151
|
Draft Genome Sequence of Streptomyces albidoflavus 09MW18-IS, Cultivated from the Atlantic Ocean off the Coast of Virginia. Microbiol Resour Announc 2022; 11:e0087221. [PMID: 34989605 PMCID: PMC8759398 DOI: 10.1128/mra.00872-21] [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] [Indexed: 11/20/2022] Open
Abstract
We report a draft genome sequence for Streptomyces albidoflavus strain 09MW18-IS, isolated from the Atlantic slope off the coast of Virginia. The whole-genome sequence will provide novel insights into biosynthetic gene clusters and ecological adaptation in an oligotrophic environment.
Collapse
|
152
|
Muñoz-Gómez SA, Susko E, Williamson K, Eme L, Slamovits CH, Moreira D, López-García P, Roger AJ. Site-and-branch-heterogeneous analyses of an expanded dataset favour mitochondria as sister to known Alphaproteobacteria. Nat Ecol Evol 2022; 6:253-262. [PMID: 35027725 DOI: 10.1038/s41559-021-01638-2] [Citation(s) in RCA: 34] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Accepted: 11/29/2021] [Indexed: 01/01/2023]
Abstract
Determining the phylogenetic origin of mitochondria is key to understanding the ancestral mitochondrial symbiosis and its role in eukaryogenesis. However, the precise evolutionary relationship between mitochondria and their closest bacterial relatives remains hotly debated. The reasons include pervasive phylogenetic artefacts as well as limited protein and taxon sampling. Here we developed a new model of protein evolution that accommodates both across-site and across-branch compositional heterogeneity. We applied this site-and-branch-heterogeneous model (MAM60 + GFmix) to a considerably expanded dataset that comprises 108 mitochondrial proteins of alphaproteobacterial origin, and novel metagenome-assembled genomes from microbial mats, microbialites and sediments. The MAM60 + GFmix model fits the data much better and agrees with analyses of compositionally homogenized datasets with conventional site-heterogenous models. The consilience of evidence thus suggests that mitochondria are sister to the Alphaproteobacteria to the exclusion of MarineProteo1 and Magnetococcia. We also show that the ancestral presence of the crista-developing mitochondrial contact site and cristae organizing system (a mitofilin-domain-containing Mic60 protein) in mitochondria and the Alphaproteobacteria only supports their close relationship.
Collapse
Affiliation(s)
- Sergio A Muñoz-Gómez
- Ecologie Systématique Evolution, CNRS, Université Paris-Saclay, AgroParisTech, Orsay, France.
| | - Edward Susko
- Department of Mathematics and Statistics, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Kelsey Williamson
- Centre for Comparative Genomics and Evolutionary Bioinformatics, Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Laura Eme
- Ecologie Systématique Evolution, CNRS, Université Paris-Saclay, AgroParisTech, Orsay, France
| | - Claudio H Slamovits
- Centre for Comparative Genomics and Evolutionary Bioinformatics, Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Nova Scotia, Canada
| | - David Moreira
- Ecologie Systématique Evolution, CNRS, Université Paris-Saclay, AgroParisTech, Orsay, France
| | | | - Andrew J Roger
- Centre for Comparative Genomics and Evolutionary Bioinformatics, Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Nova Scotia, Canada.
| |
Collapse
|
153
|
Abstract
Sialic acids are present in humans and other metazoans, playing essential roles in physiological and pathological processes. Commensal and pathogenic bacteria have evolved the capacity to utilize sialic acids as nutrient and energy sources. However, in some actinobacteria, sialic acid catabolism (SAC) is associated with free-living populations. To unravel the distribution and evolutionary history of SAC in the phylum Actinobacteria, we analyzed the presence and diversity of the putative SAC gene cluster (nan) in 7,180 high-quality, nonredundant actinobacterial genomes that covered 1,969 species. The results showed that ∼13% of actinobacterial species had the potential to utilize sialic acids, with 45 species capable of anhydro-SAC, all except two of them through the canonical pathway. These species belonged to 20 orders and 81 genera, with ∼36% of them from four genera, Actinomyces, Bifidobacterium, Corynebacterium, and Streptomyces. Moreover, ∼40% of the nan-positive species are free living. Phylogenetic analysis of the key nan genes, nanA, nanK, and nanE, revealed a strong signal of horizontal gene transfer (HGT), accompanied with vertical inheritance and gene loss. This evolutionary pattern led to high diversity and differential distribution of nan among actinobacterial taxa and might cause the cluster to spread to some free-living species while losing in some host-associated species. The evolution of SAC in actinobacteria probably represents the evolution of certain kinds of noncore bacterial functions for environmental adaptation and lifestyle switch, in which HGT plays a dominant role. IMPORTANCE Sialic acids play essential roles in the physiology of humans and other metazoan animals, and microbial sialic acid catabolism (SAC) is one of the processes critical for pathogenesis. To date, microbial SAC is studied mainly in commensals and pathogens, while its distribution in free-living microbes and evolutionary pathway remain largely unexplored. Here, by examining all actinobacterial genomes available, we demonstrate that putative SAC is present in a small proportion of actinobacterial species, of which, however, ∼40% are free-living species. We also reveal remarkable difference in the distribution of SAC among actinobacterial taxa and high diversity of the putative SAC gene clusters. HGT plays a significant role in the evolution of SAC, accompanied with vertical inheritance and gene loss. Our results provide a comprehensive and systematic picture of the distribution and evolutionary history of SAC in actinobacteria, expanding the current knowledge on bacterial adaptation and diversification.
Collapse
|
154
|
Kandel PP, Naumova M, Fautt C, Patel RR, Triplett LR, Hockett KL. Genome Mining Shows Ubiquitous Presence and Extensive Diversity of Toxin-Antitoxin Systems in Pseudomonas syringae. Front Microbiol 2022; 12:815911. [PMID: 35095819 PMCID: PMC8790059 DOI: 10.3389/fmicb.2021.815911] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Accepted: 12/13/2021] [Indexed: 11/09/2022] Open
Abstract
Bacterial toxin-antitoxin (TA) systems consist of two or more adjacent genes, encoding a toxin and an antitoxin. TA systems are implicated in evolutionary and physiological functions including genome maintenance, antibiotics persistence, phage defense, and virulence. Eight classes of TA systems have been described, based on the mechanism of toxin neutralization by the antitoxin. Although studied well in model species of clinical significance, little is known about the TA system abundance and diversity, and their potential roles in stress tolerance and virulence of plant pathogens. In this study, we screened the genomes of 339 strains representing the genetic and lifestyle diversity of the Pseudomonas syringae species complex for TA systems. Using bioinformatic search and prediction tools, including SLING, BLAST, HMMER, TADB2.0, and T1TAdb, we show that P. syringae strains encode 26 different families of TA systems targeting diverse cellular functions. TA systems in this species are almost exclusively type II. We predicted a median of 15 TA systems per genome, and we identified six type II TA families that are found in more than 80% of strains, while others are more sporadic. The majority of predicted TA genes are chromosomally encoded. Further functional characterization of the predicted TA systems could reveal how these widely prevalent gene modules potentially impact P. syringae ecology, virulence, and disease management practices.
Collapse
Affiliation(s)
- Prem P. Kandel
- Department of Plant Pathology and Environmental Microbiology, Pennsylvania State University, University Park, PA, United States,*Correspondence: Prem P. kandel,
| | - Marina Naumova
- Department of Plant Pathology and Environmental Microbiology, Pennsylvania State University, University Park, PA, United States
| | - Chad Fautt
- Department of Plant Pathology and Environmental Microbiology, Pennsylvania State University, University Park, PA, United States
| | - Ravikumar R. Patel
- Department of Plant Pathology and Ecology, The Connecticut Agricultural Experiment Station, New Haven, CT, United States
| | - Lindsay R. Triplett
- Department of Plant Pathology and Ecology, The Connecticut Agricultural Experiment Station, New Haven, CT, United States
| | - Kevin L. Hockett
- Department of Plant Pathology and Environmental Microbiology, Pennsylvania State University, University Park, PA, United States,The Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA, United States,Kevin L. Hockett,
| |
Collapse
|
155
|
Wu WJH, Kim M, Chang LC, Assie A, Saldana-Morales FB, Zegarra-Ruiz DF, Norwood K, Samuel BS, Diehl GE. Interleukin-1β secretion induced by mucosa-associated gut commensal bacteria promotes intestinal barrier repair. Gut Microbes 2022; 14:2014772. [PMID: 34989321 PMCID: PMC8741296 DOI: 10.1080/19490976.2021.2014772] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Accepted: 11/23/2021] [Indexed: 02/04/2023] Open
Abstract
The gut microbiota is essential for maintenance and repair of the intestinal epithelial barrier. As shifts in both intestinal epithelial barrier function and microbiota composition are found in inflammatory bowel disease patients, it is critical to understand the role of distinct bacteria in regulating barrier repair. We identified a mouse commensal E. coli isolate, GDAR2-2, that protects mice from Citrobacter rodentium infection and dextran sulfate sodium-induced colitis. Colonization with GDAR2-2 in mice resulted in expansion of CX3CR1+ mononuclear phagocytes, including CX3CR1+ macrophages/dendritic cells and monocytes, along with IL-22-secreting type 3 innate lymphoid cells and improved epithelial barrier function. In vitro co-culture of macrophages with GDAR2-2 resulted in IL-1β production. In vivo, protection after GDAR2-2 colonization was lost after depletion of CX3CR1+ MNPs, or blockade of IL-1β or IL-22. We further identified human commensal E. coli isolates that similarly protect mice from C. rodentium infection through CX3CR1+ MNP and IL-1β production. Together, these findings demonstrate an unexpected role for commensal bacteria in promoting IL-1β secretion to support intestinal barrier repair.
Collapse
Affiliation(s)
- Wan-Jung H. Wu
- Immunology Graduate Program, Baylor College of Medicine, Houston, TX, USA
- Memorial Sloan Kettering Cancer Center, Immunology Program of the Sloan Kettering Institute, New York, NY, USA
| | - Myunghoo Kim
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA
- Present Address: Department of Animal Science, College of Natural Resources and Life Sciences, Pusan National University, Miryang, Korea
| | - Lin-Chun Chang
- Memorial Sloan Kettering Cancer Center, Immunology Program of the Sloan Kettering Institute, New York, NY, USA
| | - Adrien Assie
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA
| | - Fatima B. Saldana-Morales
- Memorial Sloan Kettering Cancer Center, Immunology Program of the Sloan Kettering Institute, New York, NY, USA
- Neuroscience Graduate Program, Baylor College of Medicine, Houston, TX, USA
| | - Daniel F. Zegarra-Ruiz
- Memorial Sloan Kettering Cancer Center, Immunology Program of the Sloan Kettering Institute, New York, NY, USA
| | - Kendra Norwood
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA
| | - Buck S. Samuel
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA
| | - Gretchen E. Diehl
- Memorial Sloan Kettering Cancer Center, Immunology Program of the Sloan Kettering Institute, New York, NY, USA
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA
| |
Collapse
|
156
|
Garber AI, Zehnpfennig JR, Sheik CS, Henson MW, Ramírez GA, Mahon AR, Halanych KM, Learman DR. Metagenomics of Antarctic Marine Sediment Reveals Potential for Diverse Chemolithoautotrophy. mSphere 2021; 6:e0077021. [PMID: 34817234 PMCID: PMC8612310 DOI: 10.1128/msphere.00770-21] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2021] [Accepted: 11/10/2021] [Indexed: 11/30/2022] Open
Abstract
The microbial biogeochemical processes occurring in marine sediment in Antarctica remain underexplored due to limited access. Further, these polar habitats are unique, as they are being exposed to significant changes in their climate. To explore how microbes drive biogeochemistry in these sediments, we performed a shotgun metagenomic survey of marine surficial sediment (0 to 3 cm of the seafloor) collected from 13 locations in western Antarctica and assembled 16 high-quality metagenome assembled genomes for focused interrogation of the lifestyles of some abundant lineages. We observe an abundance of genes from pathways for the utilization of reduced carbon, sulfur, and nitrogen sources. Although organotrophy is pervasive, nitrification and sulfide oxidation are the dominant lithotrophic pathways and likely fuel carbon fixation via the reverse tricarboxylic acid and Calvin cycles. Oxygen-dependent terminal oxidases are common, and genes for reduction of oxidized nitrogen are sporadically present in our samples. Our results suggest that the underlying benthic communities are well primed for the utilization of settling organic matter, which is consistent with findings from highly productive surface water. Despite the genetic potential for nitrate reduction, the net catabolic pathway in our samples remains aerobic respiration, likely coupled to the oxidation of sulfur and nitrogen imported from the highly productive Antarctic water column above. IMPORTANCE The impacts of climate change in polar regions, like Antarctica, have the potential to alter numerous ecosystems and biogeochemical cycles. Increasing temperature and freshwater runoff from melting ice can have profound impacts on the cycling of organic and inorganic nutrients between the pelagic and benthic ecosystems. Within the benthos, sediment microbial communities play a critical role in carbon mineralization and the cycles of essential nutrients like nitrogen and sulfur. Metagenomic data collected from sediment samples from the continental shelf of western Antarctica help to examine this unique system and document the metagenomic potential for lithotrophic metabolisms and the cycles of both nitrogen and sulfur, which support not only benthic microbes but also life in the pelagic zone.
Collapse
Affiliation(s)
- Arkadiy I. Garber
- Biodesign Center for Mechanisms for Evolution, Arizona State University, Tempe, Arizona, USA
| | | | - Cody S. Sheik
- Biology Department and Large Lakes Observatory, University of Minnesota Duluth, Duluth, Minnesota, USA
| | - Michael W. Henson
- Department of Biology, Central Michigan University, Mt. Pleasant, Michigan, USA
| | - Gustavo A. Ramírez
- College of Veterinary Medicine, Western University of Health Sciences, Pomona, California, USA
- Department of Marine Biology, Haifa University, Haifa, Israel
| | - Andrew R. Mahon
- Department of Biology, Central Michigan University, Mt. Pleasant, Michigan, USA
| | - Kenneth M. Halanych
- Center for Marine Science, University of North Carolina Wilmington, Wilmington, North Carolina, USA
| | - Deric R. Learman
- Department of Biology, Central Michigan University, Mt. Pleasant, Michigan, USA
| |
Collapse
|
157
|
Albuquerque P, Ribeiro I, Correia S, Mucha AP, Tamagnini P, Braga-Henriques A, Carvalho MDF, Mendes MV. Complete Genome Sequence of Two Deep-Sea Streptomyces Isolates from Madeira Archipelago and Evaluation of Their Biosynthetic Potential. Mar Drugs 2021; 19:md19110621. [PMID: 34822492 PMCID: PMC8622039 DOI: 10.3390/md19110621] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Revised: 10/28/2021] [Accepted: 10/28/2021] [Indexed: 11/22/2022] Open
Abstract
The deep-sea constitutes a true unexplored frontier and a potential source of innovative drug scaffolds. Here, we present the genome sequence of two novel marine actinobacterial strains, MA3_2.13 and S07_1.15, isolated from deep-sea samples (sediments and sponge) and collected at Madeira archipelago (NE Atlantic Ocean; Portugal). The de novo assembly of both genomes was achieved using a hybrid strategy that combines short-reads (Illumina) and long-reads (PacBio) sequencing data. Phylogenetic analyses showed that strain MA3_2.13 is a new species of the Streptomyces genus, whereas strain S07_1.15 is closely related to the type strain of Streptomyces xinghaiensis. In silico analysis revealed that the total length of predicted biosynthetic gene clusters (BGCs) accounted for a high percentage of the MA3_2.13 genome, with several potential new metabolites identified. Strain S07_1.15 had, with a few exceptions, a predicted metabolic profile similar to S. xinghaiensis. In this work, we implemented a straightforward approach for generating high-quality genomes of new bacterial isolates and analyse in silico their potential to produce novel NPs. The inclusion of these in silico dereplication steps allows to minimize the rediscovery rates of traditional natural products screening methodologies and expedite the drug discovery process.
Collapse
Affiliation(s)
- Pedro Albuquerque
- i3S—Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Rua Alfredo Allen 208, 4200-135 Porto, Portugal; (P.A.); (P.T.)
- IBMC—Instituto de Biologia Molecular e Celular, Universidade do Porto, Rua Alfredo Allen 208, 4200-135 Porto, Portugal
| | - Inês Ribeiro
- CIIMAR—Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Terminal de Cruzeiros do Porto de Leixões, Avenida General Norton de Matos s/n, 4450-208 Matosinhos, Portugal; (I.R.); (S.C.); (A.P.M.); (M.d.F.C.)
- ICBAS—Instituto de Ciências Biomédicas Abel Salazar, Universidade do Porto, Rua de Jorge Viterbo Ferreira 228, 4050-313 Porto, Portugal
| | - Sofia Correia
- CIIMAR—Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Terminal de Cruzeiros do Porto de Leixões, Avenida General Norton de Matos s/n, 4450-208 Matosinhos, Portugal; (I.R.); (S.C.); (A.P.M.); (M.d.F.C.)
| | - Ana Paula Mucha
- CIIMAR—Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Terminal de Cruzeiros do Porto de Leixões, Avenida General Norton de Matos s/n, 4450-208 Matosinhos, Portugal; (I.R.); (S.C.); (A.P.M.); (M.d.F.C.)
- Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre, Edifício FC4, 4169-007 Porto, Portugal
| | - Paula Tamagnini
- i3S—Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Rua Alfredo Allen 208, 4200-135 Porto, Portugal; (P.A.); (P.T.)
- IBMC—Instituto de Biologia Molecular e Celular, Universidade do Porto, Rua Alfredo Allen 208, 4200-135 Porto, Portugal
- Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre, Edifício FC4, 4169-007 Porto, Portugal
| | - Andreia Braga-Henriques
- OOM—Oceanic Observatory of Madeira & MARE—Marine and Environmental Sciences Centre, ARDITI—Agência Regional para o Desenvolvimento da Investigação Tecnologia e Inovação, Caminho da Penteada, 9020-105 Funchal, Portugal;
- Regional Directorate for Fisheries, Regional Secretariat for the Sea and Fisheries, Government of the Azores, Rua Cônsul Dabney—Colónia Alemã, 9900-014 Horta, Portugal
| | - Maria de Fátima Carvalho
- CIIMAR—Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Terminal de Cruzeiros do Porto de Leixões, Avenida General Norton de Matos s/n, 4450-208 Matosinhos, Portugal; (I.R.); (S.C.); (A.P.M.); (M.d.F.C.)
- ICBAS—Instituto de Ciências Biomédicas Abel Salazar, Universidade do Porto, Rua de Jorge Viterbo Ferreira 228, 4050-313 Porto, Portugal
| | - Marta V. Mendes
- i3S—Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Rua Alfredo Allen 208, 4200-135 Porto, Portugal; (P.A.); (P.T.)
- IBMC—Instituto de Biologia Molecular e Celular, Universidade do Porto, Rua Alfredo Allen 208, 4200-135 Porto, Portugal
- Correspondence:
| |
Collapse
|
158
|
Saeedi A, Cummings NJ, McLean D, Connerton IF, Connerton PL. Venatorbacter cucullus gen. nov sp. nov a novel bacterial predator. Sci Rep 2021; 11:21393. [PMID: 34725408 PMCID: PMC8560859 DOI: 10.1038/s41598-021-00865-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Accepted: 10/13/2021] [Indexed: 11/09/2022] Open
Abstract
A novel Gram-stain negative, aerobic, halotolerant, motile, rod-shaped, predatory bacterium ASxL5T, was isolated from a bovine slurry tank in Nottinghamshire, UK using Campylobacter hyointestinalis as prey. Other Campylobacter species and members of the Enterobacteriaceae were subsequently found to serve as prey. Weak axenic growth on Brain Heart Infusion agar was achieved upon subculture without host cells. The optimal growth conditions were 37 °C, at pH 7. Transmission electron microscopy revealed some highly unusual morphological characteristics related to prey availability. Phylogenetic analyses using 16S rRNA gene sequences showed that the isolate was related to members of the Oceanospirillaceae family but could not be classified clearly as a member of any known genus. Whole genome sequencing of ASxL5T confirmed the relationship to members the Oceanospirillaceae. Database searches revealed that several ASxL5T share 16S rRNA gene sequences with several uncultured bacteria from marine, and terrestrial surface and subsurface water. We propose that strain ASxL5T represents a novel species in a new genus. We propose the name Venatorbacter cucullus gen. nov., sp. nov. with ASxL5T as the type strain.
Collapse
Affiliation(s)
- Ahmed Saeedi
- grid.4563.40000 0004 1936 8868Division of Microbiology, Brewing and Biotechnology, School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, LE12 5RD UK
| | - Nicola J. Cummings
- grid.4563.40000 0004 1936 8868Division of Microbiology, Brewing and Biotechnology, School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, LE12 5RD UK
| | - Denise McLean
- grid.4563.40000 0004 1936 8868Nanoscale and Microscale Research Centre, University of Nottingham, Nottingham, NG7 2RD UK
| | - Ian F. Connerton
- grid.4563.40000 0004 1936 8868Division of Microbiology, Brewing and Biotechnology, School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, LE12 5RD UK
| | - Phillippa L. Connerton
- grid.4563.40000 0004 1936 8868Division of Microbiology, Brewing and Biotechnology, School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, LE12 5RD UK
| |
Collapse
|
159
|
Vázquez-Campos X, Kinsela AS, Bligh MW, Payne TE, Wilkins MR, Waite TD. Genomic Insights Into the Archaea Inhabiting an Australian Radioactive Legacy Site. Front Microbiol 2021; 12:732575. [PMID: 34737728 PMCID: PMC8561730 DOI: 10.3389/fmicb.2021.732575] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Accepted: 09/21/2021] [Indexed: 11/29/2022] Open
Abstract
During the 1960s, small quantities of radioactive materials were co-disposed with chemical waste at the Little Forest Legacy Site (LFLS, Sydney, Australia). The microbial function and population dynamics in a waste trench during a rainfall event have been previously investigated revealing a broad abundance of candidate and potentially undescribed taxa in this iron-rich, radionuclide-contaminated environment. Applying genome-based metagenomic methods, we recovered 37 refined archaeal MAGs, mainly from undescribed DPANN Archaea lineages without standing in nomenclature and 'Candidatus Methanoperedenaceae' (ANME-2D). Within the undescribed DPANN, the newly proposed orders 'Ca. Gugararchaeales', 'Ca. Burarchaeales' and 'Ca. Anstonellales', constitute distinct lineages with a more comprehensive central metabolism and anabolic capabilities within the 'Ca. Micrarchaeota' phylum compared to most other DPANN. The analysis of new and extant 'Ca. Methanoperedens spp.' MAGs suggests metal ions as the ancestral electron acceptors during the anaerobic oxidation of methane while the respiration of nitrate/nitrite via molybdopterin oxidoreductases would have been a secondary acquisition. The presence of genes for the biosynthesis of polyhydroxyalkanoates in most 'Ca. Methanoperedens' also appears to be a widespread characteristic of the genus for carbon accumulation. This work expands our knowledge about the roles of the Archaea at the LFLS, especially, DPANN Archaea and 'Ca. Methanoperedens', while exploring their diversity, uniqueness, potential role in elemental cycling, and evolutionary history.
Collapse
Affiliation(s)
- Xabier Vázquez-Campos
- NSW Systems Biology Initiative, School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Sydney, NSW, Australia
| | - Andrew S. Kinsela
- UNSW Water Research Centre, School of Civil and Environmental Engineering, The University of New South Wales, Sydney, NSW, Australia
| | - Mark W. Bligh
- UNSW Water Research Centre, School of Civil and Environmental Engineering, The University of New South Wales, Sydney, NSW, Australia
| | - Timothy E. Payne
- Environmental Research Theme, Australian Nuclear Science and Technology Organisation, Kirrawee DC, NSW, Australia
| | - Marc R. Wilkins
- NSW Systems Biology Initiative, School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Sydney, NSW, Australia
| | - T. David Waite
- UNSW Water Research Centre, School of Civil and Environmental Engineering, The University of New South Wales, Sydney, NSW, Australia
| |
Collapse
|
160
|
McDaniel EA, Wahl SA, Ishii S, Pinto A, Ziels R, Nielsen PH, McMahon KD, Williams RBH. Prospects for multi-omics in the microbial ecology of water engineering. WATER RESEARCH 2021; 205:117608. [PMID: 34555741 DOI: 10.1016/j.watres.2021.117608] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2021] [Revised: 08/20/2021] [Accepted: 08/23/2021] [Indexed: 06/13/2023]
Abstract
Advances in high-throughput sequencing technologies and bioinformatics approaches over almost the last three decades have substantially increased our ability to explore microorganisms and their functions - including those that have yet to be cultivated in pure isolation. Genome-resolved metagenomic approaches have enabled linking powerful functional predictions to specific taxonomical groups with increasing fidelity. Additionally, related developments in both whole community gene expression surveys and metabolite profiling have permitted for direct surveys of community-scale functions in specific environmental settings. These advances have allowed for a shift in microbiome science away from descriptive studies and towards mechanistic and predictive frameworks for designing and harnessing microbial communities for desired beneficial outcomes. Water engineers, microbiologists, and microbial ecologists studying activated sludge, anaerobic digestion, and drinking water distribution systems have applied various (meta)omics techniques for connecting microbial community dynamics and physiologies to overall process parameters and system performance. However, the rapid pace at which new omics-based approaches are developed can appear daunting to those looking to apply these state-of-the-art practices for the first time. Here, we review how modern genome-resolved metagenomic approaches have been applied to a variety of water engineering applications from lab-scale bioreactors to full-scale systems. We describe integrated omics analysis across engineered water systems and the foundations for pairing these insights with modeling approaches. Lastly, we summarize emerging omics-based technologies that we believe will be powerful tools for water engineering applications. Overall, we provide a framework for microbial ecologists specializing in water engineering to apply cutting-edge omics approaches to their research questions to achieve novel functional insights. Successful adoption of predictive frameworks in engineered water systems could enable more economically and environmentally sustainable bioprocesses as demand for water and energy resources increases.
Collapse
Affiliation(s)
- Elizabeth A McDaniel
- Department of Bacteriology, University of Wisconsin - Madison, Madison, WI, USA.
| | | | - Shun'ichi Ishii
- Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Super-cutting-edge Grand and Advanced Research (SUGAR) Program, Institute for Extra-cutting-edge Science and Technology Avant-garde Research (X-star), Yokosuka 237-0061, Japan
| | - Ameet Pinto
- Department of Civil and Environmental Engineering, Northeastern University, Boston, MA, USA
| | - Ryan Ziels
- Department of Civil Engineering, The University of British Columbia, Vancouver, BC, Canada
| | | | - Katherine D McMahon
- Department of Bacteriology, University of Wisconsin - Madison, Madison, WI, USA; Department of Civil and Environmental Engineering, University of Wisconsin - Madison, Madison, WI, USA
| | - Rohan B H Williams
- Singapore Centre for Environmental Life Sciences Engineering, National University of Singapore, Republic of Singapore.
| |
Collapse
|
161
|
Zvi-Kedem T, Shemesh E, Tchernov D, Rubin-Blum M. The worm affair: fidelity and environmental adaptation in symbiont species that co-occur in vestimentiferan tubeworms. ENVIRONMENTAL MICROBIOLOGY REPORTS 2021; 13:744-752. [PMID: 34374209 DOI: 10.1111/1758-2229.12994] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Revised: 06/20/2021] [Accepted: 07/19/2021] [Indexed: 06/13/2023]
Abstract
The symbioses between the vestimentiferan tubeworms and their chemosynthetic partners (Gammaproteobacteria, Chromatiales and Sedimenticolaceae) hallmark the success of these organisms in hydrothermal vent and hydrocarbon seep deep-sea habitats. The fidelity of these associations varies, as both the hosts and the symbionts can be loose in partner choice. Some tubeworms may host distinct symbiont phylotypes, which often co-occur in a single host individual. To better understand the genetic basis for the promiscuity of tubeworm symbioses, we assembled and investigated metagenome-assembled genomes of two symbiont phylotypes (species, based on the average nucleotide identity < 95%) in Lamellibrachia anaximandri, a vestimentiferan endemic to the Mediterranean Sea, in individuals collected from Palinuro hydrothermal vents (Italy) and hydrocarbon seeps (Eratosthenes seamount and Palmahim disturbance). Using comparative genomics, we show that mainly mobilome and genes involved in defence mechanisms distinguish the symbiont genotypes. While many central metabolic functions are conserved in the tubeworm symbionts, nitrate respiration (Nar, Nap and Nas proteins) is modular, yet this modularity is not linked to phylotype, but rather to geographic location, potentially implying adaptation to the local environment. Our results hint that variation in a single moonlighting protein may be responsible for the fidelity of these symbioses.
Collapse
Affiliation(s)
- Tal Zvi-Kedem
- Morris Kahn Marine Research Station, Department of Marine Biology, Leon H. Charney School of Marine Sciences, University of Haifa, Haifa, 3498838, Israel
| | - Eli Shemesh
- Morris Kahn Marine Research Station, Department of Marine Biology, Leon H. Charney School of Marine Sciences, University of Haifa, Haifa, 3498838, Israel
| | - Dan Tchernov
- Morris Kahn Marine Research Station, Department of Marine Biology, Leon H. Charney School of Marine Sciences, University of Haifa, Haifa, 3498838, Israel
| | - Maxim Rubin-Blum
- Israel Oceanographic and Limnological Research, Haifa, 3108000, Israel
| |
Collapse
|
162
|
Mishra A, Gupta J, Kumari T, Pal R, Thakur IS. Unravelling the attributes of novel cyanobacteria Jacksonvillea sp. ISTCYN1 by draft genome sequencing. BIORESOURCE TECHNOLOGY 2021; 337:125473. [PMID: 34320753 DOI: 10.1016/j.biortech.2021.125473] [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: 05/16/2021] [Revised: 06/22/2021] [Accepted: 06/24/2021] [Indexed: 06/13/2023]
Abstract
Filamentous cyanobacteria, Jacksonvillea sp. ISTCYN1 was isolated from agriculture field and cultured in BG-11 medium. This study, report the genome sequence of cyanobacteria Jacksonvillea thatto the best of our knowledgeis the firstgenome sequenceof thisgenus. The 5.7 MB draft genome sequence of this cyanobacterium contains 5134 protein-coding genes. The phylogenetic tree was constructed based on genome and Desertifilum sp. IPPAS B-1220 validated the closest relationship with Jacksonvillea sp. ISTCYN1. The growth of strain ISTCYN1 has been reported in the presence of different types of plastic when used as a sole carbon source. SEM analysis revealed biofilm formation by cyanobacterial strain ISTCYN1 on the surface of high and low-density polyethylene and polypropylene. In the presence of these plastics, EPS production has also been reported by this strain. Whole genome sequence analysis reveals the presence of many genes involved in biofilm formation. The presence of key enzymes responsible for plastic degradation laccase, esterase, lipase, thioesterase, and peroxidase have been predicted in the genome analysis. Genome analysis also provides insight into the genes involved in biotin biosynthetic pathways. Furthermore, the presence of many selenoproteins reveals the selenium acquisition by this cyanobacterium.
Collapse
Affiliation(s)
- Arti Mishra
- Amity Institute of Microbial Technology, Amity University, Uttar Pradesh, Sector-125, Noida 201303, India
| | - Juhi Gupta
- School of Environmental Sciences, Jawaharlal Nehru University, New Delhi, Delhi 110067, India
| | - Taruna Kumari
- Department of Statistics, University of Delhi, New Delhi 110007, India
| | - Ruchita Pal
- Advanced Instrumentation Research Facility, Jawaharlal Nehru University, New Delhi 110067, India
| | - I S Thakur
- School of Environmental Sciences, Jawaharlal Nehru University, New Delhi, Delhi 110067, India.
| |
Collapse
|
163
|
Ettinger CL, Byrne FJ, Collin MA, Carter-House D, Walling LL, Atkinson PW, Redak RA, Stajich JE. Improved draft reference genome for the Glassy-winged Sharpshooter (Homalodisca vitripennis), a vector for Pierce's disease. G3-GENES GENOMES GENETICS 2021; 11:6324818. [PMID: 34568917 PMCID: PMC8496328 DOI: 10.1093/g3journal/jkab255] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Accepted: 07/09/2021] [Indexed: 11/29/2022]
Abstract
Homalodisca vitripennis (Hemiptera: Cicadellidae), known as the glassy-winged sharpshooter, is a xylem feeding leafhopper and an important agricultural pest as a vector of Xylella fastidiosa, which causes Pierce’s disease in grapes and a variety of other scorch diseases. The current H. vitripennis reference genome from the Baylor College of Medicine's i5k pilot project is a 1.4-Gb assembly with 110,000 scaffolds, which still has significant gaps making identification of genes difficult. To improve on this effort, we used a combination of Oxford Nanopore long-read sequencing technology combined with Illumina sequencing reads to generate a better assembly and first-pass annotation of the whole genome sequence of a wild-caught Californian (Tulare County) individual of H. vitripennis. The improved reference genome assembly for H. vitripennis is 1.93-Gb in length (21,254 scaffolds, N50 = 650 Mb, BUSCO completeness = 94.3%), with 33.06% of the genome masked as repetitive. In total, 108,762 gene models were predicted including 98,296 protein-coding genes and 10,466 tRNA genes. As an additional community resource, we identified 27 orthologous candidate genes of interest for future experimental work including phenotypic marker genes like white. Furthermore, as part of the assembly process, we generated four endosymbiont metagenome-assembled genomes, including a high-quality near complete 1.7-Mb Wolbachia sp. genome (1 scaffold, CheckM completeness = 99.4%). The improved genome assembly and annotation for H. vitripennis, curated set of candidate genes, and endosymbiont MAGs will be invaluable resources for future research of H. vitripennis.
Collapse
Affiliation(s)
- Cassandra L Ettinger
- Department of Microbiology and Plant Pathology, University of California, Riverside, Riverside, CA 92521, USA
| | - Frank J Byrne
- Department of Entomology, University of California, Riverside, Riverside, CA 92521, USA
| | - Matthew A Collin
- Department of Botany and Plant Sciences, University of California, Riverside, Riverside, CA 92521, USA.,Institute for Integrative Genome Biology, University of California, Riverside, Riverside, CA 92521, USA
| | - Derreck Carter-House
- Department of Microbiology and Plant Pathology, University of California, Riverside, Riverside, CA 92521, USA
| | - Linda L Walling
- Department of Botany and Plant Sciences, University of California, Riverside, Riverside, CA 92521, USA.,Institute for Integrative Genome Biology, University of California, Riverside, Riverside, CA 92521, USA
| | - Peter W Atkinson
- Department of Entomology, University of California, Riverside, Riverside, CA 92521, USA.,Institute for Integrative Genome Biology, University of California, Riverside, Riverside, CA 92521, USA
| | - Rick A Redak
- Department of Entomology, University of California, Riverside, Riverside, CA 92521, USA
| | - Jason E Stajich
- Department of Microbiology and Plant Pathology, University of California, Riverside, Riverside, CA 92521, USA.,Institute for Integrative Genome Biology, University of California, Riverside, Riverside, CA 92521, USA
| |
Collapse
|
164
|
Draft Genome Sequence of Desulfurobacterium sp. Strain AV08, a Thermophilic Chemolithoautotroph Isolated from a Deep-Sea Hydrothermal Vent. Microbiol Resour Announc 2021; 10:e0061521. [PMID: 34435861 PMCID: PMC8388535 DOI: 10.1128/mra.00615-21] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
A thermophilic chemolithoautotrophic bacterium was isolated from vent fluids at Axial Seamount, an active deep-sea volcano in the northeast Pacific Ocean. We present the draft genome sequence of Desulfurobacterium sp. strain AV08.
Collapse
|
165
|
Saati-Santamaría Z, Peral-Aranega E, Velázquez E, Rivas R, García-Fraile P. Phylogenomic Analyses of the Genus Pseudomonas Lead to the Rearrangement of Several Species and the Definition of New Genera. BIOLOGY 2021; 10:782. [PMID: 34440014 PMCID: PMC8389581 DOI: 10.3390/biology10080782] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/10/2021] [Revised: 08/03/2021] [Accepted: 08/11/2021] [Indexed: 11/17/2022]
Abstract
Pseudomonas is a large and diverse genus broadly distributed in nature. Its species play relevant roles in the biology of earth and living beings. Because of its ubiquity, the number of new species is continuously increasing although its taxonomic organization remains quite difficult to unravel. Nowadays the use of genomics is routinely employed for the analysis of bacterial systematics. In this work, we aimed to investigate the classification of species of the genus Pseudomonas on the basis of the analyses of the type strains whose genomes are currently available. Based on these analyses, we propose the creation of three new genera (Denitrificimonas gen nov. comb. nov., Neopseudomonas gen nov. comb. nov. and Parapseudomonas gen nov. comb. nov) to encompass several species currently included within the genus Pseudomonas and the reclassification of several species of this genus in already described taxa.
Collapse
Affiliation(s)
- Zaki Saati-Santamaría
- Microbiology and Genetics Department, University of Salamanca, 37007 Salamanca, Spain; (E.P.-A.); (E.V.); (R.R.); (P.G.-F.)
- Institute for Agribiotechnology Research (CIALE), 37185 Salamanca, Spain
| | - Ezequiel Peral-Aranega
- Microbiology and Genetics Department, University of Salamanca, 37007 Salamanca, Spain; (E.P.-A.); (E.V.); (R.R.); (P.G.-F.)
- Institute for Agribiotechnology Research (CIALE), 37185 Salamanca, Spain
| | - Encarna Velázquez
- Microbiology and Genetics Department, University of Salamanca, 37007 Salamanca, Spain; (E.P.-A.); (E.V.); (R.R.); (P.G.-F.)
- Institute for Agribiotechnology Research (CIALE), 37185 Salamanca, Spain
- Associated Research Unit of Plant-Microorganism Interaction, University of Salamanca-IRNASA-CSIC, 37008 Salamanca, Spain
| | - Raúl Rivas
- Microbiology and Genetics Department, University of Salamanca, 37007 Salamanca, Spain; (E.P.-A.); (E.V.); (R.R.); (P.G.-F.)
- Institute for Agribiotechnology Research (CIALE), 37185 Salamanca, Spain
- Associated Research Unit of Plant-Microorganism Interaction, University of Salamanca-IRNASA-CSIC, 37008 Salamanca, Spain
| | - Paula García-Fraile
- Microbiology and Genetics Department, University of Salamanca, 37007 Salamanca, Spain; (E.P.-A.); (E.V.); (R.R.); (P.G.-F.)
- Institute for Agribiotechnology Research (CIALE), 37185 Salamanca, Spain
- Associated Research Unit of Plant-Microorganism Interaction, University of Salamanca-IRNASA-CSIC, 37008 Salamanca, Spain
| |
Collapse
|
166
|
Haverkamp THA, Lossouarn J, Zhaxybayeva O, Lyu J, Bienvenu N, Geslin C, Nesbø CL. Newly identified proviruses in Thermotogota suggest that viruses are the vehicles on the highways of interphylum gene sharing. Environ Microbiol 2021; 23:7105-7120. [PMID: 34398506 DOI: 10.1111/1462-2920.15723] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Revised: 07/24/2021] [Accepted: 08/13/2021] [Indexed: 11/30/2022]
Abstract
Phylogenomic analyses of bacteria from the phylum Thermotogota have shown extensive lateral gene transfer with distantly related organisms, particularly with Firmicutes. One likely mechanism of such DNA transfer is viruses. However, to date, only three temperate viruses have been characterized in this phylum, all infecting bacteria from the Marinitoga genus. Here we report 17 proviruses integrated into genomes of bacteria belonging to eight Thermotogota genera and induce viral particle production from one of the proviruses. All except an incomplete provirus from Mesotoga fall into two groups based on sequence similarity, gene synteny and taxonomic classification. Proviruses of Group 1 are found in the genera Geotoga, Kosmotoga, Marinitoga, Thermosipho and Mesoaciditoga and are similar to the previously characterized Marinitoga viruses, while proviruses from Group 2 are distantly related to the Group 1 proviruses, have different genome organization and are found in Petrotoga and Defluviitoga. Genes carried by both groups are closely related to Firmicutes and Firmicutes (pro)viruses in phylogenetic analyses. Moreover, one of the groups show evidence of recent gene exchange and may be capable of infecting cells from both phyla. We hypothesize that viruses are responsible for a large portion of the observed gene flow between Firmicutes and Thermotogota.
Collapse
Affiliation(s)
- Thomas H A Haverkamp
- Centre for Ecological and Evolutionary Synthesis, Department of Biosciences, University of Oslo, Oslo, Norway
| | - Julien Lossouarn
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, Jouy-en-Josas, 78350, France
| | - Olga Zhaxybayeva
- Department of Biological Sciences, Dartmouth College, Hanover, NH, USA
| | - Jie Lyu
- Université Brest, CNRS, IFREMER, Laboratoire de Microbiologie des Environnements Extrêmes, Plouzané, F-29280, France
| | - Nadège Bienvenu
- Université Brest, CNRS, IFREMER, Laboratoire de Microbiologie des Environnements Extrêmes, Plouzané, F-29280, France
| | - Claire Geslin
- Université Brest, CNRS, IFREMER, Laboratoire de Microbiologie des Environnements Extrêmes, Plouzané, F-29280, France
| | - Camilla L Nesbø
- Department of Biological Sciences, University of Alberta, Edmonton, AB, Canada.,Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, ON, M5S 3E5, Canada
| |
Collapse
|
167
|
Garber AI, Kupper M, Laetsch DR, Weldon SR, Ladinsky MS, Bjorkman PJ, McCutcheon JP. The Evolution of Interdependence in a Four-Way Mealybug Symbiosis. Genome Biol Evol 2021; 13:evab123. [PMID: 34061185 PMCID: PMC8331144 DOI: 10.1093/gbe/evab123] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/24/2021] [Indexed: 01/03/2023] Open
Abstract
Mealybugs are insects that maintain intracellular bacterial symbionts to supplement their nutrient-poor plant sap diets. Some mealybugs have a single betaproteobacterial endosymbiont, a Candidatus Tremblaya species (hereafter Tremblaya) that alone provides the insect with its required nutrients. Other mealybugs have two nutritional endosymbionts that together provision these same nutrients, where Tremblaya has gained a gammaproteobacterial partner that resides in its cytoplasm. Previous work had established that Pseudococcus longispinus mealybugs maintain not one but two species of gammaproteobacterial endosymbionts along with Tremblaya. Preliminary genomic analyses suggested that these two gammaproteobacterial endosymbionts have large genomes with features consistent with a relatively recent origin as insect endosymbionts, but the patterns of genomic complementarity between members of the symbiosis and their relative cellular locations were unknown. Here, using long-read sequencing and various types of microscopy, we show that the two gammaproteobacterial symbionts of P. longispinus are mixed together within Tremblaya cells, and that their genomes are somewhat reduced in size compared with their closest nonendosymbiotic relatives. Both gammaproteobacterial genomes contain thousands of pseudogenes, consistent with a relatively recent shift from a free-living to an endosymbiotic lifestyle. Biosynthetic pathways of key metabolites are partitioned in complex interdependent patterns among the two gammaproteobacterial genomes, the Tremblaya genome, and horizontally acquired bacterial genes that are encoded on the mealybug nuclear genome. Although these two gammaproteobacterial endosymbionts have been acquired recently in evolutionary time, they have already evolved codependencies with each other, Tremblaya, and their insect host.
Collapse
Affiliation(s)
- Arkadiy I Garber
- Division of Biological Sciences, University of Montana, Missoula, Montana, USA
- Biodesign Center for Mechanisms of Evolution and School of Life Sciences, Arizona State University, Tempe, Arizona, USA
| | - Maria Kupper
- Division of Biological Sciences, University of Montana, Missoula, Montana, USA
- Biodesign Center for Mechanisms of Evolution and School of Life Sciences, Arizona State University, Tempe, Arizona, USA
| | - Dominik R Laetsch
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, United Kingdom
| | - Stephanie R Weldon
- Division of Biological Sciences, University of Montana, Missoula, Montana, USA
| | - Mark S Ladinsky
- Department of Biology and Biological Engineering, California Institute of Technology, Pasadena, California, USA
| | - Pamela J Bjorkman
- Department of Biology and Biological Engineering, California Institute of Technology, Pasadena, California, USA
| | - John P McCutcheon
- Division of Biological Sciences, University of Montana, Missoula, Montana, USA
- Biodesign Center for Mechanisms of Evolution and School of Life Sciences, Arizona State University, Tempe, Arizona, USA
| |
Collapse
|
168
|
Metagenomes, metatranscriptomes and microbiomes of naturally decomposing deadwood. Sci Data 2021; 8:198. [PMID: 34344895 PMCID: PMC8333335 DOI: 10.1038/s41597-021-00987-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Accepted: 07/01/2021] [Indexed: 12/22/2022] Open
Abstract
Deadwood represents significant carbon (C) stock in a temperate forests. Its decomposition and C mobilization is accomplished by decomposer microorganisms – fungi and bacteria – who also supply the foodweb of commensalist microbes. Due to the ecosystem-level importance of deadwood habitat as a C and nutrient stock with significant nitrogen fixation, the deadwood microbiome composition and function are critical to understanding the microbial processes related to its decomposition. We present a comprehensive suite of data packages obtained through environmental DNA and RNA sequencing from natural deadwood. Data provide a complex picture of the composition and function of microbiome on decomposing trunks of European beech (Fagus sylvatica L.) in a natural forest. Packages include deadwood metagenomes, metatranscriptomes, sequences of total RNA, bacterial genomes resolved from metagenomic data and the 16S rRNA gene and ITS2 metabarcoding markers to characterize the bacterial and fungal communities. This project will be of use to microbiologists, environmental biologists and biogeochemists interested in the microbial processes associated with the transformation of recalcitrant plant biomass. Measurement(s) | metagenomic data • metatranscriptomic data • microbiome • RNA-seq of total RNA | Technology Type(s) | DNA sequencing • RNA-seq of total RNA • amplicon sequencing • RNA sequencing | Factor Type(s) | time of decomposition | Sample Characteristic - Organism | Fungi • Bacteria | Sample Characteristic - Environment | wood | Sample Characteristic - Location | Narodni prirodni rezervace Zofinsky prales |
Machine-accessible metadata file describing the reported data: 10.6084/m9.figshare.14821752
Collapse
|
169
|
Johnson MD, Scott JJ, Leray M, Lucey N, Bravo LMR, Wied WL, Altieri AH. Rapid ecosystem-scale consequences of acute deoxygenation on a Caribbean coral reef. Nat Commun 2021; 12:4522. [PMID: 34312399 PMCID: PMC8313580 DOI: 10.1038/s41467-021-24777-3] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Accepted: 06/30/2021] [Indexed: 02/07/2023] Open
Abstract
Loss of oxygen in the global ocean is accelerating due to climate change and eutrophication, but how acute deoxygenation events affect tropical marine ecosystems remains poorly understood. Here we integrate analyses of coral reef benthic communities with microbial community sequencing to show how a deoxygenation event rapidly altered benthic community composition and microbial assemblages in a shallow tropical reef ecosystem. Conditions associated with the event precipitated coral bleaching and mass mortality, causing a 50% loss of live coral and a shift in the benthic community that persisted a year later. Conversely, the unique taxonomic and functional profile of hypoxia-associated microbes rapidly reverted to a normoxic assemblage one month after the event. The decoupling of ecological trajectories among these major functional groups following an acute event emphasizes the need to incorporate deoxygenation as an emerging stressor into coral reef research and management plans to combat escalating threats to reef persistence.
Collapse
Affiliation(s)
- Maggie D Johnson
- Smithsonian Tropical Research Institute, Balboa, Ancon, Republic of Panama.
- Tennenbaum Marine Observatories Network, MarineGEO, Smithsonian Institution, Edgewater, MD, USA.
- Biology Department, Woods Hole Oceanographic Institution, Woods Hole, MA, USA.
| | - Jarrod J Scott
- Smithsonian Tropical Research Institute, Balboa, Ancon, Republic of Panama
| | - Matthieu Leray
- Smithsonian Tropical Research Institute, Balboa, Ancon, Republic of Panama
| | - Noelle Lucey
- Smithsonian Tropical Research Institute, Balboa, Ancon, Republic of Panama
| | - Lucia M Rodriguez Bravo
- Smithsonian Tropical Research Institute, Balboa, Ancon, Republic of Panama
- Facultad de Ciencias Marinas, Universidad Autónoma de Baja California, Ensenada, Mexico
| | - William L Wied
- Smithsonian Tropical Research Institute, Balboa, Ancon, Republic of Panama
- Department of Biological Sciences, Center for Coastal Oceans Research, Florida International University, Miami, FL, USA
| | - Andrew H Altieri
- Smithsonian Tropical Research Institute, Balboa, Ancon, Republic of Panama
- Department of Environmental Engineering Sciences, University of Florida, Gainesville, FL, USA
| |
Collapse
|
170
|
Zajkowski T, Lee MD, Mondal SS, Carbajal A, Dec R, Brennock PD, Piast RW, Snyder JE, Bense NB, Dzwolak W, Jarosz DF, Rothschild LJ. The Hunt for Ancient Prions: Archaeal Prion-Like Domains Form Amyloid-Based Epigenetic Elements. Mol Biol Evol 2021; 38:2088-2103. [PMID: 33480998 DOI: 10.1093/molbev/msab010] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Prions, proteins that can convert between structurally and functionally distinct states and serve as non-Mendelian mechanisms of inheritance, were initially discovered and only known in eukaryotes, and consequently considered to likely be a relatively late evolutionary acquisition. However, the recent discovery of prions in bacteria and viruses has intimated a potentially more ancient evolutionary origin. Here, we provide evidence that prion-forming domains exist in the domain archaea, the last domain of life left unexplored with regard to prions. We searched for archaeal candidate prion-forming protein sequences computationally, described their taxonomic distribution and phylogeny, and analyzed their associated functional annotations. Using biophysical in vitro assays, cell-based and microscopic approaches, and dye-binding analyses, we tested select candidate prion-forming domains for prionogenic characteristics. Out of the 16 tested, eight formed amyloids, and six acted as protein-based elements of information transfer driving non-Mendelian patterns of inheritance. We also identified short peptides from our archaeal prion candidates that can form amyloid fibrils independently. Lastly, candidates that tested positively in our assays had significantly higher tyrosine and phenylalanine content than candidates that tested negatively, an observation that may help future archaeal prion predictions. Taken together, our discovery of functional prion-forming domains in archaea provides evidence that multiple archaeal proteins are capable of acting as prions-thus expanding our knowledge of this epigenetic phenomenon to the third and final domain of life and bolstering the possibility that they were present at the time of the last universal common ancestor.
Collapse
Affiliation(s)
- Tomasz Zajkowski
- Centre of New Technologies, University of Warsaw, Warsaw, Poland.,University Space Research Association, Mountain View, CA, USA.,Blue Marble Space Institute of Science, Seattle, WA, USA
| | - Michael D Lee
- Blue Marble Space Institute of Science, Seattle, WA, USA
| | - Shamba S Mondal
- Laboratory of Bioinformatics, Nencki Institute of Experimental Biology of Polish Academy of Sciences, Warsaw, Poland
| | - Amanda Carbajal
- University Space Research Association, Mountain View, CA, USA.,University of California Santa Cruz, Santa Cruz, CA, USA
| | - Robert Dec
- Faculty of Chemistry, Biological and Chemical Research Centre, University of Warsaw, Warsaw, Poland
| | | | - Radoslaw W Piast
- Faculty of Chemistry, Biological and Chemical Research Centre, University of Warsaw, Warsaw, Poland
| | | | | | - Wojciech Dzwolak
- Faculty of Chemistry, Biological and Chemical Research Centre, University of Warsaw, Warsaw, Poland
| | - Daniel F Jarosz
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA, USA.,Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA, USA
| | - Lynn J Rothschild
- Space Science and Astrobiology Division, NASA Ames Research Center, Moffett Field, CA, USA
| |
Collapse
|
171
|
Lambrecht N, Stevenson Z, Sheik CS, Pronschinske MA, Tong H, Swanner ED. " Candidatus Chlorobium masyuteum," a Novel Photoferrotrophic Green Sulfur Bacterium Enriched From a Ferruginous Meromictic Lake. Front Microbiol 2021; 12:695260. [PMID: 34305861 PMCID: PMC8302410 DOI: 10.3389/fmicb.2021.695260] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Accepted: 06/07/2021] [Indexed: 11/13/2022] Open
Abstract
Anoxygenic phototrophic bacteria can be important primary producers in some meromictic lakes. Green sulfur bacteria (GSB) have been detected in ferruginous lakes, with some evidence that they are photosynthesizing using Fe(II) as an electron donor (i.e., photoferrotrophy). However, some photoferrotrophic GSB can also utilize reduced sulfur compounds, complicating the interpretation of Fe-dependent photosynthetic primary productivity. An enrichment (BLA1) from meromictic ferruginous Brownie Lake, Minnesota, United States, contains an Fe(II)-oxidizing GSB and a metabolically flexible putative Fe(III)-reducing anaerobe. "Candidatus Chlorobium masyuteum" grows photoautotrophically with Fe(II) and possesses the putative Fe(II) oxidase-encoding cyc2 gene also known from oxygen-dependent Fe(II)-oxidizing bacteria. It lacks genes for oxidation of reduced sulfur compounds. Its genome encodes for hydrogenases and a reverse TCA cycle that may allow it to utilize H2 and acetate as electron donors, an inference supported by the abundance of this organism when the enrichment was supplied by these substrates and light. The anaerobe "Candidatus Pseudopelobacter ferreus" is in low abundance (∼1%) in BLA1 and is a putative Fe(III)-reducing bacterium from the Geobacterales ord. nov. While "Ca. C. masyuteum" is closely related to the photoferrotrophs C. ferroooxidans strain KoFox and C. phaeoferrooxidans strain KB01, it is unique at the genomic level. The main light-harvesting molecule was identified as bacteriochlorophyll c with accessory carotenoids of the chlorobactene series. BLA1 optimally oxidizes Fe(II) at a pH of 6.8, and the rate of Fe(II) oxidation was 0.63 ± 0.069 mmol day-1, comparable to other photoferrotrophic GSB cultures or enrichments. Investigation of BLA1 expands the genetic basis for phototrophic Fe(II) oxidation by GSB and highlights the role these organisms may play in Fe(II) oxidation and carbon cycling in ferruginous lakes.
Collapse
Affiliation(s)
- Nicholas Lambrecht
- Department of Geological and Atmospheric Sciences, Iowa State University, Ames, IA, United States
| | - Zackry Stevenson
- Department of Geological and Atmospheric Sciences, Iowa State University, Ames, IA, United States
| | - Cody S. Sheik
- Department of Biology, University of Minnesota Duluth, Duluth, MN, United States
- Large Lakes Observatory, University of Minnesota Duluth, Duluth, MN, United States
| | - Matthew A. Pronschinske
- Department of Geological and Atmospheric Sciences, Iowa State University, Ames, IA, United States
| | - Hui Tong
- Department of Geological and Atmospheric Sciences, Iowa State University, Ames, IA, United States
- Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Institute of Eco-environmental Science and Technology, Guangdong Academy of Sciences, Guangzhou, China
| | - Elizabeth D. Swanner
- Department of Geological and Atmospheric Sciences, Iowa State University, Ames, IA, United States
| |
Collapse
|
172
|
Draft Genome Sequence of Staphylococcus succinus Strain GN1, Isolated from a Basement Floor in Milwaukee, WI. Microbiol Resour Announc 2021; 10:e0058021. [PMID: 34236223 PMCID: PMC8265232 DOI: 10.1128/mra.00580-21] [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] [Indexed: 11/29/2022] Open
Abstract
A strain of Staphylococcus succinus was sampled from the floor of the basement of a house and isolated in an undergraduate classroom in Milwaukee, WI. Here, we report the draft genome sequence of this strain.
Collapse
|
173
|
Tláskal V, Baldrian P. Deadwood-Inhabiting Bacteria Show Adaptations to Changing Carbon and Nitrogen Availability During Decomposition. Front Microbiol 2021; 12:685303. [PMID: 34220772 PMCID: PMC8247643 DOI: 10.3389/fmicb.2021.685303] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Accepted: 05/04/2021] [Indexed: 01/01/2023] Open
Abstract
Deadwood decomposition is responsible for a significant amount of carbon (C) turnover in natural forests. While fresh deadwood contains mainly plant compounds and is extremely low in nitrogen (N), fungal biomass and N content increase during decomposition. Here, we examined 18 genome-sequenced bacterial strains representing the dominant deadwood taxa to assess their adaptations to C and N utilization in deadwood. Diverse gene sets for the efficient decomposition of plant and fungal cell wall biopolymers were found in Acidobacteria, Bacteroidetes, and Actinobacteria. In contrast to these groups, Alphaproteobacteria and Gammaproteobacteria contained fewer carbohydrate-active enzymes and depended either on low-molecular-mass C sources or on mycophagy. This group, however, showed rich gene complements for N2 fixation and nitrate/nitrite reduction—key assimilatory and dissimilatory steps in the deadwood N cycle. We show that N2 fixers can obtain C independently from either plant biopolymers or fungal biomass. The succession of bacteria on decomposing deadwood reflects their ability to cope with the changing quality of C-containing compounds and increasing N content.
Collapse
Affiliation(s)
- Vojtěch Tláskal
- Laboratory of Environmental Microbiology, Institute of Microbiology of the Czech Academy of Sciences, Praha, Czechia
| | - Petr Baldrian
- Laboratory of Environmental Microbiology, Institute of Microbiology of the Czech Academy of Sciences, Praha, Czechia
| |
Collapse
|
174
|
Li Y, Wang M, Sun ZZ, Xie BB. Comparative Genomic Insights Into the Taxonomic Classification, Diversity, and Secondary Metabolic Potentials of Kitasatospora, a Genus Closely Related to Streptomyces. Front Microbiol 2021; 12:683814. [PMID: 34194415 PMCID: PMC8236941 DOI: 10.3389/fmicb.2021.683814] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Accepted: 05/20/2021] [Indexed: 11/25/2022] Open
Abstract
While the genus Streptomyces (family Streptomycetaceae) has been studied as a model for bacterial secondary metabolism and genetics, its close relatives have been less studied. The genus Kitasatospora is the second largest genus in the family Streptomycetaceae. However, its taxonomic position within the family remains under debate and the secondary metabolic potential remains largely unclear. Here, we performed systematic comparative genomic and phylogenomic analyses of Kitasatospora. Firstly, the three genera within the family Streptomycetaceae (Kitasatospora, Streptomyces, and Streptacidiphilus) showed common genomic features, including high G + C contents, high secondary metabolic potentials, and high recombination frequencies. Secondly, phylogenomic and comparative genomic analyses revealed phylogenetic distinctions and genome content differences among these three genera, supporting Kitasatospora as a separate genus within the family. Lastly, the pan-genome analysis revealed extensive genetic diversity within the genus Kitasatospora, while functional annotation and genome content comparison suggested genomic differentiation among lineages. This study provided new insights into genomic characteristics of the genus Kitasatospora, and also uncovered its previously underestimated and complex secondary metabolism.
Collapse
Affiliation(s)
- Yisong Li
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao, China
| | - Meng Wang
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao, China
| | - Zhong-Zhi Sun
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao, China
| | - Bin-Bin Xie
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao, China
| |
Collapse
|
175
|
Kim J, Na SI, Kim D, Chun J. UBCG2: Up-to-date bacterial core genes and pipeline for phylogenomic analysis. J Microbiol 2021; 59:609-615. [PMID: 34052993 DOI: 10.1007/s12275-021-1231-4] [Citation(s) in RCA: 87] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Revised: 05/11/2021] [Accepted: 05/11/2021] [Indexed: 11/29/2022]
Abstract
Phylogenomic tree reconstruction has recently become a routine and critical task to elucidate the evolutionary relationships among bacterial species. The most widely used method utilizes the concatenated core genes, universally present in a single-copy throughout the bacterial domain. In our previous study, a bioinformatics pipeline termed Up-to-date Bacterial Core Genes (UBCG) was developed with a set of bacterial core genes selected from 1,429 species covering 28 phyla. In this study, we revised a new bacterial core gene set, named UBCG2, that was selected from the more extensive genome sequence set belonging to 3,508 species spanning 43 phyla. UBCG2 comprises 81 genes with nine Clusters of Orthologous Groups of proteins (COGs) functional categories. The new gene set and complete pipeline are available at http://leb.snu.ac.kr/ubcg2 .
Collapse
Affiliation(s)
- Jihyeon Kim
- Interdisciplinary Program in Bioinformatics, Seoul National University, Seoul, 00826, Republic of Korea
- Institute of Molecular Biology & Genetics, Seoul National University, Seoul, 00826, Republic of Korea
| | - Seong-In Na
- Interdisciplinary Program in Bioinformatics, Seoul National University, Seoul, 00826, Republic of Korea
| | - Dongwook Kim
- Interdisciplinary Program in Bioinformatics, Seoul National University, Seoul, 00826, Republic of Korea
- Institute of Molecular Biology & Genetics, Seoul National University, Seoul, 00826, Republic of Korea
| | - Jongsik Chun
- Interdisciplinary Program in Bioinformatics, Seoul National University, Seoul, 00826, Republic of Korea.
- Institute of Molecular Biology & Genetics, Seoul National University, Seoul, 00826, Republic of Korea.
- School of Biological Sciences, Seoul National University, Seoul, 00826, Republic of Korea.
| |
Collapse
|
176
|
Leung MHY, Tong X, Bøifot KO, Bezdan D, Butler DJ, Danko DC, Gohli J, Green DC, Hernandez MT, Kelly FJ, Levy S, Mason-Buck G, Nieto-Caballero M, Syndercombe-Court D, Udekwu K, Young BG, Mason CE, Dybwad M, Lee PKH. Characterization of the public transit air microbiome and resistome reveals geographical specificity. MICROBIOME 2021; 9:112. [PMID: 34039416 PMCID: PMC8157753 DOI: 10.1186/s40168-021-01044-7] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/08/2021] [Accepted: 03/09/2021] [Indexed: 05/21/2023]
Abstract
BACKGROUND The public transit is a built environment with high occupant density across the globe, and identifying factors shaping public transit air microbiomes will help design strategies to minimize the transmission of pathogens. However, the majority of microbiome works dedicated to the public transit air are limited to amplicon sequencing, and our knowledge regarding the functional potentials and the repertoire of resistance genes (i.e. resistome) is limited. Furthermore, current air microbiome investigations on public transit systems are focused on single cities, and a multi-city assessment of the public transit air microbiome will allow a greater understanding of whether and how broad environmental, building, and anthropogenic factors shape the public transit air microbiome in an international scale. Therefore, in this study, the public transit air microbiomes and resistomes of six cities across three continents (Denver, Hong Kong, London, New York City, Oslo, Stockholm) were characterized. RESULTS City was the sole factor associated with public transit air microbiome differences, with diverse taxa identified as drivers for geography-associated functional potentials, concomitant with geographical differences in species- and strain-level inferred growth profiles. Related bacterial strains differed among cities in genes encoding resistance, transposase, and other functions. Sourcetracking estimated that human skin, soil, and wastewater were major presumptive resistome sources of public transit air, and adjacent public transit surfaces may also be considered presumptive sources. Large proportions of detected resistance genes were co-located with mobile genetic elements including plasmids. Biosynthetic gene clusters and city-unique coding sequences were found in the metagenome-assembled genomes. CONCLUSIONS Overall, geographical specificity transcends multiple aspects of the public transit air microbiome, and future efforts on a global scale are warranted to increase our understanding of factors shaping the microbiome of this unique built environment.
Collapse
Affiliation(s)
- M H Y Leung
- School of Energy and Environment, City University of Hong Kong, Hong Kong SAR, China
| | - X Tong
- School of Energy and Environment, City University of Hong Kong, Hong Kong SAR, China
| | - K O Bøifot
- Comprehensive Defence Division, Norwegian Defence Research Establishment FFI, Kjeller, Norway
- Department of Analytical, Environmental & Forensic Sciences, King's College London, London, UK
| | - D Bezdan
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA
| | - D J Butler
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA
| | - D C Danko
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA
| | - J Gohli
- Comprehensive Defence Division, Norwegian Defence Research Establishment FFI, Kjeller, Norway
| | - D C Green
- Department of Analytical, Environmental & Forensic Sciences, King's College London, London, UK
| | - M T Hernandez
- Environmental Engineering Program, College of Engineering and Applied Science, University of Colorado, Boulder, CO, USA
| | - F J Kelly
- Department of Analytical, Environmental & Forensic Sciences, King's College London, London, UK
| | - S Levy
- HudsonAlpha Institute of Biotechnology, Huntsville, AL, USA
| | - G Mason-Buck
- Department of Analytical, Environmental & Forensic Sciences, King's College London, London, UK
| | - M Nieto-Caballero
- Environmental Engineering Program, College of Engineering and Applied Science, University of Colorado, Boulder, CO, USA
| | - D Syndercombe-Court
- Department of Analytical, Environmental & Forensic Sciences, King's College London, London, UK
| | - K Udekwu
- Department of Aquatic Sciences & Assessment, Swedish University of Agriculture, Uppsala, Sweden
| | - B G Young
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA
| | - C E Mason
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA.
- The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, USA.
- The WorldQuant Initiative for Quantitative Prediction, Weill Cornell Medicine, New York, NY, USA.
- The Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, New York, NY, USA.
| | - M Dybwad
- Comprehensive Defence Division, Norwegian Defence Research Establishment FFI, Kjeller, Norway.
- Department of Analytical, Environmental & Forensic Sciences, King's College London, London, UK.
| | - P K H Lee
- School of Energy and Environment, City University of Hong Kong, Hong Kong SAR, China.
| |
Collapse
|
177
|
Makhlouf J, Merhi G, Salloum T, Abboud E, Tokajian S. Molecular characterization of a carbapenem-resistant Enterobacter hormaechei ssp. xiangfangensis co-harbouring bla NDM-1 and a chromosomally encoded phage-linked bla CTX-M-15 genes. INFECTION GENETICS AND EVOLUTION 2021; 93:104924. [PMID: 34004359 DOI: 10.1016/j.meegid.2021.104924] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/20/2020] [Revised: 03/22/2021] [Accepted: 05/13/2021] [Indexed: 10/21/2022]
Abstract
Enterobacter cloacae complex (ECC) members are rapidly emerging as successful nosocomial pathogens, especially, with the emergence of carbapenem-resistant clones. In this study, we performed a comprehensive molecular characterization of a carbapenem-resistant E. hormaechei ssp. xiangfangensis LAU_ENC1. hsp60 and average nucleotide identity (ANI) were used for its identification. The repertoire of resistance genes and phage content were analyzed. Plasmid sequences were extracted and compared to closest references. The isolate LAU_ENC1 was identified as an E. hormaechei ssp. xiangfangensis and belonged to ST-114A sub-cluster. blaNDM-1, blaCTX-M-15, blaOXA-1, and blaACT-16 genes were detected as β-lactam resistance determinants. A chromosomal hybrid intact phage, Enterobacter phage LAU1, with blaCTX-M-15 integrated in its direct vicinity within an ISEcp1 - blaCTX-M-15 - wbuC - ∆Tn2 rare cassette was detected. blaNDM-1 was integrated within a novel IncFII conjugative plasmid, pLAU_ENC1, through an IS3000- ΔISAba125-blaNDM-1-bleMBL-//-Tn5403 cassette. To our knowledge, this is the first report of a multi-drug resistant (MDR) E. hormaechei ssp. xiangfangensis carrying a blaCTX-M-15 integrated within the proximity of a provirus chromosomal region. Treatment options for MDR ECC members are becoming scarce, thus warranting an increased monitoring of the dissemination of these pathogens in clinical settings.
Collapse
Affiliation(s)
- Jana Makhlouf
- Department of Natural Sciences, Lebanese American University, Lebanon
| | - Georgi Merhi
- Department of Natural Sciences, Lebanese American University, Lebanon
| | - Tamara Salloum
- Department of Natural Sciences, Lebanese American University, Lebanon
| | - Edmond Abboud
- Laboratory Department, Middle East Institute of Health University Hospital, Lebanon
| | - Sima Tokajian
- Department of Natural Sciences, Lebanese American University, Lebanon.
| |
Collapse
|
178
|
Rasmussen JA, Villumsen KR, Duchêne DA, Puetz LC, Delmont TO, Sveier H, Jørgensen LVG, Præbel K, Martin MD, Bojesen AM, Gilbert MTP, Kristiansen K, Limborg MT. Genome-resolved metagenomics suggests a mutualistic relationship between Mycoplasma and salmonid hosts. Commun Biol 2021; 4:579. [PMID: 33990699 PMCID: PMC8121932 DOI: 10.1038/s42003-021-02105-1] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Accepted: 04/14/2021] [Indexed: 11/08/2022] Open
Abstract
Salmonids are important sources of protein for a large proportion of the human population. Mycoplasma species are a major constituent of the gut microbiota of salmonids, often representing the majority of microbiota. Despite the frequent reported dominance of salmonid-related Mycoplasma species, little is known about the phylogenomic placement, functions and potential evolutionary relationships with their salmonid hosts. In this study, we utilise 2.9 billion metagenomic reads generated from 12 samples from three different salmonid host species to I) characterise and curate the first metagenome-assembled genomes (MAGs) of Mycoplasma dominating the intestines of three different salmonid species, II) establish the phylogeny of these salmonid candidate Mycoplasma species, III) perform a comprehensive pangenomic analysis of Mycoplasma, IV) decipher the putative functionalities of the salmonid MAGs and reveal specific functions expected to benefit the host. Our data provide a basis for future studies examining the composition and function of the salmonid microbiota.
Collapse
Affiliation(s)
- Jacob A Rasmussen
- Laboratory of Genomics and Molecular Medicine, Department of Biology, University of Copenhagen, Copenhagen, Denmark.
- Center for Evolutionary Hologenomics, GLOBE institute, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.
| | - Kasper R Villumsen
- Department of Veterinary and Animal Sciences, University of Copenhagen, Veterinary Clinical Microbiology, Copenhagen, Denmark
| | - David A Duchêne
- Center for Evolutionary Hologenomics, GLOBE institute, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Lara C Puetz
- Center for Evolutionary Hologenomics, GLOBE institute, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Tom O Delmont
- Center for Evolutionary Hologenomics, GLOBE institute, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, Evry, France
| | | | - Louise von Gersdorff Jørgensen
- Department of Veterinary and Animal Sciences, University of Copenhagen, Parasitology and Aquatic Pathobiology, Copenhagen, Denmark
| | - Kim Præbel
- Norwegian College of Fishery Science, UiT the Arctic University of Norway, Tromsø, Norway
| | - Michael D Martin
- Department of Natural History, NTNU University Museum, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
| | - Anders M Bojesen
- Department of Veterinary and Animal Sciences, University of Copenhagen, Veterinary Clinical Microbiology, Copenhagen, Denmark
| | - M Thomas P Gilbert
- Center for Evolutionary Hologenomics, GLOBE institute, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- Department of Natural History, NTNU University Museum, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
| | - Karsten Kristiansen
- Laboratory of Genomics and Molecular Medicine, Department of Biology, University of Copenhagen, Copenhagen, Denmark
- Institute of Metagenomics, BGI-Shenzhen, Shenzhen, China
| | - Morten T Limborg
- Laboratory of Genomics and Molecular Medicine, Department of Biology, University of Copenhagen, Copenhagen, Denmark.
- Center for Evolutionary Hologenomics, GLOBE institute, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.
| |
Collapse
|
179
|
Sieradzki ET, Morando M, Fuhrman JA. Metagenomics and Quantitative Stable Isotope Probing Offer Insights into Metabolism of Polycyclic Aromatic Hydrocarbon Degraders in Chronically Polluted Seawater. mSystems 2021; 6:e00245-21. [PMID: 33975968 PMCID: PMC8125074 DOI: 10.1128/msystems.00245-21] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Accepted: 04/12/2021] [Indexed: 11/21/2022] Open
Abstract
Bacterial biodegradation is a significant contributor to remineralization of polycyclic aromatic hydrocarbons (PAHs)-toxic and recalcitrant components of crude oil as well as by-products of partial combustion chronically introduced into seawater via atmospheric deposition. The Deepwater Horizon oil spill demonstrated the speed at which a seed PAH-degrading community maintained by chronic inputs responds to acute pollution. We investigated the diversity and functional potential of a similar seed community in the chronically polluted Port of Los Angeles (POLA), using stable isotope probing with naphthalene, deep-sequenced metagenomes, and carbon incorporation rate measurements at the port and in two sites in the San Pedro Channel. We demonstrate the ability of the community of degraders at the POLA to incorporate carbon from naphthalene, leading to a quick shift in microbial community composition to be dominated by the normally rare Colwellia and Cycloclasticus We show that metagenome-assembled genomes (MAGs) belonged to these naphthalene degraders by matching their 16S-rRNA gene with experimental stable isotope probing data. Surprisingly, we did not find a full PAH degradation pathway in those genomes, even when combining genes from the entire microbial community, leading us to hypothesize that promiscuous dehydrogenases replace canonical naphthalene degradation enzymes in this site. We compared metabolic pathways identified in 29 genomes whose abundance increased in the presence of naphthalene to generate genomic-based recommendations for future optimization of PAH bioremediation at the POLA, e.g., ammonium as opposed to urea, heme or hemoproteins as an iron source, and polar amino acids.IMPORTANCE Oil spills in the marine environment have a devastating effect on marine life and biogeochemical cycles through bioaccumulation of toxic hydrocarbons and oxygen depletion by hydrocarbon-degrading bacteria. Oil-degrading bacteria occur naturally in the ocean, especially where they are supported by chronic inputs of oil or other organic carbon sources, and have a significant role in degradation of oil spills. Polycyclic aromatic hydrocarbons are the most persistent and toxic component of crude oil. Therefore, the bacteria that can break those molecules down are of particular importance. We identified such bacteria at the Port of Los Angeles (POLA), one of the busiest ports worldwide, and characterized their metabolic capabilities. We propose chemical targets based on those analyses to stimulate the activity of these bacteria in case of an oil spill in the Port POLA.
Collapse
Affiliation(s)
- Ella T Sieradzki
- Department of Biological Sciences, University of Southern California, Los Angeles, California, USA
| | - Michael Morando
- Department of Biological Sciences, University of Southern California, Los Angeles, California, USA
| | - Jed A Fuhrman
- Department of Biological Sciences, University of Southern California, Los Angeles, California, USA
| |
Collapse
|
180
|
Unraveling the Metabolic Potential of Asgardarchaeota in a Sediment from the Mediterranean Hydrocarbon-Contaminated Water Basin Mar Piccolo (Taranto, Italy). Microorganisms 2021; 9:microorganisms9040859. [PMID: 33923677 PMCID: PMC8072921 DOI: 10.3390/microorganisms9040859] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Revised: 04/10/2021] [Accepted: 04/14/2021] [Indexed: 12/02/2022] Open
Abstract
Increasing number of metagenome sequencing studies have proposed a central metabolic role of still understudied Archaeal members in natural and artificial ecosystems. However, their role in hydrocarbon cycling, particularly in the anaerobic biodegradation of aliphatic and aromatic hydrocarbons, is still mostly unknown in both marine and terrestrial environments. In this work, we focused our study on the metagenomic characterization of the archaeal community inhabiting the Mar Piccolo (Taranto, Italy, central Mediterranean) sediments heavily contaminated by petroleum hydrocarbons and polychlorinated biphenyls (PCB). Among metagenomic bins reconstructed from Mar Piccolo microbial community, we have identified members of the Asgardarchaeota superphylum that has been recently proposed to play a central role in hydrocarbon cycling in natural ecosystems under anoxic conditions. In particular, we found members affiliated with Thorarchaeota, Heimdallarchaeota, and Lokiarchaeota phyla and analyzed their genomic potential involved in central metabolism and hydrocarbon biodegradation. Metabolic prediction based on metagenomic analysis identified the malonyl-CoA and benzoyl-CoA routes as the pathways involved in aliphatic and aromatic biodegradation in these Asgardarchaeota members. This is the first study to give insight into the archaeal community functionality and connection to hydrocarbon degradation in marine sediment historically contaminated by hydrocarbons.
Collapse
|
181
|
Otaru N, Ye K, Mujezinovic D, Berchtold L, Constancias F, Cornejo FA, Krzystek A, de Wouters T, Braegger C, Lacroix C, Pugin B. GABA Production by Human Intestinal Bacteroides spp.: Prevalence, Regulation, and Role in Acid Stress Tolerance. Front Microbiol 2021; 12:656895. [PMID: 33936013 PMCID: PMC8082179 DOI: 10.3389/fmicb.2021.656895] [Citation(s) in RCA: 72] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Accepted: 03/24/2021] [Indexed: 12/11/2022] Open
Abstract
The high neuroactive potential of metabolites produced by gut microbes has gained traction over the last few years, with metagenomic-based studies suggesting an important role of microbiota-derived γ-aminobutyric acid (GABA) in modulating mental health. Emerging evidence has revealed the presence of the glutamate decarboxylase (GAD)-encoding gene, a key enzyme to produce GABA, in the prominent human intestinal genus Bacteroides. Here, we investigated GABA production by Bacteroides in culture and metabolic assays combined with comparative genomics and phylogenetics. A total of 961 Bacteroides genomes were analyzed in silico and 17 metabolically and genetically diverse human intestinal isolates representing 11 species were screened in vitro. Using the model organism Bacteroides thetaiotaomicron DSM 2079, we determined GABA production kinetics, its impact on milieu pH, and we assessed its role in mitigating acid-induced cellular damage. We showed that the GAD-system consists of at least four highly conserved genes encoding a GAD, a glutaminase, a glutamate/GABA antiporter, and a potassium channel. We demonstrated a high prevalence of the GAD-system among Bacteroides with 90% of all Bacteroides genomes (96% in human gut isolates only) harboring all genes of the GAD-system and 16 intestinal Bacteroides strains producing GABA in vitro (ranging from 0.09 to 60.84 mM). We identified glutamate and glutamine as precursors of GABA production, showed that the production is regulated by pH, and that the GAD-system acts as a protective mechanism against acid stress in Bacteroides, mitigating cell death and preserving metabolic activity. Our data also indicate that the GAD-system might represent the only amino acid-dependent acid tolerance system in Bacteroides. Altogether, our results suggest an important contribution of Bacteroides in the regulation of the GABAergic system in the human gut.
Collapse
Affiliation(s)
- Nize Otaru
- Laboratory of Food Biotechnology, Department of Health Sciences and Technology, ETH Zürich, Zürich, Switzerland.,Nutrition Research Unit, University Children's Hospital Zürich, Zürich, Switzerland
| | - Kun Ye
- Laboratory of Food Biotechnology, Department of Health Sciences and Technology, ETH Zürich, Zürich, Switzerland
| | - Denisa Mujezinovic
- Laboratory of Food Biotechnology, Department of Health Sciences and Technology, ETH Zürich, Zürich, Switzerland
| | - Laura Berchtold
- Laboratory of Food Biotechnology, Department of Health Sciences and Technology, ETH Zürich, Zürich, Switzerland.,PharmaBiome AG, Zürich, Switzerland
| | - Florentin Constancias
- Laboratory of Food Biotechnology, Department of Health Sciences and Technology, ETH Zürich, Zürich, Switzerland
| | - Fabián A Cornejo
- Max Planck Unit for the Science of Pathogens, Berlin, Germany.,Laboratory of Molecular Microbiology, Faculty of Chemistry and Biology, University of Santiago, Santiago, Chile
| | - Adam Krzystek
- Laboratory of Human Nutrition, Department of Health Sciences and Technology, ETH Zürich, Zürich, Switzerland
| | | | - Christian Braegger
- Nutrition Research Unit, University Children's Hospital Zürich, Zürich, Switzerland
| | - Christophe Lacroix
- Laboratory of Food Biotechnology, Department of Health Sciences and Technology, ETH Zürich, Zürich, Switzerland
| | - Benoit Pugin
- Laboratory of Food Biotechnology, Department of Health Sciences and Technology, ETH Zürich, Zürich, Switzerland
| |
Collapse
|
182
|
Shen W, Ren H. TaxonKit: A practical and efficient NCBI taxonomy toolkit. J Genet Genomics 2021; 48:844-850. [PMID: 34001434 DOI: 10.1016/j.jgg.2021.03.006] [Citation(s) in RCA: 93] [Impact Index Per Article: 31.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Revised: 03/15/2021] [Accepted: 03/27/2021] [Indexed: 01/09/2023]
Abstract
The National Center for Biotechnology Information (NCBI) Taxonomy is widely applied in biomedical and ecological studies. Typical demands include querying taxonomy identifier (TaxIds) by taxonomy names, querying complete taxonomic lineages by TaxIds, listing descendants of given TaxIds, and others. However, existed tools are either limited in functionalities or inefficient in terms of runtime. In this work, we present TaxonKit, a command-line toolkit for comprehensive and efficient manipulation of NCBI Taxonomy data. TaxonKit comprises seven core subcommands providing functions, including TaxIds querying, listing, filtering, lineage retrieving and reformatting, lowest common ancestor computation, and TaxIds change tracking. The practical functions, competitive processing performance, scalability with different scales of datasets and good accessibility could facilitate taxonomy data manipulations. TaxonKit provides free access under the permissive MIT license on GitHub, Brewsci, and Bioconda. The documents are also available at https://bioinf.shenwei.me/taxonkit/.
Collapse
Affiliation(s)
- Wei Shen
- Institute for Viral Hepatitis, Department of Infectious Diseases, Key Laboratory of Molecular Biology for Infectious Diseases, Ministry of Education, The Second Affiliated Hospital of Chongqing Medical University, Chongqing, 400010, China.
| | - Hong Ren
- Institute for Viral Hepatitis, Department of Infectious Diseases, Key Laboratory of Molecular Biology for Infectious Diseases, Ministry of Education, The Second Affiliated Hospital of Chongqing Medical University, Chongqing, 400010, China.
| |
Collapse
|
183
|
Cambon-Bonavita MA, Aubé J, Cueff-Gauchard V, Reveillaud J. Niche partitioning in the Rimicaris exoculata holobiont: the case of the first symbiotic Zetaproteobacteria. MICROBIOME 2021; 9:87. [PMID: 33845886 PMCID: PMC8042907 DOI: 10.1186/s40168-021-01045-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/19/2020] [Accepted: 03/09/2021] [Indexed: 06/12/2023]
Abstract
BACKGROUND Free-living and symbiotic chemosynthetic microbial communities support primary production and higher trophic levels in deep-sea hydrothermal vents. The shrimp Rimicaris exoculata, which dominates animal communities along the Mid-Atlantic Ridge, houses a complex bacterial community in its enlarged cephalothorax. The dominant bacteria present are from the taxonomic groups Campylobacteria, Desulfobulbia (formerly Deltaproteobacteria), Alphaproteobacteria, Gammaproteobacteria, and some recently discovered iron oxyhydroxide-coated Zetaproteobacteria. This epibiotic consortium uses iron, sulfide, methane, and hydrogen as energy sources. Here, we generated shotgun metagenomes from Rimicaris exoculata cephalothoracic epibiotic communities to reconstruct and investigate symbiotic genomes. We collected specimens from three geochemically contrasted vent fields, TAG, Rainbow, and Snake Pit, to unravel the specificity, variability, and adaptation of Rimicaris-microbe associations. RESULTS Our data enabled us to reconstruct 49 metagenome-assembled genomes (MAGs) from the TAG and Rainbow vent fields, including 16 with more than 90% completion and less than 5% contamination based on single copy core genes. These MAGs belonged to the dominant Campylobacteria, Desulfobulbia, Thiotrichaceae, and some novel candidate phyla radiation (CPR) lineages. In addition, most importantly, two MAGs in our collection were affiliated to Zetaproteobacteria and had no close relatives (average nucleotide identity ANI < 77% with the closest relative Ghiorsea bivora isolated from TAG, and 88% with each other), suggesting potential novel species. Genes for Calvin-Benson Bassham (CBB) carbon fixation, iron, and sulfur oxidation, as well as nitrate reduction, occurred in both MAGs. However, genes for hydrogen oxidation and multicopper oxidases occurred in one MAG only, suggesting shared and specific potential functions for these two novel Zetaproteobacteria symbiotic lineages. Overall, we observed highly similar symbionts co-existing in a single shrimp at both the basaltic TAG and ultramafic Rainbow vent sites. Nevertheless, further examination of the seeming functional redundancy among these epibionts revealed important differences. CONCLUSION These data highlight microniche partitioning in the Rimicaris holobiont and support recent studies showing that functional diversity enables multiple symbiont strains to coexist in animals colonizing hydrothermal vents. Video Abstract.
Collapse
Affiliation(s)
- Marie-Anne Cambon-Bonavita
- Univ Brest, CNRS, IFREMER, Laboratoire de Microbiologie des Environnements Extrêmes, 29280 Plouzané, France
| | - Johanne Aubé
- Univ Brest, CNRS, IFREMER, Laboratoire de Microbiologie des Environnements Extrêmes, 29280 Plouzané, France
| | - Valérie Cueff-Gauchard
- Univ Brest, CNRS, IFREMER, Laboratoire de Microbiologie des Environnements Extrêmes, 29280 Plouzané, France
| | - Julie Reveillaud
- Univ Brest, CNRS, IFREMER, Laboratoire de Microbiologie des Environnements Extrêmes, 29280 Plouzané, France
- MIVEGEC, Univ. Montpellier, INRAe, CNRS, IRD, Montpellier, France
| |
Collapse
|
184
|
Kröber E, Cunningham MR, Peixoto J, Spurgin L, Wischer D, Kruger R, Kumaresan D. Comparative genomics analyses indicate differential methylated amine utilization trait within members of the genus Gemmobacter. ENVIRONMENTAL MICROBIOLOGY REPORTS 2021; 13:195-208. [PMID: 33484104 DOI: 10.1111/1758-2229.12927] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/08/2020] [Revised: 01/11/2021] [Accepted: 01/11/2021] [Indexed: 05/22/2023]
Abstract
Methylated amines are ubiquitous in the environment and play a role in regulating the earth's climate via a set of complex biological and chemical reactions. Microbial degradation of these compounds is thought to be a major sink. Recently we isolated a facultative methylotroph, Gemmobacter sp. LW-1, an isolate from the unique environment Movile Cave, Romania, which is capable of methylated amine utilization as a carbon source. Here, using a comparative genomics approach, we investigate how widespread methylated amine utilization is within members of the bacterial genus Gemmobacter. Seven genomes of different Gemmobacter species isolated from diverse environments, such as activated sludge, fresh water, sulphuric cave waters (Movile Cave) and the marine environment were available from the public repositories and used for the analysis. Our results indicate that methylamine utilization is a distinctive feature of selected members of the genus Gemmobacter, namely G. aquatilis, G. lutimaris, G. sp. HYN0069, G. caeni and G. sp. LW-1 have the genetic potential while others (G. megaterium and G. nectariphilus) have not.
Collapse
Affiliation(s)
- Eileen Kröber
- Department of Symbiosis, Max-Planck Institute for Marine Microbiology, Bremen, Germany
| | - Mark R Cunningham
- School of Biological Sciences, Institute for Global Food Security, Queen's University Belfast, Belfast, UK
| | - Julianna Peixoto
- Department of Cellular Biology, University of Brasília, Brasília, Brazil
| | - Lewis Spurgin
- School of Environmental Sciences, University of East Anglia, Norwich, UK
| | - Daniela Wischer
- School of Environmental Sciences, University of East Anglia, Norwich, UK
| | - Ricardo Kruger
- Department of Cellular Biology, University of Brasília, Brasília, Brazil
| | - Deepak Kumaresan
- School of Biological Sciences, Institute for Global Food Security, Queen's University Belfast, Belfast, UK
| |
Collapse
|
185
|
Niche dimensions of a marine bacterium are identified using invasion studies in coastal seawater. Nat Microbiol 2021; 6:524-532. [PMID: 33495621 DOI: 10.1038/s41564-020-00851-2] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Accepted: 12/11/2020] [Indexed: 01/29/2023]
Abstract
Niche theory is a foundational ecological concept that explains the distribution of species in natural environments. Identifying the dimensions of any organism's niche is challenging because numerous environmental factors can affect organism viability. We used serial invasion experiments to introduce Ruegeria pomeroyi DSS-3, a heterotrophic marine bacterium, into a coastal phytoplankton bloom on 14 dates. RNA-sequencing analysis of R. pomeroyi was conducted after 90 min to assess its niche dimensions in this dynamic ecosystem. We identified ~100 external conditions eliciting transcriptional responses, which included substrates, nutrients, metals and biotic interactions such as antagonism, resistance and cofactor synthesis. The peak bloom was characterized by favourable states for most of the substrate dimensions, but low inferred growth rates of R. pomeroyi at this stage indicated that its niche was narrowed by factors other than substrate availability, most probably negative biotic interactions with the bloom dinoflagellate. Our findings indicate chemical and biological features of the ocean environment that can constrain where heterotrophic bacteria survive.
Collapse
|
186
|
Hanson BT, Dimitri Kits K, Löffler J, Burrichter AG, Fiedler A, Denger K, Frommeyer B, Herbold CW, Rattei T, Karcher N, Segata N, Schleheck D, Loy A. Sulfoquinovose is a select nutrient of prominent bacteria and a source of hydrogen sulfide in the human gut. ISME JOURNAL 2021; 15:2779-2791. [PMID: 33790426 PMCID: PMC8397734 DOI: 10.1038/s41396-021-00968-0] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/11/2020] [Revised: 03/01/2021] [Accepted: 03/17/2021] [Indexed: 12/26/2022]
Abstract
Responses of the microbiota to diet are highly personalized but mechanistically not well understood because many metabolic capabilities and interactions of human gut microorganisms are unknown. Here we show that sulfoquinovose (SQ), a sulfonated monosaccharide omnipresent in green vegetables, is a selective yet relevant substrate for few but ubiquitous bacteria in the human gut. In human feces and in defined co-culture, Eubacterium rectale and Bilophila wadsworthia used recently identified pathways to cooperatively catabolize SQ with 2,3-dihydroxypropane-1-sulfonate as a transient intermediate to hydrogen sulfide (H2S), a key intestinal metabolite with disparate effects on host health. SQ-degradation capability is encoded in almost half of E. rectale genomes but otherwise sparsely distributed among microbial species in the human intestine. However, re-analysis of fecal metatranscriptome datasets of four human cohorts showed that SQ degradation (mostly from E. rectale and Faecalibacterium prausnitzii) and H2S production (mostly from B. wadsworthia) pathways were expressed abundantly across various health states, demonstrating that these microbial functions are core attributes of the human gut. The discovery of green-diet-derived SQ as an exclusive microbial nutrient and an additional source of H2S in the human gut highlights the role of individual dietary compounds and organosulfur metabolism on microbial activity and has implications for precision editing of the gut microbiota by dietary and prebiotic interventions.
Collapse
Affiliation(s)
- Buck T Hanson
- Division of Microbial Ecology, Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria.,FFoQSI GmbH, Austrian Competence Centre for Feed and Food Quality Safety & Innovation, Tulln, Austria
| | - K Dimitri Kits
- Division of Microbial Ecology, Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
| | - Jessica Löffler
- Division of Microbial Ecology, Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
| | - Anna G Burrichter
- Department of Biology, University of Konstanz, Konstanz, Germany.,Konstanz Research School Chemical Biology, University of Konstanz, Konstanz, Germany
| | | | - Karin Denger
- Department of Biology, University of Konstanz, Konstanz, Germany
| | - Benjamin Frommeyer
- Department of Biology, University of Konstanz, Konstanz, Germany.,Konstanz Research School Chemical Biology, University of Konstanz, Konstanz, Germany
| | - Craig W Herbold
- Division of Microbial Ecology, Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
| | - Thomas Rattei
- Division of Computational Systems Biology, Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
| | | | - Nicola Segata
- CIBIO Department, University of Trento, Trento, Italy
| | - David Schleheck
- Department of Biology, University of Konstanz, Konstanz, Germany. .,Konstanz Research School Chemical Biology, University of Konstanz, Konstanz, Germany.
| | - Alexander Loy
- Division of Microbial Ecology, Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria. .,Joint Microbiome Facility of the Medical University of Vienna and the University of Vienna, Vienna, Austria.
| |
Collapse
|
187
|
Bijlani S, Singh NK, Eedara VVR, Podile AR, Mason CE, Wang CCC, Venkateswaran K. Methylobacterium ajmalii sp. nov., Isolated From the International Space Station. Front Microbiol 2021; 12:639396. [PMID: 33790880 PMCID: PMC8005752 DOI: 10.3389/fmicb.2021.639396] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Accepted: 02/22/2021] [Indexed: 11/22/2022] Open
Abstract
Four strains belonging to the family of Methylobacteriaceae were isolated from different locations on the International Space Station (ISS) across two consecutive flights. Of these, three were identified as Gram-negative, rod-shaped, catalase-positive, oxidase-positive, motile bacteria, designated as IF7SW-B2T, IIF1SW-B5, and IIF4SW-B5, whereas the fourth was identified as Methylorubrum rhodesianum. The sequence similarity of these three ISS strains, designated as IF7SW-B2T, IIF1SW-B5, and IIF4SW-B5, was <99.4% for 16S rRNA genes and <97.3% for gyrB gene, with the closest being Methylobacterium indicum SE2.11T. Furthermore, the multi-locus sequence analysis placed these three ISS strains in the same clade of M. indicum. The average nucleotide identity (ANI) values of these three ISS strains were <93% and digital DNA-DNA hybridization (dDDH) values were <46.4% with any described Methylobacterium species. Based on the ANI and dDDH analyses, these three ISS strains were considered as novel species belonging to the genus Methylobacterium. The three ISS strains showed 100% ANI similarity and dDDH values with each other, indicating that these three ISS strains, isolated during various flights and from different locations, belong to the same species. These three ISS strains were found to grow optimally at temperatures from 25 to 30°C, pH 6.0 to 8.0, and NaCl 0 to 1%. Phenotypically, these three ISS strains resemble M. aquaticum and M. terrae since they assimilate similar sugars as sole carbon substrate when compared to other Methylobacterium species. Fatty acid analysis showed that the major fatty acid produced by the ISS strains are C18:1−ω7c and C18:1−ω6c. The predominant quinone was ubiquinone 10, and the major polar lipids were diphosphatidylglycerol, phosphatidylcholine, phosphatidylethanolamine, phosphatidylglycerol, and an unidentified lipid. Therefore, based on genomic, phylogenetic, biochemical, and fatty acid analyses, strains IF7SW-B2T, IIF1SW-B5, and IIF4SW-B5, are assigned to a novel species within the genus Methylobacterium, and the name Methylobacterium ajmalii sp. nov. is proposed. The type strain is IF7SW-B2T (NRRL B-65601T and LMG 32165T).
Collapse
Affiliation(s)
- Swati Bijlani
- Department of Pharmacology and Pharmaceutical Sciences, School of Pharmacy, University of Southern California, Los Angeles, CA, United States
| | - Nitin K Singh
- Jet Propulsion Laboratory, California Institute of Technology, Pasadena, CA, United States
| | - V V Ramprasad Eedara
- Department of Plant Science, School of Life Sciences, University of Hyderabad, Hyderabad, India
| | - Appa Rao Podile
- Department of Plant Science, School of Life Sciences, University of Hyderabad, Hyderabad, India
| | - Christopher E Mason
- WorldQuant Initiative for Quantitative Prediction, Weill Cornell Medicine, New York, NY, United States
| | - Clay C C Wang
- Department of Pharmacology and Pharmaceutical Sciences, School of Pharmacy, University of Southern California, Los Angeles, CA, United States
| | - Kasthuri Venkateswaran
- Jet Propulsion Laboratory, California Institute of Technology, Pasadena, CA, United States
| |
Collapse
|
188
|
Ruiz-Perez CA, Bertagnolli AD, Tsementzi D, Woyke T, Stewart FJ, Konstantinidis KT. Description of Candidatus Mesopelagibacter carboxydoxydans and Candidatus Anoxipelagibacter denitrificans: Nitrate-reducing SAR11 genera that dominate mesopelagic and anoxic marine zones. Syst Appl Microbiol 2021; 44:126185. [PMID: 33676264 DOI: 10.1016/j.syapm.2021.126185] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2020] [Revised: 11/25/2020] [Accepted: 12/09/2020] [Indexed: 11/29/2022]
Abstract
The diverse and ubiquitous members of the SAR11 lineage (Alphaproteobacteria) represent up to 30-40% of the surface and mesopelagic oceanic microbial communities. However, the molecular and ecological mechanisms that differentiate closely related, yet distinct, SAR11 members that often co-occur under similar environmental conditions remain speculative. Recently, two mesopelagic and oxygen minimum zone (OMZ)-associated subclades of SAR11 (Ic and IIa.A) were described using single-cell amplified genomes (SAGs) linked to nitrate reduction in OMZs. In this current study, the collection of genomes belonging to these two subclades was expanded with thirteen new metagenome-assembled genomes (MAGs), thus providing a more detailed phylogenetic and functional characterization of these subclades. Gene content-based predictions of metabolic functions revealed similarities in central carbon metabolism between subclades Ic and IIa.A and surface SAR11 clades, with small variations in central pathways. These variations included more versatile sulfur assimilation pathways, as well as a previously predicted capacity for nitrate reduction that conferred unique versatility on mesopelagic-adapted clades compared to their surface counterparts. Finally, consistent with previously reported abundances of carbon monoxide (CO) in surface and mesopelagic waters, subclades Ia (surface) and Ic (mesopelagic) have the genetic potential to oxidize carbon monoxide (CO), presumably taking advantage of this abundant compound as an electron donor. Based on genomic analyses, environmental distribution and metabolic reconstruction, we propose two new SAR11 genera, Ca. Mesopelagibacter carboxydoxydans (subclade Ic) and Ca. Anoxipelagibacter denitrificans (subclade IIa.A), which represent members of the mesopelagic and OMZ-adapted SAR11 clades.
Collapse
Affiliation(s)
- Carlos A Ruiz-Perez
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Anthony D Bertagnolli
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Despina Tsementzi
- School of Civil and Environmental Engineering, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Tanja Woyke
- DOE Joint Genome Institute, One Cyclotron Road, Mail Stop 91R0183, Berkeley, CA 94720, USA
| | - Frank J Stewart
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332, USA; Center for Microbial Dynamics and Infection, Georgia Institute of Technology, Atlanta, GA 30332, USA; Department of Microbiology & Immunology, Montana State University, Bozeman, MT 59717, USA
| | - Konstantinos T Konstantinidis
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332, USA; School of Civil and Environmental Engineering, Georgia Institute of Technology, Atlanta, GA 30332, USA; Center for Bioinformatics and Computational Genomics, Georgia Institute of Technology, Atlanta, GA 30332, USA.
| |
Collapse
|
189
|
Lee MD, O'Rourke A, Lorenzi H, Bebout BM, Dupont CL, Everroad RC. Reference-guided metagenomics reveals genome-level evidence of potential microbial transmission from the ISS environment to an astronaut's microbiome. iScience 2021; 24:102114. [PMID: 33659879 PMCID: PMC7892915 DOI: 10.1016/j.isci.2021.102114] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2020] [Revised: 11/22/2020] [Accepted: 01/22/2021] [Indexed: 11/16/2022] Open
Abstract
Monitoring microbial communities aboard the International Space Station (ISS) is essential to maintaining astronaut health and the integrity of life-support systems. Using assembled genomes of ISS-derived microbial isolates as references, recruiting metagenomic reads from an astronaut's nasal microbiome revealed no recruitment to a Staphylococcus aureus isolate from samples before launch, yet systematic recruitment across the genome when sampled after 3 months aboard the ISS, with a median percent identity of 100%. This suggests that either a highly similar S. aureus population colonized the astronaut's nasal microbiome while the astronaut was aboard the ISS or that it may have been below detection before spaceflight, instead supporting a shift in community composition. This work highlights the value in generating genomic libraries of microbes from built-environments such as the ISS and demonstrates one way such data can be integrated with metagenomics to facilitate the tracking and monitoring of astronaut microbiomes and health. Understanding built-environment microbiomes is critical for human space exploration Reference-guided metagenomics is a powerful approach for monitoring microbiomes We show potential microbial colonization of an astronaut microbiome while aboard the ISS
Collapse
Affiliation(s)
- Michael D Lee
- Exobiology Branch, NASA Ames Research Center, Mountain View, CA, USA.,Blue Marble Space Institute of Science, Seattle, WA, USA
| | - Aubrie O'Rourke
- Space Life Sciences, NASA Kennedy Space Center, Merritt Island, FL, USA
| | - Hernan Lorenzi
- Department of Infectious Diseases, J. Craig Venter Institute, Rockville, MD, USA
| | - Brad M Bebout
- Exobiology Branch, NASA Ames Research Center, Mountain View, CA, USA
| | | | - R Craig Everroad
- Exobiology Branch, NASA Ames Research Center, Mountain View, CA, USA
| |
Collapse
|
190
|
Sidhu C, Saini MK, Srinivas Tanuku NR, Pinnaka AK. Arenibacter amylolyticus sp. nov., an amylase-producing bacterium of the family Flavobacteriaceae isolated from marine water in India. Int J Syst Evol Microbiol 2021; 71. [PMID: 33502300 DOI: 10.1099/ijsem.0.004664] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A novel Gram-stain-negative, curved rod-shaped, 0.5-0.7 µm wide and 3.0-10.0 µm long, non-motile bacterium, designated strain AK53T, was isolated from a 5 m depth water sample collected from the Bay of Bengal, Visakhapatnam, India. Colonies on marine agar were circular, small, dark orange, shiny, smooth, translucent, flat, with an entire margin. The major fatty acids included iso-C15 : 0, iso-C15 : 0 3OH, anteiso-C15 : 0, iso-C15 : 1 G, iso-C17 : 0 3OH and summed feature 3 (C16 : 1 ω7c and/or C16 : 1 ω6c and/or iso-C15 : 0-2OH). Polar lipids included phosphatidylethanolamine and five unidentified lipids. The DNA G+C content of the strain AK53T was found to be 40.8 mol%. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain AK53T was closely related to Arenibacter latericius KMM 426T and Arenibacter certesii KMM3941T (pair-wise sequence similarity of 99.17 and 98.89 %, respectively), forming a distinct branch within the genus Arenibacter and clustering with A. latericius. Strain AK53T shared average nucleotide identity (ANIb, based on blast) of 78.07 and 77.44 % with A. latericius JCM 13508T and A. certesii JCM 13507T, respectively. Based on the observed phenotypic, chemotaxonomic characteristics and phylogenetic analysis, strain AK53T is described in this study as representing a novel species in the genus Arenibacter, for which the name Arenibacter amylolyticus sp. nov. is proposed. The type strain of Arenibacter amylolyticus is AK53T (=MTCC 12004T= JCM 19206T=KCTC 62553T).
Collapse
Affiliation(s)
- Chandni Sidhu
- Present address: Department of Molecular Ecology, Max Planck Institute for Marine Microbiology, Celsiusstrasse 1, D-28359, Bremen, Germany.,MTCC-Microbial Type Culture Collection & Gene Bank, CSIR-Institute of Microbial Technology, Chandigarh 160036, India
| | - Mohit Kumar Saini
- Present address: Department of Biological Sciences, Tokyo Metropolitan University, 1-1 Minami-Osawa, Hachioji, Tokyo 1920397, Japan.,MTCC-Microbial Type Culture Collection & Gene Bank, CSIR-Institute of Microbial Technology, Chandigarh 160036, India
| | - Naga Radha Srinivas Tanuku
- CSIR-National Institute of Oceanography, Regional Centre, 176, Lawsons Bay Colony, Visakhapatnam 530017, India
| | - Anil Kumar Pinnaka
- MTCC-Microbial Type Culture Collection & Gene Bank, CSIR-Institute of Microbial Technology, Chandigarh 160036, India
| |
Collapse
|
191
|
Rathour R, Medhi K, Gupta J, Thakur IS. Integrated approach of whole-genome analysis, toxicological evaluation and life cycle assessment for pyrene biodegradation by a psychrophilic strain, Shewanella sp. ISTPL2. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2021; 269:116176. [PMID: 33307397 DOI: 10.1016/j.envpol.2020.116176] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/14/2020] [Revised: 11/18/2020] [Accepted: 11/27/2020] [Indexed: 06/12/2023]
Abstract
Polycyclic aromatic hydrocarbons (PAHs) such as pyrene are universal contaminants existing in the environment which have known cancer-causing and mutagenic characteristics. A psychrophilic bacterial strain Shewanella sp. ISTPL2 was isolated from the sediment sample collected from the Pangong lake, Jammu & Kashmir, India. In our previous study, the pyrene degradation potential of the ISTPL2 strain was studied in both mineral salt media as well as in soil artificially spiked with different concentrations of pyrene. Whole-genome sequencing of ISTPL2 strain in the current study highlighted the key genes of pyrene metabolism, including alcohol dehydrogenase and ring hydroxylating dioxygenase alpha-subunit. Pyrene cytotoxicity was evaluated on HepG2, a human hepato-carcinoma cell line. The cytotoxicity of the organic extract decreased with the increasing duration of bacterial treatment. To develop a more sustainable biodegradation approach, the potential impacts were evaluated for human health and ecosystem using life-cycle assessment (LCA) following the ReCiPe methodology for the considered PAH. The results implemented that global warming potential (GWP) had the highest impact, whereas both ecotoxicity and human toxicity had least from this study.
Collapse
Affiliation(s)
- Rashmi Rathour
- School of Environmental Sciences, Jawaharlal Nehru University, Delhi, 110067, India.
| | - Kristina Medhi
- School of Environmental Sciences, Jawaharlal Nehru University, Delhi, 110067, India; Central Pollution Control Board (CPCB), Regional Directorate (North), PICUP Bhawan, Lucknow, Uttar Pradesh, 226010, India.
| | - Juhi Gupta
- School of Environmental Sciences, Jawaharlal Nehru University, Delhi, 110067, India.
| | - Indu Shekhar Thakur
- School of Environmental Sciences, Jawaharlal Nehru University, Delhi, 110067, India.
| |
Collapse
|
192
|
Gomez-Alvarez V, Liu H, Pressman JG, Wahman DG. Metagenomic Profile of Microbial Communities in a Drinking Water Storage Tank Sediment after Sequential Exposure to Monochloramine, Free Chlorine, and Monochloramine. ACS ES&T WATER 2021; 1:1283-1294. [PMID: 34337601 PMCID: PMC8318090 DOI: 10.1021/acsestwater.1c00016] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
Sediment accumulation in drinking water storage facilities may lead to water quality degradation, including biological growth and disinfectant decay. The current research evaluated the microbiome present in a sediment after sequential exposure to monochloramine, free chlorine, and monochloramine. Chemical profiles within the sediment based on microelectrodes showed evidence of nitrification, and monochloramine slowly penetrated the sediment but was not measurable at lower depths. A metagenomic approach was used to characterize the microbial communities and functional potential of top (0-1 cm) and bottom (1-2 cm) layers in sediment cores. Differential abundance analysis revealed both an enrichment and depletion associated with depth of microbial populations. We assembled 30 metagenome-assembled genomes (MAGs) representing bacterial and archaeal microorganisms. Most metabolic functions were represented in both layers, suggesting the capability of the microbiomes to respond to environmental fluctuations. However, niche-specific abundance differences were identified in biotransformation processes (e.g., nitrogen). Metagenome-level analyses indicated that nitrification and denitrification can potentially occur simultaneously in the sediments, but the exact location of their occurrence within the sediment will depend on the localized physicochemical conditions. Even though monochloramine was maintained in the bulk water there was limited penetration into the sediment, and the microbial community remained functionally diverse and active.
Collapse
Affiliation(s)
- Vicente Gomez-Alvarez
- Center for Environmental Solutions & Emergency Response, U.S. Environmental Protection Agency, Cincinnati, Ohio 45268, United States
| | - Hong Liu
- Oak Ridge Institute for Science and Education (ORISE), Post-Doctoral Fellow at U.S. Environmental Protection Agency, Cincinnati, Ohio 45268, United States
| | - Jonathan G Pressman
- Center for Environmental Solutions & Emergency Response, U.S. Environmental Protection Agency, Cincinnati, Ohio 45268, United States
| | - David G Wahman
- Center for Environmental Solutions & Emergency Response, U.S. Environmental Protection Agency, Cincinnati, Ohio 45268, United States
| |
Collapse
|
193
|
Sevillano M, Dai Z, Calus S, Bautista-de Los Santos QM, Eren AM, van der Wielen PWJJ, Ijaz UZ, Pinto AJ. Differential prevalence and host-association of antimicrobial resistance traits in disinfected and non-disinfected drinking water systems. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 749:141451. [PMID: 32836121 DOI: 10.1016/j.scitotenv.2020.141451] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Revised: 07/10/2020] [Accepted: 08/01/2020] [Indexed: 06/11/2023]
Abstract
Antimicrobial resistance (AMR) in drinking water has received less attention than its counterparts in the urban water cycle. While culture-based techniques or gene-centric PCR have been used to probe the impact of treatment approaches (e.g., disinfection) on AMR in drinking water, to our knowledge there is no systematic comparison of AMR trait distribution and prevalence between disinfected and disinfectant residual-free drinking water systems. We used metagenomics to assess the associations between disinfectant residuals and AMR prevalence and its host association in full-scale drinking water distribution systems (DWDSs) with and without disinfectant residuals. While the differences in AMR profiles between DWDSs were associated with the presence or absence of disinfectant, they were also associated with overall water chemistry and more importantly with microbial community structure. AMR genes and mechanisms differentially abundant in disinfected systems were primarily associated with nontuberculous mycobacteria (NTM). Finally, evaluation of metagenome assembled genomes (MAGs) also suggests that NTM possessing AMR genes conferring intrinsic resistance to key antibiotics were prevalent in disinfected systems, whereas such NTM genomes were not detected in disinfectant residual free DWDSs. Altogether, our findings provide insights into the drinking water resistome and its association with potential opportunistic pathogens, particularly in systems with disinfectant residual.
Collapse
Affiliation(s)
- Maria Sevillano
- Department of Civil and Environmental Engineering, Northeastern University, Boston, MA, USA
| | - Zihan Dai
- Infrastructure and Environmental Research Division, School of Engineering, University of Glasgow, G12 8LT Glasgow, UK
| | - Szymon Calus
- Infrastructure and Environmental Research Division, School of Engineering, University of Glasgow, G12 8LT Glasgow, UK
| | | | - A Murat Eren
- Department of Medicine, University of Chicago, Chicago, IL, USA; Bay Paul Center, Marine Biological Laboratory, Woods Hole, MA, USA
| | - Paul W J J van der Wielen
- KWR Watercycle Research Institute, Nieuwegein, Netherlands; Laboratory of Microbiology, Wageningen University, Wageningen, Netherlands
| | - Umer Z Ijaz
- Infrastructure and Environmental Research Division, School of Engineering, University of Glasgow, G12 8LT Glasgow, UK
| | - Ameet J Pinto
- Department of Civil and Environmental Engineering, Northeastern University, Boston, MA, USA.
| |
Collapse
|
194
|
Broddrick JT, Szubin R, Norsigian CJ, Monk JM, Palsson BO, Parenteau MN. High-Quality Genome-Scale Models From Error-Prone, Long-Read Assemblies. Front Microbiol 2020; 11:596626. [PMID: 33281796 PMCID: PMC7688782 DOI: 10.3389/fmicb.2020.596626] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2020] [Accepted: 10/19/2020] [Indexed: 11/13/2022] Open
Abstract
Advances in nanopore-based sequencing techniques have enabled rapid characterization of genomes and transcriptomes. An emerging application of this sequencing technology is point-of-care characterization of pathogenic bacteria. However, genome assessments alone are unable to provide a complete understanding of the pathogenic phenotype. Genome-scale metabolic reconstruction and analysis is a bottom-up Systems Biology technique that has elucidated the phenotypic nuances of antimicrobial resistant (AMR) bacteria and other human pathogens. Combining these genome-scale models (GEMs) with point-of-care nanopore sequencing is a promising strategy for combating the emerging health challenge of AMR pathogens. However, the sequencing errors inherent to the nanopore technique may negatively affect the quality, and therefore the utility, of GEMs reconstructed from nanopore assemblies. Here we describe and validate a workflow for rapid construction of GEMs from nanopore (MinION) derived assemblies. Benchmarking the pipeline against a high-quality reference GEM of Escherichia coli K-12 resulted in nanopore-derived models that were >99% complete even at sequencing depths of less than 10× coverage. Applying the pipeline to clinical isolates of pathogenic bacteria resulted in strain-specific GEMs that identified canonical AMR genome content and enabled simulations of strain-specific microbial growth. Additionally, we show that treating the sequencing run as a mock metagenome did not degrade the quality of models derived from metagenome assemblies. Taken together, this study demonstrates that combining nanopore sequencing with GEM construction pipelines enables rapid, in situ characterization of microbial metabolism.
Collapse
Affiliation(s)
- Jared T Broddrick
- Exobiology Branch, Space Science and Astrobiology Division, NASA Ames Research Center, Moffett Field, CA, United States
| | - Richard Szubin
- Department of Bioengineering, University of California, San Diego, La Jolla, CA, United States
| | - Charles J Norsigian
- Department of Bioengineering, University of California, San Diego, La Jolla, CA, United States
| | - Jonathan M Monk
- Department of Bioengineering, University of California, San Diego, La Jolla, CA, United States
| | - Bernhard O Palsson
- Department of Bioengineering, University of California, San Diego, La Jolla, CA, United States
| | - Mary N Parenteau
- Exobiology Branch, Space Science and Astrobiology Division, NASA Ames Research Center, Moffett Field, CA, United States
| |
Collapse
|
195
|
Utter DR, He X, Cavanaugh CM, McLean JS, Bor B. The saccharibacterium TM7x elicits differential responses across its host range. THE ISME JOURNAL 2020; 14:3054-3067. [PMID: 32839546 PMCID: PMC7784981 DOI: 10.1038/s41396-020-00736-6] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/22/2020] [Revised: 07/01/2020] [Accepted: 08/03/2020] [Indexed: 12/28/2022]
Abstract
Host range is a fundamental component of symbiotic interactions, yet it remains poorly characterized for the prevalent yet enigmatic subcategory of bacteria/bacteria symbioses. The recently characterized obligate bacterial epibiont Candidatus Nanosynbacter lyticus TM7x with its bacterial host Actinomyces odontolyticus XH001 offers an ideal system to study such a novel relationship. In this study, the host range of TM7x was investigated by coculturing TM7x with various related Actinomyces strains and characterizing their growth dynamics from initial infection through subsequent co-passages. Of the twenty-seven tested Actinomyces, thirteen strains, including XH001, could host TM7x, and further classified into "permissive" and "nonpermissive" based on their varying initial responses to TM7x. Ten permissive strains exhibited growth/crash/recovery phases following TM7x infection, with crash timing and extent dependent on initial TM7x dosage. Meanwhile, three nonpermissive strains hosted TM7x without a growth-crash phase despite high TM7x dosage. The physical association of TM7x with all hosts, including nonpermissive strains, was confirmed by microscopy. Comparative genomic analyses revealed distinguishing genomic features between permissive and nonpermissive hosts. Our results expand the concept of host range beyond a binary to a wider spectrum, and the varying susceptibility of Actinomyces strains to TM7x underscores how small genetic differences between hosts can underly divergent selective trajectories.
Collapse
Affiliation(s)
- Daniel R Utter
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, 02138, USA
| | - Xuesong He
- Department of Microbiology, The Forsyth Institute, Cambridge, MA, 02142, USA
- Department of Oral Medicine, Infection and Immunity, Harvard School of Dental Medicine, Boston, MA, 02115, USA
| | - Colleen M Cavanaugh
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, 02138, USA
| | - Jeffrey S McLean
- Department of Periodontics, University of Washington, Seattle, WA, 98119, USA
| | - Batbileg Bor
- Department of Microbiology, The Forsyth Institute, Cambridge, MA, 02142, USA.
- Department of Oral Medicine, Infection and Immunity, Harvard School of Dental Medicine, Boston, MA, 02115, USA.
| |
Collapse
|
196
|
Hunter ES, Paight C, Lane CE. Metabolic Contributions of an Alphaproteobacterial Endosymbiont in the Apicomplexan Cardiosporidium cionae. Front Microbiol 2020; 11:580719. [PMID: 33335517 PMCID: PMC7737231 DOI: 10.3389/fmicb.2020.580719] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Accepted: 11/05/2020] [Indexed: 12/27/2022] Open
Abstract
Apicomplexa is a diverse protistan phylum composed almost exclusively of metazoan-infecting parasites, including the causative agents of malaria, cryptosporidiosis, and toxoplasmosis. A single apicomplexan genus, Nephromyces, was described in 2010 as a mutualist partner to its tunicate host. Here we present genomic and transcriptomic data from the parasitic sister species to this mutualist, Cardiosporidium cionae, and its associated bacterial endosymbiont. Cardiosporidium cionae and Nephromyces both infect tunicate hosts, localize to similar organs within these hosts, and maintain bacterial endosymbionts. Though many other protists are known to harbor bacterial endosymbionts, these associations are completely unknown in Apicomplexa outside of the Nephromycidae clade. Our data indicate that a vertically transmitted α-proteobacteria has been retained in each lineage since Nephromyces and Cardiosporidium diverged. This α-proteobacterial endosymbiont has highly reduced metabolic capabilities, but contributes the essential amino acid lysine, and essential cofactor lipoic acid to C. cionae. This partnership likely reduces resource competition with the tunicate host. However, our data indicate that the contribution of the single α-proteobacterial endosymbiont in C. cionae is minimal compared to the three taxa of endosymbionts present in the Nephromyces system, and is a potential explanation for the virulence disparity between these lineages.
Collapse
Affiliation(s)
- Elizabeth Sage Hunter
- Department of Biological Sciences, University of Rhode Island, Kingston, RI, United States
| | - Christopher Paight
- Department of Ecology, Evolution & Marine Biology, University of California, Santa Barbara, Santa Barbara, CA, United States
| | - Christopher E. Lane
- Department of Biological Sciences, University of Rhode Island, Kingston, RI, United States
| |
Collapse
|
197
|
Complete Genome Sequence of Microbacterium sp. Strain Nx66, Isolated from Waters Contaminated with Petrochemicals in El Saf-Saf Valley, Algeria. Microbiol Resour Announc 2020; 9:9/47/e01130-20. [PMID: 33214306 PMCID: PMC7679099 DOI: 10.1128/mra.01130-20] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
Microbacterium sp. strain Nx66 was isolated from waters contaminated by petrochemical effluents collected in Algeria. Its genome was sequenced using Illumina MiSeq (2 × 150-bp read pairs) and Oxford Nanopore (long reads) technologies and was assembled using Unicycler. It is composed of one chromosome of 3.42 Mb and one plasmid of 34.22 kb. Microbacterium sp. strain Nx66 was isolated from waters contaminated by petrochemical effluents collected in Algeria. Its genome was sequenced using Illumina MiSeq (2 × 150-bp read pairs) and Oxford Nanopore (long reads) technologies and was assembled using Unicycler. It is composed of one chromosome of 3.42 Mb and one plasmid of 34.22 kb.
Collapse
|
198
|
Tsuji JM, Tran N, Schiff SL, Venkiteswaran JJ, Molot LA, Tank M, Hanada S, Neufeld JD. Anoxygenic photosynthesis and iron-sulfur metabolic potential of Chlorobia populations from seasonally anoxic Boreal Shield lakes. THE ISME JOURNAL 2020; 14:2732-2747. [PMID: 32747714 PMCID: PMC7784702 DOI: 10.1038/s41396-020-0725-0] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/28/2019] [Revised: 07/02/2020] [Accepted: 07/20/2020] [Indexed: 12/16/2022]
Abstract
Aquatic environments with high levels of dissolved ferrous iron and low levels of sulfate serve as an important systems for exploring biogeochemical processes relevant to the early Earth. Boreal Shield lakes, which number in the tens of millions globally, commonly develop seasonally anoxic waters that become iron rich and sulfate poor, yet the iron-sulfur microbiology of these systems has been poorly examined. Here we use genome-resolved metagenomics and enrichment cultivation to explore the metabolic diversity and ecology of anoxygenic photosynthesis and iron/sulfur cycling in the anoxic water columns of three Boreal Shield lakes. We recovered four high-completeness and low-contamination draft genome bins assigned to the class Chlorobia (formerly phylum Chlorobi) from environmental metagenome data and enriched two novel sulfide-oxidizing species, also from the Chlorobia. The sequenced genomes of both enriched species, including the novel "Candidatus Chlorobium canadense", encoded the cyc2 gene that is associated with photoferrotrophy among cultured Chlorobia members, along with genes for phototrophic sulfide oxidation. One environmental genome bin also encoded cyc2. Despite the presence of cyc2 in the corresponding draft genome, we were unable to induce photoferrotrophy in "Ca. Chlorobium canadense". Genomic potential for phototrophic sulfide oxidation was more commonly detected than cyc2 among environmental genome bins of Chlorobia, and metagenome and cultivation data suggested the potential for cryptic sulfur cycling to fuel sulfide-based growth. Overall, our results provide an important basis for further probing the functional role of cyc2 and indicate that anoxygenic photoautotrophs in Boreal Shield lakes could have underexplored photophysiology pertinent to understanding Earth's early microbial communities.
Collapse
Affiliation(s)
- J M Tsuji
- University of Waterloo, 200 University Avenue West, Waterloo, ON, N2L 3G1, Canada
| | - N Tran
- University of Waterloo, 200 University Avenue West, Waterloo, ON, N2L 3G1, Canada
| | - S L Schiff
- University of Waterloo, 200 University Avenue West, Waterloo, ON, N2L 3G1, Canada
| | - J J Venkiteswaran
- University of Waterloo, 200 University Avenue West, Waterloo, ON, N2L 3G1, Canada
- Wilfrid Laurier University, 75 University Avenue West, Waterloo, ON, N2L 3C5, Canada
| | - L A Molot
- York University, 4700 Keele Street, Toronto, ON, M3J 1P3, Canada
| | - M Tank
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures GmbH, Inhoffenstrasse 7B, 38124, Braunschweig, Germany
- Tokyo Metropolitan University, 1-1 Minami-osawa, Hachioji, Tokyo, 192-0397, Japan
| | - S Hanada
- Tokyo Metropolitan University, 1-1 Minami-osawa, Hachioji, Tokyo, 192-0397, Japan
| | - J D Neufeld
- University of Waterloo, 200 University Avenue West, Waterloo, ON, N2L 3G1, Canada.
| |
Collapse
|
199
|
Alker AT, Delherbe N, Purdy TN, Moore BS, Shikuma NJ. Genetic examination of the marine bacterium Pseudoalteromonas luteoviolacea and effects of its metamorphosis-inducing factors. Environ Microbiol 2020; 22:4689-4701. [PMID: 32840026 PMCID: PMC8214333 DOI: 10.1111/1462-2920.15211] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Revised: 08/14/2020] [Accepted: 08/22/2020] [Indexed: 12/13/2022]
Abstract
Pseudoalteromonas luteoviolacea is a globally distributed marine bacterium that stimulates the metamorphosis of marine animal larvae, an important bacteria-animal interaction that can promote the recruitment of animals to benthic ecosystems. Recently, different P. luteoviolacea isolates have been shown to produce two stimulatory factors that can induce tubeworm and coral metamorphosis; Metamorphosis-Associated Contractile structures (MACs) and tetrabromopyrrole (TBP) respectively. However, it remains unclear what proportion of P. luteoviolacea isolates possess the genes encoding MACs, and what phenotypic effect MACs and TBP have on other larval species. Here, we show that 9 of 19 sequenced P. luteoviolacea genomes genetically encode both MACs and TBP. While P. luteoviolacea biofilms producing MACs stimulate the metamorphosis of the tubeworm Hydroides elegans, TBP biosynthesis genes had no effect under the conditions tested. Although MACs are lethal to larvae of the cnidarian Hydractinia symbiologicarpus, P. luteoviolacea mutants unable to produce MACs are capable of stimulating metamorphosis. Our findings reveal a hidden complexity of interactions between a single bacterial species, the factors it produces and two species of larvae belonging to different phyla.
Collapse
Affiliation(s)
- Amanda T. Alker
- Department of Biology and Viral Information Institute, San Diego State University, San Diego, CA, 92182
| | - Nathalie Delherbe
- Department of Biology and Viral Information Institute, San Diego State University, San Diego, CA, 92182
| | - Trevor N. Purdy
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, CA, 92093
| | - Bradley S. Moore
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, CA, 92093
| | - Nicholas J. Shikuma
- Department of Biology and Viral Information Institute, San Diego State University, San Diego, CA, 92182
| |
Collapse
|
200
|
Duar RM, Casaburi G, Mitchell RD, Scofield LN, Ortega Ramirez CA, Barile D, Henrick BM, Frese SA. Comparative Genome Analysis of Bifidobacterium longum subsp. infantis Strains Reveals Variation in Human Milk Oligosaccharide Utilization Genes among Commercial Probiotics. Nutrients 2020; 12:nu12113247. [PMID: 33114073 PMCID: PMC7690671 DOI: 10.3390/nu12113247] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Revised: 10/16/2020] [Accepted: 10/19/2020] [Indexed: 12/23/2022] Open
Abstract
Dysbiosis is associated with acute and long-term consequences for neonates. Probiotics can be effective in limiting the growth of bacteria associated with dysbiosis and promoting the healthy development of the infant microbiome. Given its adaptation to the infant gut, and promising data from animal and in vitro models, Bifidobacterium longum subsp. infantis is an attractive candidate for use in infant probiotics. However, strain-level differences in the ability of commercialized strains to utilize human milk oligosaccharides (HMOs) may have implications in the performance of strains in the infant gut. In this study, we characterized twelve B. infantis probiotic strains and identified two main variants in one of the HMO utilization gene clusters. Some strains possessed the full repertoire of HMO utilization genes (H5-positive strains), while H5-negative strains lack an ABC-type transporter known to bind core HMO structures. H5-positive strains achieved significantly superior growth on lacto-N-tetraose and lacto-N-neotetraose. In vitro, H5-positive strains had a significant fitness advantage over H5-negative strains, which was also observed in vivo in breastfed infants. This work provides evidence of the functional implications of genetic differences among B. infantis strains and highlights that genotype and HMO utilization phenotype should be considered when selecting a strain for probiotic use in infants.
Collapse
Affiliation(s)
- Rebbeca M. Duar
- Evolve BioSystems, Inc., Davis, CA 95618, USA; (R.M.D.); (G.C.); (R.D.M.); (L.N.C.S.); (C.A.O.R.); (B.M.H.)
| | - Giorgio Casaburi
- Evolve BioSystems, Inc., Davis, CA 95618, USA; (R.M.D.); (G.C.); (R.D.M.); (L.N.C.S.); (C.A.O.R.); (B.M.H.)
| | - Ryan D. Mitchell
- Evolve BioSystems, Inc., Davis, CA 95618, USA; (R.M.D.); (G.C.); (R.D.M.); (L.N.C.S.); (C.A.O.R.); (B.M.H.)
| | - Lindsey N.C. Scofield
- Evolve BioSystems, Inc., Davis, CA 95618, USA; (R.M.D.); (G.C.); (R.D.M.); (L.N.C.S.); (C.A.O.R.); (B.M.H.)
| | - Camila A. Ortega Ramirez
- Evolve BioSystems, Inc., Davis, CA 95618, USA; (R.M.D.); (G.C.); (R.D.M.); (L.N.C.S.); (C.A.O.R.); (B.M.H.)
| | - Daniela Barile
- Foods for Health Institute, University of California at Davis, Davis, CA 95616, USA;
- Department of Food Science and Technology, University of California at Davis, Davis, CA 95616, USA
| | - Bethany M. Henrick
- Evolve BioSystems, Inc., Davis, CA 95618, USA; (R.M.D.); (G.C.); (R.D.M.); (L.N.C.S.); (C.A.O.R.); (B.M.H.)
- Department of Food Science and Technology, University of Nebraska, Lincoln, NE 68588, USA
| | - Steven A. Frese
- Evolve BioSystems, Inc., Davis, CA 95618, USA; (R.M.D.); (G.C.); (R.D.M.); (L.N.C.S.); (C.A.O.R.); (B.M.H.)
- Department of Food Science and Technology, University of Nebraska, Lincoln, NE 68588, USA
- Correspondence: ; Tel.: +1-530-747-2045
| |
Collapse
|