https://phys.org/ en-us Latest news from DOE/Joint Genome Institute To boost crops more efficiently in the future, the evolutionary past may hold key insights. The way that plants process nutrients has a rich back story—they rely on enzymes that have been evolving for billions of years. However, these enzymes are often loosely understood, leaving potential targets for crop engineering untouched. https://phys.org/news/2024-12-enzymes-evolved-characteristics-nitrogen-metabolism.html Evolution Thu, 12 Dec 2024 13:26:04 EST news653232361 The products of photosynthesis are easy to point out. Plants, algae and cyanobacteria create the air we breathe and the fuel for food webs as they turn carbon dioxide and water into oxygen and sugars. How photosynthesis works, though, is much harder to pin down. https://phys.org/news/2024-06-insights-cyanobacterial-proteins-carbon-conditions.html Cell & Microbiology Fri, 07 Jun 2024 09:40:20 EDT news636972014 If a tree falls in the forest—whether or not anyone registers the sound—one thing is for sure: there are lots of fungi around. Within a forest's soil, hundreds of species decompose debris, mobilize nutrients from that decay, and deliver those nutrients to tree roots and soil. These fungi help shape a forest's ecology. They store carbon and cycle key nutrients like nitrogen and phosphorus. https://phys.org/news/2024-04-scientists-soil-rna-fungal-genomes.html Ecology Wed, 24 Apr 2024 15:19:12 EDT news633190748 Most organisms use oxygen to convert food into energy. However, in environments with little or no oxygen, life found other ways to produce energy, using a process called fermentation. https://phys.org/news/2024-03-interactive-comprehensive-database-fermentative-prokaryotes.html Cell & Microbiology Mon, 25 Mar 2024 09:56:25 EDT news630579382 Eelgrass, one of the most abundant plants in the ocean, originated in Japan before spreading around the globe. Now, scientists have shed light on both when and how eelgrass adapted and evolved throughout its history. https://phys.org/news/2023-12-eelgrass-evolutionarily-younger-thought.html Plants & Animals Wed, 13 Dec 2023 11:27:33 EST news621689251 Scientists have discovered flagella in an unexpected place: hot spring-dwelling bacteria from the phylum Chloroflexota. Research shows that flagella were lost in other forms of Chloroflexota that adapted to marine environments hundreds of millions of years ago. https://phys.org/news/2023-10-marine-bacteria-ditched-flagella-traits.html Evolution Fri, 20 Oct 2023 09:45:48 EDT news617013944 Mobile genetic elements (MGEs) are genetic entities that seek to replicate themselves and spread from cell to cell. Two of the most common forms of MGEs are viruses and plasmids. They can be found in virtually all of Earth's ecosystems. https://phys.org/news/2023-09-tool-quickly-accurately-mobile-genetic.html Biotechnology Fri, 22 Sep 2023 09:37:16 EDT news614594227 Shiitake mushrooms get their name from the same place they often source their nutrients—the shii tree, a Japanese relative of the oak. These fungi are part of the genus Lentinula, which have evolved to decompose hardwoods on every continent besides Europe and Antarctica. https://phys.org/news/2023-03-evolution-shiitake-mushrooms.html Plants & Animals Wed, 01 Mar 2023 10:45:03 EST news596889901 Since its launch 25 years ago, the Genomes OnLine Database (GOLD) has matured from six projects on a spreadsheet into a flagship genomic metadata repository, making curated microbiome metadata that follows community standards freely available, and enabling large-scale comparative genomics analysis initiatives. https://phys.org/news/2022-11-genomes-online-database-features.html Biotechnology Tue, 29 Nov 2022 15:00:13 EST news588956409 The planet's microbial diversity is immense, yet much of it remains unknown. For more than a decade, researchers around the world have collaborated with the U.S. Department of Energy (DOE) Joint Genome Institute (JGI), a DOE Office of Science User Facility located at Lawrence Berkeley National Laboratory (Berkeley Lab), to fill in these gaps of knowledge. https://phys.org/news/2022-11-large-scale-analysis-identification-biosynthetic-gene.html Cell & Microbiology Mon, 14 Nov 2022 12:26:03 EST news587651161 A zoo once offered a coloring book featuring polar bears in winter scenes that came with crayons in various shades of white. To researchers searching for sequences of RNA viruses in large data sets, their work may be akin to finding a single snowflake on a colored-in page of that book. https://phys.org/news/2022-10-rna-virus-needles-database-haystacks.html Biotechnology Mon, 03 Oct 2022 11:28:07 EDT news584015283 Microbial secondary metabolites, those molecules not essential for growth yet essential for survival, may now be easier to characterize following a proof-of-concept study in which researchers paired CRISPR and CRAGE technologies. https://phys.org/news/2022-08-secrets-secondary-metabolites.html Biochemistry Tue, 23 Aug 2022 09:20:02 EDT news580465201 A collaborative team led by researchers at the University of Texas (UT) at Austin, the HudsonAlpha Institute for Biotechnology (HudsonAlpha), and the U.S. Department of Energy (DOE) Joint Genome Institute (JGI), a DOE Office of Science User Facility, has discovered that the candidate bioenergy feedstock switchgrass has adapted to expand its habitat range, but at what cost? In the following guest piece, postdoctoral researcher Joseph Napier from the Juenger lab and computational biologist Paul Grabowski of HudsonAlpha outline the questions they asked—and answered—in the study that recently appeared in the Proceedings of the National Academy of Sciences (PNAS). https://phys.org/news/2022-04-multiple-switchgrass-gene.html Molecular & Computational biology Wed, 13 Apr 2022 09:22:26 EDT news569060541 Researchers demonstrated the value of conducting large-scale single cell genomics by collecting nearly 500 single cells from a single low diversity hot spring sediment sample. Their work showed that single cell genomics can add significant value to the other commonly used culture-independent sequencing approaches including amplicon and metagenomic sequencing. For example, they showed that the composition of the community was similar across sequencing approaches, that species specific sets of single cells harbored mobile genetic elements that were missed within paired metagenome assembled genomes (MAGs), and that dominant populations varied with respect to the amount of within species recombination, indicating variation in gene flow between the analyzed community members. https://phys.org/news/2022-04-large-scale-cell-genomics-complements-metagenomics.html Biotechnology Tue, 12 Apr 2022 10:43:04 EDT news568978974 A collaborative team led by Geoffrey Schiebinger at the University of British Columbia, Philip Benfey at Duke University and Uwe Ohler at Humboldt Universität zu Berlin has developed an atlas that maps gene expression patterns in the Arabidopsis root, profiling nearly 100,000 single root cells and combining the information with previously published datasets. The work was recently published in the journal Developmental Cell and provides a community resource that could help researchers track cell development and how they determine identity, as well as the roles played by neighboring cells in these processes. https://phys.org/news/2022-03-root-atlas-tracking-developmental-trajectories.html Plants & Animals Tue, 08 Mar 2022 11:07:33 EST news565960032 In a text file, the rows of letters A, T, C and G appearing over and over in a dizzying array of combinations, are unremarkable, save perhaps for the absence of all the other letters of the alphabet. Yet the specific sequence of these four letters represents an organism's genetic code, or genome, which underlies physical features and functions. https://phys.org/news/2021-11-enlarging-windows-gene-functions.html Molecular & Computational biology Fri, 26 Nov 2021 11:10:06 EST news557147031 A deep dive into microbial genomics reveals one bacterial species is made of four ecologically distinct groups with different lifestyles. https://phys.org/news/2021-11-marine-microbe-multitudes.html Ecology Fri, 19 Nov 2021 08:51:35 EST news556534290 Since early 2020, people all over the world have been forced to confront the awesome power that viruses have to affect nearly every aspect of our daily lives. But for researchers who study viruses that infect organisms much smaller than humans, like bacteria, this power is not surprising at all. In fact, even in non-pandemic times such viruses are well known to play major roles in a vast range of globe-straddling phenomena. For example, viruses which infect the photosynthetic cyanobacteria found throughout the planet's oceans can exert great influence on earth's carbon and nitrogen cycles. https://phys.org/news/2021-09-power-viral-metagenomics.html Molecular & Computational biology Thu, 30 Sep 2021 09:34:04 EDT news552213242 Altiarchaea are carbon-fixing microbes and targets of multiple viruses in Earth's deep subsurface. They are abundant representatives of deep subsurface ecosystems. A team of researchers described how the viruses repeatedly attempted to infect and destroy the host archaea—and how the microbes resist. The battle waged below the Earth's surface is reconstructed by combining a study of microbial communities (metagenomics) and a chemical labeling approach. https://phys.org/news/2021-09-plotting-virus-host-warfare-deep-ground.html Cell & Microbiology Thu, 23 Sep 2021 09:56:34 EDT news551609790 Anaerobic fungi, which die in the presence of oxygen, dwell in herbivore guts and help them digest their last leafy meal. In their evolutionary history, these fungi branched off early from aerobic fungi, which can breathe oxygen—just like we do. Oxygen is a rich source of energy, and because anaerobic fungi can't harness it, scientists long held that these fungi don't have the energy to make complex compounds called natural products. Yet, combing through the genomes of four anaerobic fungal species has revealed, for the first time, that this group is unexpectedly powerful: they can whip up dozens of complex natural products, including new ones. https://phys.org/news/2021-04-gut-fungi-unexpected-source-chemicals.html Cell & Microbiology Thu, 29 Apr 2021 09:55:00 EDT news538908897 In 2019, the JGI's Yasuo Yoshikuni and his team announced in Nature Microbiology an important addition to the synthetic biologist's toolkit: a technique for chassis (or strain)-independent recombinase-assisted genome engineering (CRAGE). CRAGE enables scientists to insert large pieces of DNA (up to 60 kb) in a single step, directly into the genome. https://phys.org/news/2021-02-age-crage-advances-rapidly-non-model.html Biotechnology Tue, 09 Feb 2021 08:26:57 EST news532081615 Through advances in sequencing technologies and computational approaches, more and more virus sequences are being recovered and identified from environmental samples (metagenomes). However, the quality and completeness of metagenome-assembled virus sequences vary widely. In a previous effort, an international consortium recommended specific guidelines and best practices for characterizing uncultivated viruses. Following up on those guidelines, JGI researchers have now developed CheckV (pronounced "Check-Vee") to help researchers assess and improve the quality of metagenome-assembled viral genomes. https://phys.org/news/2020-12-automated-tool-virus-quality.html Biotechnology Tue, 22 Dec 2020 08:57:36 EST news527849849 Interested in the genomes of algae? You now have one place where you can browse the genetic blueprints of these photosynthetic organisms. PhycoCosm is one of the largest data repositories of its kind, with an interactive browser that allows algal scientists and enthusiasts to look deep into more than 100 algal genomes, compare them, and visualize supporting experimental data. https://phys.org/news/2020-12-one-stop-algal-genomes.html Biotechnology Tue, 22 Dec 2020 08:49:05 EST news527849342 Maize (Zea mays) produces a plethora of antibiotics called zealexins. Even though scientists have identified at least 15 zealexins, they suspect there are even more to find. Zealexins are produced in every corn variety and protect maize by fending off fungal and microbial infections. Scientists had assumed that maize synthesizes these compounds via clear, straight pathways, entailing the function of more than a dozen enzymes. But researchers have now revealed that just a handful of enzymes are needed to transform zealexins and related precursors into a bonanza of diverse structures. https://phys.org/news/2020-12-maize-antibiotic-cocktail.html Plants & Animals Wed, 09 Dec 2020 08:55:42 EST news526726480 Despite advances in sequencing technologies and computational methods in the past decade, researchers have uncovered genomes for just a small fraction of Earth's microbial diversity. Because most microbes cannot be cultivated under laboratory conditions, their genomes can't be sequenced using traditional approaches. Identifying and characterizing the planet's microbial diversity is key to understanding the roles of microorganisms in regulating nutrient cycles, as well as gaining insights into potential applications they may have in a wide range of research fields. https://phys.org/news/2020-11-uncovering-genomes-earth-microbiomes.html Ecology Tue, 10 Nov 2020 09:27:19 EST news524222739 In microbial mats, communities of microorganisms live among viruses that infect them. But what trends govern those virus-host interactions? Do generalist viruses run rampant, capable of infecting different host species? Or, do they tend to specialize, infecting just a single host? Another wrinkle in the mystery is that viruses can affect their prey in different ways. They have the capacity to kill outright, replicating so thoroughly that they lyse the cell—a process called lytic infection. But some viruses are also able to play a long game. In a lifestyle called lysogeny, they can insinuate themselves inside the host's genome, living quietly and replicating with their host indefinitely. https://phys.org/news/2020-09-host-virus-dynamics-microbial-mat-hot.html Cell & Microbiology Wed, 09 Sep 2020 08:37:24 EDT news518859435 Flowering plants abide by the concept, "the more the merrier," with respect to their genomes. In their base state, they are diploids with two genome copies, one from each parent. Having three or more genome copies from additional parents or duplication, also known as "polyploidy," is common among flowering plants; at least once during their evolution, the genomes of flowering plants multiply. Over time, plants lose many genes after such events, returning their genomes to a diploid state while retaining multiple copies of some genes. https://phys.org/news/2020-08-brachypodium-polyploid-genome-evolution.html Evolution Wed, 26 Aug 2020 08:22:15 EDT news517648932 Scientists have developed a more nuanced library approach to tuning gene expression in metabolic pathways. Compared to the traditional way, which leverages an all-or-nothing approach to expression, scientists can now opt for various shades of gray. The ability to fine-tune the level of gene expression allowed researchers to identify variations of essential genes in metabolic networks that were missed using traditional approaches. https://phys.org/news/2020-08-fine-tuning-metabolic-gene-variants-yeast.html Cell & Microbiology Fri, 07 Aug 2020 08:10:01 EDT news516006443 As a proof of concept, researchers developed an algorithm that "taught" a computer how to classify 101 representative genomes of Dothideomycetes, the largest class of fungi, by lifestyles. The machine "learned" to identify data generated in part through the 1000 Fungal Genomes Project, including 55 newly-sequenced species. https://phys.org/news/2020-07-computationally-fungal-lifestyles.html Molecular & Computational biology Wed, 22 Jul 2020 10:03:28 EDT news514630998 A team led by researchers at the Max Planck Institute (MPI) for Marine Microbiology has developed, tested and deployed a pipeline to first target cells from communities of uncultivated microbes, and then efficiently retrieve and characterize their genomes. https://phys.org/news/2020-04-microbial-needle-haystack.html Cell & Microbiology Fri, 24 Apr 2020 09:03:20 EDT news506937798