دورية أكاديمية
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Stable-Isotope-Informed, Genome-Resolved Metagenomics Uncovers Potential Cross-Kingdom Interactions in Rhizosphere Soil.

التفاصيل البيبلوغرافية
العنوان: Stable-Isotope-Informed, Genome-Resolved Metagenomics Uncovers Potential Cross-Kingdom Interactions in Rhizosphere Soil.
المؤلفون: Starr EP; Department of Plant and Microbial Biology, University of California, Berkeleygrid.47840.3f, California, USA., Shi S; Lincoln Science Centre, AgResearch Ltd., Christchurch, New Zealand., Blazewicz SJ; Physical and Life Sciences Directorate, Lawrence Livermore National Laboratorygrid.250008.f, Livermore, California, USA., Koch BJ; Department of Biological Sciences, Northern Arizona Universitygrid.261120.6, Flagstaff, Arizona, USA.; Center for Ecosystem Science and Society, Northern Arizona Universitygrid.261120.6, Flagstaff, Arizona, USA., Probst AJ; Biofilm Center, University of Duisburg-Essen, Essen, Germany., Hungate BA; Department of Biological Sciences, Northern Arizona Universitygrid.261120.6, Flagstaff, Arizona, USA.; Center for Ecosystem Science and Society, Northern Arizona Universitygrid.261120.6, Flagstaff, Arizona, USA., Pett-Ridge J; Physical and Life Sciences Directorate, Lawrence Livermore National Laboratorygrid.250008.f, Livermore, California, USA., Firestone MK; Department of Environmental Science, Policy, and Management, University of California, Berkeleygrid.47840.3f, California, USA.; Earth and Environmental Sciences, Lawrence Berkeley National Laboratory, Berkeley, California, USA., Banfield JF; Department of Environmental Science, Policy, and Management, University of California, Berkeleygrid.47840.3f, California, USA.; Earth and Environmental Sciences, Lawrence Berkeley National Laboratory, Berkeley, California, USA.; Department of Earth and Planetary Science, University of California, Berkeleygrid.47840.3f, California, USA.; Innovative Genomics Institute, Berkeley, California, USA.; Chan Zuckerberg Biohub, San Francisco, California, USA.
المصدر: MSphere [mSphere] 2021 Oct 27; Vol. 6 (5), pp. e0008521. Date of Electronic Publication: 2021 Sep 01.
نوع المنشور: Journal Article; Research Support, Non-U.S. Gov't; Research Support, U.S. Gov't, Non-P.H.S.
اللغة: English
بيانات الدورية: Publisher: American Society for Microbiology Country of Publication: United States NLM ID: 101674533 Publication Model: Print-Electronic Cited Medium: Internet ISSN: 2379-5042 (Electronic) Linking ISSN: 23795042 NLM ISO Abbreviation: mSphere Subsets: MEDLINE
أسماء مطبوعة: Original Publication: Washington, DC : American Society for Microbiology, [2015]-
مواضيع طبية MeSH: Bacteria/*genetics , Bacteria/*metabolism , DNA, Bacterial/*biosynthesis , Genome, Bacterial/*genetics , RNA, Bacterial/*biosynthesis, Bacteria/classification ; Carbon/metabolism ; DNA, Bacterial/genetics ; Isotope Labeling ; Metagenomics ; Phylogeny ; Plant Roots/microbiology ; RNA, Bacterial/genetics ; Rhizosphere ; Soil Microbiology
مستخلص: The functioning, health, and productivity of soil are intimately tied to a complex network of interactions, particularly in plant root-associated rhizosphere soil. We conducted a stable-isotope-informed, genome-resolved metagenomic study to trace carbon from Avena fatua grown in a 13 CO 2 atmosphere into soil. We collected paired rhizosphere and nonrhizosphere soil at 6 and 9 weeks of plant growth and extracted DNA that was then separated by density using ultracentrifugation. Thirty-two fractions from each of five samples were grouped by density, sequenced, assembled, and binned to generate 55 unique bacterial genomes that were ≥70% complete. We also identified complete 18S rRNA sequences of several 13 C-enriched microeukaryotic bacterivores and fungi. We generated 10 circularized bacteriophage (phage) genomes, some of which were the most labeled entities in the rhizosphere, suggesting that phage may be important agents of turnover of plant-derived C in soil. CRISPR locus targeting connected one of these phage to a Burkholderiales host predicted to be a plant pathogen. Another highly labeled phage is predicted to replicate in a Catenulispora sp., a possible plant growth-promoting bacterium. We searched the genome bins for traits known to be used in interactions involving bacteria, microeukaryotes, and plant roots and found DNA from heavily 13 C-labeled bacterial genes thought to be involved in modulating plant signaling hormones, plant pathogenicity, and defense against microeukaryote grazing. Stable-isotope-informed, genome-resolved metagenomics indicated that phage can be important agents of turnover of plant-derived carbon in soil. IMPORTANCE Plants grow in intimate association with soil microbial communities; these microbes can facilitate the availability of essential resources to plants. Thus, plant productivity commonly depends on interactions with rhizosphere bacteria, viruses, and eukaryotes. Our work is significant because we identified the organisms that took up plant-derived organic C in rhizosphere soil and determined that many of the active bacteria are plant pathogens or can impact plant growth via hormone modulation. Further, by showing that bacteriophage accumulate CO 2 -derived carbon, we demonstrated their vital roles in redistribution of plant-derived C into the soil environment through bacterial cell lysis. The use of stable-isotope probing (SIP) to identify consumption (or lack thereof) of root-derived C by key microbial community members within highly complex microbial communities opens the way for assessing manipulations of bacteria and phage with potentially beneficial and detrimental traits, ultimately providing a path to improved plant health and soil carbon storage.
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فهرسة مساهمة: Keywords: bacteriophages; metagenomics; plant-microbe interactions; rhizosphere; stable-isotope probing
سلسلة جزيئية: figshare 10.6084/m9.figshare.c.5405805
المشرفين على المادة: 0 (DNA, Bacterial)
0 (RNA, Bacterial)
7440-44-0 (Carbon)
تواريخ الأحداث: Date Created: 20210901 Date Completed: 20220202 Latest Revision: 20220202
رمز التحديث: 20221213
مُعرف محوري في PubMed: PMC8550312
DOI: 10.1128/mSphere.00085-21
PMID: 34468166
قاعدة البيانات: MEDLINE
الوصف
تدمد:2379-5042
DOI:10.1128/mSphere.00085-21