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Wei S, Jespersen ML, Baunwall SMD, Myers PN, Smith EM, Dahlerup JF, Rasmussen S, Nielsen HB, Licht TR, Bahl MI, Hvas CL. Cross-generational bacterial strain transfer to an infant after fecal microbiota transplantation to a pregnant patient: a case report. MICROBIOME 2022; 10:193. [PMID: 36352460 PMCID: PMC9647999 DOI: 10.1186/s40168-022-01394-w] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Accepted: 10/13/2022] [Indexed: 06/14/2023]
Abstract
BACKGROUND Fecal microbiota transplantation (FMT) effectively prevents the recurrence of Clostridioides difficile infection (CDI). Long-term engraftment of donor-specific microbial consortia may occur in the recipient, but potential further transfer to other sites, including the vertical transmission of donor-specific strains to future generations, has not been investigated. Here, we report, for the first time, the cross-generational transmission of specific bacterial strains from an FMT donor to a pregnant patient with CDI and further to her child, born at term, 26 weeks after the FMT treatment. METHODS A pregnant woman (gestation week 12 + 5) with CDI was treated with FMT via colonoscopy. She gave vaginal birth at term to a healthy baby. Fecal samples were collected from the feces donor, the mother (before FMT, and 1, 8, 15, 22, 26, and 50 weeks after FMT), and the infant (meconium at birth and 3 and 6 months after birth). Fecal samples were profiled by deep metagenomic sequencing for strain-level analysis. The microbial transfer was monitored using single nucleotide variants in metagenomes and further compared to a collection of metagenomic samples from 651 healthy infants and 58 healthy adults. RESULTS The single FMT procedure led to an uneventful and sustained clinical resolution in the patient, who experienced no further CDI-related symptoms up to 50 weeks after treatment. The gut microbiota of the patient with CDI differed considerably from the healthy donor and was characterized as low in alpha diversity and enriched for several potential pathogens. The FMT successfully normalized the patient's gut microbiota, likely by donor microbiota transfer and engraftment. Importantly, our analysis revealed that some specific strains were transferred from the donor to the patient and then further to the infant, thus demonstrating cross-generational microbial transfer. CONCLUSIONS The evidence for cross-generational strain transfer following FMT provides novel insights into the dynamics and engraftment of bacterial strains from healthy donors. The data suggests FMT treatment of pregnant women as a potential strategy to introduce beneficial strains or even bacterial consortia to infants, i.e., neonatal seeding. Video Abstract.
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Affiliation(s)
- Shaodong Wei
- National Food Institute, Technical University of Denmark, Kemitorvet 202, 2800, Kgs Lyngby, Denmark
| | - Marie Louise Jespersen
- National Food Institute, Technical University of Denmark, Kemitorvet 202, 2800, Kgs Lyngby, Denmark
- Clinical-Microbiomics A/S, Copenhagen, Denmark
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Simon Mark Dahl Baunwall
- Department of Hepatology and Gastroenterology, Aarhus University Hospital, Aarhus, Denmark
- Institute of Clinical Medicine, Aarhus University, Aarhus, Denmark
| | | | - Emilie Milton Smith
- National Food Institute, Technical University of Denmark, Kemitorvet 202, 2800, Kgs Lyngby, Denmark
| | - Jens Frederik Dahlerup
- Department of Hepatology and Gastroenterology, Aarhus University Hospital, Aarhus, Denmark
| | - Simon Rasmussen
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | | | - Tine Rask Licht
- National Food Institute, Technical University of Denmark, Kemitorvet 202, 2800, Kgs Lyngby, Denmark
| | - Martin Iain Bahl
- National Food Institute, Technical University of Denmark, Kemitorvet 202, 2800, Kgs Lyngby, Denmark.
| | - Christian Lodberg Hvas
- Department of Hepatology and Gastroenterology, Aarhus University Hospital, Aarhus, Denmark
- Institute of Clinical Medicine, Aarhus University, Aarhus, Denmark
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Roux S, Emerson JB. Diversity in the soil virosphere: to infinity and beyond? Trends Microbiol 2022; 30:1025-1035. [PMID: 35644779 DOI: 10.1016/j.tim.2022.05.003] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Revised: 05/02/2022] [Accepted: 05/03/2022] [Indexed: 01/13/2023]
Abstract
Viruses are key members of Earth's microbiomes, shaping microbial community composition and metabolism. Here, we describe recent advances in 'soil viromics', that is, virus-focused metagenome and metatranscriptome analyses that offer unprecedented windows into the soil virosphere. Given the emerging picture of high soil viral activity, diversity, and dynamics over short spatiotemporal scales, we then outline key eco-evolutionary processes that we hypothesize are the major diversity drivers for soil viruses. We argue that a community effort is needed to establish a 'global soil virosphere atlas' that can be used to address the roles of viruses in soil microbiomes and terrestrial biogeochemical cycles across spatiotemporal scales.
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Affiliation(s)
- Simon Roux
- DOE (Department of Energy) Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
| | - Joanne B Emerson
- Department of Plant Pathology, University of California, Davis, Davis, CA, USA; Genome Center, University of California, Davis, Davis, CA, USA.
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Truu M, Ligi T, Nõlvak H, Peeb A, Tiirik K, Devarajan AK, Oopkaup K, Kasemets K, Kõiv-Vainik M, Kasak K, Truu J. Impact of synthetic silver nanoparticles on the biofilm microbial communities and wastewater treatment efficiency in experimental hybrid filter system treating municipal wastewater. JOURNAL OF HAZARDOUS MATERIALS 2022; 440:129721. [PMID: 35963093 DOI: 10.1016/j.jhazmat.2022.129721] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Revised: 07/22/2022] [Accepted: 08/04/2022] [Indexed: 06/15/2023]
Abstract
Silver nanoparticles (AgNPs) threaten human and ecosystem health, and are among the most widely used engineered nanomaterials that reach wastewater during production, usage, and disposal phases. This study evaluated the effect of a 100-fold increase in collargol (protein-coated AgNP) and Ag+ ions concentrations in municipal wastewater on the microbial community composition of the filter material biofilms (FMB) and the purification efficiency of the hybrid treatment system consisting of vertical (VF) and horizontal (HF) subsurface flow filters. We found that increased amounts of collargol and AgNO3 in wastewater had a modest effect on the prokaryotic community composition in FMB and did not significantly affect the performance of the studied system. Regardless of how Ag was introduced, 99.9% of it was removed by the system. AgNPs and AgNO3 concentrations did not significantly affect the purification efficiency of the system. AgNO3 induced a higher increase in the genetic potential of certain Ag resistance mechanisms in VFs than collargol; however, the increase in Ag resistance potential was similar for both substances in HF. Hence, the microbial community composition in biofilms of vertical and horizontal flow filters is largely resistant, resilient, or functionally redundant in response to AgNPs addition in the form of collargol.
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Affiliation(s)
- Marika Truu
- Institute of Molecular and Cell Biology, University of Tartu, Riia 23, 51010 Tartu, Estonia.
| | - Teele Ligi
- Institute of Molecular and Cell Biology, University of Tartu, Riia 23, 51010 Tartu, Estonia.
| | - Hiie Nõlvak
- Institute of Molecular and Cell Biology, University of Tartu, Riia 23, 51010 Tartu, Estonia.
| | - Angela Peeb
- Institute of Molecular and Cell Biology, University of Tartu, Riia 23, 51010 Tartu, Estonia.
| | - Kertu Tiirik
- Institute of Molecular and Cell Biology, University of Tartu, Riia 23, 51010 Tartu, Estonia.
| | - Arun Kumar Devarajan
- Institute of Molecular and Cell Biology, University of Tartu, Riia 23, 51010 Tartu, Estonia.
| | - Kristjan Oopkaup
- Institute of Molecular and Cell Biology, University of Tartu, Riia 23, 51010 Tartu, Estonia.
| | - Kaja Kasemets
- Laboratory of Environmental Toxicology, National Institute of Chemical Physics and Biophysics, Akadeemia tee 23, 12618 Tallinn, Estonia.
| | - Margit Kõiv-Vainik
- Institute of Ecology and Earth Sciences, University of Tartu, Vanemuise 46, 51014 Tartu, Estonia.
| | - Kuno Kasak
- Institute of Ecology and Earth Sciences, University of Tartu, Vanemuise 46, 51014 Tartu, Estonia.
| | - Jaak Truu
- Institute of Molecular and Cell Biology, University of Tartu, Riia 23, 51010 Tartu, Estonia.
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Kim M, Rodriguez-R LM, Hatt JK, Kayali O, Nalá R, Dunlop AL, Brennan PA, Corwin E, Smith AK, Brown J, Konstantinidis KT. Higher pathogen load in children from Mozambique vs. USA revealed by comparative fecal microbiome profiling. ISME COMMUNICATIONS 2022; 2:74. [PMID: 37938667 PMCID: PMC9723681 DOI: 10.1038/s43705-022-00154-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2022] [Revised: 07/08/2022] [Accepted: 07/20/2022] [Indexed: 07/05/2023]
Abstract
The infant gut microbiome has lifelong implications on health and immunity but there is still limited understanding of the microbiome differences and similarities between children in low- and middle-income countries (LMICs) vs. high-income countries (HICs). Here, we describe and compare the microbiome profile of children aged under 48 months in two urban areas: Maputo, Mozambique and Atlanta, USA using shotgun metagenomics. The gut microbiome of American children showed distinct development, characterized by higher alpha diversity after infancy, compared to the same age group of African children, and the microbiomes clustered separately based on geographic location or age. The abundances of antibiotic resistance genes (ARGs) and virulence factors (VFs) were significantly higher in Maputo children, driven primarily by several primary and opportunistic pathogens. Most notably, about 50% of Maputo children under the age of two were positive for enterotoxigenic (ETEC) and typical enteropathogenic (EPEC) Escherichia coli diagnostic genes while none of the Atlanta age-matched children showed such a positive signal. In contrast, commensal species such as Phocaeicola vulgatus and Bacteroides caccae were more abundant in Atlanta, potentially reflecting diets rich in animal protein and susceptibility to inflammatory diseases. Overall, our results suggest that the different environments characterizing the two cities have significant, distinctive signatures on the microbiota of children and its development over time. Lack of safe water, sanitation, and hygiene (WASH) conditions and/or unsafe food sources may explain the higher enteric pathogen load among children in Maputo.
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Affiliation(s)
- Minjae Kim
- School of Civil and Environmental Engineering, Georgia Institute of Technology, Atlanta, GA, 30332, USA
- Natural Resource Ecology Laboratory, Colorado State University, Fort Collins, CO, 80523, USA
| | - Luis M Rodriguez-R
- Department of Microbiology and Digital Science Center (DiSC), University of Innsbruck, 6020, Innsbruck, Tyrol, Austria
| | - Janet K Hatt
- School of Civil and Environmental Engineering, Georgia Institute of Technology, Atlanta, GA, 30332, USA
| | - Osman Kayali
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, 30332, USA
| | - Rassul Nalá
- Instituto Nacional de Saúde, Marracuene, Mozambique
| | - Anne L Dunlop
- Department of Gynecology and Obstetrics, Emory University School of Medicine, Atlanta, GA, 30332, USA
| | | | - Elizabeth Corwin
- School of Nursing, Columbia University, New York, NY, 10032, USA
| | - Alicia K Smith
- Department of Gynecology and Obstetrics, Department of Psychiatry and Behavioral Sciences, Emory University, Atlanta, GA, 30322, USA
| | - Joe Brown
- Department of Environmental Sciences and Engineering, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, North, Carolina, NC, 27599, USA.
| | - Konstantinos T Konstantinidis
- School of Civil and Environmental Engineering, Georgia Institute of Technology, Atlanta, GA, 30332, USA.
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, 30332, USA.
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Keenum I, Wind L, Ray P, Guron G, Chen C, Knowlton K, Ponder M, Pruden A. Metagenomic tracking of antibiotic resistance genes through a pre-harvest vegetable production system: an integrated lab-, microcosm- and greenhouse-scale analysis. Environ Microbiol 2022; 24:3705-3721. [PMID: 35466491 PMCID: PMC9541739 DOI: 10.1111/1462-2920.16022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Revised: 04/14/2022] [Accepted: 04/18/2022] [Indexed: 11/30/2022]
Abstract
Prior research demonstrated the potential for agricultural production systems to contribute to the environmental spread of antibiotic resistance genes (ARGs). However, there is a need for integrated assessment of critical management points for minimizing this potential. Shotgun metagenomic sequencing data were analysed to comprehensively compare total ARG profiles characteristic of amendments (manure or compost) derived from either beef or dairy cattle (with and without dosing antibiotics according to conventional practice), soil (loamy sand or silty clay loam) and vegetable (lettuce or radish) samples collected across studies carried out at laboratory-, microcosm- and greenhouse-scale. Vegetables carried the greatest diversity of ARGs (n = 838) as well as the most ARG-mobile genetic element co-occurrences (n = 945). Radishes grown in manure- or compost-amended soils harboured a higher relative abundance of total (0.91 and 0.91 ARGs/16S rRNA gene) and clinically relevant ARGs than vegetables from other experimental conditions (average: 0.36 ARGs/16S rRNA gene). Lettuce carried the highest relative abundance of pathogen gene markers among the metagenomes examined. Total ARG relative abundances were highest on vegetables grown in loamy sand receiving antibiotic-treated beef amendments. The findings emphasize that additional barriers, such as post-harvest processes, merit further study to minimize potential exposure to consumers.
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Affiliation(s)
- Ishi Keenum
- Department of Civil and Environmental EngineeringVirginia TechBlacksburgVAUSA
| | - Lauren Wind
- Department of Biological Systems EngineeringVirginia TechBlacksburgVAUSA
| | - Partha Ray
- Department of Animal Sciences, School of Agriculture, Policy and DevelopmentUniversity of ReadingReadingRG6 6ARUK
| | - Giselle Guron
- Department of Food Science and TechnologyVirginia TechBlacksburgVAUSA
| | - Chaoqi Chen
- Department of Crop and Soil Environmental SciencesVirginia TechBlacksburgVAUSA
| | | | - Monica Ponder
- Department of Food Science and TechnologyVirginia TechBlacksburgVAUSA
| | - Amy Pruden
- Department of Civil and Environmental EngineeringVirginia TechBlacksburgVAUSA
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Comparative Metagenomic Analysis of Biosynthetic Diversity across Sponge Microbiomes Highlights Metabolic Novelty, Conservation, and Diversification. mSystems 2022; 7:e0035722. [PMID: 35862823 PMCID: PMC9426513 DOI: 10.1128/msystems.00357-22] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Marine sponges and their microbial symbiotic communities are rich sources of diverse natural products (NPs) that often display biological activity, yet little is known about the global distribution of NPs and the symbionts that produce them. Since the majority of sponge symbionts remain uncultured, it is a challenge to characterize their NP biosynthetic pathways, assess their prevalence within the holobiont, and measure the diversity of NP biosynthetic gene clusters (BGCs) across sponge taxa and environments. Here, we explore the microbial biosynthetic landscapes of three high-microbial-abundance (HMA) sponges from the Atlantic Ocean and the Mediterranean Sea. This data set reveals striking novelty, with <1% of the recovered gene cluster families (GCFs) showing similarity to any characterized BGC. When zooming in on the microbial communities of each sponge, we observed higher variability of specialized metabolic and taxonomic profiles between sponge species than within species. Nonetheless, we identified conservation of GCFs, with 20% of sponge GCFs being shared between at least two sponge species and a GCF core comprised of 6% of GCFs shared across all species. Within this functional core, we identified a set of widespread and diverse GCFs encoding nonribosomal peptide synthetases that are potentially involved in the production of diversified ether lipids, as well as GCFs putatively encoding the production of highly modified proteusins. The present work contributes to the small, yet growing body of data characterizing NP landscapes of marine sponge symbionts and to the cryptic biosynthetic potential contained in this environmental niche. IMPORTANCE Marine sponges and their microbial symbiotic communities are a rich source of diverse natural products (NPs). However, little is known about the sponge NP global distribution landscape and the symbionts that produce them. Here, we make use of recently developed tools to perform untargeted mining and comparative analysis of sponge microbiome metagenomes of three sponge species in the first study considering replicate metagenomes of multiple sponge species. We present an overview of the biosynthetic diversity across these sponge holobionts, which displays extreme biosynthetic novelty. We report not only the conservation of biosynthetic and taxonomic diversity but also a core of conserved specialized metabolic pathways. Finally, we highlight several novel GCFs with unknown ecological function, and observe particularly high biosynthetic potential in Acidobacteriota and Latescibacteria symbionts. This study paves the way toward a better understanding of the marine sponge holobionts' biosynthetic potential and the functional and ecological role of sponge microbiomes.
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Fernández-López M, Sánchez-Reyes A, Barcelos C, Sidón-Ceseña K, Leite RB, Lago-Lestón A. Deep-Sea Sediments from the Southern Gulf of Mexico Harbor a Wide Diversity of PKS I Genes. Antibiotics (Basel) 2022; 11:antibiotics11070887. [PMID: 35884142 PMCID: PMC9311598 DOI: 10.3390/antibiotics11070887] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2022] [Revised: 06/08/2022] [Accepted: 06/20/2022] [Indexed: 11/19/2022] Open
Abstract
The excessive use of antibiotics has triggered the appearance of new resistant strains, which is why great interest has been taken in the search for new bioactive compounds capable of overcoming this emergency in recent years. Massive sequencing tools have enabled the detection of new microorganisms that cannot be cultured in a laboratory, thus opening the door to the search for new biosynthetic genes. The great variety in oceanic environments in terms of pressure, salinity, temperature, and nutrients enables marine microorganisms to develop unique biochemical and physiological properties for their survival, enhancing the production of secondary metabolites that can vary from those produced by terrestrial microorganisms. We performed a search for type I PKS genes in metagenomes obtained from the marine sediments of the deep waters of the Gulf of Mexico using Hidden Markov Models. More than 2000 candidate genes were detected in the metagenomes that code for type I PKS domains, while biosynthetic pathways that may code for other secondary metabolites were also detected. Our research demonstrates the great potential use of the marine sediments of the Gulf of Mexico for identifying genes that code for new secondary metabolites.
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Affiliation(s)
- Maikel Fernández-López
- Centro de Investigación en Dinámica Celular, Instituto de Investigación en Ciencias Básicas y Aplicadas, Universidad Autónoma del Estado de Morelos, Av. Universidad 1001, Col. Chamilpa, Cuernavaca 62209, Mexico;
| | - Ayixon Sánchez-Reyes
- CONACYT-Instituto de Biotecnología, Universidad Nacional Autónoma de México (UNAM), Av. Universidad 2001, Col. Chamilpa, Cuernavaca 62210, Mexico;
| | - Clara Barcelos
- Posgrado de Ciencias de la Vida, Centro de Investigación Científica y de Educación Superior de Ensenada, Carretera Ensenada-Tijuana No. 3918, Zona Playitas, Ensenada 22860, Mexico; (C.B.); (K.S.-C.)
- Departamento de Innovación Biomédica, Centro de Investigación Científica y de Educación Superior de Ensenada, Carretera Ensenada-Tijuana No. 3918, Zona Playitas, Ensenada 22860, Mexico
| | - Karla Sidón-Ceseña
- Posgrado de Ciencias de la Vida, Centro de Investigación Científica y de Educación Superior de Ensenada, Carretera Ensenada-Tijuana No. 3918, Zona Playitas, Ensenada 22860, Mexico; (C.B.); (K.S.-C.)
- Departamento de Innovación Biomédica, Centro de Investigación Científica y de Educación Superior de Ensenada, Carretera Ensenada-Tijuana No. 3918, Zona Playitas, Ensenada 22860, Mexico
| | - Ricardo B. Leite
- Instituto Gulbenkian de Ciência, Rua da Quinta Grande, 6, 2780-156 Oeiras, Portugal;
| | - Asunción Lago-Lestón
- Departamento de Innovación Biomédica, Centro de Investigación Científica y de Educación Superior de Ensenada, Carretera Ensenada-Tijuana No. 3918, Zona Playitas, Ensenada 22860, Mexico
- Correspondence:
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Cannon JL, Seabolt MH, Xu R, Montmayeur A, Suh SH, Diez-Valcarce M, Bucardo F, Becker-Dreps S, Vinjé J. Gut Microbiome Changes Occurring with Norovirus Infection and Recovery in Infants Enrolled in a Longitudinal Birth Cohort in Leon, Nicaragua. Viruses 2022; 14:v14071395. [PMID: 35891376 PMCID: PMC9323674 DOI: 10.3390/v14071395] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Revised: 06/07/2022] [Accepted: 06/13/2022] [Indexed: 02/05/2023] Open
Abstract
Noroviruses are associated with one fifth of diarrheal illnesses globally and are not yet preventable with vaccines. Little is known about the effects of norovirus infection on infant gut microbiome health, which has a demonstrated role in protecting hosts from pathogens and a possible role in oral vaccine performance. In this study, we characterized infant gut microbiome changes occurring with norovirus-associated acute gastroenteritis (AGE) and the extent of recovery. Metagenomic sequencing was performed on the stools of five infants participating in a longitudinal birth cohort study conducted in León, Nicaragua. Taxonomic and functional diversities of gut microbiomes were profiled at time points before, during, and after norovirus infection. Initially, the gut microbiomes resembled those of breastfeeding infants, rich in probiotic species. When disturbed by AGE, Gammaproteobacteria dominated, particularly Pseudomonas species. Alpha diversity increased but the genes involved in carbohydrate metabolism and glycan biosynthesis decreased. After the symptoms subsided, the gut microbiomes rebounded with their taxonomic and functional communities resembling those of the pre-infection microbiomes. In this study, during disruptive norovirus-associated AGE, the gut microbiome was temporarily altered, returning to a pre-infection composition a median of 58 days later. Our study provides new insights for developing probiotic treatments and furthering our understanding of the role that episodes of AGE have in shaping the infant gut microbiome, their long-term outcomes, and implications for oral vaccine effectiveness.
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Affiliation(s)
- Jennifer L. Cannon
- Division of Viral Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, GA 30329, USA; (R.X.); (A.M.); (S.H.S.); (M.D.-V.); (J.V.)
- CDC Foundation, Atlanta, GA 30329, USA
- Correspondence: ; Tel.: +1-404-639-2396
| | - Matthew H. Seabolt
- Office of Advanced Molecular Detection, National Center for Emerging & Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, GA 30329, USA;
- Leidos Inc., Reston, VA 20190, USA
| | - Ruijie Xu
- Division of Viral Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, GA 30329, USA; (R.X.); (A.M.); (S.H.S.); (M.D.-V.); (J.V.)
| | - Anna Montmayeur
- Division of Viral Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, GA 30329, USA; (R.X.); (A.M.); (S.H.S.); (M.D.-V.); (J.V.)
| | - Soo Hwan Suh
- Division of Viral Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, GA 30329, USA; (R.X.); (A.M.); (S.H.S.); (M.D.-V.); (J.V.)
- Ministry of Food and Drug Safety, Cheonju-Si 28159, Korea
| | - Marta Diez-Valcarce
- Division of Viral Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, GA 30329, USA; (R.X.); (A.M.); (S.H.S.); (M.D.-V.); (J.V.)
| | - Filemón Bucardo
- Center for Infectious Diseases Research, National Autonomous University of Nicaragua—León (UNAN-León), León 21000, Nicaragua;
| | - Sylvia Becker-Dreps
- Department of Family Medicine and Epidemiology, University of North Carolina Chapel Hill, Chapel Hill, NC 27599, USA;
| | - Jan Vinjé
- Division of Viral Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, GA 30329, USA; (R.X.); (A.M.); (S.H.S.); (M.D.-V.); (J.V.)
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Ren W, Zhong Y, Ding Y, Wu Y, Xu X, Zhou P. Mismatches in 16S rRNA Gene Primers: An Area Worth Further Exploring. Front Microbiol 2022; 13:888803. [PMID: 35770162 PMCID: PMC9234566 DOI: 10.3389/fmicb.2022.888803] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Accepted: 05/02/2022] [Indexed: 11/13/2022] Open
Affiliation(s)
- Wenting Ren
- Key Laboratory of Marine Ecosystem Dynamics, Ministry of Natural Resources and Second Institute of Oceanography, Ministry of Natural Resources, Hangzhou, China
| | - Yingwen Zhong
- Key Laboratory of Marine Ecosystem Dynamics, Ministry of Natural Resources and Second Institute of Oceanography, Ministry of Natural Resources, Hangzhou, China
- School of Oceanography, Shanghai Jiao Tong University, Shanghai, China
| | - Yi Ding
- Key Laboratory of Marine Ecosystem Dynamics, Ministry of Natural Resources and Second Institute of Oceanography, Ministry of Natural Resources, Hangzhou, China
- School of Oceanography, Shanghai Jiao Tong University, Shanghai, China
| | - Yuehong Wu
- Key Laboratory of Marine Ecosystem Dynamics, Ministry of Natural Resources and Second Institute of Oceanography, Ministry of Natural Resources, Hangzhou, China
- School of Oceanography, Shanghai Jiao Tong University, Shanghai, China
| | - XueWei Xu
- Key Laboratory of Marine Ecosystem Dynamics, Ministry of Natural Resources and Second Institute of Oceanography, Ministry of Natural Resources, Hangzhou, China
- School of Oceanography, Shanghai Jiao Tong University, Shanghai, China
| | - Peng Zhou
- Key Laboratory of Marine Ecosystem Dynamics, Ministry of Natural Resources and Second Institute of Oceanography, Ministry of Natural Resources, Hangzhou, China
- *Correspondence: Peng Zhou
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Marasco R, Fusi M, Ramond JB, Van Goethem MW, Seferji K, Maggs-Kölling G, Cowan DA, Daffonchio D. The plant rhizosheath-root niche is an edaphic "mini-oasis" in hyperarid deserts with enhanced microbial competition. ISME COMMUNICATIONS 2022; 2:47. [PMID: 37938683 PMCID: PMC9723607 DOI: 10.1038/s43705-022-00130-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Revised: 05/04/2022] [Accepted: 05/09/2022] [Indexed: 06/17/2023]
Abstract
Plants have evolved unique morphological and developmental adaptations to cope with the abiotic stresses imposed by (hyper)arid environments. Such adaptations include the formation of rhizosheath-root system in which mutualistic plant-soil microbiome associations are established: the plant provides a nutrient-rich and shielded environment to microorganisms, which in return improve plant-fitness through plant growth promoting services. We hypothesized that the rhizosheath-root systems represent refuge niches and resource islands for the desert edaphic microbial communities. As a corollary, we posited that microorganisms compete intensively to colonize such "oasis" and only those beneficial microorganisms improving host fitness are preferentially selected by plant. Our results show that the belowground rhizosheath-root micro-environment is largely more hospitable than the surrounding gravel plain soil with higher nutrient and humidity contents, and cooler temperatures. By combining metabarcoding and shotgun metagenomics, we demonstrated that edaphic microbial biomass and community stability increased from the non-vegetated soils to the rhizosheath-root system. Concomitantly, non-vegetated soil communities favored autotrophy lifestyle while those associated with the plant niches were mainly heterotrophs and enriched in microbial plant growth promoting capacities. An intense inter-taxon microbial competition is involved in the colonization and homeostasis of the rhizosheath zone, as documented by significant enrichment of antibiotic resistance genes and CRISPR-Cas motifs. Altogether, our results demonstrate that rhizosheath-root systems are "edaphic mini-oases" and microbial diversity hotspots in hyperarid deserts. However, to colonize such refuge niches, the desert soil microorganisms compete intensively and are therefore prepared to outcompete potential rivals.
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Affiliation(s)
- Ramona Marasco
- King Abdullah University of Science and Technology (KAUST), Biological and Environmental Sciences and Engineering Division (BESE), Thuwal, 23955-6900, Saudi Arabia.
| | - Marco Fusi
- King Abdullah University of Science and Technology (KAUST), Biological and Environmental Sciences and Engineering Division (BESE), Thuwal, 23955-6900, Saudi Arabia
| | - Jean-Baptiste Ramond
- Centre for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa
- Department of Molecular Genetics and Microbiology, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Marc W Van Goethem
- King Abdullah University of Science and Technology (KAUST), Biological and Environmental Sciences and Engineering Division (BESE), Thuwal, 23955-6900, Saudi Arabia
- Centre for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa
| | - Kholoud Seferji
- King Abdullah University of Science and Technology (KAUST), Biological and Environmental Sciences and Engineering Division (BESE), Thuwal, 23955-6900, Saudi Arabia
| | | | - Don A Cowan
- Centre for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa
| | - Daniele Daffonchio
- King Abdullah University of Science and Technology (KAUST), Biological and Environmental Sciences and Engineering Division (BESE), Thuwal, 23955-6900, Saudi Arabia.
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61
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Shi LD, Dong X, Liu Z, Yang Y, Lin JG, Li M, Gu JD, Zhu LZ, Zhao HP. A mixed blessing of viruses in wastewater treatment plants. WATER RESEARCH 2022; 215:118237. [PMID: 35245718 DOI: 10.1016/j.watres.2022.118237] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Revised: 02/23/2022] [Accepted: 02/24/2022] [Indexed: 06/14/2023]
Abstract
Activated sludge of wastewater treatment plants harbors a very high diversity of both microorganisms and viruses, wherein the latter control microbial dynamics and metabolisms by infection and lysis of cells. However, it remains poorly understood how viruses impact the biochemical processes of activated sludge, for example in terms of treatment efficiency and pollutant removal. Using metagenomic and metatranscriptomic deep sequencing, the present study recovered thousands of viral sequences from activated sludge samples of three conventional wastewater treatment plants. Gene-sharing network indicated that most of viruses could not be assigned to known viral genera, implying activated sludge as an underexplored reservoir for new viruses and viral diversity. In silico predictions of virus-host linkages demonstrated that infected microbial hosts, mostly belonging to bacteria, were transcriptionally active and able to hydrolyze polymers including starches, celluloses, and proteins. Some viruses encode auxiliary metabolic genes (AMGs) involved in carbon, nitrogen, and sulfur cycling, and antibiotic resistance genes (ARGs) for resistance to multiple drugs. The virus-encoded AMGs may enhance the biodegradation of contaminants like starches and celluloses, suggesting a positive role for viruses in strengthening the performance of activated sludge. However, ARGs would be disseminated to different microorganisms using viruses as gene shuttles, demonstrating the possibility for viruses to facilitate the spread of antibiotic resistance in the environment. Collectively, this study highlights the mixed blessing of viruses in wastewater treatment plants, and deciphers how they manipulate the biochemical processes in the activated sludge, with implications for both environmental protection and ecosystem security.
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Affiliation(s)
- Ling-Dong Shi
- MOE Key Lab of Environmental Remediation and Ecosystem Health, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, Zhejiang, China
| | - Xiyang Dong
- School of Marine Sciences, Sun Yat-Sen University, Zhuhai, China; Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, China
| | - Zongbao Liu
- Archaeal Biology Center, Institute for Advanced Study, Shenzhen University, Shenzhen 518060, China
| | - Yuchun Yang
- State Key Laboratory of Biocontrol, School of Ecology, Sun Yat-sen University, Guangzhou 510275, China
| | - Jih-Gaw Lin
- Institute of Environmental Engineering, National Yang Ming Chiao Tung University, 1001 University Road, Hsinchu 30010, Taiwan
| | - Meng Li
- Archaeal Biology Center, Institute for Advanced Study, Shenzhen University, Shenzhen 518060, China; Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen 518060, China
| | - Ji-Dong Gu
- Environmental Science and Engineering Program, Guangdong Technion - Israel Institute of Technology, 241 Daxue Road, Shantou, Guangdong 515063, China
| | - Li-Zhong Zhu
- MOE Key Lab of Environmental Remediation and Ecosystem Health, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, Zhejiang, China
| | - He-Ping Zhao
- MOE Key Lab of Environmental Remediation and Ecosystem Health, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, Zhejiang, China.
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Vuong P, Moreira-Grez B, Wise MJ, Whiteley AS, Kumaresan D, Kaur P. From Rags to Enriched: Metagenomic Insights into Ammonia-oxidizing Archaea Following Ammonia Enrichment of a Denuded Oligotrophic Soil Ecosystem. Environ Microbiol 2022; 24:3097-3110. [PMID: 35384236 PMCID: PMC9545067 DOI: 10.1111/1462-2920.15994] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2021] [Accepted: 03/28/2022] [Indexed: 11/29/2022]
Abstract
Stored topsoil acts as a microbial inoculant for ecological restoration of land after disturbance, but the altered circumstances frequently create unfavorable conditions for microbial survival. Nitrogen cycling is a critical indicator for ecological success and this study aimed to investigate the cornerstone taxa driving the process. Previous in-silico studies investigating stored topsoil discovered persistent archaeal taxa with the potential for re-establishing ecological activity. Ammonia oxidization is the limiting step in nitrification and as such, ammonia oxidizing archaea (AOA) can be considered as the one of the gatekeepers for the re-establishment of the nitrogen cycle in disturbed soils. Semi-arid soil samples were enriched with ammonium sulfate to promote the selective enrichment of ammonia oxidizers for targeted genomic recovery, and to investigate the microbial response of the microcosm to nitrogen input. Ammonia addition produced an increase in AOA population, particularly within the genus Candidatus Nitrosotalea, from which metagenome-assembled genomes (MAGs) were successfully recovered. The Ca. Nitrosotalea archaeon candidates' ability to survive in extreme conditions and rapidly respond to ammonia input makes it a potential bioprospecting target for application in ecological restoration of semi-arid soils and the recovered MAGs provide a metabolic blueprint for developing potential strategies towards isolation of these acclimated candidates. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Paton Vuong
- UWA School of Agriculture & Environment, University of Western Australia, Perth, Australia
| | - Benjamin Moreira-Grez
- UWA School of Agriculture & Environment, University of Western Australia, Perth, Australia
| | - Michael J Wise
- School of Physics, Mathematics and Computing, University of Western Australia, Perth, Australia.,The Marshall Centre of Infectious Diseases, School of Biological Sciences, The University of Western Australia, Perth, Australia
| | - Andrew S Whiteley
- Centre for Environment & Life Sciences, Commonwealth Scientific and Industrial Research Organisation (CSIRO), Floreat, Australia
| | - Deepak Kumaresan
- School of Biological Sciences, Queen's University of Belfast, Belfast, UK
| | - Parwinder Kaur
- UWA School of Agriculture & Environment, University of Western Australia, Perth, Australia
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Wang J, Tang X, Mo Z, Mao Y. Metagenome-Assembled Genomes From Pyropia haitanensis Microbiome Provide Insights Into the Potential Metabolic Functions to the Seaweed. Front Microbiol 2022; 13:857901. [PMID: 35401438 PMCID: PMC8984609 DOI: 10.3389/fmicb.2022.857901] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Accepted: 02/28/2022] [Indexed: 12/24/2022] Open
Abstract
Pyropia is an economically important edible red alga worldwide. The aquaculture industry and Pyropia production have grown considerably in recent decades. Microbial communities inhabit the algal surface and produce a variety of compounds that can influence host adaptation. Previous studies on the Pyropia microbiome were focused on the microbial components or the function of specific microbial lineages, which frequently exclude metabolic information and contained only a small fraction of the overall community. Here, we performed a genome-centric analysis to study the metabolic potential of the Pyropia haitanensis phycosphere bacteria. We reconstructed 202 unique metagenome-assembled genomes (MAGs) comprising all major taxa present within the P. haitanensis microbiome. The addition of MAGs to the genome tree containing all publicly available Pyropia-associated microorganisms increased the phylogenetic diversity by 50% within the bacteria. Metabolic reconstruction of the MAGs showed functional redundancy across taxa for pathways including nitrate reduction, taurine metabolism, organophosphorus, and 1-aminocyclopropane-1-carboxylate degradation, auxin, and vitamin B12 synthesis. Some microbial functions, such as auxin and vitamin B12 synthesis, that were previously assigned to a few Pyropia-associated microorganisms were distributed across the diverse epiphytic taxa. Other metabolic pathways, such as ammonia oxidation, denitrification, and sulfide oxidation, were confined to specific keystone taxa.
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Affiliation(s)
- Junhao Wang
- Key Laboratory of Marine Genetics and Breeding (Ministry of Education), College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Xianghai Tang
- Key Laboratory of Marine Genetics and Breeding (Ministry of Education), College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Zhaolan Mo
- Key Laboratory of Marine Genetics and Breeding (Ministry of Education), College of Marine Life Sciences, Ocean University of China, Qingdao, China
- Key Laboratory of Tropical Aquatic Germplasm of Hainan Province, Sanya Oceanographic Institution, Ocean University of China, Sanya, China
| | - Yunxiang Mao
- Key Laboratory of Utilization and Conservation of Tropical Marine Bioresource (Ministry of Education), College of Fisheries and Life Sciences, Hainan Tropical Ocean University, Sanya, China
- Yazhou Bay Innovation Research Institute, Hainan Tropical Ocean University, Sanya, China
- Key Laboratory for Conservation and Utilization of Tropical Marine Fishery Resources of Hainan Province, Hainan Tropical Ocean University, Sanya, China
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64
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Skipper PJA, Skipper LK, Dixon RA. A metagenomic analysis of the bacterial microbiome of limestone, and the role of associated biofilms in the biodeterioration of heritage stone surfaces. Sci Rep 2022; 12:4877. [PMID: 35318388 PMCID: PMC8940931 DOI: 10.1038/s41598-022-08851-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2021] [Accepted: 03/02/2022] [Indexed: 12/14/2022] Open
Abstract
There is growing concern surrounding the aesthetic and physical effects of microbial biofilms on heritage buildings and monuments. Carboniferous stones, such as limestone and marble, are soluble in weak acid solutions and therefore particularly vulnerable to biocorrosion. This paper aims to determine the differences and commonalities between the microbiome of physically damaged and undamaged Lincolnshire limestone, an area of research which has not been previously studied. A lack of information about the core microbiome has resulted in conflicting claims in the literature regarding the biodeteriorative potential of many microorganisms. To address this, we used metagenomics alongside traditional microbiological techniques to produce an in-depth analysis of differences between the bacterial microbiomes found on deteriorated and undamaged external limestone surfaces. We demonstrate there is a core microbiome on Lincolnshire limestone present on both damaged and undamaged surfaces. In addition to the core microbiome, significant differences were found between species isolated from undamaged compared to damaged surfaces. Isolated species were characterised for biofilm formation and biodeteriorative processes, resulting in the association of species with biodeterioration that had not been previously described. Additionally, we have identified a previously undescribed method of biofilm-associated biomechanical damage. This research adds significant new understanding to the field, aiding decision making in conservation of stone surfaces.
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Affiliation(s)
| | - Lynda K Skipper
- School of History and Heritage, University of Lincoln, Lincoln, UK
| | - Ronald A Dixon
- School of Life Sciences, University of Lincoln, Lincoln, UK
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Marcoleta AE, Arros P, Varas MA, Costa J, Rojas-Salgado J, Berríos-Pastén C, Tapia-Fuentes S, Silva D, Fierro J, Canales N, Chávez FP, Gaete A, González M, Allende ML, Lagos R. The highly diverse Antarctic Peninsula soil microbiota as a source of novel resistance genes. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 810:152003. [PMID: 34856283 DOI: 10.1016/j.scitotenv.2021.152003] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Revised: 11/22/2021] [Accepted: 11/23/2021] [Indexed: 06/13/2023]
Abstract
The rise of multiresistant bacterial pathogens is currently one of the most critical threats to global health, encouraging a better understanding of the evolution and spread of antimicrobial resistance. In this regard, the role of the environment as a source of resistance mechanisms remains poorly understood. Moreover, we still know a minimal part of the microbial diversity and resistome present in remote and extreme environments, hosting microbes that evolved to resist harsh conditions and thus a potentially rich source of novel resistance genes. This work demonstrated that the Antarctic Peninsula soils host a remarkable microbial diversity and a widespread presence of autochthonous antibiotic-resistant bacteria and resistance genes. We observed resistance to a wide array of antibiotics among isolates, including Pseudomonas resisting ten or more different compounds, with an overall increased resistance in bacteria from non-intervened areas. In addition, genome analysis of selected isolates showed several genes encoding efflux pumps, as well as a lack of known resistance genes for some of the resisted antibiotics, including colistin, suggesting novel uncharacterized mechanisms. By combining metagenomic approaches based on analyzing raw reads, assembled contigs, and metagenome-assembled genomes, we found hundreds of widely distributed genes potentially conferring resistance to different antibiotics (including an outstanding variety of inactivation enzymes), metals, and biocides, hosted mainly by Polaromonas, Pseudomonas, Streptomyces, Variovorax, and Burkholderia. Furthermore, a proportion of these genes were found inside predicted plasmids and other mobile elements, including a putative OXA-like carbapenemase from Polaromonas harboring conserved key residues and predicted structural features. All this evidence indicates that the Antarctic Peninsula soil microbiota has a broad natural resistome, part of which could be transferred horizontally to pathogenic bacteria, acting as a potential source of novel resistance genes.
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Affiliation(s)
- Andrés E Marcoleta
- Grupo de Microbiología Integrativa, Laboratorio de Biología Estructural y Molecular BEM, Departamento de Biología, Facultad de Ciencias, Universidad de Chile, Santiago, Chile.
| | - Patricio Arros
- Grupo de Microbiología Integrativa, Laboratorio de Biología Estructural y Molecular BEM, Departamento de Biología, Facultad de Ciencias, Universidad de Chile, Santiago, Chile
| | - Macarena A Varas
- Grupo de Microbiología Integrativa, Laboratorio de Biología Estructural y Molecular BEM, Departamento de Biología, Facultad de Ciencias, Universidad de Chile, Santiago, Chile
| | - José Costa
- Grupo de Microbiología Integrativa, Laboratorio de Biología Estructural y Molecular BEM, Departamento de Biología, Facultad de Ciencias, Universidad de Chile, Santiago, Chile
| | - Johanna Rojas-Salgado
- Grupo de Microbiología Integrativa, Laboratorio de Biología Estructural y Molecular BEM, Departamento de Biología, Facultad de Ciencias, Universidad de Chile, Santiago, Chile
| | - Camilo Berríos-Pastén
- Grupo de Microbiología Integrativa, Laboratorio de Biología Estructural y Molecular BEM, Departamento de Biología, Facultad de Ciencias, Universidad de Chile, Santiago, Chile
| | - Sofía Tapia-Fuentes
- Grupo de Microbiología Integrativa, Laboratorio de Biología Estructural y Molecular BEM, Departamento de Biología, Facultad de Ciencias, Universidad de Chile, Santiago, Chile
| | - Daniel Silva
- Grupo de Microbiología Integrativa, Laboratorio de Biología Estructural y Molecular BEM, Departamento de Biología, Facultad de Ciencias, Universidad de Chile, Santiago, Chile
| | - José Fierro
- Grupo de Microbiología Integrativa, Laboratorio de Biología Estructural y Molecular BEM, Departamento de Biología, Facultad de Ciencias, Universidad de Chile, Santiago, Chile
| | - Nicolás Canales
- Grupo de Microbiología Integrativa, Laboratorio de Biología Estructural y Molecular BEM, Departamento de Biología, Facultad de Ciencias, Universidad de Chile, Santiago, Chile
| | - Francisco P Chávez
- Laboratorio de Microbiología de Sistemas, Departamento de Biología, Facultad de Ciencias, Universidad de Chile, Santiago, Chile
| | - Alexis Gaete
- Laboratorio de Bioinformática y Expresión Génica, Instituto de Nutrición y Tecnología de los Alimentos, Universidad de Chile, Santiago, Chile; FONDAP Center for Genome Regulation, Facultad de Ciencias, Universidad de Chile, Santiago, Chile
| | - Mauricio González
- Laboratorio de Bioinformática y Expresión Génica, Instituto de Nutrición y Tecnología de los Alimentos, Universidad de Chile, Santiago, Chile
| | - Miguel L Allende
- FONDAP Center for Genome Regulation, Facultad de Ciencias, Universidad de Chile, Santiago, Chile
| | - Rosalba Lagos
- Grupo de Microbiología Integrativa, Laboratorio de Biología Estructural y Molecular BEM, Departamento de Biología, Facultad de Ciencias, Universidad de Chile, Santiago, Chile
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Hiraoka S, Sumida T, Hirai M, Toyoda A, Kawagucci S, Yokokawa T, Nunoura T. Diverse DNA modification in marine prokaryotic and viral communities. Nucleic Acids Res 2022; 50:1531-1550. [PMID: 35051998 PMCID: PMC8919816 DOI: 10.1093/nar/gkab1292] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Revised: 11/30/2021] [Accepted: 12/17/2021] [Indexed: 11/15/2022] Open
Abstract
DNA chemical modifications, including methylation, are widespread and play important roles in prokaryotes and viruses. However, current knowledge of these modification systems is severely biased towards a limited number of culturable prokaryotes, despite the fact that a vast majority of microorganisms have not yet been cultured. Here, using single-molecule real-time sequencing, we conducted culture-independent 'metaepigenomic' analyses (an integrated analysis of metagenomics and epigenomics) of marine microbial communities. A total of 233 and 163 metagenomic-assembled genomes (MAGs) were constructed from diverse prokaryotes and viruses, respectively, and 220 modified motifs and 276 DNA methyltransferases (MTases) were identified. Most of the MTase genes were not genetically linked with the endonuclease genes predicted to be involved in defense mechanisms against extracellular DNA. The MTase-motif correspondence found in the MAGs revealed 10 novel pairs, 5 of which showed novel specificities and experimentally confirmed the catalytic specificities of the MTases. We revealed novel alternative specificities in MTases that are highly conserved in Alphaproteobacteria, which may enhance our understanding of the co-evolutionary history of the methylation systems and the genomes. Our findings highlight diverse unexplored DNA modifications that potentially affect the ecology and evolution of prokaryotes and viruses in nature.
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Affiliation(s)
- Satoshi Hiraoka
- Research Center for Bioscience and Nanoscience (CeBN),
Research Institute for Marine Resources Utilization, Japan Agency for
Marine-Earth Science and Technology (JAMSTEC),
Yokosuka,
Kanagawa 237–0061,
Japan
| | - Tomomi Sumida
- Research Center for Bioscience and Nanoscience (CeBN),
Research Institute for Marine Resources Utilization, Japan Agency for
Marine-Earth Science and Technology (JAMSTEC),
Yokosuka,
Kanagawa 237–0061,
Japan
| | - Miho Hirai
- Institute for Extra-cutting-edge Science and Technology
Avant-garde Research (X-star), Japan Agency for Marine-Earth Science and
Technology (JAMSTEC), Yokosuka,
Kanagawa 237–0061,
Japan
| | - Atsushi Toyoda
- Advanced Genomics Center, National Institute of
Genetics, Mishima,
Shizuoka 411-8540,
Japan
| | - Shinsuke Kawagucci
- Institute for Extra-cutting-edge Science and Technology
Avant-garde Research (X-star), Japan Agency for Marine-Earth Science and
Technology (JAMSTEC), Yokosuka,
Kanagawa 237–0061,
Japan
- Marine Biodiversity and Environmental Assessment Research
Center (BioEnv), Research Institute for Global Change (RIGC), Japan
Agency for Marine-Earth Science and Technology (JAMSTEC),
Yokosuka,
Kanagawa 237–0061,
Japan
| | - Taichi Yokokawa
- Institute for Extra-cutting-edge Science and Technology
Avant-garde Research (X-star), Japan Agency for Marine-Earth Science and
Technology (JAMSTEC), Yokosuka,
Kanagawa 237–0061,
Japan
| | - Takuro Nunoura
- Research Center for Bioscience and Nanoscience (CeBN),
Research Institute for Marine Resources Utilization, Japan Agency for
Marine-Earth Science and Technology (JAMSTEC),
Yokosuka,
Kanagawa 237–0061,
Japan
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67
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Clinical Metagenomics Is Increasingly Accurate and Affordable to Detect Enteric Bacterial Pathogens in Stool. Microorganisms 2022; 10:microorganisms10020441. [PMID: 35208895 PMCID: PMC8880012 DOI: 10.3390/microorganisms10020441] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2021] [Revised: 01/29/2022] [Accepted: 02/09/2022] [Indexed: 02/04/2023] Open
Abstract
Stool culture is the gold standard method to diagnose enteric bacterial infections; however, many clinical laboratories are transitioning to syndromic multiplex PCR panels. PCR is rapid, accurate, and affordable, yet does not yield subtyping information critical for foodborne disease surveillance. A metagenomics-based stool testing approach could simultaneously provide diagnostic and public health information. Here, we evaluated shotgun metagenomics to assess the detection of common enteric bacterial pathogens in stool. We sequenced 304 stool specimens from 285 patients alongside routine diagnostic testing for Salmonella spp., Campylobacter spp., Shigella spp., and shiga-toxin producing Escherichia coli. Five analytical approaches were assessed for pathogen detection: microbiome profiling, Kraken2, MetaPhlAn, SRST2, and KAT-SECT. Among analysis tools and databases compared, KAT-SECT analysis provided the best sensitivity and specificity for all pathogens tested compared to culture (91.2% and 96.2%, respectively). Where metagenomics detected a pathogen in culture-negative specimens, standard PCR was positive 85% of the time. The cost of metagenomics is approaching the current combined cost of PCR, reflex culture, and whole genome sequencing for pathogen detection and subtyping. As cost, speed, and analytics for single-approach metagenomics improve, it may be more routinely applied in clinical and public health laboratories.
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68
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Lindner BG, Suttner B, Zhu KJ, Conrad RE, Rodriguez-R LM, Hatt JK, Brown J, Konstantinidis KT. Toward shotgun metagenomic approaches for microbial source tracking sewage spills based on laboratory mesocosms. WATER RESEARCH 2022; 210:117993. [PMID: 34979467 DOI: 10.1016/j.watres.2021.117993] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/04/2021] [Revised: 12/17/2021] [Accepted: 12/18/2021] [Indexed: 06/14/2023]
Abstract
Little is known about the genomic diversity of the microbial communities associated with raw municipal wastewater (sewage), including whether microbial populations specific to sewage exist and how such populations could be used to improve source attribution and apportioning in contaminated waters. Herein, we used the influent of three wastewater treatment plants in Atlanta, Georgia (USA) to perturb laboratory freshwater mesocosms, simulating sewage contamination events, and followed these mesocosms with shotgun metagenomics over a 7-day observational period. We describe 15 abundant non-redundant bacterial metagenome-assembled genomes (MAGs) ubiquitous within all sewage inocula yet absent from the unperturbed freshwater control at our analytical limit of detection. Tracking the dynamics of the populations represented by these MAGs revealed varied decay kinetics, depending on (inferred) phenotypes, e.g., anaerobes decayed faster than aerobes under the well-aerated incubation conditions. Notably, a portion of these populations showed decay patterns similar to those of common markers, Enterococcus and HF183. Despite the apparent decay of these populations, the abundance of β-lactamase encoding genes remained high throughout incubation relative to the control. Lastly, we constructed genomic libraries representing several different fecal sources and outline a bioinformatic approach which leverages these libraries for identifying and apportioning contamination signal among multiple probable sources using shotgun metagenomic data.
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Affiliation(s)
- Blake G Lindner
- School of Civil and Environmental Engineering, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Brittany Suttner
- School of Civil and Environmental Engineering, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Kevin J Zhu
- School of Civil and Environmental Engineering, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Roth E Conrad
- Ocean Science and Engineering, Georgia Institute of Technology, 311 Ferst Drive, ES&T Building, Room 3321, Atlanta, GA 30332, USA
| | - Luis M Rodriguez-R
- School of Civil and Environmental Engineering, Georgia Institute of Technology, Atlanta, GA 30332, USA; Department of Microbiology and Digital Science Center (DiSC), University of Innsbruck, Innsbruck, Tyrol 6020, Austria
| | - Janet K Hatt
- School of Civil and Environmental Engineering, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Joe Brown
- School of Civil and Environmental Engineering, Georgia Institute of Technology, Atlanta, GA 30332, USA
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Hu J, Hellgeth N, Cabay C, Clark J, Oliaro FJ, Van Bonn W, Hartmann EM. Towards understanding microbial degradation of chloroquine in large saltwater systems. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 807:150532. [PMID: 34606868 DOI: 10.1016/j.scitotenv.2021.150532] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Revised: 08/30/2021] [Accepted: 09/19/2021] [Indexed: 06/13/2023]
Abstract
Circulating saltwater aquariums hosting marine animals contain a wide range of microorganisms, which have strong implications on promoting animal health. In this study, we investigated the degradation of chloroquine phosphate, an anti-parasitic bath pharmaceutical used in saltwater quarantine and exhibition systems, and attributed the reduction in drug concentration to microbial degradation of chloroquine associated with pipeline microbial communities. To advance our knowledge on chloroquine degradation in aquatic systems, we conducted microbial and chemical analyses on three tropical saltwater systems. Our findings show that aquarium microbiome composition is shaped by sampling location (i.e., tank water and pipeline; PERMANOVA R2 = 0.09992, p = 0.0134), chloroquine dosing (PERMANOVA R2 = 0.05700, p = 0.0030), and whether the aquarium is occupied by marine animals (PERMANOVA R2 = 0.07019, p = 0.0009). Several microbial taxa belonging to the phyla Actinobacteria, Bacteroidetes, Chloroflexi, and Proteobacteria, along with functional genes related to pathways such as phenylethylamine degradation and denitrification, appeared to have differential (relative) abundance between samples where chloroquine degradation was observed and those without degradation (Benjamini-Hochberg adjusted p-value <0.05). Together, these results provide practical mitigation options to prevent or delay the development of chloroquine-degrading microbial communities in saltwater aquariums. Our results further demonstrate the need to improve our understanding of the interactions between nitrogen availability and microbial activity in saltwater systems.
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Affiliation(s)
- Jinglin Hu
- Department of Civil and Environmental Engineering, Northwestern University, Evanston, IL, USA
| | - Nancy Hellgeth
- Department of Civil and Environmental Engineering, Northwestern University, Evanston, IL, USA
| | - Chrissy Cabay
- Animal Care and Science Division, John G. Shedd Aquarium, Chicago, IL, USA
| | - James Clark
- Animal Care and Science Division, John G. Shedd Aquarium, Chicago, IL, USA
| | - Francis J Oliaro
- Animal Care and Science Division, John G. Shedd Aquarium, Chicago, IL, USA
| | - William Van Bonn
- Animal Care and Science Division, John G. Shedd Aquarium, Chicago, IL, USA
| | - Erica M Hartmann
- Department of Civil and Environmental Engineering, Northwestern University, Evanston, IL, USA.
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Bornemann TLV, Adam PS, Turzynski V, Schreiber U, Figueroa-Gonzalez PA, Rahlff J, Köster D, Schmidt TC, Schunk R, Krauthausen B, Probst AJ. Genetic diversity in terrestrial subsurface ecosystems impacted by geological degassing. Nat Commun 2022; 13:284. [PMID: 35022403 PMCID: PMC8755723 DOI: 10.1038/s41467-021-27783-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2020] [Accepted: 12/02/2021] [Indexed: 12/30/2022] Open
Abstract
Earth’s mantle releases 38.7 ± 2.9 Tg/yr CO2 along with other reduced and oxidized gases to the atmosphere shaping microbial metabolism at volcanic sites across the globe, yet little is known about its impact on microbial life under non-thermal conditions. Here, we perform comparative metagenomics coupled to geochemical measurements of deep subsurface fluids from a cold-water geyser driven by mantle degassing. Key organisms belonging to uncultivated Candidatus Altiarchaeum show a global biogeographic pattern and site-specific adaptations shaped by gene loss and inter-kingdom horizontal gene transfer. Comparison of the geyser community to 16 other publicly available deep subsurface sites demonstrate a conservation of chemolithoautotrophic metabolism across sites. In silico replication measures suggest a linear relationship of bacterial replication with ecosystems depth with the exception of impacted sites, which show near surface characteristics. Our results suggest that subsurface ecosystems affected by geological degassing are hotspots for microbial life in the deep biosphere. Geological degassing can impact subsurface metabolism. Here, the authors describe microbial communities from a cold-water geyser are described and compared with other deep subsurface sites, finding a key role for an uncultivated archaeon.
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Affiliation(s)
- Till L V Bornemann
- Environmental Microbiology and Biotechnology, Faculty of Chemistry, University Duisburg-Essen, Essen, Germany
| | - Panagiotis S Adam
- Environmental Microbiology and Biotechnology, Faculty of Chemistry, University Duisburg-Essen, Essen, Germany
| | - Victoria Turzynski
- Environmental Microbiology and Biotechnology, Faculty of Chemistry, University Duisburg-Essen, Essen, Germany
| | - Ulrich Schreiber
- Department of Geology, University Duisburg-Essen, Essen, Germany
| | | | - Janina Rahlff
- Environmental Microbiology and Biotechnology, Faculty of Chemistry, University Duisburg-Essen, Essen, Germany.,Centre for Ecology and Evolution in Microbial Model Systems (EEMiS), Department of Biology and Environmental Science, Linneaus University, Kalmar, Sweden
| | - Daniel Köster
- Instrumental Analytical Chemistry and Centre for Water and Environmental Research (ZWU), University of Duisburg-Essen, Essen, Germany
| | - Torsten C Schmidt
- Instrumental Analytical Chemistry and Centre for Water and Environmental Research (ZWU), University of Duisburg-Essen, Essen, Germany.,Centre of Water and Environmental Research (ZWU), University of Duisburg-Essen, Universitätsstraße 5, Essen, Germany
| | | | - Bernhard Krauthausen
- Institute of Applied Geosciences, Karlsruhe Institute of Technology, Karlsruhe, Germany
| | - Alexander J Probst
- Environmental Microbiology and Biotechnology, Faculty of Chemistry, University Duisburg-Essen, Essen, Germany. .,Centre of Water and Environmental Research (ZWU), University of Duisburg-Essen, Universitätsstraße 5, Essen, Germany.
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71
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Bornemann TLV, Adam PS, Probst AJ. Reconstruction of Archaeal Genomes from Short-Read Metagenomes. Methods Mol Biol 2022; 2522:487-527. [PMID: 36125772 DOI: 10.1007/978-1-0716-2445-6_33] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
As the majority of biological diversity remains unexplored and uncultured, investigating it requires culture-independent approaches. Archaea in particular suffer from a multitude of issues that make their culturing problematic, from them being frequently members of the rare biosphere, to low growth rates, to them thriving under very specific and often extreme environmental and community conditions that are difficult to replicate. OMICs techniques are state of the art approaches that allow direct high-throughput investigations of environmental samples at all levels from nucleic acids to proteins, lipids, and secondary metabolites. Metagenomics, as the foundation for other OMICs techniques, facilitates the identification and functional characterization of the microbial community members and can be combined with other methods to provide insights into the microbial activities, both on the RNA and protein levels. In this chapter, we provide a step-by-step workflow for the recovery of archaeal genomes from metagenomes, starting from raw short-read sequences. This workflow can be applied to recover bacterial genomes as well.
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Affiliation(s)
- Till L V Bornemann
- Environmental Microbiology and Biotechnology, Faculty of Chemistry, University of Duisburg-Essen, Essen, Germany.
| | - Panagiotis S Adam
- Environmental Microbiology and Biotechnology, Faculty of Chemistry, University of Duisburg-Essen, Essen, Germany
| | - Alexander J Probst
- Environmental Microbiology and Biotechnology, Faculty of Chemistry, University of Duisburg-Essen, Essen, Germany.
- Centre of Water and Environmental Research (ZWU), University of Duisburg-Essen, Essen, Germany.
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72
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The Edible Plant Microbiome represents a diverse genetic reservoir with functional potential in the human host. Sci Rep 2021; 11:24017. [PMID: 34911987 PMCID: PMC8674285 DOI: 10.1038/s41598-021-03334-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Accepted: 11/24/2021] [Indexed: 12/15/2022] Open
Abstract
Plant microbiomes have been extensively studied for their agricultural relevance on growth promotion and pathogenesis, but little is known about their role as part of the diet when fresh fruits and vegetables are consumed raw. Most studies describing these communities are based on 16S rRNA gene amplicon surveys, limiting our understanding of the taxonomic resolution at the species level and functional capabilities. In this study, we characterized microbes colonizing tomatoes, spinach, brined olives, and dried figs using shotgun metagenomics. We recovered metagenome-assembled genomes of novel lactic acid bacteria from green olives and identified high intra- and inter-specific diversity of Pseudomonas in tomatoes. All samples were colonized by Pseudomonas, consistent with other reports with distinct community structure. Functional characterization showed the presence of enzymes involved in vitamin and short chain fatty acid metabolism and degradation of diverse carbohydrate substrates including plant fibers. The dominant bacterial members were isolated, sequenced, and mapped to its metagenome confirming their identity and indicating the microbiota is culturable. Our results reveal high genetic diversity, previously uncultured genera, and specific functions reflecting a likely plant host association. This study highlights the potential that plant microbes can play when consumed as part of our diet and proposes these as transient contributors to the gut microbiome.
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73
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Sevillano M, Vosloo S, Cotto I, Dai Z, Jiang T, Santiago Santana JM, Padilla IY, Rosario-Pabon Z, Velez Vega C, Cordero JF, Alshawabkeh A, Gu A, Pinto AJ. Spatial-temporal targeted and non-targeted surveys to assess microbiological composition of drinking water in Puerto Rico following Hurricane Maria. WATER RESEARCH X 2021; 13:100123. [PMID: 34704006 PMCID: PMC8524244 DOI: 10.1016/j.wroa.2021.100123] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Revised: 09/28/2021] [Accepted: 09/30/2021] [Indexed: 05/05/2023]
Abstract
Loss of basic utilities, such as drinking water and electricity distribution, were sustained for months in the aftermath of Hurricane Maria's (HM) landfall in Puerto Rico (PR) in September 2017. The goal of this study was to assess if there was deterioration in biological quality of drinking water due to these disruptions. This study characterized the microbial composition of drinking water following HM across nine drinking water systems (DWSs) in PR and utilized an extended temporal sampling campaign to determine if changes in the drinking water microbiome were indicative of HM associated disturbance followed by recovery. In addition to monitoring water chemistry, the samples were subjected to culture independent targeted and non-targeted microbial analysis including quantitative PCR (qPCR) and genome-resolved metagenomics. The qPCR results showed that residual disinfectant was the major driver of bacterial concentrations in tap water with marked decrease in concentrations from early to late sampling timepoints. While Mycobacterium avium and Pseudomonas aeruginosa were not detected in any sampling locations and timepoints, genetic material from Leptospira and Legionella pneumophila were transiently detected in a few sampling locations. The majority of metagenome assembled genomes (MAGs) recovered from these samples were not associated with pathogens and were consistent with bacterial community members routinely detected in DWSs. Further, whole metagenome-level comparisons between drinking water samples collected in this study with samples from other full-scale DWS indicated no significant deviation from expected community membership of the drinking water microbiome. Overall, our results suggest that disruptions due to HM did not result in significant and sustained deterioration of biological quality of drinking water at our study sites.
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Affiliation(s)
- Maria Sevillano
- Department of Civil and Environmental Engineering, Northeastern University, Boston, MA, United States of America
| | - Solize Vosloo
- School of Civil and Environmental Engineering, Georgia Institute of Technology, Atlanta, GA, United States of America
| | - Irmarie Cotto
- Department of Civil and Environmental Engineering, Northeastern University, Boston, MA, United States of America
| | - Zihan Dai
- Key Laboratory of Drinking Water Science and Technology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Tao Jiang
- Department of Civil and Environmental Engineering, Northeastern University, Boston, MA, United States of America
| | - Jose M. Santiago Santana
- Department of Natural Sciences, University of Puerto Rico, Carolina, PR, United States of America
| | - Ingrid Y. Padilla
- Department of Civil Engineering and Surveying, University of Puerto Rico, Mayagüez, PR, United States of America
| | - Zaira Rosario-Pabon
- University of Puerto Rico—Medical Sciences Campus, San Juan, PR, United States of America
| | - Carmen Velez Vega
- University of Puerto Rico—Medical Sciences Campus, San Juan, PR, United States of America
| | - José F. Cordero
- Department of Epidemiology and Biostatistics, University of Georgia, Athens, Georgia, United States of America
| | - Akram Alshawabkeh
- Department of Civil and Environmental Engineering, Northeastern University, Boston, MA, United States of America
| | - April Gu
- School of Civil and Environmental Engineering, Cornell University, Ithaca, NY, United States of America
| | - Ameet J. Pinto
- School of Civil and Environmental Engineering, Georgia Institute of Technology, Atlanta, GA, United States of America
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Santiago LD, DeLeon-Rodriguez N, LaSanta-Pagán K, Hatt JK, Kurt Z, Massol-Deyá A, Konstantinidis KT. Microbial diversity in a military impacted lagoon (Vieques, Puerto Rico) and description of "Candidatus Biekeibacterium resiliens" gen. nov., sp. nov. comprising a new bacterial family. Syst Appl Microbiol 2021; 45:126288. [PMID: 34933230 DOI: 10.1016/j.syapm.2021.126288] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Revised: 11/21/2021] [Accepted: 11/23/2021] [Indexed: 10/19/2022]
Abstract
The Anones Lagoon, located in the Island Municipality of Vieques, Puerto Rico (PR), received extensive bombing by the US Navy during military exercises for decades until 2003 when military activities ceased. Here, we employed shotgun metagenomic sequencing to investigate how microbial communities responded to pollution by heavy metals and explosives at this lagoon. Sediment samples (0-5 cm) from Anones were collected in 2005 and 2014 and compared to samples from two reference lagoons, i.e., Guaniquilla, Cabo Rojo (a natural reserve) and Condado, San Juan (PR's capital city). Consistent with low anthropogenic inputs, Guaniquilla exhibited the highest degree of diversity with a lower frequency of genes related to xenobiotics metabolism between the three lagoons. Notably, a clear shift was observed in Anones, with Euryarchaeota becoming enriched (9% of total) and a concomitant increase in community diversity, by about one order of magnitude, after almost 10 years without bombing activities. In contrast, genes associated with explosives biodegradation and heavy metal transformation significantly decreased in abundance in Anones 2014 (by 91.5%). Five unique metagenome-assembled genomes (MAGs) were recovered from the Anones 2005 sample that encoded genetic determinants implicated in biodegradation of contaminants, and we propose to name one of them as "Candidatus Biekeibacterium resiliens" gen. nov., sp. nov. within the Gammaproteobacteria class. Collectively, these results provide new insights into the natural attenuation of explosive contaminants by the benthic microbial communities of the Anones lagoon and provide a reference point for assessing other similarly impacted sites and associated bioremediation efforts.
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Affiliation(s)
- Lizbeth-Dávila Santiago
- Department of Biology, University of Puerto Rico, Mayagüez, Puerto Rico; School of Civil and Environmental Engineering, Georgia Institute of Technology, Atlanta, GA, United States; School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, United States
| | - Natasha DeLeon-Rodriguez
- School of Civil and Environmental Engineering, Georgia Institute of Technology, Atlanta, GA, United States
| | | | - Janet K Hatt
- School of Civil and Environmental Engineering, Georgia Institute of Technology, Atlanta, GA, United States
| | - Zohre Kurt
- School of Civil and Environmental Engineering, Georgia Institute of Technology, Atlanta, GA, United States
| | - Arturo Massol-Deyá
- Department of Biology, University of Puerto Rico, Mayagüez, Puerto Rico; Casa Pueblo, Adjuntas, Puerto Rico.
| | - Konstantinos T Konstantinidis
- School of Civil and Environmental Engineering, Georgia Institute of Technology, Atlanta, GA, United States; School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, United States.
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75
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Microbial Community Dynamics during Biodegradation of Crude Oil and Its Response to Biostimulation in Svalbard Seawater at Low Temperature. Microorganisms 2021; 9:microorganisms9122425. [PMID: 34946026 PMCID: PMC8707851 DOI: 10.3390/microorganisms9122425] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Revised: 11/19/2021] [Accepted: 11/22/2021] [Indexed: 11/17/2022] Open
Abstract
The development of oil exploration activities and an increase in shipping in Arctic areas have increased the risk of oil spills in this cold marine environment. The objective of this experimental study was to assess the effect of biostimulation on microbial community abundance, structure, dynamics, and metabolic potential for oil hydrocarbon degradation in oil-contaminated Arctic seawater. The combination of amplicon-based and shotgun sequencing, together with the integration of genome-resolved metagenomics and omics data, was applied to assess microbial community structure and metabolic properties in naphthenic crude oil-amended microcosms. The comparison of estimates for oil-degrading microbial taxa obtained with different sequencing and taxonomic assignment methods showed substantial discrepancies between applied methods. Consequently, the data acquired with different methods was integrated for the analysis of microbial community structure, and amended with quantitative PCR, producing a more objective description of microbial community dynamics and evaluation of the effect of biostimulation on particular microbial taxa. Implementing biostimulation of the seawater microbial community with the addition of nutrients resulted in substantially elevated prokaryotic community abundance (103-fold), a distinctly different bacterial community structure from that in the initial seawater, 1.3-fold elevation in the normalized abundance of hydrocarbon degradation genes, and 12% enhancement of crude oil biodegradation. The bacterial communities in biostimulated microcosms after four months of incubation were dominated by Gammaproteobacterial genera Pseudomonas, Marinomonas, and Oleispira, which were succeeded by Cycloclasticus and Paraperlucidibaca after eight months of incubation. The majority of 195 compiled good-quality metagenome-assembled genomes (MAGs) exhibited diverse hydrocarbon degradation gene profiles. The results reveal that biostimulation with nutrients promotes naphthenic oil degradation in Arctic seawater, but this strategy alone might not be sufficient to effectively achieve bioremediation goals within a reasonable timeframe.
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76
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Long-read metagenomics of soil communities reveals phylum-specific secondary metabolite dynamics. Commun Biol 2021; 4:1302. [PMID: 34795375 PMCID: PMC8602731 DOI: 10.1038/s42003-021-02809-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Accepted: 10/25/2021] [Indexed: 01/04/2023] Open
Abstract
Microbial biosynthetic gene clusters (BGCs) encoding secondary metabolites are thought to impact a plethora of biologically mediated environmental processes, yet their discovery and functional characterization in natural microbiomes remains challenging. Here we describe deep long-read sequencing and assembly of metagenomes from biological soil crusts, a group of soil communities that are rich in BGCs. Taking advantage of the unusually long assemblies produced by this approach, we recovered nearly 3,000 BGCs for analysis, including 712 full-length BGCs. Functional exploration through metatranscriptome analysis of a 3-day wetting experiment uncovered phylum-specific BGC expression upon activation from dormancy, elucidating distinct roles and complex phylogenetic and temporal dynamics in wetting processes. For example, a pronounced increase in BGC transcription occurs at night primarily in cyanobacteria, implicating BGCs in nutrient scavenging roles and niche competition. Taken together, our results demonstrate that long-read metagenomic sequencing combined with metatranscriptomic analysis provides a direct view into the functional dynamics of BGCs in environmental processes and suggests a central role of secondary metabolites in maintaining phylogenetically conserved niches within biocrusts.
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77
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Abstract
Reconstructing microbial genomes from metagenomic short-read data can be challenging due to the unknown and uneven complexity of microbial communities. This complexity encompasses highly diverse populations, which often includes strain variants. Reconstructing high-quality genomes is a crucial part of the metagenomic workflow, as subsequent ecological and metabolic inferences depend on their accuracy, quality, and completeness. In contrast to microbial communities in other ecosystems, there has been no systematic assessment of genome-centric metagenomic workflows for drinking water microbiomes. In this study, we assessed the performance of a combination of assembly and binning strategies for time series drinking water metagenomes that were collected over 6 months. The goal of this study was to identify the combination of assembly and binning approaches that result in high-quality and -quantity metagenome-assembled genomes (MAGs), representing most of the sequenced metagenome. Our findings suggest that the metaSPAdes coassembly strategies had the best performance, as they resulted in larger and less fragmented assemblies, with at least 85% of the sequence data mapping to contigs greater than 1 kbp. Furthermore, a combination of metaSPAdes coassembly strategies and MetaBAT2 produced the highest number of medium-quality MAGs while capturing at least 70% of the metagenomes based on read recruitment. Utilizing different assembly/binning approaches also assists in the reconstruction of unique MAGs from closely related species that would have otherwise collapsed into a single MAG using a single workflow. Overall, our study suggests that leveraging multiple binning approaches with different metaSPAdes coassembly strategies may be required to maximize the recovery of good-quality MAGs. IMPORTANCE Drinking water contains phylogenetic diverse groups of bacteria, archaea, and eukarya that affect the esthetic quality of water, water infrastructure, and public health. Taxonomic, metabolic, and ecological inferences of the drinking water microbiome depend on the accuracy, quality, and completeness of genomes that are reconstructed through the application of genome-resolved metagenomics. Using time series metagenomic data, we present reproducible genome-centric metagenomic workflows that result in high-quality and -quantity genomes, which more accurately signifies the sequenced drinking water microbiome. These genome-centric metagenomic workflows will allow for improved taxonomic and functional potential analysis that offers enhanced insights into the stability and dynamics of drinking water microbial communities.
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78
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Heritier-Robbins P, Karthikeyan S, Hatt JK, Kim M, Huettel M, Kostka JE, Konstantinidis KT, Rodriguez-R LM. Beach sand oil spills select for generalist microbial populations. THE ISME JOURNAL 2021; 15:3418-3422. [PMID: 34088976 PMCID: PMC8528907 DOI: 10.1038/s41396-021-01017-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Revised: 05/09/2021] [Accepted: 05/14/2021] [Indexed: 11/15/2022]
Abstract
The specialization-disturbance hypothesis predicts that, in the event of a disturbance, generalists are favored, while specialists are selected against. This hypothesis has not been rigorously tested in microbial systems and it remains unclear to what extent it could explain microbial community succession patterns following perturbations. Previous field observations of Pensacola Beach sands that were impacted by the Deepwater Horizon (DWH) oil spill provided evidence in support of the specialization-disturbance hypothesis. However, ecological drift as well as uncounted environmental fluctuations (e.g., storms) could not be ruled out as confounding factors driving these field results. In this study, the specialization-disturbance hypothesis was tested on beach sands, disturbed by DWH crude oil, ex situ in closed laboratory advective-flow chambers that mimic in situ conditions in saturated beach sediments. The chambers were inoculated with weathered DWH oil and unamended chambers served as controls. The time series of shotgun metagenomic and 16S rRNA gene amplicon sequence data from a two-month long incubation showed that functional diversity significantly increased while taxonomic diversity significantly declined, indicating a decrease in specialist taxa. Thus, results from this laboratory study corroborate field observations, providing verification that the specialization-disturbance hypothesis can explain microbial succession patterns in crude oil impacted beach sands.
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Affiliation(s)
- Patrick Heritier-Robbins
- School of Civil and Environmental Engineering, Georgia Institute of Technology, Atlanta, GA, USA
| | - Smruthi Karthikeyan
- School of Civil and Environmental Engineering, Georgia Institute of Technology, Atlanta, GA, USA
| | - Janet K Hatt
- School of Civil and Environmental Engineering, Georgia Institute of Technology, Atlanta, GA, USA
| | - Minjae Kim
- School of Civil and Environmental Engineering, Georgia Institute of Technology, Atlanta, GA, USA
| | - Markus Huettel
- Department of Earth, Ocean and Atmospheric Sciences, Florida State University, Tallahassee, FL, USA
| | - Joel E Kostka
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA
- School of Earth and Atmospheric Sciences, Georgia Institute of Technology, Atlanta, GA, USA
- Center for Microbial Dynamics and Infection, Georgia Institute of Technology, Atlanta, GA, USA
| | - Konstantinos T Konstantinidis
- School of Civil and Environmental Engineering, Georgia Institute of Technology, Atlanta, GA, USA.
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA.
| | - Luis M Rodriguez-R
- School of Civil and Environmental Engineering, Georgia Institute of Technology, Atlanta, GA, USA.
- Department of Microbiology, University of Innsbruck, Innsbruck, Austria.
- Digital Science Center (DiSC), University of Innsbruck, Innsbruck, Austria.
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79
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Metagenomic Sequencing of Multiple Soil Horizons and Sites in Close Vicinity Revealed Novel Secondary Metabolite Diversity. mSystems 2021; 6:e0101821. [PMID: 34636675 PMCID: PMC8510542 DOI: 10.1128/msystems.01018-21] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Discovery of novel antibiotics is crucial for combating rapidly spreading antimicrobial resistance and new infectious diseases. Most of the clinically used antibiotics are natural products—secondary metabolites produced by soil microbes that can be cultured in the lab. Rediscovery of these secondary metabolites during discovery expeditions costs both time and resources. Metagenomics approaches can overcome this challenge by capturing both culturable and unculturable hidden microbial diversity. To be effective, such an approach should address questions like the following. Which sequencing method is better at capturing the microbial diversity and biosynthesis potential? What part of the soil should be sampled? Can patterns and correlations from such big-data explorations guide future novel natural product discovery surveys? Here, we address these questions by a paired amplicon and shotgun metagenomic sequencing survey of samples from soil horizons of multiple forest sites very close to each other. Metagenome mining identified numerous novel biosynthetic gene clusters (BGCs) and enzymatic domain sequences. Hybrid assembly of both long reads and short reads improved the metagenomic assembly and resulted in better BGC annotations. A higher percentage of novel domains was recovered from shotgun metagenome data sets than from amplicon data sets. Overall, in addition to revealing the biosynthetic potential of soil microbes, our results suggest the importance of sampling not only different soils but also their horizons to capture microbial and biosynthetic diversity and highlight the merits of metagenome sequencing methods. IMPORTANCE This study helped uncover the biosynthesis potential of forest soils via exploration of shotgun metagenome and amplicon sequencing methods and showed that both methods are needed to expose the full microbial diversity in soil. Based on our metagenome mining results, we suggest revising the historical strategy of sampling soils from far-flung places, as we found a significant number of novel and diverse BGCs and domains even in different soils that are very close to each other. Furthermore, sampling of different soil horizons can reveal the additional diversity that often remains hidden and is mainly caused by differences in environmental key parameters such as soil pH and nutrient content. This paired metagenomic survey identified diversity patterns and correlations, a step toward developing a rational approach for future natural product discovery surveys.
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80
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Sun Y, Debeljak P, Obernosterer I. Microbial iron and carbon metabolism as revealed by taxonomy-specific functional diversity in the Southern Ocean. THE ISME JOURNAL 2021; 15:2933-2946. [PMID: 33941887 PMCID: PMC8443675 DOI: 10.1038/s41396-021-00973-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Revised: 03/16/2021] [Accepted: 03/30/2021] [Indexed: 02/01/2023]
Abstract
Marine microbes are major drivers of all elemental cycles. The processing of organic carbon by heterotrophic prokaryotes is tightly coupled to the availability of the trace element iron in large regions of the Southern Ocean. However, the functional diversity in iron and carbon metabolism within diverse communities remains a major unresolved issue. Using novel Southern Ocean meta-omics resources including 133 metagenome-assembled genomes (MAGs), we show a mosaic of taxonomy-specific ecological strategies in naturally iron-fertilized and high nutrient low chlorophyll (HNLC) waters. Taxonomic profiling revealed apparent community shifts across contrasting nutrient regimes. Community-level and genome-resolved metatranscriptomics evidenced a moderate association between taxonomic affiliations and iron and carbon-related functional roles. Diverse ecological strategies emerged when considering the central metabolic pathways of individual MAGs. Closely related lineages appear to adapt to distinct ecological niches, based on their distribution and gene regulation patterns. Our in-depth observations emphasize the complex interplay between the genetic repertoire of individual taxa and their environment and how this shapes prokaryotic responses to iron and organic carbon availability in the Southern Ocean.
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Affiliation(s)
- Ying Sun
- CNRS, Sorbonne Université, Laboratoire d'Océanographie Microbienne, LOMIC, F-66650, Banyuls/mer, France.
| | - Pavla Debeljak
- CNRS, Sorbonne Université, Laboratoire d'Océanographie Microbienne, LOMIC, F-66650, Banyuls/mer, France
- University of Vienna, Department of Functional and Evolutionary Ecology, A-1090, Vienna, Austria
| | - Ingrid Obernosterer
- CNRS, Sorbonne Université, Laboratoire d'Océanographie Microbienne, LOMIC, F-66650, Banyuls/mer, France
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81
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Kwon MJ, Tripathi BM, Göckede M, Shin SC, Myeong NR, Lee YK, Kim M. Disproportionate microbial responses to decadal drainage on a Siberian floodplain. GLOBAL CHANGE BIOLOGY 2021; 27:5124-5140. [PMID: 34216067 DOI: 10.1111/gcb.15785] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/20/2021] [Accepted: 06/11/2021] [Indexed: 06/13/2023]
Abstract
Permafrost thaw induces soil hydrological changes which in turn affects carbon cycle processes in the Arctic terrestrial ecosystems. However, hydrological impacts of thawing permafrost on microbial processes and greenhouse gas (GHG) dynamics are poorly understood. This study examined changes in microbial communities using gene and genome-centric metagenomics on an Arctic floodplain subject to decadal drainage, and linked them to CO2 and CH4 flux and soil chemistry. Decadal drainage led to significant changes in the abundance, taxonomy, and functional potential of microbial communities, and these modifications well explained the changes in CO2 and CH4 fluxes between ecosystem and atmosphere-increased fungal abundances potentially increased net CO2 emission rates and highly reduced CH4 emissions in drained sites corroborated the marked decrease in the abundance of methanogens and methanotrophs. Interestingly, various microbial taxa disproportionately responded to drainage: Methanoregula, one of the key players in methanogenesis under saturated conditions, almost disappeared, and also Methylococcales methanotrophs were markedly reduced in response to drainage. Seven novel methanogen population genomes were recovered, and the metabolic reconstruction of highly correlated population genomes revealed novel syntrophic relationships between methanogenic archaea and syntrophic partners. These results provide a mechanistic view of microbial processes regulating GHG dynamics in the terrestrial carbon cycle, and disproportionate microbial responses to long-term drainage provide key information for understanding the effects of warming-induced soil drying on microbial processes in Arctic wetland ecosystems.
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Affiliation(s)
- Min Jung Kwon
- Korea Polar Research Institute, Incheon, Republic of Korea
| | | | | | | | - Nu Ri Myeong
- Korea Polar Research Institute, Incheon, Republic of Korea
| | - Yoo Kyung Lee
- Korea Polar Research Institute, Incheon, Republic of Korea
| | - Mincheol Kim
- Korea Polar Research Institute, Incheon, Republic of Korea
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82
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Cha G, Meinhardt KA, Orellana LH, Hatt JK, Pannu MW, Stahl DA, Konstantinidis KT. The influence of alfalfa-switchgrass intercropping on microbial community structure and function. Environ Microbiol 2021; 23:6828-6843. [PMID: 34554631 DOI: 10.1111/1462-2920.15785] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Accepted: 09/17/2021] [Indexed: 11/30/2022]
Abstract
The use of nitrogen fertilizer on bioenergy crops such as switchgrass results in increased costs, nitrogen leaching and emissions of N2 O, a potent greenhouse gas. Intercropping with nitrogen-fixing alfalfa has been proposed as an environmentally sustainable alternative, but the effects of synthetic fertilizer versus intercropping on soil microbial community functionality remain uncharacterized. We analysed 24 metagenomes from the upper soil layer of agricultural fields from Prosser, WA over two growing seasons and representing three agricultural practices: unfertilized switchgrass (control), fertilized switchgrass and switchgrass intercropped with alfalfa. The synthetic fertilization and intercropping did not result in major shifts of microbial community taxonomic and functional composition compared with the control plots, but a few significant changes were noted. Most notably, mycorrhizal fungi, ammonia-oxidizing archaea and bacteria increased in abundance with intercropping and fertilization. However, only betaproteobacterial ammonia-oxidizing bacteria abundance in fertilized plots significantly correlated to N2 O emission and companion qPCR data. Collectively, a short period of intercropping elicits minor but significant changes in the soil microbial community toward nitrogen preservation and that intercropping may be a viable alternative to synthetic fertilization.
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Affiliation(s)
- Gyuhyon Cha
- School of Civil and Environmental Engineering, Georgia Institute of Technology, Atlanta, GA, 30332, USA
| | - Kelley A Meinhardt
- Civil and Environmental Engineering, University of Washington, Seattle, WA, 98195, USA
| | - Luis H Orellana
- School of Civil and Environmental Engineering, Georgia Institute of Technology, Atlanta, GA, 30332, USA
| | - Janet K Hatt
- School of Civil and Environmental Engineering, Georgia Institute of Technology, Atlanta, GA, 30332, USA
| | - Manmeet W Pannu
- Civil and Environmental Engineering, University of Washington, Seattle, WA, 98195, USA
| | - David A Stahl
- Civil and Environmental Engineering, University of Washington, Seattle, WA, 98195, USA
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83
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High arsenic levels increase activity rather than diversity or abundance of arsenic metabolism genes in paddy soils. Appl Environ Microbiol 2021; 87:e0138321. [PMID: 34378947 DOI: 10.1128/aem.01383-21] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Arsenic (As) metabolism genes are generally present in soils but their diversity, relative abundance, and transcriptional activity in response to different As concentrations remain unclear, limiting our understanding of the microbial activities that control the fate of an important environmental pollutant. To address this issue, we applied metagenomics and metatranscriptomics to paddy soils showing a gradient of As concentrations to investigate As resistance genes (ars) including arsR, acr3, arsB, arsC, arsM, arsI, arsP, and arsH as well as energy-generating As respiratory oxidation (aioA) and reduction (arrA) genes. Somewhat unexpectedly, the relative DNA abundances and diversity of ars, aioA, and arrA genes were not significantly different between low and high (∼10 vs ∼100 mg kg-1) As soils. By comparison to available metagenomes from other soils, geographic distance rather than As levels drove the different compositions of microbial communities. Arsenic significantly increased ars genes abundance only when its concentration was higher than 410 mg kg-1. In contrast, between low and high As soils, metatranscriptomics revealed a significant increase in transcription of ars and aioA genes, which are induced by arsenite, the dominant As species in paddy soils, but not arrA genes, which are induced by arsenate. These patterns appeared to be community-wide as opposed to taxon-specific. Collectively, our findings advance understanding of how microbes respond to high As levels and the diversity of As metabolism genes in paddy soils and indicated that future studies of As metabolism in soil, or other environments, should include the function (transcriptome) level. IMPORTANCE Arsenic (As) is a toxic metalloid pervasively present in the environment. Microorganisms have evolved the capacity to metabolize As, and As metabolism genes are ubiquitously present in the environment even in the absence of high concentrations of As. However, these previous studies were carried out at the DNA level and thus, the activity of the As metabolism genes detected remains essentially speculative. Here, we show that the high As levels in paddy soils increased the transcriptional activity rather than the relative DNA abundance and diversity of As metabolism genes. These findings advance our understanding of how microbes respond to and cope with high As levels and have implications for better monitoring and managing an important toxic metalloid in agricultural soils and possibly other ecosystems.
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84
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Metabolic Features of Ganjang (a Korean Traditional Soy Sauce) Fermentation Revealed by Genome-Centered Metatranscriptomics. mSystems 2021; 6:e0044121. [PMID: 34342543 PMCID: PMC8407349 DOI: 10.1128/msystems.00441-21] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
Abstract
The taste and quality of soy sauce, a fermented liquid condiment popular worldwide, is greatly influenced by microbial metabolism during fermentation. To investigate the fermentative features of ganjang (a Korean traditional soy sauce), ganjang batches using meju (fermented soybean) bricks and solar salts were prepared, and organic compounds, microbial communities, metagenomes, and metatranscriptomes of ganjang were quantitively analyzed during fermentation. Polymeric compound analysis in the ganjang treated with/without microbial inhibitors revealed that indigenous enzymes of meju bricks might be primarily responsible for degrading polymeric compounds. Through metagenome binning and microbe sequencing, 17 high-quality genome sequences representing all major ganjang microbiota were obtained, and their transcriptional expressions were quantitatively analyzed by mapping metatranscriptome reads normalized by spike-in RNA sequencing to the 17 genomes, which revealed that microbial metabolism might primarily occur while meju bricks are in the ganjang solution and decrease significantly after the removal of meju bricks. Metabolic pathways for carbohydrates, proteins, and lipids of the major ganjang microbiota were reconstructed, and their metabolic genes were transcriptionally analyzed, revealing that facultative lactic acid fermentation by Tetragenococcus was the major fermentation process active in the ganjang fermentation and that aerobic respiration by facultatively aerobic bacteria such as Chromohalobacter, Halomonas, and Marinobacter was also an important metabolic process during fermentation. Although the abundances of Fungi and the corresponding transcriptional expression levels were generally much lower than those of Bacteria, our analysis suggests that yeasts such as Debaryomyces and Wickerhamomyces might be in large part responsible for producing biogenic amines and flavors. IMPORTANCE The taste and quality of soy sauce, a popular fermented liquid condiment worldwide, is greatly influenced by microbial metabolism during fermentation. Spontaneous fermentation of ganjang (a Korean traditional soy sauce) in a nonsterile environment leads to the growth of diverse bacteria and fungi during fermentation, making it difficult to understand the mechanism of ganjang fermentation. Genome-centered metatranscriptomic analysis, combined with organic compound analysis, quantitative metagenome and metatranscriptome analyses, and metabolic pathway reconstruction and expressional analysis of the major ganjang microbiota during fermentation, would provide comprehensive insights into the metabolic features of ganjang fermentation.
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85
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Patin NV, Dietrich ZA, Stancil A, Quinan M, Beckler JS, Hall ER, Culter J, Smith CG, Taillefert M, Stewart FJ. Gulf of Mexico blue hole harbors high levels of novel microbial lineages. THE ISME JOURNAL 2021; 15:2206-2232. [PMID: 33612832 PMCID: PMC8319197 DOI: 10.1038/s41396-021-00917-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2020] [Revised: 01/14/2021] [Accepted: 01/27/2021] [Indexed: 01/31/2023]
Abstract
Exploration of oxygen-depleted marine environments has consistently revealed novel microbial taxa and metabolic capabilities that expand our understanding of microbial evolution and ecology. Marine blue holes are shallow karst formations characterized by low oxygen and high organic matter content. They are logistically challenging to sample, and thus our understanding of their biogeochemistry and microbial ecology is limited. We present a metagenomic and geochemical characterization of Amberjack Hole on the Florida continental shelf (Gulf of Mexico). Dissolved oxygen became depleted at the hole's rim (32 m water depth), remained low but detectable in an intermediate hypoxic zone (40-75 m), and then increased to a secondary peak before falling below detection in the bottom layer (80-110 m), concomitant with increases in nutrients, dissolved iron, and a series of sequentially more reduced sulfur species. Microbial communities in the bottom layer contained heretofore undocumented levels of the recently discovered phylum Woesearchaeota (up to 58% of the community), along with lineages in the bacterial Candidate Phyla Radiation (CPR). Thirty-one high-quality metagenome-assembled genomes (MAGs) showed extensive biochemical capabilities for sulfur and nitrogen cycling, as well as for resisting and respiring arsenic. One uncharacterized gene associated with a CPR lineage differentiated hypoxic from anoxic zone communities. Overall, microbial communities and geochemical profiles were stable across two sampling dates in the spring and fall of 2019. The blue hole habitat is a natural marine laboratory that provides opportunities for sampling taxa with under-characterized but potentially important roles in redox-stratified microbial processes.
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Affiliation(s)
- N V Patin
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA.
- Center for Microbial Dynamics and Infection, Georgia Institute of Technology, Atlanta, GA, USA.
- Ocean Chemistry and Ecosystems Division, Atlantic Oceanographic and Meteorological Laboratory, National Oceanic and Atmospheric Administration, Miami, FL, USA.
- Cooperative Institute for Marine and Atmospheric Studies, Rosenstiel School of Marine and Atmospheric Science, University of Miami, Miami, FL, USA.
- Stationed at Southwest Fisheries Science Center, National Marine Fisheries Service, National Oceanic and Atmospheric Administration, La Jolla, CA, USA.
| | | | - A Stancil
- Harbor Branch Oceanographic Institute, Florida Atlantic University, Ft. Pierce, FL, USA
| | - M Quinan
- Harbor Branch Oceanographic Institute, Florida Atlantic University, Ft. Pierce, FL, USA
| | - J S Beckler
- Harbor Branch Oceanographic Institute, Florida Atlantic University, Ft. Pierce, FL, USA
| | - E R Hall
- Mote Marine Laboratory, Sarasota, FL, USA
| | - J Culter
- Mote Marine Laboratory, Sarasota, FL, USA
| | - C G Smith
- U.S. Geological Survey, St. Petersburg Coastal and Marine Science Center, St. Petersburg, FL, USA
| | - M Taillefert
- School of Earth & Atmospheric Sciences, Georgia Institute of Technology, Atlanta, GA, USA
| | - F J Stewart
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA
- Center for Microbial Dynamics and Infection, Georgia Institute of Technology, Atlanta, GA, USA
- Department of Microbiology & Immunology, Montana State University, Bozeman, MT, USA
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86
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Priest T, Orellana LH, Huettel B, Fuchs BM, Amann R. Microbial metagenome-assembled genomes of the Fram Strait from short and long read sequencing platforms. PeerJ 2021; 9:e11721. [PMID: 34249520 PMCID: PMC8254474 DOI: 10.7717/peerj.11721] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Accepted: 06/14/2021] [Indexed: 01/21/2023] Open
Abstract
The impacts of climate change on the Arctic Ocean are manifesting throughout the ecosystem at an unprecedented rate. Of global importance are the impacts on heat and freshwater exchange between the Arctic and North Atlantic Oceans. An expanding Atlantic influence in the Arctic has accelerated sea-ice decline, weakened water column stability and supported the northward shift of temperate species. The only deep-water gateway connecting the Arctic and North Atlantic and thus, fundamental for these exchange processes is the Fram Strait. Previous research in this region is extensive, however, data on the ecology of microbial communities is limited, reflecting the wider bias towards temperate and tropical latitudes. Therefore, we present 14 metagenomes, 11 short-read from Illumina and three long-read from PacBio Sequel II, of the 0.2-3 µm fraction to help alleviate such biases and support future analyses on changing ecological patterns. Additionally, we provide 136 species-representative, manually refined metagenome-assembled genomes which can be used for comparative genomics analyses and addressing questions regarding functionality or distribution of taxa.
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Affiliation(s)
- Taylor Priest
- Department of Molecular Ecology, Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Luis H. Orellana
- Department of Molecular Ecology, Max Planck Institute for Marine Microbiology, Bremen, Germany
| | | | - Bernhard M. Fuchs
- Department of Molecular Ecology, Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Rudolf Amann
- Department of Molecular Ecology, Max Planck Institute for Marine Microbiology, Bremen, Germany
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87
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Detman A, Bucha M, Treu L, Chojnacka A, Pleśniak Ł, Salamon A, Łupikasza E, Gromadka R, Gawor J, Gromadka A, Drzewicki W, Jakubiak M, Janiga M, Matyasik I, Błaszczyk MK, Jędrysek MO, Campanaro S, Sikora A. Evaluation of acidogenesis products' effect on biogas production performed with metagenomics and isotopic approaches. BIOTECHNOLOGY FOR BIOFUELS 2021; 14:125. [PMID: 34051845 PMCID: PMC8164749 DOI: 10.1186/s13068-021-01968-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Accepted: 05/06/2021] [Indexed: 06/09/2023]
Abstract
BACKGROUND During the acetogenic step of anaerobic digestion, the products of acidogenesis are oxidized to substrates for methanogenesis: hydrogen, carbon dioxide and acetate. Acetogenesis and methanogenesis are highly interconnected processes due to the syntrophic associations between acetogenic bacteria and hydrogenotrophic methanogens, allowing the whole process to become thermodynamically favorable. The aim of this study is to determine the influence of the dominant acidic products on the metabolic pathways of methane formation and to find a core microbiome and substrate-specific species in a mixed biogas-producing system. RESULTS Four methane-producing microbial communities were fed with artificial media having one dominant component, respectively, lactate, butyrate, propionate and acetate, for 896 days in 3.5-L Up-flow Anaerobic Sludge Blanket (UASB) bioreactors. All the microbial communities showed moderately different methane production and utilization of the substrates. Analyses of stable carbon isotope composition of the fermentation gas and the substrates showed differences in average values of δ13C(CH4) and δ13C(CO2) revealing that acetate and lactate strongly favored the acetotrophic pathway, while butyrate and propionate favored the hydrogenotrophic pathway of methane formation. Genome-centric metagenomic analysis recovered 234 Metagenome Assembled Genomes (MAGs), including 31 archaeal and 203 bacterial species, mostly unknown and uncultivable. MAGs accounted for 54%-67% of the entire microbial community (depending on the bioreactor) and evidenced that the microbiome is extremely complex in terms of the number of species. The core microbiome was composed of Methanothrix soehngenii (the most abundant), Methanoculleus sp., unknown Bacteroidales and Spirochaetaceae. Relative abundance analysis of all the samples revealed microbes having substrate preferences. Substrate-specific species were mostly unknown and not predominant in the microbial communities. CONCLUSIONS In this experimental system, the dominant fermentation products subjected to methanogenesis moderately modified the final effect of bioreactor performance. At the molecular level, a different contribution of acetotrophic and hydrogenotrophic pathways for methane production, a very high level of new species recovered, and a moderate variability in microbial composition depending on substrate availability were evidenced. Propionate was not a factor ceasing methane production. All these findings are relevant because lactate, acetate, propionate and butyrate are the universal products of acidogenesis, regardless of feedstock.
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Affiliation(s)
- Anna Detman
- Institute of Biochemistry and Biophysics PAS, Warsaw, Poland
| | - Michał Bucha
- Institute of Biochemistry and Biophysics PAS, Warsaw, Poland
- Faculty of Earth Sciences, University of Silesia in Katowice, Sosnowiec, Poland
| | - Laura Treu
- Department of Biology, University of Padova, Padova, Italy
| | - Aleksandra Chojnacka
- Institute of Biochemistry and Biophysics PAS, Warsaw, Poland
- Department of Biochemistry and Microbiology, Institute of Biology, Warsaw, University of Life Sciences, Warsaw, Poland
| | - Łukasz Pleśniak
- Institute of Biochemistry and Biophysics PAS, Warsaw, Poland
- Institute of Geological Sciences, University of Wroclaw, Wrocław, Poland
| | | | - Ewa Łupikasza
- Faculty of Earth Sciences, University of Silesia in Katowice, Sosnowiec, Poland
| | - Robert Gromadka
- Institute of Biochemistry and Biophysics PAS, Warsaw, Poland
| | - Jan Gawor
- Institute of Biochemistry and Biophysics PAS, Warsaw, Poland
| | | | - Wojciech Drzewicki
- Institute of Geological Sciences, University of Wroclaw, Wrocław, Poland
| | - Marta Jakubiak
- Institute of Geological Sciences, University of Wroclaw, Wrocław, Poland
| | - Marek Janiga
- Oil and Gas Institute, National Research Institute, Cracow, Poland
| | - Irena Matyasik
- Oil and Gas Institute, National Research Institute, Cracow, Poland
| | - Mieczysław K Błaszczyk
- Department of Biochemistry and Microbiology, Institute of Biology, Warsaw, University of Life Sciences, Warsaw, Poland
| | | | | | - Anna Sikora
- Institute of Biochemistry and Biophysics PAS, Warsaw, Poland.
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Qian X, Gunturu S, Guo J, Chai B, Cole JR, Gu J, Tiedje JM. Metagenomic analysis reveals the shared and distinct features of the soil resistome across tundra, temperate prairie, and tropical ecosystems. MICROBIOME 2021; 9:108. [PMID: 33990222 PMCID: PMC8122544 DOI: 10.1186/s40168-021-01047-4] [Citation(s) in RCA: 61] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Accepted: 03/11/2021] [Indexed: 05/02/2023]
Abstract
BACKGROUND Soil is an important reservoir of antibiotic resistance genes (ARGs), but their potential risk in different ecosystems as well as response to anthropogenic land use change is unknown. We used a metagenomic approach and datasets with well-characterized metadata to investigate ARG types and amounts in soil DNA of three native ecosystems: Alaskan tundra, US Midwestern prairie, and Amazon rainforest, as well as the effect of conversion of the latter two to agriculture and pasture, respectively. RESULTS High diversity (242 ARG subtypes) and abundance (0.184-0.242 ARG copies per 16S rRNA gene copy) were observed irrespective of ecosystem, with multidrug resistance and efflux pump the dominant class and mechanism. Ten regulatory genes were identified and they accounted for 13-35% of resistome abundances in soils, among them arlR, cpxR, ompR, vanR, and vanS were dominant and observed in all studied soils. We identified 55 non-regulatory ARGs shared by all 26 soil metagenomes of the three ecosystems, which accounted for more than 81% of non-regulatory resistome abundance. Proteobacteria, Firmicutes, and Actinobacteria were primary ARG hosts, 7 of 10 most abundant ARGs were found in all of them. No significant differences in both ARG diversity and abundance were observed between native prairie soil and adjacent long-term cultivated agriculture soil. We chose 12 clinically important ARGs to evaluate at the sequence level and found them to be distinct from those in human pathogens, and when assembled they were even more dissimilar. Significant correlation was found between bacterial community structure and resistome profile, suggesting that variance in resistome profile was mainly driven by the bacterial community composition. CONCLUSIONS Our results identify candidate background ARGs (shared in all 26 soils), classify ARG hosts, quantify resistance classes, and provide quantitative and sequence information suggestive of very low risk but also revealing resistance gene variants that might emerge in the future. Video abstract.
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Affiliation(s)
- Xun Qian
- Interdisciplinary Research Center for Soil Microbial Ecology and Land Sustainable Productivity in Dry Areas, Northwest A&F University, Yangling, 712100 Shaanxi China
- Center for Microbial Ecology, Michigan State University, East Lansing, MI 48824 USA
- College of Natural Resources and Environment, Northwest A&F University, Yangling, 712100 Shaanxi China
| | - Santosh Gunturu
- Center for Microbial Ecology, Michigan State University, East Lansing, MI 48824 USA
| | - Jiarong Guo
- Center for Microbial Ecology, Michigan State University, East Lansing, MI 48824 USA
| | - Benli Chai
- Center for Microbial Ecology, Michigan State University, East Lansing, MI 48824 USA
| | - James R. Cole
- Center for Microbial Ecology, Michigan State University, East Lansing, MI 48824 USA
| | - Jie Gu
- Interdisciplinary Research Center for Soil Microbial Ecology and Land Sustainable Productivity in Dry Areas, Northwest A&F University, Yangling, 712100 Shaanxi China
- College of Natural Resources and Environment, Northwest A&F University, Yangling, 712100 Shaanxi China
| | - James M. Tiedje
- Interdisciplinary Research Center for Soil Microbial Ecology and Land Sustainable Productivity in Dry Areas, Northwest A&F University, Yangling, 712100 Shaanxi China
- Center for Microbial Ecology, Michigan State University, East Lansing, MI 48824 USA
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89
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Li X, Stokholm J, Brejnrod A, Vestergaard GA, Russel J, Trivedi U, Thorsen J, Gupta S, Hjelmsø MH, Shah SA, Rasmussen MA, Bisgaard H, Sørensen SJ. The infant gut resistome associates with E. coli, environmental exposures, gut microbiome maturity, and asthma-associated bacterial composition. Cell Host Microbe 2021; 29:975-987.e4. [PMID: 33887206 DOI: 10.1016/j.chom.2021.03.017] [Citation(s) in RCA: 58] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2020] [Revised: 03/03/2021] [Accepted: 03/26/2021] [Indexed: 02/06/2023]
Abstract
Antimicrobial resistance (AMR) is an accelerating global threat, yet the nature of AMR in the gut microbiome and how AMR is acquired during early life remain largely unknown. In a cohort of 662 Danish children, we characterized the antibiotic resistance genes (ARGs) acquired during the first year of life and assessed the impacts of diverse environmental exposures on ARG load. Our study reveals a clear bimodal distribution of ARG richness that is driven by the composition of the gut microbiome, especially E. coli. ARG profiles were significantly affected by various environmental factors. Among these factors, the importance of antibiotics diminished with time since treatment. Finally, ARG load and ARG clusters were also associated with the maturity of the gut microbiome and a bacterial composition associated with increased risk of asthma. These findings broaden our understanding of AMR in early life and have critical implications for efforts to mitigate its spread.
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Affiliation(s)
- Xuanji Li
- Department of Biology, Section of Microbiology, University of Copenhagen, 2100 Copenhagen, Denmark
| | - Jakob Stokholm
- COPSAC, Copenhagen Prospective Studies on Asthma in Childhood, Herlev and Gentofte Hospital, University of Copenhagen, 2820 Copenhagen, Denmark
| | - Asker Brejnrod
- Skaggs School of Pharmacy, University of California, San Diego, La Jolla, CA 9500, USA
| | - Gisle Alberg Vestergaard
- Technical University of Denmark, Section of Bioinformatics, Department of Health Technology, 2800 Kongens Lyngby, Denmark
| | - Jakob Russel
- Department of Biology, Section of Microbiology, University of Copenhagen, 2100 Copenhagen, Denmark
| | - Urvish Trivedi
- Department of Biology, Section of Microbiology, University of Copenhagen, 2100 Copenhagen, Denmark
| | - Jonathan Thorsen
- COPSAC, Copenhagen Prospective Studies on Asthma in Childhood, Herlev and Gentofte Hospital, University of Copenhagen, 2820 Copenhagen, Denmark
| | - Shashank Gupta
- Department of Biology, Section of Microbiology, University of Copenhagen, 2100 Copenhagen, Denmark
| | - Mathis Hjort Hjelmsø
- COPSAC, Copenhagen Prospective Studies on Asthma in Childhood, Herlev and Gentofte Hospital, University of Copenhagen, 2820 Copenhagen, Denmark
| | - Shiraz A Shah
- COPSAC, Copenhagen Prospective Studies on Asthma in Childhood, Herlev and Gentofte Hospital, University of Copenhagen, 2820 Copenhagen, Denmark
| | - Morten Arendt Rasmussen
- COPSAC, Copenhagen Prospective Studies on Asthma in Childhood, Herlev and Gentofte Hospital, University of Copenhagen, 2820 Copenhagen, Denmark
| | - Hans Bisgaard
- COPSAC, Copenhagen Prospective Studies on Asthma in Childhood, Herlev and Gentofte Hospital, University of Copenhagen, 2820 Copenhagen, Denmark
| | - Søren Johannes Sørensen
- Department of Biology, Section of Microbiology, University of Copenhagen, 2100 Copenhagen, Denmark.
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90
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Soto-Girón MJ, Peña-Gonzalez A, Hatt JK, Montero L, Páez M, Ortega E, Smith S, Cevallos W, Trueba G, Konstantinidis KT, Levy K. Gut Microbiome Changes with Acute Diarrheal Disease in Urban Versus Rural Settings in Northern Ecuador. Am J Trop Med Hyg 2021; 104:2275-2285. [PMID: 33872206 DOI: 10.4269/ajtmh.20-0831] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Accepted: 02/15/2021] [Indexed: 12/12/2022] Open
Abstract
Previous studies have reported lower fecal bacterial diversity in urban populations compared with those living in rural settings. However, most of these studies compare geographically distant populations from different countries and even continents. The extent of differences in the gut microbiome in adjacent rural versus urban populations, and the role of such differences, if any, during enteric infections remain poorly understood. To provide new insights into these issues, we sampled the gut microbiome of young children with and without acute diarrheal disease (ADD) living in rural and urban areas in northern Ecuador. Shotgun metagenomic analyses of non-ADD samples revealed small but significant differences in the abundance of microbial taxa, including a greater abundance of Prevotella and a lower abundance of Bacteroides and Alistipes in rural populations. Greater and more significant shifts in taxon abundance, metabolic pathway abundance, and diversity were observed between ADD and non-ADD status when comparing urban to rural sites (Welch's t-test, P < 0.05). Collectively our data show substantial functional, diversity, and taxonomic shifts in the gut microbiome of urban populations with, ADD supporting the idea that the microbiome of rural populations may be more resilient to ADD episodes.
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Affiliation(s)
- Maria J Soto-Girón
- 1School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia
| | - Angela Peña-Gonzalez
- 1School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia
| | - Janet K Hatt
- 2School of Civil and Environmental Engineering, Georgia Institute of Technology, Atlanta, Georgia
| | - Lorena Montero
- 3Instituto de Microbiologia, Universidad San Francisco de Quito, Quito, Ecuador
| | - Maritza Páez
- 3Instituto de Microbiologia, Universidad San Francisco de Quito, Quito, Ecuador
| | - Estefania Ortega
- 3Instituto de Microbiologia, Universidad San Francisco de Quito, Quito, Ecuador
| | - Shanon Smith
- 4School of Public Health, University of Washington, Seattle, Washington
| | - William Cevallos
- 5Centro de Biomedicina, Universidad Central del Ecuador, Quito, Ecuador
| | - Gabriel Trueba
- 3Instituto de Microbiologia, Universidad San Francisco de Quito, Quito, Ecuador
| | - Konstantinos T Konstantinidis
- 1School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia.,2School of Civil and Environmental Engineering, Georgia Institute of Technology, Atlanta, Georgia
| | - Karen Levy
- 4School of Public Health, University of Washington, Seattle, Washington
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Nayfach S, Roux S, Seshadri R, Udwary D, Varghese N, Schulz F, Wu D, Paez-Espino D, Chen IM, Huntemann M, Palaniappan K, Ladau J, Mukherjee S, Reddy TBK, Nielsen T, Kirton E, Faria JP, Edirisinghe JN, Henry CS, Jungbluth SP, Chivian D, Dehal P, Wood-Charlson EM, Arkin AP, Tringe SG, Visel A, Woyke T, Mouncey NJ, Ivanova NN, Kyrpides NC, Eloe-Fadrosh EA. A genomic catalog of Earth's microbiomes. Nat Biotechnol 2021; 39:499-509. [PMID: 33169036 PMCID: PMC8041624 DOI: 10.1038/s41587-020-0718-6] [Citation(s) in RCA: 352] [Impact Index Per Article: 117.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2019] [Accepted: 09/28/2020] [Indexed: 01/02/2023]
Abstract
The reconstruction of bacterial and archaeal genomes from shotgun metagenomes has enabled insights into the ecology and evolution of environmental and host-associated microbiomes. Here we applied this approach to >10,000 metagenomes collected from diverse habitats covering all of Earth's continents and oceans, including metagenomes from human and animal hosts, engineered environments, and natural and agricultural soils, to capture extant microbial, metabolic and functional potential. This comprehensive catalog includes 52,515 metagenome-assembled genomes representing 12,556 novel candidate species-level operational taxonomic units spanning 135 phyla. The catalog expands the known phylogenetic diversity of bacteria and archaea by 44% and is broadly available for streamlined comparative analyses, interactive exploration, metabolic modeling and bulk download. We demonstrate the utility of this collection for understanding secondary-metabolite biosynthetic potential and for resolving thousands of new host linkages to uncultivated viruses. This resource underscores the value of genome-centric approaches for revealing genomic properties of uncultivated microorganisms that affect ecosystem processes.
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Affiliation(s)
| | - Simon Roux
- DOE Joint Genome Institute, Berkeley, CA, USA
| | | | | | | | | | - Dongying Wu
- DOE Joint Genome Institute, Berkeley, CA, USA
| | | | - I-Min Chen
- DOE Joint Genome Institute, Berkeley, CA, USA
| | | | | | | | | | - T B K Reddy
- DOE Joint Genome Institute, Berkeley, CA, USA
| | | | | | | | | | | | - Sean P Jungbluth
- DOE Joint Genome Institute, Berkeley, CA, USA
- Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Dylan Chivian
- Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Paramvir Dehal
- Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | | | - Adam P Arkin
- Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | | | - Axel Visel
- DOE Joint Genome Institute, Berkeley, CA, USA
| | - Tanja Woyke
- DOE Joint Genome Institute, Berkeley, CA, USA
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92
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Wei ZG, Zhang XD, Cao M, Liu F, Qian Y, Zhang SW. Comparison of Methods for Picking the Operational Taxonomic Units From Amplicon Sequences. Front Microbiol 2021; 12:644012. [PMID: 33841367 PMCID: PMC8024490 DOI: 10.3389/fmicb.2021.644012] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2020] [Accepted: 02/17/2021] [Indexed: 12/31/2022] Open
Abstract
With the advent of next-generation sequencing technology, it has become convenient and cost efficient to thoroughly characterize the microbial diversity and taxonomic composition in various environmental samples. Millions of sequencing data can be generated, and how to utilize this enormous sequence resource has become a critical concern for microbial ecologists. One particular challenge is the OTUs (operational taxonomic units) picking in 16S rRNA sequence analysis. Lucky, this challenge can be directly addressed by sequence clustering that attempts to group similar sequences. Therefore, numerous clustering methods have been proposed to help to cluster 16S rRNA sequences into OTUs. However, each method has its clustering mechanism, and different methods produce diverse outputs. Even a slight parameter change for the same method can also generate distinct results, and how to choose an appropriate method has become a challenge for inexperienced users. A lot of time and resources can be wasted in selecting clustering tools and analyzing the clustering results. In this study, we introduced the recent advance of clustering methods for OTUs picking, which mainly focus on three aspects: (i) the principles of existing clustering algorithms, (ii) benchmark dataset construction for OTU picking and evaluation metrics, and (iii) the performance of different methods with various distance thresholds on benchmark datasets. This paper aims to assist biological researchers to select the reasonable clustering methods for analyzing their collected sequences and help algorithm developers to design more efficient sequences clustering methods.
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Affiliation(s)
- Ze-Gang Wei
- Institute of Physics and Optoelectronics Technology, Baoji University of Arts and Sciences, Baoji, China
- Key Laboratory of Information Fusion Technology of Ministry of Education, School of Automation, Northwestern Polytechnical University, Xi’an, China
| | - Xiao-Dan Zhang
- Institute of Physics and Optoelectronics Technology, Baoji University of Arts and Sciences, Baoji, China
| | - Ming Cao
- Faculty of Electronic and Information Engineering, Xi’an Jiaotong University, Xi’an, China
- School of Mathematics and Statistics, Shaanxi Xueqian Normal University, Xi’an, China
| | - Fei Liu
- Institute of Physics and Optoelectronics Technology, Baoji University of Arts and Sciences, Baoji, China
| | - Yu Qian
- Institute of Physics and Optoelectronics Technology, Baoji University of Arts and Sciences, Baoji, China
| | - Shao-Wu Zhang
- Key Laboratory of Information Fusion Technology of Ministry of Education, School of Automation, Northwestern Polytechnical University, Xi’an, China
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93
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The Effect of the Effluent from a Small-Scale Conventional Wastewater Treatment Plant Treating Municipal Wastewater on the Composition and Abundance of the Microbial Community, Antibiotic Resistome, and Pathogens in the Sediment and Water of a Receiving Stream. WATER 2021. [DOI: 10.3390/w13060865] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
The effluents of wastewater treatment plants (WWTPs) are major contributors of nutrients, microbes—including those carrying antibiotic resistance genes (ARGs)—and pathogens to receiving waterbodies. The effect of the effluent of a small-scale activated sludge WWTP treating municipal wastewater on the composition and abundance of the microbial community as well as the antibiotic resistome and pathogens in the sediment and water of the receiving stream and river was studied using metagenome sequencing and a quantitative approach. Elevated Bacteroidetes proportions in the prokaryotic community, heightened sulfonamide and aminoglycoside resistance determinants proportions, and an increase of up to three orders of magnitude of sul1–sul2–aadA–blaOXA2 gene cluster abundances were recorded in stream water and sediments 0.3 km downstream of a WWTP discharge point. Further downstream, a gradual recovery of affected microbial communities along a distance gradient from WWTP was recorded, culminating in the mostly comparable state of river water and sediment parameters 3.7 km downstream of WWTP and stream water and sediments upstream of the WWTP discharge point. Archaea, especially Methanosarcina, Methanothrix, and Methanoregula, formed a substantial proportion of the microbial community of WWTP effluent as well as receiving stream water and sediment, and were linked to the spread of ARGs. Opportunistic environmental-origin pathogens were predominant in WWTP effluent and receiving stream bacterial communities, with Citrobacter freundii proportion being especially elevated in the close vicinity downstream of the WWTP discharge point.
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94
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The Fennoscandian Shield deep terrestrial virosphere suggests slow motion 'boom and burst' cycles. Commun Biol 2021; 4:307. [PMID: 33686191 PMCID: PMC7940616 DOI: 10.1038/s42003-021-01810-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Accepted: 02/08/2021] [Indexed: 12/22/2022] Open
Abstract
The deep biosphere contains members from all three domains of life along with viruses. Here we investigate the deep terrestrial virosphere by sequencing community nucleic acids from three groundwaters of contrasting chemistries, origins, and ages. These viromes constitute a highly unique community compared to other environmental viromes and sequenced viral isolates. Viral host prediction suggests that many of the viruses are associated with Firmicutes and Patescibacteria, a superphylum lacking previously described active viruses. RNA transcript-based activity implies viral predation in the shallower marine water-fed groundwater, while the deeper and more oligotrophic waters appear to be in ‘metabolic standby’. Viral encoded antibiotic production and resistance systems suggest competition and antagonistic interactions. The data demonstrate a viral community with a wide range of predicted hosts that mediates nutrient recycling to support a higher microbial turnover than previously anticipated. This suggests the presence of ‘kill-the-winner’ oscillations creating slow motion ‘boom and burst’ cycles. Karin Holmfeldt et al. sequence metagenomes and metatranscriptomes of viruses in deep groundwaters down to 448 m below the surface. The results reveal ecological dynamics of viruses including slow motion ‘boom and burst’ cycles and a ‘kill the winner’ model potentially driven by viral predation.
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95
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Cissell EC, McCoy SJ. Shotgun metagenomic sequencing reveals the full taxonomic, trophic, and functional diversity of a coral reef benthic cyanobacterial mat from Bonaire, Caribbean Netherlands. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 755:142719. [PMID: 33077235 DOI: 10.1016/j.scitotenv.2020.142719] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/25/2020] [Revised: 09/25/2020] [Accepted: 09/26/2020] [Indexed: 06/11/2023]
Abstract
Anthropogenic forcing is spurring cyanobacterial proliferation in aquatic ecosystems worldwide. While planktonic cyanobacterial blooms have received substantial research attention, benthic blooms of mat-forming cyanobacteria have received considerably less attention, especially benthic mat blooms on coral reefs. Resultingly, numerous aspects of coral reef benthic cyanobacterial bloom ecology remain unknown, including underlying biodiversity in the mat communities. Most previous characterizations of coral reef cyanobacterial mat composition have only considered the cyanobacterial component. Without an unbiased characterization of full community diversity, we cannot predict whole-community response to anthropogenic inputs or effectively determine appropriate mitigation strategies. Here, we advocate for the implementation of shotgun sequencing techniques to study coral reef cyanobacterial mats worldwide, utilizing a case study of a coral reef benthic cyanobacterial mat sampled from the island of Bonaire, Caribbean Netherlands. Read-based taxonomic profiling revealed that Cyanobacteria was present at only 47.57% relative abundance in a coral reef cyanobacterial mat, with non-cyanobacterial members of the sampled mat community, including diatoms (0.78%), fungi (0.25%), Archaea (0.34%), viruses (0.08%), and other bacteria (45.78%), co-dominating the community. We found numerous gene families for regulatory systems and for functional pathways (both aerobic and anaerobic). These gene families were involved in community coordination; photosynthesis; nutrient scavenging; and the cycling of sulfur, nitrogen, phosphorous, and iron. We also report bacteriophage (including prophage) sequences associated with this subtidal coral reef cyanobacterial mat, which could contribute to intra-mat nutrient cycling and bloom dynamics. Overall, our results suggest that Cyanobacteria-focused analysis of coral reef cyanobacterial mats underestimates mat diversity and fails to capture community members possessing broad metabolic potential for intra-mat nutrient scavenging, recycling, and retention that likely contribute to the contemporary success of cyanobacterial mats on reefs. We advocate for increased collaboration between microbiologists and coral reef ecologists to unite insights from each discipline and improve efforts to understand mat ecology.
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Affiliation(s)
- Ethan C Cissell
- Department of Biological Science, Florida State University, Tallahassee, FL, USA.
| | - Sophie J McCoy
- Department of Biological Science, Florida State University, Tallahassee, FL, USA
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96
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Matsuura N, Masakke Y, Karthikeyan S, Kanazawa S, Honda R, Yamamoto-Ikemoto R, Konstantinidis KT. Metagenomic insights into the effect of sulfate on enhanced biological phosphorus removal. Appl Microbiol Biotechnol 2021; 105:2181-2193. [PMID: 33555362 DOI: 10.1007/s00253-021-11113-4] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Revised: 12/25/2020] [Accepted: 01/12/2021] [Indexed: 11/30/2022]
Abstract
Excess phosphorus in water supplies causes eutrophication, which degrades water quality. Hence, the efficient removal of phosphorus from wastewater represents a highly desirable process. Here, we evaluated the effect of sulfate concentration on enhanced biological phosphorus removal (EBPR), in which phosphorus is typically removed under anaerobic-oxic cycles, with sulfate reduction the predominant process in the anaerobic phase. Two sequencing batch EBPR reactors operated under high- (SBR-H) vs. low-sulfate (SBR-L) concentrations for 189 days and under three periods, i.e., start-up, sufficient acetate, and limited acetate. Under acetate-rich conditions, phosphorus removal efficiency was > 90% for both reactors; however, under acetate-limited conditions, only 34% and 91.3% of the phosphorus were removed for the SBR-L and the SBR-H, respectively. Metagenomic sequencing of the reactors showed that the relative abundance of the polyphosphate-accumulating and sulfur-reducing bacteria (SRB) was higher in the SBR-H, consistent with its higher phosphorus removal activity. Ten high-quality metagenome-assembled genomes, including one closely related to the genus Thiothrix disciformis (99.81% average amino acid identity), were recovered and predicted to simultaneously metabolize phosphorus and sulfur by the presence of phosphorus (ppk, ppx, pst, and pit) and sulfur (sul, sox, dsr, sqr, apr, cys, and sat) metabolism marker genes. The omics-based analysis provided a holistic view of the microbial ecosystem in the EBPR process and revealed that SRB and Thiothrix play key roles in the presence of high sulfate.Key points• We observed high phosphorus-removal efficiency in high-sulfate EBPR.• Metagenome-based analysis revealed sulfate-related metabolic mechanisms in EBPR.• SRB and PAOs showed interrelationships in the EBPR-sulfur systems.
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Affiliation(s)
- Norihisa Matsuura
- Faculty of Geosciences and Civil Engineering, Kanazawa University, Kanazawa, Ishikawa, Japan.
| | - Yalkhin Masakke
- Graduate School of Natural Science and Technology, Kanazawa University, Kanazawa, Ishikawa, Japan
| | - Smruthi Karthikeyan
- School of Civil and Environmental Engineering, Georgia Institute of Technology, Atlanta, GA, USA
| | - Sui Kanazawa
- Graduate School of Natural Science and Technology, Kanazawa University, Kanazawa, Ishikawa, Japan
| | - Ryo Honda
- Faculty of Geosciences and Civil Engineering, Kanazawa University, Kanazawa, Ishikawa, Japan
| | - Ryoko Yamamoto-Ikemoto
- Faculty of Geosciences and Civil Engineering, Kanazawa University, Kanazawa, Ishikawa, Japan
| | - Konstantinos T Konstantinidis
- School of Civil and Environmental Engineering, Georgia Institute of Technology, Atlanta, GA, USA.,School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA
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97
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Blaustein RA, Michelitsch LM, Glawe AJ, Lee H, Huttelmaier S, Hellgeth N, Ben Maamar S, Hartmann EM. Toothbrush microbiomes feature a meeting ground for human oral and environmental microbiota. MICROBIOME 2021; 9:32. [PMID: 33517907 PMCID: PMC7849112 DOI: 10.1186/s40168-020-00983-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Accepted: 12/16/2020] [Indexed: 05/10/2023]
Abstract
BACKGROUND While indoor microbiomes impact our health and well-being, much remains unknown about taxonomic and functional transitions that occur in human-derived microbial communities once they are transferred away from human hosts. Toothbrushes are a model to investigate the potential response of oral-derived microbiota to conditions of the built environment. Here, we characterize metagenomes of toothbrushes from 34 subjects to define the toothbrush microbiome and resistome and possible influential factors. RESULTS Toothbrush microbiomes often comprised a dominant subset of human oral taxa and less abundant or site-specific environmental strains. Although toothbrushes contained lower taxonomic diversity than oral-associated counterparts (determined by comparison with the Human Microbiome Project), they had relatively broader antimicrobial resistance gene (ARG) profiles. Toothbrush resistomes were enriched with a variety of ARGs, notably those conferring multidrug efflux and putative resistance to triclosan, which were primarily attributable to versatile environmental taxa. Toothbrush microbial communities and resistomes correlated with a variety of factors linked to personal health, dental hygiene, and bathroom features. CONCLUSIONS Selective pressures in the built environment may shape the dynamic mixture of human (primarily oral-associated) and environmental microbiota that encounter each other on toothbrushes. Harboring a microbial diversity and resistome distinct from human-associated counterparts suggests toothbrushes could potentially serve as a reservoir that may enable the transfer of ARGs. Video abstract.
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Affiliation(s)
- Ryan A. Blaustein
- Department of Civil and Environmental Engineering, Northwestern University, Evanston, IL USA
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD USA
| | | | - Adam J. Glawe
- Department of Civil and Environmental Engineering, Northwestern University, Evanston, IL USA
| | - Hansung Lee
- Department of Civil and Environmental Engineering, Northwestern University, Evanston, IL USA
| | - Stefanie Huttelmaier
- Department of Civil and Environmental Engineering, Northwestern University, Evanston, IL USA
| | - Nancy Hellgeth
- Department of Civil and Environmental Engineering, Northwestern University, Evanston, IL USA
| | - Sarah Ben Maamar
- Department of Civil and Environmental Engineering, Northwestern University, Evanston, IL USA
| | - Erica M. Hartmann
- Department of Civil and Environmental Engineering, Northwestern University, Evanston, IL USA
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98
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Meier DV, Imminger S, Gillor O, Woebken D. Distribution of Mixotrophy and Desiccation Survival Mechanisms across Microbial Genomes in an Arid Biological Soil Crust Community. mSystems 2021; 6:e00786-20. [PMID: 33436509 PMCID: PMC7901476 DOI: 10.1128/msystems.00786-20] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Accepted: 12/08/2020] [Indexed: 02/06/2023] Open
Abstract
Desert surface soils devoid of plant cover are populated by a variety of microorganisms, many with yet unresolved physiologies and lifestyles. Nevertheless, a common feature vital for these microorganisms inhabiting arid soils is their ability to survive long drought periods and reactivate rapidly in rare incidents of rain. Chemolithotrophic processes such as oxidation of atmospheric hydrogen and carbon monoxide are suggested to be a widespread energy source to support dormancy and resuscitation in desert soil microorganisms. Here, we assessed the distribution of chemolithotrophic, phototrophic, and desiccation-related metabolic potential among microbial populations in arid biological soil crusts (BSCs) from the Negev Desert, Israel, via population-resolved metagenomic analysis. While the potential to utilize light and atmospheric hydrogen as additional energy sources was widespread, carbon monoxide oxidation was less common than expected. The ability to utilize continuously available energy sources might decrease the dependency of mixotrophic populations on organic storage compounds and carbon provided by the BSC-founding cyanobacteria. Several populations from five different phyla besides the cyanobacteria encoded CO2 fixation potential, indicating further potential independence from photoautotrophs. However, we also found population genomes with a strictly heterotrophic genetic repertoire. The highly abundant Rubrobacteraceae (Actinobacteriota) genomes showed particular specialization for this extreme habitat, different from their closest cultured relatives. Besides the ability to use light and hydrogen as energy sources, they encoded extensive O2 stress protection and unique DNA repair potential. The uncovered differences in metabolic potential between individual, co-occurring microbial populations enable predictions of their ecological niches and generation of hypotheses on the dynamics and interactions among them.IMPORTANCE This study represents a comprehensive community-wide genome-centered metagenome analysis of biological soil crust (BSC) communities in arid environments, providing insights into the distribution of genes encoding different energy generation mechanisms, as well as survival strategies, among populations in an arid soil ecosystem. It reveals the metabolic potential of several uncultured and previously unsequenced microbial genera, families, and orders, as well as differences in the metabolic potential between the most abundant BSC populations and their cultured relatives, highlighting once more the danger of inferring function on the basis of taxonomy. Assigning functional potential to individual populations allows for the generation of hypotheses on trophic interactions and activity patterns in arid soil microbial communities and represents the basis for future resuscitation and activity studies of the system, e.g., involving metatranscriptomics.
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Affiliation(s)
- Dimitri V Meier
- Division of Microbial Ecology, Department of Microbiology and Ecosystem Science, Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
| | - Stefanie Imminger
- Division of Microbial Ecology, Department of Microbiology and Ecosystem Science, Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
| | - Osnat Gillor
- Zuckerberg Institute for Water Research, Blaustein Institutes for Desert Research, Ben Gurion University of the Negev, Sde Boker, Israel
| | - Dagmar Woebken
- Division of Microbial Ecology, Department of Microbiology and Ecosystem Science, Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
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99
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Yu J, Pavia MJ, Deem LM, Crow SE, Deenik JL, Penton CR. DNA-Stable Isotope Probing Shotgun Metagenomics Reveals the Resilience of Active Microbial Communities to Biochar Amendment in Oxisol Soil. Front Microbiol 2020; 11:587972. [PMID: 33329461 PMCID: PMC7717982 DOI: 10.3389/fmicb.2020.587972] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Accepted: 10/08/2020] [Indexed: 12/03/2022] Open
Abstract
The functions and interactions of individual microbial populations and their genes in agricultural soils amended with biochar remain elusive but are crucial for a deeper understanding of nutrient cycling and carbon (C) sequestration. In this study, we coupled DNA stable isotope probing (SIP) with shotgun metagenomics in order to target the active community in microcosms which contained soil collected from biochar-amended and control plots under napiergrass cultivation. Our analyses revealed that the active community was composed of high-abundant and low-abundant populations, including Actinobacteria, Proteobacteria, Gemmatimonadetes, and Acidobacteria. Although biochar did not significantly shift the active taxonomic and functional communities, we found that the narG (nitrate reductase) gene was significantly more abundant in the control metagenomes. Interestingly, putative denitrifier genomes generally encoded one gene or a partial denitrification pathway, suggesting denitrification is typically carried out by an assembly of different populations within this Oxisol soil. Altogether, these findings indicate that the impact of biochar on the active soil microbial community are transient in nature. As such, the addition of biochar to soils appears to be a promising strategy for the long-term C sequestration in agricultural soils, does not impart lasting effects on the microbial functional community, and thus mitigates un-intended microbial community shifts that may lead to fertilizer loss through increased N cycling.
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Affiliation(s)
- Julian Yu
- School of Life Sciences, Arizona State University, Tempe, AZ, United States.,Center for Fundamental and Applied Microbiomics, The Biodesign Institute, Arizona State University, Tempe, AZ, United States
| | - Michael J Pavia
- School of Life Sciences, Arizona State University, Tempe, AZ, United States.,Center for Fundamental and Applied Microbiomics, The Biodesign Institute, Arizona State University, Tempe, AZ, United States.,Swette Center for Environmental Biotechnology, The Biodesign Institute, Arizona State University, Tempe, AZ, United States
| | - Lauren M Deem
- Natural Resources and Environmental Management, University of Hawai'i at Mânoa, Honolulu, HI, United States
| | - Susan E Crow
- Natural Resources and Environmental Management, University of Hawai'i at Mânoa, Honolulu, HI, United States
| | - Jonathan L Deenik
- Tropical Plant and Soil Sciences, University of Hawai'i at Mânoa, Honolulu, HI, United States
| | - Christopher Ryan Penton
- Center for Fundamental and Applied Microbiomics, The Biodesign Institute, Arizona State University, Tempe, AZ, United States.,College of Integrative Sciences and Arts, Arizona State University, Mesa, AZ, United States
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100
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Patin NV, Peña-Gonzalez A, Hatt JK, Moe C, Kirby A, Konstantinidis KT. The Role of the Gut Microbiome in Resisting Norovirus Infection as Revealed by a Human Challenge Study. mBio 2020; 11:e02634-20. [PMID: 33203758 PMCID: PMC7683401 DOI: 10.1128/mbio.02634-20] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2020] [Accepted: 10/16/2020] [Indexed: 12/11/2022] Open
Abstract
Norovirus infections take a heavy toll on worldwide public health. While progress has been made toward understanding host responses to infection, the role of the gut microbiome in determining infection outcome is unknown. Moreover, data are lacking on the nature and duration of the microbiome response to norovirus infection, which has important implications for diagnostics and host recovery. Here, we characterized the gut microbiomes of subjects enrolled in a norovirus challenge study. We analyzed microbiome features of asymptomatic and symptomatic individuals at the genome (population) and gene levels and assessed their response over time in symptomatic individuals. We show that the preinfection microbiomes of subjects with asymptomatic infections were enriched in Bacteroidetes and depleted in Clostridia relative to the microbiomes of symptomatic subjects. These compositional differences were accompanied by differences in genes involved in the metabolism of glycans and sphingolipids that may aid in host resilience to infection. We further show that microbiomes shifted in composition following infection and that recovery times were variable among human hosts. In particular, Firmicutes increased immediately following the challenge, while Bacteroidetes and Proteobacteria decreased over the same time. Genes enriched in the microbiomes of symptomatic subjects, including the adenylyltransferase glgC, were linked to glycan metabolism and cell-cell signaling, suggesting as-yet unknown roles for these processes in determining infection outcome. These results provide important context for understanding the gut microbiome role in host susceptibility to symptomatic norovirus infection and long-term health outcomes.IMPORTANCE The role of the human gut microbiome in determining whether an individual infected with norovirus will be symptomatic is poorly understood. This study provides important data on microbes that distinguish asymptomatic from symptomatic microbiomes and links these features to infection responses in a human challenge study. The results have implications for understanding resistance to and treatment of norovirus infections.
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Affiliation(s)
- N V Patin
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - A Peña-Gonzalez
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia, USA
- Max Planck Tandem Group in Computational Biology, Department of Biological Sciences, Universidad de los Andes, Bogotá, Colombia
| | - J K Hatt
- School of Civil and Environmental Engineering, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - C Moe
- Rollins School of Public Health, Emory University, Atlanta, Georgia, USA
| | - A Kirby
- Waterborne Disease Prevention Branch, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - K T Konstantinidis
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia, USA
- School of Civil and Environmental Engineering, Georgia Institute of Technology, Atlanta, Georgia, USA
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