/wiki\/Metagenomics\" target=\"_blank\" rel=\"noopener\">gene sequences<\/a> of microorganisms and additional rRNA datasets, provided important information<br \/>\non aspects such as the impact of intensive agriculture on microbial profiles, the role of microorganisms in <a href=\"https:\/\/resoilfoundation.org\/en\/agricultural-industry\/nitrogen-emissions-ozone-layer\/\" target=\"_blank\" rel=\"noopener\">nitrogen emission<\/a> dynamics, and that of <a href=\"https:\/\/resoilfoundation.org\/en\/environment\/fertilizer-eu-nitrogen-targets\/\" target=\"_blank\" rel=\"noopener\">fertilizers<\/a>. <strong>This contributes to the monitoring of microbial responses<\/strong> to land use and climate change.<\/p>\n<div class=\"avia-iframe-wrap\"><\/div>\n<div class=\"avia-iframe-wrap\"><\/div>\n","protected":false},"excerpt":{"rendered":"<p>A group of researchers led by Johns Hopkins University is exploring the US microbiome by collecting soil samples from urban and rural locations to identify genetic connections between the environment and microorganisms<\/p>\n","protected":false},"author":4,"featured_media":42192,"comment_status":"closed","ping_status":"open","sticky":false,"template":"","format":"standard","meta":{"footnotes":""},"categories":[152,134],"tags":[200,49,303,204,247,188,322,163],"class_list":["post-42189","post","type-post","status-publish","format-standard","has-post-thumbnail","hentry","category-innovation-technology","category-articles","tag-biodiversity","tag-ecosistemi","tag-ecosystems-2-en","tag-ecosystems","tag-monitoraggio-en","tag-research","tag-suolo-en","tag-usa-en"],"yoast_head":"<!-- This site is optimized with the Yoast SEO plugin v27.3 - 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