201
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Bunse C, Koch H, Breider S, Simon M, Wietz M. Sweet spheres: succession and CAZyme expression of marine bacterial communities colonizing a mix of alginate and pectin particles. Environ Microbiol 2021; 23:3130-3148. [PMID: 33876546 DOI: 10.1111/1462-2920.15536] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Revised: 04/06/2021] [Accepted: 04/15/2021] [Indexed: 12/24/2022]
Abstract
Polysaccharide particles are important substrates and microhabitats for marine bacteria. However, substrate-specific bacterial dynamics in mixtures of particle types with different polysaccharide composition, as likely occurring in natural habitats, are undescribed. Here, we studied the composition, functional diversity and gene expression of marine bacterial communities colonizing a mix of alginate and pectin particles. Amplicon, metagenome and metatranscriptome sequencing revealed that communities on alginate and pectin particles significantly differed from their free-living counterparts. Unexpectedly, microbial dynamics on alginate and pectin particles were similar, with predominance of amplicon sequence variants (ASVs) from Tenacibaculum, Colwellia, Psychrobium and Psychromonas. Corresponding metagenome-assembled genomes (MAGs) expressed diverse alginate lyases, several colocalized in polysaccharide utilization loci. Only a single, low-abundant MAG showed elevated transcript abundances of pectin-degrading enzymes. One specific Glaciecola ASV dominated the free-living fraction, possibly persisting on particle-derived oligomers through different glycoside hydrolases. Elevated ammonium uptake and metabolism signified nitrogen as an important factor for degrading carbon-rich particles, whereas elevated methylcitrate and glyoxylate cycles suggested nutrient limitation in surrounding waters. The bacterial preference for alginate, whereas pectin primarily served as colonization scaffold, illuminates substrate-driven dynamics within mixed polysaccharide pools. These insights expand our understanding of bacterial niche specialization and the biological carbon pump in macroalgae-rich habitats.
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Affiliation(s)
- Carina Bunse
- Helmholtz Institute for Functional Marine Biodiversity at the University of Oldenburg, Oldenburg, Germany.,Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Bremerhaven, Germany
| | - Hanna Koch
- Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, Oldenburg, Germany.,Department of Microbiology, Radboud University Nijmegen, Nijmegen, The Netherlands
| | - Sven Breider
- Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, Oldenburg, Germany
| | - Meinhard Simon
- Helmholtz Institute for Functional Marine Biodiversity at the University of Oldenburg, Oldenburg, Germany.,Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, Oldenburg, Germany
| | - Matthias Wietz
- Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Bremerhaven, Germany.,Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, Oldenburg, Germany
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202
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Doña J, Virrueta Herrera S, Nyman T, Kunnasranta M, Johnson KP. Patterns of Microbiome Variation Among Infrapopulations of Permanent Bloodsucking Parasites. Front Microbiol 2021; 12:642543. [PMID: 33935998 PMCID: PMC8085356 DOI: 10.3389/fmicb.2021.642543] [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: 12/16/2020] [Accepted: 03/26/2021] [Indexed: 12/22/2022] Open
Abstract
While interspecific variation in microbiome composition can often be readily explained by factors such as host species identity, there is still limited knowledge of how microbiomes vary at scales lower than the species level (e.g., between individuals or populations). Here, we evaluated variation in microbiome composition of individual parasites among infrapopulations (i.e., populations of parasites of the same species living on a single host individual). To address this question, we used genome-resolved and shotgun metagenomic data of 17 infrapopulations (balanced design) of the permanent, bloodsucking seal louse Echinophthirius horridus sampled from individual Saimaa ringed seals Pusa hispida saimensis. Both genome-resolved and read-based metagenomic classification approaches consistently show that parasite infrapopulation identity is a significant factor that explains both qualitative and quantitative patterns of microbiome variation at the intraspecific level. This study contributes to the general understanding of the factors driving patterns of intraspecific variation in microbiome composition, especially of bloodsucking parasites, and has implications for understanding how well-known processes occurring at higher taxonomic levels, such as phylosymbiosis, might arise in these systems.
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Affiliation(s)
- Jorge Doña
- Illinois Natural History Survey, Prairie Research Institute, University of Illinois at Urbana-Champaign, Champaign, IL, United States.,Departamento de Biología Animal, Universidad de Granada, Granada, Spain
| | - Stephany Virrueta Herrera
- Illinois Natural History Survey, Prairie Research Institute, University of Illinois at Urbana-Champaign, Champaign, IL, United States
| | - Tommi Nyman
- Department of Ecosystems in the Barents Region, Norwegian Institute of Bioeconomy Research, Svanvik, Norway
| | - Mervi Kunnasranta
- Department of Environmental and Biological Sciences, University of Eastern Finland, Joensuu, Finland.,Natural Resources Institute Finland, Joensuu, Finland
| | - Kevin P Johnson
- Illinois Natural History Survey, Prairie Research Institute, University of Illinois at Urbana-Champaign, Champaign, IL, United States
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203
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Madeira CL, Menezes O, Park D, Jog KV, Hatt JK, Gavazza S, Krzmarzick MJ, Sierra-Alvarez R, Spain JC, Konstantinidis KT, Field JA. Bacteria Make a Living Breathing the Nitroheterocyclic Insensitive Munitions Compound 3-Nitro-1,2,4-triazol-5-one (NTO). ENVIRONMENTAL SCIENCE & TECHNOLOGY 2021; 55:5806-5814. [PMID: 33835790 DOI: 10.1021/acs.est.0c07161] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
The nitroheterocyclic 3-nitro-1,2,4-triazol-5-one (NTO) is an ingredient of insensitive explosives increasingly used by the military, becoming an emergent environmental pollutant. Cometabolic biotransformation of NTO occurs in mixed microbial cultures in soils and sludges with excess electron-donating substrates. Herein, we present the unusual energy-yielding metabolic process of NTO respiration, in which the NTO reduction to 3-amino-1,2,4-triazol-5-one (ATO) is linked to the anoxic acetate oxidation to CO2 by a culture enriched from municipal anaerobic digester sludge. Cell growth was observed simultaneously with NTO reduction, whereas the culture was unable to grow in the presence of acetate only. Extremely low concentrations (0.06 mg L-1) of the uncoupler carbonyl cyanide m-chlorophenyl hydrazone inhibited NTO reduction, indicating that the process was linked to respiration. The ultimate evidence of NTO respiration was adenosine triphosphate production due to simultaneous exposure to NTO and acetate. Metagenome sequencing revealed that the main microorganisms (and relative abundances) were Geobacter anodireducens (89.3%) and Thauera sp. (5.5%). This study is the first description of a nitroheterocyclic compound being reduced by anaerobic respiration, shedding light on creative microbial processes that enable bacteria to make a living reducing NTO.
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Affiliation(s)
- Camila L Madeira
- Department of Chemical and Environmental Engineering, University of Arizona, Tucson, Arizona 85721-0011, United States
| | - Osmar Menezes
- Department of Chemical and Environmental Engineering, University of Arizona, Tucson, Arizona 85721-0011, United States
- Laboratório de Saneamento Ambiental, Departamento de Engenharia Civil e Ambiental, Universidade Federal de Pernambuco, Recife, Pernambuco 50740-530, Brazil
| | - Doyoung Park
- School of Civil and Environmental Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332-0355, United States
| | - Kalyani V Jog
- Department of Chemical and Environmental Engineering, University of Arizona, Tucson, Arizona 85721-0011, United States
| | - Janet K Hatt
- School of Civil and Environmental Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332-0355, United States
| | - Savia Gavazza
- Laboratório de Saneamento Ambiental, Departamento de Engenharia Civil e Ambiental, Universidade Federal de Pernambuco, Recife, Pernambuco 50740-530, Brazil
| | - Mark J Krzmarzick
- School of Civil and Environmental Engineering, Oklahoma State University, Stillwater, Oklahoma 74078, United States
| | - Reyes Sierra-Alvarez
- Department of Chemical and Environmental Engineering, University of Arizona, Tucson, Arizona 85721-0011, United States
| | - Jim C Spain
- School of Civil and Environmental Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332-0355, United States
- Center for Environmental Diagnostics & Bioremediation, University of West Florida, Pensacola, Florida 32514, United States
| | - Konstantinos T Konstantinidis
- School of Civil and Environmental Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332-0355, United States
| | - Jim A Field
- Department of Chemical and Environmental Engineering, University of Arizona, Tucson, Arizona 85721-0011, United States
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204
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McLean JS, Bor B, Kerns KA, Liu Q, To TT, Solden L, Hendrickson EL, Wrighton K, Shi W, He X. Acquisition and Adaptation of Ultra-small Parasitic Reduced Genome Bacteria to Mammalian Hosts. Cell Rep 2021; 32:107939. [PMID: 32698001 PMCID: PMC7427843 DOI: 10.1016/j.celrep.2020.107939] [Citation(s) in RCA: 61] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2019] [Revised: 06/20/2020] [Accepted: 06/30/2020] [Indexed: 12/31/2022] Open
Abstract
The first cultivated representative of the enigmatic phylum Saccharibacteria (formerly TM7) was isolated from humans and revealed an ultra-small cell size (200-300 nm), a reduced genome with limited biosynthetic capabilities, and a unique parasitic lifestyle. TM7x was the only cultivated member of the candidate phyla radiation (CPR), estimated to encompass 26% of the domain Bacteria. Here we report on divergent genomes from major lineages across the Saccharibacteria phylum in humans and mammals, as well as from ancient dental calculus. These lineages are present at high prevalence within hosts. Direct imaging reveals that all groups are ultra-small in size, likely feeding off commensal bacteria. Analyses suggest that multiple acquisition events in the past led to the current wide diversity, with convergent evolution of key functions allowing Saccharibacteria from the environment to adapt to mammals. Ultra-small, parasitic CPR bacteria represent a relatively unexplored paradigm of prokaryotic interactions within mammalian microbiomes.
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Affiliation(s)
- Jeffrey S McLean
- Department of Periodontics, University of Washington, Seattle, WA 98195, USA; Department of Microbiology, University of Washington, Seattle, WA 98195, 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
| | - Kristopher A Kerns
- Department of Periodontics, University of Washington, Seattle, WA 98195, USA
| | - Quanhui Liu
- Department of Periodontics, University of Washington, Seattle, WA 98195, USA
| | - Thao T To
- Department of Periodontics, University of Washington, Seattle, WA 98195, USA
| | - Lindsey Solden
- Department of Microbiology, The Ohio State University, Columbus, OH 43210, USA
| | - Erik L Hendrickson
- Department of Periodontics, University of Washington, Seattle, WA 98195, USA
| | - Kelly Wrighton
- Department of Microbiology, The Ohio State University, Columbus, OH 43210, USA
| | - Wenyuan Shi
- Department of Microbiology, The Forsyth Institute, Cambridge, MA 02142, 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
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205
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Bédard E, Trigui H, Liang J, Doberva M, Paranjape K, Lalancette C, Allegra S, Faucher SP, Prévost M. Local Adaptation of Legionella pneumophila within a Hospital Hot Water System Increases Tolerance to Copper. Appl Environ Microbiol 2021; 87:e00242-21. [PMID: 33674435 PMCID: PMC8117758 DOI: 10.1128/aem.00242-21] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Accepted: 02/25/2021] [Indexed: 11/20/2022] Open
Abstract
In large-building water systems, Legionella pneumophila is exposed to common environmental stressors such as copper. The aim of this study was to evaluate the susceptibility to copper of L. pneumophila isolates recovered from various sites: two clinical and seven environmental isolates from hot water system biofilm and water and from cooling tower water. After a 1-week acclimation in simulated drinking water, strains were exposed to various copper concentrations (0.8 to 5 mg/liter) for over 672 h. Complete loss of culturability was observed for three isolates following copper exposure to 5 mg/liter for 672 h. Two sequence type 1427 (ST1427)-like isolates were highly sensitive to copper, while the other two, isolated from biofilm samples, maintained higher culturability. The expression of the copper resistance gene copA evaluated by reverse transcription-quantitative PCR (RT-qPCR) was significantly higher for the biofilm isolates. All four ST1427-like isolates were recovered from the same water system during an outbreak. Whole-genome sequencing results confirmed that the four isolates are very close phylogenetically, differing by only 29 single nucleotide polymorphisms, suggesting in situ adaptation to microenvironmental conditions, possibly due to epigenetic regulation. These results indicate that the immediate environment within a building water distribution system influences the tolerance of L. pneumophila to copper. Increased contact of L. pneumophila biofilm strains with copper piping or copper alloys in the heat exchanger might lead to local adaptation. The phenotypic differences observed between water and biofilm isolates from the hot water system of a health care facility warrants further investigation to assess the relevance of evaluating disinfection performances based on water sampling alone.IMPORTANCELegionella pneumophila is a pathogen indigenous to natural and large building water systems in the bulk and the biofilm phases. The immediate environment within a system can impact the tolerance of L. pneumophila to environmental stressors, including copper. In health care facilities, copper levels in water can vary, depending on water quality, plumbing materials, and age. This study evaluated the impact of the isolation site (water versus biofilm, hot water system versus cooling tower) within building water systems. Closely related strains isolated from a health care facility hot water system exhibited variable tolerance to copper stress, shown by differential expression of copA, with biofilm isolates displaying highest expression and tolerance. Relying on the detection of L. pneumophila in water samples following exposure to environmental stressors such as copper may underestimate the prevalence of L. pneumophila, leading to inappropriate risk management strategies and increasing the risk of exposure for vulnerable patients.
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Affiliation(s)
- Emilie Bédard
- Department of Civil Engineering, Polytechnique Montréal, Montréal, Quebec, Canada
- Department of Natural Resource Sciences, Faculty of Agricultural and Environmental Sciences, McGill University, Sainte-Anne-de-Bellevue, Quebec, Canada
| | - Hana Trigui
- Department of Civil Engineering, Polytechnique Montréal, Montréal, Quebec, Canada
| | - Jeffrey Liang
- Department of Natural Resource Sciences, Faculty of Agricultural and Environmental Sciences, McGill University, Sainte-Anne-de-Bellevue, Quebec, Canada
| | - Margot Doberva
- Department of Civil Engineering, Polytechnique Montréal, Montréal, Quebec, Canada
| | - Kiran Paranjape
- Department of Natural Resource Sciences, Faculty of Agricultural and Environmental Sciences, McGill University, Sainte-Anne-de-Bellevue, Quebec, Canada
| | - Cindy Lalancette
- Laboratoire de Santé Publique du Québec, Sainte-Anne-de-Bellevue, Quebec, Canada
| | - Séverine Allegra
- University of Lyon, UJM-Saint-Etienne, UMR 5600 CNRS, EVS-ISTHME, Saint-Etienne, France
| | - Sebastien P Faucher
- Department of Natural Resource Sciences, Faculty of Agricultural and Environmental Sciences, McGill University, Sainte-Anne-de-Bellevue, Quebec, Canada
| | - Michèle Prévost
- Department of Civil Engineering, Polytechnique Montréal, Montréal, Quebec, Canada
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206
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Thaler DS. Is Global Microbial Biodiversity Increasing, Decreasing, or Staying the Same? Front Ecol Evol 2021. [DOI: 10.3389/fevo.2021.565649] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Animal and plant biodiversity is decreasing. In contrast, the global direction and the pace of change in microbial, including viral, biodiversity is unknown. Important niches for microbial diversity occur in highly specific associations with plants and animals, and these niches are lost as hosts become extinct. The taxonomic diversity of human gut bacteria is reported to be decreasing. On the other hand, SARS-CoV-2 variation is increasing. Where microbes are concerned, Darwin’s “tangled bank” of interdependent organisms may be composed mostly of other microbes. There is the likelihood that as some classes of microbes become extinct, others evolve and diversify. A better handle on all processes that affect microbial biodiversity and their net balance is needed. Lack of insight into the dynamics of evolution of microbial biodiversity is arguably the single most profound and consequential unknown with regard to human knowledge of the biosphere. If some or all parts of microbial diversity are relentlessly increasing, then survey approaches may be too slow to ever catch up. New approaches, including single-molecule or single-cell sequencing in populations, as well as focused attention on modulators and vectors of vertical and horizontal evolution may offer more direct insights into some aspects of the pace of microbial evolution.
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207
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Soto-Girón MJ, Peña-Gonzalez A, Hatt JK, Montero L, Páez M, Ortega E, Smith S, Cevallos W, Trueba G, Konstantinidis KT, Levy K. Gut Microbiome Changes with Acute Diarrheal Disease in Urban Versus Rural Settings in Northern Ecuador. Am J Trop Med Hyg 2021; 104:2275-2285. [PMID: 33872206 DOI: 10.4269/ajtmh.20-0831] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Accepted: 02/15/2021] [Indexed: 12/12/2022] Open
Abstract
Previous studies have reported lower fecal bacterial diversity in urban populations compared with those living in rural settings. However, most of these studies compare geographically distant populations from different countries and even continents. The extent of differences in the gut microbiome in adjacent rural versus urban populations, and the role of such differences, if any, during enteric infections remain poorly understood. To provide new insights into these issues, we sampled the gut microbiome of young children with and without acute diarrheal disease (ADD) living in rural and urban areas in northern Ecuador. Shotgun metagenomic analyses of non-ADD samples revealed small but significant differences in the abundance of microbial taxa, including a greater abundance of Prevotella and a lower abundance of Bacteroides and Alistipes in rural populations. Greater and more significant shifts in taxon abundance, metabolic pathway abundance, and diversity were observed between ADD and non-ADD status when comparing urban to rural sites (Welch's t-test, P < 0.05). Collectively our data show substantial functional, diversity, and taxonomic shifts in the gut microbiome of urban populations with, ADD supporting the idea that the microbiome of rural populations may be more resilient to ADD episodes.
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Affiliation(s)
- Maria J Soto-Girón
- 1School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia
| | - Angela Peña-Gonzalez
- 1School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia
| | - Janet K Hatt
- 2School of Civil and Environmental Engineering, Georgia Institute of Technology, Atlanta, Georgia
| | - Lorena Montero
- 3Instituto de Microbiologia, Universidad San Francisco de Quito, Quito, Ecuador
| | - Maritza Páez
- 3Instituto de Microbiologia, Universidad San Francisco de Quito, Quito, Ecuador
| | - Estefania Ortega
- 3Instituto de Microbiologia, Universidad San Francisco de Quito, Quito, Ecuador
| | - Shanon Smith
- 4School of Public Health, University of Washington, Seattle, Washington
| | - William Cevallos
- 5Centro de Biomedicina, Universidad Central del Ecuador, Quito, Ecuador
| | - Gabriel Trueba
- 3Instituto de Microbiologia, Universidad San Francisco de Quito, Quito, Ecuador
| | - Konstantinos T Konstantinidis
- 1School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia.,2School of Civil and Environmental Engineering, Georgia Institute of Technology, Atlanta, Georgia
| | - Karen Levy
- 4School of Public Health, University of Washington, Seattle, Washington
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208
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Tian L, Mazloom R, Heath LS, Vinatzer BA. LINflow: a computational pipeline that combines an alignment-free with an alignment-based method to accelerate generation of similarity matrices for prokaryotic genomes. PeerJ 2021; 9:e10906. [PMID: 33828908 PMCID: PMC8000461 DOI: 10.7717/peerj.10906] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2020] [Accepted: 01/14/2021] [Indexed: 01/21/2023] Open
Abstract
Background Computing genomic similarity between strains is a prerequisite for genome-based prokaryotic classification and identification. Genomic similarity was first computed as Average Nucleotide Identity (ANI) values based on the alignment of genomic fragments. Since this is computationally expensive, faster and computationally cheaper alignment-free methods have been developed to estimate ANI. However, these methods do not reach the level of accuracy of alignment-based methods. Methods Here we introduce LINflow, a computational pipeline that infers pairwise genomic similarity in a set of genomes. LINflow takes advantage of the speed of the alignment-free sourmash tool to identify the genome in a dataset that is most similar to a query genome and the precision of the alignment-based pyani software to precisely compute ANI between the query genome and the most similar genome identified by sourmash. This is repeated for each new genome that is added to a dataset. The sequentially computed ANI values are stored as Life Identification Numbers (LINs), which are then used to infer all other pairwise ANI values in the set. We tested LINflow on four sets, 484 genomes in total, and compared the needed time and the generated similarity matrices with other tools. Results LINflow is up to 150 times faster than pyani and pairwise ANI values generated by LINflow are highly correlated with those computed by pyani. However, because LINflow infers most pairwise ANI values instead of computing them directly, ANI values occasionally depart from the ANI values computed by pyani. In conclusion, LINflow is a fast and memory-efficient pipeline to infer similarity among a large set of prokaryotic genomes. Its ability to quickly add new genome sequences to an already computed similarity matrix makes LINflow particularly useful for projects when new genome sequences need to be regularly added to an existing dataset.
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Affiliation(s)
- Long Tian
- School of Plant and Environmental Sciences, Virginia Tech, Blacksburg, VA, USA
| | - Reza Mazloom
- Department of Computer Science, Virginia Tech, Blacksburg, VA, USA
| | - Lenwood S Heath
- Department of Computer Science, Virginia Tech, Blacksburg, VA, USA
| | - Boris A Vinatzer
- School of Plant and Environmental Sciences, Virginia Tech, Blacksburg, VA, USA
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209
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Viver T, Conrad RE, Orellana LH, Urdiain M, González-Pastor JE, Hatt JK, Amann R, Antón J, Konstantinidis KT, Rosselló-Móra R. Distinct ecotypes within a natural haloarchaeal population enable adaptation to changing environmental conditions without causing population sweeps. THE ISME JOURNAL 2021; 15:1178-1191. [PMID: 33342997 PMCID: PMC8182817 DOI: 10.1038/s41396-020-00842-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Revised: 10/26/2020] [Accepted: 11/11/2020] [Indexed: 01/29/2023]
Abstract
Microbial communities thriving in hypersaline brines of solar salterns are highly resistant and resilient to environmental changes, and salinity is a major factor that deterministically influences community structure. Here, we demonstrate that this resilience occurs even after rapid osmotic shocks caused by a threefold change in salinity (a reduction from 34 to 12% salts) leading to massive amounts of archaeal cell lysis. Specifically, our temporal metagenomic datasets identified two co-occurring ecotypes within the most dominant archaeal population of the brines Haloquadratum walsbyi that exhibited different salt concentration preferences. The dominant ecotype was generally more abundant and occurred in high-salt conditions (34%); the low abundance ecotype always co-occurred but was enriched at salinities around 20% or lower and carried unique gene content related to solute transport and gene regulation. Despite their apparent distinct ecological preferences, the ecotypes did not outcompete each other presumably due to weak functional differentiation between them. Further, the osmotic shock selected for a temporal increase in taxonomic and functional diversity at both the Hqr. walsbyi population and whole-community levels supporting the specialization-disturbance hypothesis, that is, the expectation that disturbance favors generalists. Altogether, our results provide new insights into how intraspecies diversity is maintained in light of substantial gene-content differences and major environmental perturbations.
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Affiliation(s)
- Tomeu Viver
- grid.466857.e0000 0000 8518 7126Marine Microbiology Group, Department of Animal and Microbial Biodiversity, Mediterranean Institute for Advanced Studies (IMEDEA, CSIC-UIB), Esporles, Spain
| | - Roth E. Conrad
- grid.213917.f0000 0001 2097 4943School of Civil and Environmental Engineering, Georgia Institute of Technology, Atlanta, GA USA
| | - Luis H. Orellana
- grid.419529.20000 0004 0491 3210Department of Molecular Ecology, Max-Planck-Institut für Marine Mikrobiologie, Bremen, D-28359 Germany
| | - Mercedes Urdiain
- grid.466857.e0000 0000 8518 7126Marine Microbiology Group, Department of Animal and Microbial Biodiversity, Mediterranean Institute for Advanced Studies (IMEDEA, CSIC-UIB), Esporles, Spain
| | - José E. González-Pastor
- grid.462011.00000 0001 2199 0769Laboratory of Molecular Adaptation, Department of Molecular Evolution, Centro de Astrobiología, Consejo Superior de Investigaciones Científicas—Instituto Nacional de Técnica Aeroespacial, Madrid, Spain
| | - Janet K. Hatt
- grid.213917.f0000 0001 2097 4943School of Civil and Environmental Engineering, Georgia Institute of Technology, Atlanta, GA USA
| | - Rudolf Amann
- grid.419529.20000 0004 0491 3210Department of Molecular Ecology, Max-Planck-Institut für Marine Mikrobiologie, Bremen, D-28359 Germany
| | - Josefa Antón
- grid.5268.90000 0001 2168 1800Department of Physiology, Genetics and Microbiology, University of Alicante, Alicante, Spain
| | - Konstantinos T. Konstantinidis
- grid.213917.f0000 0001 2097 4943School of Civil and Environmental Engineering, Georgia Institute of Technology, Atlanta, GA USA
| | - Ramon Rosselló-Móra
- grid.466857.e0000 0000 8518 7126Marine Microbiology Group, Department of Animal and Microbial Biodiversity, Mediterranean Institute for Advanced Studies (IMEDEA, CSIC-UIB), Esporles, Spain
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210
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Mehta P, Deshmukh K, Dagar SS, Dhakephalkar PK, Lanjekar VB. Genome sequencing and analysis of a psychrotrophic methanogen Methanosarcina sp. nov. MSH10X1 cultured from methane hydrate deposits of Krishna Godavari Basin of India. Mar Genomics 2021; 59:100864. [PMID: 33810993 DOI: 10.1016/j.margen.2021.100864] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Revised: 03/12/2021] [Accepted: 03/13/2021] [Indexed: 10/21/2022]
Abstract
Methanosarcina sp. strain MSH10X1, a psychrotrophic methanogen, was isolated from sub-seafloor methane hydrate deposits of Krishna Godavari Basin on India's east coast. The strain could grow from 5 to 40 °C following all three i.e. methylotrophic, acetoclastic, and hydrogenotrophic modes of methanogenesis utilizing different substrates like methanol, trimethylamine, H2/CO2 (80/20), acetate, valerate, isobutyrate, isopropanol, and isobutanol. The genome sequencing and analysis of this strain revealed a circular chromosome of 3,557,383 bp length having 42.47 mol% G + C content, which consisted of 3110 coding genes, 58 tRNA genes, and 3 rRNA operons. The KEGG analysis highlighted the presence of genes responsible for all three modes of methanogenesis. The presence of genes like mtaB, mtaC, and mttB in the genome provided evidence for possible adaptation of strain MSH10X1 in the deep sea's low-temperature conditions.
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Affiliation(s)
- Pooja Mehta
- Bioenergy Group, Agharkar Research Institute, G.G Agarkar Road, Pune 411004, Maharashtra, India; Max Planck Institute for Chemical Ecology, Hans-Knöll-Straße 8, Jena 07745, Germany
| | - Kalyani Deshmukh
- Bioenergy Group, Agharkar Research Institute, G.G Agarkar Road, Pune 411004, Maharashtra, India; Savitribai Phule Pune University, Ganeshkhind, Pune 411007, Maharashtra, India
| | - Sumit Singh Dagar
- Bioenergy Group, Agharkar Research Institute, G.G Agarkar Road, Pune 411004, Maharashtra, India; Savitribai Phule Pune University, Ganeshkhind, Pune 411007, Maharashtra, India
| | - Prashant K Dhakephalkar
- Bioenergy Group, Agharkar Research Institute, G.G Agarkar Road, Pune 411004, Maharashtra, India; Savitribai Phule Pune University, Ganeshkhind, Pune 411007, Maharashtra, India
| | - Vikram B Lanjekar
- Bioenergy Group, Agharkar Research Institute, G.G Agarkar Road, Pune 411004, Maharashtra, India; Savitribai Phule Pune University, Ganeshkhind, Pune 411007, Maharashtra, India.
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211
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Vorimore F, Hölzer M, Liebler-Tenorio EM, Barf LM, Delannoy S, Vittecoq M, Wedlarski R, Lécu A, Scharf S, Blanchard Y, Fach P, Hsia RC, Bavoil PM, Rosselló-Móra R, Laroucau K, Sachse K. Evidence for the existence of a new genus Chlamydiifrater gen. nov. inside the family Chlamydiaceae with two new species isolated from flamingo (Phoenicopterus roseus): Chlamydiifrater phoenicopteri sp. nov. and Chlamydiifrater volucris sp. nov. Syst Appl Microbiol 2021; 44:126200. [PMID: 34298369 DOI: 10.1016/j.syapm.2021.126200] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Revised: 03/01/2021] [Accepted: 03/18/2021] [Indexed: 11/17/2022]
Abstract
The family Chlamydiaceae currently comprises a single genus Chlamydia, with 11 validly published species and seven more taxa. It includes the human pathogens Chlamydia (C.) trachomatis, C. pneumoniae and C. psittaci, a zoonotic agent causing avian chlamydiosis and human psittacosis, as well as other proven or potential pathogens in ruminants, birds, snakes, reptiles and turtles. During routine testing of 15 apparently healthy captive flamingos in a zoo in 2011, an atypical strain of Chlamydiaceae was detected by real-time PCR of cloacal swab samples. Sequence analysis of the 16S rRNA gene revealed high similarity to the uncultured Chlamydiales bacterium clone 122, which previously had been found in gulls. As more samples were collected during annual campaigns of the flamingo ringing program in southern France from 2012 to 2015, Chlamydiaceae-specific DNA was detected by PCR in 30.9% of wild birds. From these samples, three strains were successfully grown in cell culture. Ultrastructural analysis, comparison of 16S and 23S rRNA gene sequences, whole-genome analysis based on de novo hybrid-assembled sequences of the new strains as well as subsequent calculation of taxonomic parameters revealed that the relatedness of the flamingo isolates to established members of the family Chlamydiaceae was sufficiently distant to indicate that the three strains belong to two distinct species within a new genus. Based on these data, we propose the introduction of Chlamydiifrater gen. nov., as a new genus, and Chlamydiifrater phoenicopteri sp. nov. and Chlamydiifrater volucris sp. nov., as two new species of the genus.
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Affiliation(s)
- F Vorimore
- University Paris-Est, Anses, Animal Health Laboratory, Bacterial Zoonoses Unit, Maisons-Alfort, France.
| | - M Hölzer
- Robert Koch Institute, MF1 Bioinformatics, Berlin, Germany
| | - E M Liebler-Tenorio
- Friedrich-Loeffler-Institut (Federal Research Institute for Animal Health), Institute of Molecular Pathogenesis, Germany
| | - L-M Barf
- Friedrich-Schiller-Universität Jena, RNA Bioinformatics and High-Throughput Analysis, Jena, Germany
| | - S Delannoy
- University Paris-Est, Anses, Food Research Laboratory, IdentyPath Platform, Maisons-Alfort, France
| | - M Vittecoq
- Tour du Valat, Centre de recherche pour la conservation des zones humides méditerranéennes, Le Sambuc, Arles, France
| | - R Wedlarski
- Bioparc - Zoo de Doué la fontaine, 103 rue de Cholet, 49700 Doué la Fontaine, France
| | - A Lécu
- Parc Zoologique de Paris, avenue de Daumesnil, 75012 Paris, France
| | - S Scharf
- Friedrich-Loeffler-Institut (Federal Research Institute for Animal Health), Institute of Molecular Pathogenesis, Germany
| | - Y Blanchard
- Unit of Viral Genetics and Biosafety, ANSES, Laboratory of Ploufragan, Ploufragan, France
| | - P Fach
- University Paris-Est, Anses, Food Research Laboratory, IdentyPath Platform, Maisons-Alfort, France
| | - R C Hsia
- University of Maryland, Electron Microscopy Core Imaging Facility, Baltimore, MD 21201, USA
| | - P M Bavoil
- University of Maryland, Department of Microbial Pathogenesis, Baltimore, MD 21201, USA
| | - R Rosselló-Móra
- Marine Microbiology Group, Department of Animal and Microbial Biodiversity, Mediterranean Institute for Advanced Studies, 07190 Esporles, Spain
| | - K Laroucau
- University Paris-Est, Anses, Animal Health Laboratory, Bacterial Zoonoses Unit, Maisons-Alfort, France
| | - K Sachse
- Friedrich-Schiller-Universität Jena, RNA Bioinformatics and High-Throughput Analysis, Jena, Germany
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212
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Fanelli F, Caputo L, Quintieri L. Phenotypic and genomic characterization of Pseudomonas putida ITEM 17297 spoiler of fresh vegetables: Focus on biofilm and antibiotic resistance interaction. Curr Res Food Sci 2021; 4:74-82. [PMID: 33718885 PMCID: PMC7932912 DOI: 10.1016/j.crfs.2021.02.001] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Revised: 02/01/2021] [Accepted: 02/02/2021] [Indexed: 11/30/2022] Open
Abstract
Pseudomonas putida is widely recognized as a spoiler of fresh foods under cold storage, and recently associated also with infections in clinical settings. The presence of antibiotic resistance genes (ARGs) could be acquired and transmitted by horizontal genetic transfer and further increase the risk associated with its persistence in food and the need to be deeper investigated. Thus, in this work we presented a genomic and phenotypic analysis of the psychrotrophic P. putida ITEM 17297 to provide new insight into AR mechanisms by this species until now widely studied only for its spoilage traits. ITEM 17297 displayed resistance to several classes of antibiotics and it also formed huge amounts of biofilm; this latter registered increases at 15 °C in comparison to the optimum growth condition (30 °C). After ITEM 17297 biofilms exposure to antibiotic concentrations higher than 10-fold their MIC values no eradication occurred; interestingly, biomasses of biofilm cultivated at 15 °C increased their amount in a dose-dependent manner. Genomic analyses revealed determinants (RND-systems, ABC-transporters, and MFS-efflux pumps) for multi-drugs resistance (β-lactams, macrolides, nalidixic acid, tetracycline, fusidic acid and bacitracin) and a novel ampC allele. Biofilm and motility related pathways were depicted underlying their contribution to AR. Based on these results, underestimated psychrotrophic pseudomonas, such as the herein studied ITEM 17297 strain, might assume relevance in relation to the risk associated with the transfer of antimicrobial resistance genes to humans through cold stored contaminated foods. P. putida biofilm and AR related molecular targets herein identified will provide a basis to clarify the interaction between AR and biofilm formation and to develop novel strategies to counteract the persistence of multidrug resistant P. putida in the food chain. Multidrug resistant Pseudomonas putida ITEM 17297 was isolated from fresh vegetables. Determinants for AR and biofilm formation were identified by genomic analysis. Biofilm increased more than 10-fold antibiotic MIC value of planktonic cells. Cold adapted biofilm increased its biomass under CHL, NA, and ERY pressure. New insight into the risk for P. putida spread in the food chain were provided.
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Affiliation(s)
- Francesca Fanelli
- Institute of Sciences of Food Production, National Research Council of Italy, V. G. Amendola 122/O, 70126, Bari, Italy
| | - Leonardo Caputo
- Institute of Sciences of Food Production, National Research Council of Italy, V. G. Amendola 122/O, 70126, Bari, Italy
| | - Laura Quintieri
- Institute of Sciences of Food Production, National Research Council of Italy, V. G. Amendola 122/O, 70126, Bari, Italy
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213
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Rathore DS, Sheikh MA, Gohel SD, Singh SP. Genetic and Phenotypic Heterogeneity of the Nocardiopsis alba Strains of Seawater. Curr Microbiol 2021; 78:1377-1387. [PMID: 33646381 DOI: 10.1007/s00284-021-02420-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2020] [Accepted: 02/10/2021] [Indexed: 11/29/2022]
Abstract
This study deals with the genetic and phenotypic heterogeneity of the marine Nocardiopsis alba strains isolated during pre-monsoon, monsoon and post-monsoon seasons. The isolates were characterized for their morphological and biochemical attributes, growth media preferences, antibiotic susceptibility and extracellular enzyme secretion. Nocardiopsis alba strains were assessed against 12 different antibiotics, and the responses were expressed in terms of the multiple antibiotic resistance (MAR) number. The majority of the strains produced multiple extracellular enzymes: proteases, amylases and lipases. Further, the strains were characterized on the basis of 16S rRNA gene sequencing and the majority were identified as Nocardiopsis alba along with few strains of Streptomyces lopnurensis, Nocardiopsis synnemataformans and Nocardiopsis dassonvillei. Neighbor-joining (NJ) phylogenetic tree suggested variation among the genetically similar Nocardiopsis alba species. The study establishes significant heterogeneity with respect to genetic and phenotypic characteristics of the strains of Nocardiopsis alba. Phylogenetic tree and phenogram-based comparison reflect the heterogeneity in terms of different clustering patterns of the strains. Further, the whole genome sequence data available in the literature also confirm the observed heterogeneity. Nocardiopsis alba strains displayed a relatively regressive pattern of dependence on the environmental factors based on the canonical correspondence analysis plot. The study represents cultivation, characterization, phylogenetic analysis and enzymatic potential of the Nocardiopsis alba species of seawater origin.
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Affiliation(s)
- Dalip Singh Rathore
- Department of Biosciences, UGC Centre for Advanced Studies (CAS), Saurashtra University, Rajkot, Gujarat, India
| | - Mahejbin A Sheikh
- Department of Biosciences, UGC Centre for Advanced Studies (CAS), Saurashtra University, Rajkot, Gujarat, India
| | - Sangeeta D Gohel
- Department of Biosciences, UGC Centre for Advanced Studies (CAS), Saurashtra University, Rajkot, Gujarat, India
| | - Satya P Singh
- Department of Biosciences, UGC Centre for Advanced Studies (CAS), Saurashtra University, Rajkot, Gujarat, India.
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214
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The Reliability of Metagenome-Assembled Genomes (MAGs) in Representing Natural Populations: Insights from Comparing MAGs against Isolate Genomes Derived from the Same Fecal Sample. Appl Environ Microbiol 2021; 87:AEM.02593-20. [PMID: 33452027 DOI: 10.1128/aem.02593-20] [Citation(s) in RCA: 67] [Impact Index Per Article: 22.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Accepted: 01/06/2021] [Indexed: 12/24/2022] Open
Abstract
The recovery of metagenome-assembled genomes (MAGs) from metagenomic data has recently become a common task for microbial studies. The strengths and limitations of the underlying bioinformatics algorithms are well appreciated by now based on performance tests with mock data sets of known composition. However, these mock data sets do not capture the complexity and diversity often observed within natural populations, since their construction typically relies on only a single genome of a given organism. Further, it remains unclear if MAGs can recover population-variable genes (those shared by >10% but <90% of the members of the population) as efficiently as core genes (those shared by >90% of the members). To address these issues, we compared the gene variabilities of pathogenic Escherichia coli isolates from eight diarrheal samples, for which the isolate was the causative agent, against their corresponding MAGs recovered from the companion metagenomic data set. Our analysis revealed that MAGs with completeness estimates near 95% captured only 77% of the population core genes and 50% of the variable genes, on average. Further, about 5% of the genes of these MAGs were conservatively identified as missing in the isolate and were of different (non-Enterobacteriaceae) taxonomic origin, suggesting errors at the genome-binning step, even though contamination estimates based on commonly used pipelines were only 1.5%. Therefore, the quality of MAGs may often be worse than estimated, and we offer examples of how to recognize and improve such MAGs to sufficient quality by (for instance) employing only contigs longer than 1,000 bp for binning.IMPORTANCE Metagenome assembly and the recovery of metagenome-assembled genomes (MAGs) have recently become common tasks for microbiome studies across environmental and clinical settings. However, the extent to which MAGs can capture the genes of the population they represent remains speculative. Current approaches to evaluating MAG quality are limited to the recovery and copy number of universal housekeeping genes, which represent a small fraction of the total genome, leaving the majority of the genome essentially inaccessible. If MAG quality in reality is lower than these approaches would estimate, this could have dramatic consequences for all downstream analyses and interpretations. In this study, we evaluated this issue using an approach that employed comparisons of the gene contents of MAGs to the gene contents of isolate genomes derived from the same sample. Further, our samples originated from a diarrhea case-control study, and thus, our results are relevant for recovering the virulence factors of pathogens from metagenomic data sets.
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215
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Metagenomes and Assembled Genomes from Diarrhea-Affected Cattle (Bos taurus). Microbiol Resour Announc 2021; 10:10/7/e01411-20. [PMID: 33602735 PMCID: PMC7892668 DOI: 10.1128/mra.01411-20] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
Abstract
The de novo metagenome assembly for C1-TPA is 68,577,389 bp long spread over 10,108 contigs, while that of C3-TPA is 55,517,929 bp distributed over 9,415 contigs. A total of 8 metagenome-assembled genomes (MAGs) were extracted from C1-TPA, and 10 were extracted from C3-TPA. Both samples have a Flavobacterium sp. and a Pseudomonas sp. in common among their bacterial communities. The de novo metagenome assembly for C1-TPA is 68,577,389 bp long spread over 10,108 contigs, while that of C3-TPA is 55,517,929 bp distributed over 9,415 contigs. A total of 8 metagenome-assembled genomes (MAGs) were extracted from C1-TPA, and 10 were extracted from C3-TPA. Both samples have a Flavobacterium sp. and a Pseudomonas sp. in common among their bacterial communities.
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216
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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.
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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.
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217
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Matsuura N, Masakke Y, Karthikeyan S, Kanazawa S, Honda R, Yamamoto-Ikemoto R, Konstantinidis KT. Metagenomic insights into the effect of sulfate on enhanced biological phosphorus removal. Appl Microbiol Biotechnol 2021; 105:2181-2193. [PMID: 33555362 DOI: 10.1007/s00253-021-11113-4] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Revised: 12/25/2020] [Accepted: 01/12/2021] [Indexed: 11/30/2022]
Abstract
Excess phosphorus in water supplies causes eutrophication, which degrades water quality. Hence, the efficient removal of phosphorus from wastewater represents a highly desirable process. Here, we evaluated the effect of sulfate concentration on enhanced biological phosphorus removal (EBPR), in which phosphorus is typically removed under anaerobic-oxic cycles, with sulfate reduction the predominant process in the anaerobic phase. Two sequencing batch EBPR reactors operated under high- (SBR-H) vs. low-sulfate (SBR-L) concentrations for 189 days and under three periods, i.e., start-up, sufficient acetate, and limited acetate. Under acetate-rich conditions, phosphorus removal efficiency was > 90% for both reactors; however, under acetate-limited conditions, only 34% and 91.3% of the phosphorus were removed for the SBR-L and the SBR-H, respectively. Metagenomic sequencing of the reactors showed that the relative abundance of the polyphosphate-accumulating and sulfur-reducing bacteria (SRB) was higher in the SBR-H, consistent with its higher phosphorus removal activity. Ten high-quality metagenome-assembled genomes, including one closely related to the genus Thiothrix disciformis (99.81% average amino acid identity), were recovered and predicted to simultaneously metabolize phosphorus and sulfur by the presence of phosphorus (ppk, ppx, pst, and pit) and sulfur (sul, sox, dsr, sqr, apr, cys, and sat) metabolism marker genes. The omics-based analysis provided a holistic view of the microbial ecosystem in the EBPR process and revealed that SRB and Thiothrix play key roles in the presence of high sulfate.Key points• We observed high phosphorus-removal efficiency in high-sulfate EBPR.• Metagenome-based analysis revealed sulfate-related metabolic mechanisms in EBPR.• SRB and PAOs showed interrelationships in the EBPR-sulfur systems.
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Affiliation(s)
- Norihisa Matsuura
- Faculty of Geosciences and Civil Engineering, Kanazawa University, Kanazawa, Ishikawa, Japan.
| | - Yalkhin Masakke
- Graduate School of Natural Science and Technology, Kanazawa University, Kanazawa, Ishikawa, Japan
| | - Smruthi Karthikeyan
- School of Civil and Environmental Engineering, Georgia Institute of Technology, Atlanta, GA, USA
| | - Sui Kanazawa
- Graduate School of Natural Science and Technology, Kanazawa University, Kanazawa, Ishikawa, Japan
| | - Ryo Honda
- Faculty of Geosciences and Civil Engineering, Kanazawa University, Kanazawa, Ishikawa, Japan
| | - Ryoko Yamamoto-Ikemoto
- Faculty of Geosciences and Civil Engineering, Kanazawa University, Kanazawa, Ishikawa, Japan
| | - Konstantinos T Konstantinidis
- School of Civil and Environmental Engineering, Georgia Institute of Technology, Atlanta, GA, USA.,School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA
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218
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An antimicrobial Staphylococcus sciuri with broad temperature and salt spectrum isolated from the surface of the African social spider, Stegodyphus dumicola. Antonie Van Leeuwenhoek 2021; 114:325-335. [PMID: 33543432 DOI: 10.1007/s10482-021-01526-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Accepted: 01/22/2021] [Indexed: 10/22/2022]
Abstract
Some social arthropods engage in mutualistic symbiosis with antimicrobial compound-producing microorganisms that provide protection against pathogens. Social spiders live in communal nests and contain specific endosymbionts with unknown function. Bacteria are also found on the spiders' surface, including prevalent staphylococci, which may have protective potential. Here we present the genomic and phenotypic characterization of strain i1, isolated from the surface of the social spider Stegodyphus dumicola. Phylogenomic analysis identified i1 as novel strain of Staphylococcus sciuri within subgroup 2 of three newly defined genomic subgroups. Further phenotypic investigations showed that S. sciuri i1 is an extremophile that can grow at a broad range of temperatures (4 °C-45 °C), high salt concentrations (up to 27%), and has antimicrobial activity against closely related species. We identified a lactococcin 972-like bacteriocin gene cluster, likely responsible for the antimicrobial activity, and found it conserved in two of the three subgroups of S. sciuri. These features indicate that S. sciuri i1, though not a specific symbiont, is well-adapted to survive on the surface of social spiders and may gain a competitive advantage by inhibiting closely related species.
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219
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Ping M, Yun-Lin Z, Jun L, Jian G, Zheng-Gang X. Proposal of Lentzea deserti (Okoro et al. 2010) Nouioui et al. 2018 as a later heterotypic synonym of Lentzea atacamensis (Okoro et al. 2010) Nouioui et al. 2018 and an emended description of Lentzea atacamensis. PLoS One 2021; 16:e0246533. [PMID: 33539471 PMCID: PMC7861442 DOI: 10.1371/journal.pone.0246533] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Accepted: 01/20/2021] [Indexed: 11/19/2022] Open
Abstract
The taxonomic relationship of Lentzea atacamensis and Lentzea deserti were re-evaluated using comparative genome analysis. The 16S rRNA gene sequence analysis indicated that the type strains of L. atacamensis and L. deserti shared 99.7% sequence similarity. The digital DNA-DNA hybridization (dDDH) and average nucleotide identity (ANI) values between the genomes of two type strains were 88.6% and 98.8%, respectively, greater than the two recognized thresholds values of 70% dDDH and 95-96% ANI for bacterial species delineation. These results suggested that L. atacamensis and L. deserti should share the same taxonomic position. And this conclusion was further supported by similar phenotypic and chemotaxonomic features between them. Therefore, we propose that L. deserti is a later heterotypic synonym of L. atacamensis.
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Affiliation(s)
- Mo Ping
- Hunan Research Center of Engineering Technology for Utilization of Environmental and Resources Plant, Central South University of Forestry and Technology, Changsha, Hunan, China
| | - Zhao Yun-Lin
- Hunan Research Center of Engineering Technology for Utilization of Environmental and Resources Plant, Central South University of Forestry and Technology, Changsha, Hunan, China
| | - Liu Jun
- Hunan Research Center of Engineering Technology for Utilization of Environmental and Resources Plant, Central South University of Forestry and Technology, Changsha, Hunan, China
| | - Gao Jian
- School of Life Science, Hunan University of Science and Technology, Xiangtan, Hunan, China
| | - Xu Zheng-Gang
- Hunan Research Center of Engineering Technology for Utilization of Environmental and Resources Plant, Central South University of Forestry and Technology, Changsha, Hunan, China
- College of Forestry, Northwest A & F University, Yangling, Shaanxi, China
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220
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Yamaguchi M, Win HPM, Higashi K, Ono M, Hirose Y, Motooka D, Okuzaki D, Aye MM, Htun MM, Thu HM, Kawabata S. Epidemiological analysis of pneumococcal strains isolated at Yangon Children's Hospital in Myanmar via whole-genome sequencing-based methods. Microb Genom 2021; 7:000523. [PMID: 33565958 PMCID: PMC8208701 DOI: 10.1099/mgen.0.000523] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2020] [Accepted: 01/10/2021] [Indexed: 11/21/2022] Open
Abstract
Streptococcus pneumoniae causes over one million deaths from lower respiratory infections per annum worldwide. Although mortality is very high in Southeast Asian countries, molecular epidemiological information remains unavailable for some countries. In this study, we report, for the first time, the whole-genome sequences and genetic profiles of pneumococcal strains isolated in Myanmar. We isolated 60 streptococcal strains from 300 children with acute respiratory infection at Yangon Children's Hospital in Myanmar. We obtained whole-genome sequences and identified the species, serotypes, sequence types, antimicrobial resistance (AMR) profiles, virulence factor profiles and pangenome structure using sequencing-based analysis. Average nucleotide identity analysis indicated that 58 strains were S. pneumoniae and the other 2 strains were Streptococcus mitis. The major serotype was 19F (11 strains), followed by 6E (6B genetic variant; 7 strains) and 15 other serotypes; 5 untypable strains were also detected. Multilocus sequence typing analysis revealed 39 different sequence types, including 11 novel ones. In addition, genetic profiling indicated that AMR genes and mutations spread among pneumococcal strains in Myanmar. A minimum inhibitory concentration assay indicated that several pneumococcal strains had acquired azithromycin and tetracycline resistance, whereas no strains were found to be resistant against levofloxacin and high-dose penicillin G. Phylogenetic and pangenome analysis showed various pneumococcal lineages and that the pneumococcal strains contain a rich and mobile gene pool, providing them with the ability to adapt to selective pressures. This molecular epidemiological information can help in tracking global infection and supporting AMR control in addition to public health interventions in Myanmar.
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Affiliation(s)
- Masaya Yamaguchi
- Department of Oral and Molecular Microbiology, Osaka University Graduate School of Dentistry, Osaka, Japan
| | - Hpoo Pwint Myo Win
- Bacteriology Research Division, Department of Medical Research, Ministry of Health and Sports, Yangon, Myanmar
| | - Kotaro Higashi
- Department of Oral and Molecular Microbiology, Osaka University Graduate School of Dentistry, Osaka, Japan
| | - Masayuki Ono
- Department of Oral and Molecular Microbiology, Osaka University Graduate School of Dentistry, Osaka, Japan
| | - Yujiro Hirose
- Department of Oral and Molecular Microbiology, Osaka University Graduate School of Dentistry, Osaka, Japan
| | - Daisuke Motooka
- Genome Information Research Center, Research Institute for Microbial Diseases, Osaka University, Suita, Osaka, Japan
| | - Daisuke Okuzaki
- Genome Information Research Center, Research Institute for Microbial Diseases, Osaka University, Suita, Osaka, Japan
| | - Mya Mya Aye
- Bacteriology Research Division, Department of Medical Research, Ministry of Health and Sports, Yangon, Myanmar
| | - Moh Moh Htun
- Bacteriology Research Division, Department of Medical Research, Ministry of Health and Sports, Yangon, Myanmar
| | - Hlaing Myat Thu
- Bacteriology Research Division, Department of Medical Research, Ministry of Health and Sports, Yangon, Myanmar
| | - Shigetada Kawabata
- Department of Oral and Molecular Microbiology, Osaka University Graduate School of Dentistry, Osaka, Japan
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221
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Freitas-Silva J, de Oliveira BFR, Vigoder FDM, Muricy G, Dobson ADW, Laport MS. Peeling the Layers Away: The Genomic Characterization of Bacillus pumilus 64-1, an Isolate With Antimicrobial Activity From the Marine Sponge Plakina cyanorosea (Porifera, Homoscleromorpha). Front Microbiol 2021; 11:592735. [PMID: 33488540 PMCID: PMC7820076 DOI: 10.3389/fmicb.2020.592735] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Accepted: 12/09/2020] [Indexed: 11/30/2022] Open
Abstract
Bacillus pumilus 64-1, a bacterial strain isolated from the marine sponge Plakina cyanorosea, which exhibits antimicrobial activity against both pathogenic and drug-resistant Gram-positive and Gram-negative bacteria. This study aimed to conduct an in-depth genomic analysis of this bioactive sponge-derived strain. The nearly complete genome of strain 64-1 consists of 3.6 Mbp (41.5% GC), which includes 3,705 coding sequences (CDS). An open pangenome was observed when limiting to the type strains of the B. pumilus group and aquatic-derived B. pumilus representatives. The genome appears to encode for at least 12 potential biosynthetic gene clusters (BGCs), including both types I and III polyketide synthases (PKS), non-ribosomal peptide synthetases (NRPS), and one NRPS-T1PKS hybrid, among others. In particular, bacilysin and other bacteriocin-coding genes were found and may be associated with the detected antimicrobial activity. Strain 64-1 also appears to possess a broad repertoire of genes encoding for plant cell wall-degrading carbohydrate-active enzymes (CAZymes). A myriad of genes which may be involved in various process required by the strain in its marine habitat, such as those encoding for osmoprotectory transport systems and the biosynthesis of compatible solutes were also present. Several heavy metal tolerance genes are also present, together with various mobile elements including a region encoding for a type III-B Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) region, four prophage segments and transposase elements. This is the first report on the genomic characterization of a cultivable bacterial member of the Plakina cyanorosea holobiont.
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Affiliation(s)
- Jéssyca Freitas-Silva
- Institute of Microbiology Paulo de Góes, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Bruno Francesco Rodrigues de Oliveira
- Institute of Microbiology Paulo de Góes, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil.,School of Microbiology, University College Cork, Cork, Ireland
| | - Felipe de Mello Vigoder
- Department of Genetics, Institute of Biology, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Guilherme Muricy
- Department of Invertebrates, National Museum, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Alan D W Dobson
- School of Microbiology, University College Cork, Cork, Ireland.,Environmental Research Institute, University College Cork, Cork, Ireland
| | - Marinella Silva Laport
- Institute of Microbiology Paulo de Góes, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
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222
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Draft Genome Sequence of the Phosphate-Solubilizing Rhizobacterium Burkholderia pseudomultivorans Strain MPSB1, Isolated from a Copper Mined-Out Site. Microbiol Resour Announc 2021; 10:10/1/e01304-20. [PMID: 33414315 PMCID: PMC8407738 DOI: 10.1128/mra.01304-20] [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: 11/30/2022] Open
Abstract
Burkholderia pseudomultivorans MPSB1 was isolated from a copper mined-out soil sample collected from Mogpog, Marinduque, Philippines. Here, we report the draft genome sequence with predicted gene inventories supporting rhizosphere bioremediation, such as heavy metal tolerance, phosphate solubilization, and siderophore production. Burkholderia pseudomultivorans MPSB1 was isolated from a copper mined-out soil sample collected from Mogpog, Marinduque, Philippines. Here, we report the draft genome sequence with predicted gene inventories supporting rhizosphere bioremediation, such as heavy metal tolerance, phosphate solubilization, and siderophore production.
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223
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Complete Genome Sequences of Four Atrazine-Degrading Bacterial Strains, Pseudomonas sp. Strain ADPe, Arthrobacter sp. Strain TES, Variovorax sp. Strain 38R, and Chelatobacter sp. Strain SR38. Microbiol Resour Announc 2021; 10:10/1/e01080-20. [PMID: 33414292 PMCID: PMC8407692 DOI: 10.1128/mra.01080-20] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
We report here the complete genome sequences of four atrazine-degrading bacteria. Their genomes will serve as references for determining the genetic changes that have occurred during an evolution experiment. We report here the complete genome sequences of four atrazine-degrading bacteria. Their genomes will serve as references for determining the genetic changes that have occurred during an evolution experiment.
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224
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Draft Genome Sequence of Streptomyces sp. Isolate H28 from the Meycauayan River, Philippines. Microbiol Resour Announc 2021; 10:10/1/e01269-20. [PMID: 33414351 PMCID: PMC8407727 DOI: 10.1128/mra.01269-20] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
In this paper, we report the draft genome sequence of Streptomyces sp. isolate H28, isolated from sediments of the Meycauayan River in the Philippines. This species exhibits production of melanin as well as the ability to utilize and degrade both high-density polyethylene (HDPE) and low-density polyethylene (LDPE).
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225
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Guo Y, Hu S, Li K, Xinke T, Sun Y, Gao J. Proposal of Bacillus ciccensis Liu et al. as a Later Heterotypic Synonym of Cytobacillus solani (Liu et al.) Patel and Gupta Using Comparative Genomic Analysis. Curr Microbiol 2021; 78:843-847. [PMID: 33410954 DOI: 10.1007/s00284-020-02307-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2020] [Accepted: 11/24/2020] [Indexed: 12/14/2022]
Abstract
Bacillus ciccensis and Cytobacillus solani were reported to belong to separate genomic species based on a polyphasic taxonomic approach. However, we found that type strains of B. ciccensis and C. solani should belong to the same genomic species based on the clustering patterns resulting from genome phylogenetic analysis. The average nucleotide identity and digital DNA-DNA hybridization values between the genomes of two type strains were 99.6% and 96.9%, respectively, much higher than 95 ~ 96% and 70% cut-off point proposed and generally accepted species boundary. This result was also supported by a comprehensive comparison of phenotypic characteristics between the two type strains. These results suggested that B. ciccensis and C. solani had the same taxonomic position. Consequently, we propose that B. ciccensis is a later heterotypic synonym of C. solani.
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Affiliation(s)
- Yihui Guo
- School of Life Science, Hunan University of Science and Technology, Xiangtan, 411201, China
| | - Siren Hu
- School of Life Science, Hunan University of Science and Technology, Xiangtan, 411201, China
| | - Kaiqin Li
- School of Life Science, Hunan University of Science and Technology, Xiangtan, 411201, China
| | - Tang Xinke
- School of Life Science, Hunan University of Science and Technology, Xiangtan, 411201, China
| | - Yuandong Sun
- School of Life Science, Hunan University of Science and Technology, Xiangtan, 411201, China
| | - Jian Gao
- School of Life Science, Hunan University of Science and Technology, Xiangtan, 411201, China.
- Key Laboratory of Ecological Remediation and Safe Utilization of Heavy Metal-Polluted Soils, College of Hunan Province, Xiangtan, 411201, China.
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226
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Meziti A, Nikouli E, Hatt JK, Konstantinidis KT, Kormas KA. Time series metagenomic sampling of the Thermopyles, Greece, geothermal springs reveals stable microbial communities dominated by novel sulfur-oxidizing chemoautotrophs. Environ Microbiol 2021; 23:3710-3726. [PMID: 33350070 DOI: 10.1111/1462-2920.15373] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Accepted: 12/19/2020] [Indexed: 11/29/2022]
Abstract
Geothermal springs are essentially unaffected by environmental conditions aboveground as they are continuously supplied with subsurface water with little variability in chemistry. Therefore, changes in their microbial community composition and function, especially over a long period, are expected to be limited but this assumption has not yet been rigorously tested. Toward closing this knowledge gap, we applied whole metagenome sequencing to 17 water samples collected between 2010 and 2016 from the Thermopyles sulfur-rich geothermal springs in central Greece. As revealed by 16S rRNA gene fragments recovered in the metagenomes, Epsilonproteobacteria-related operational taxonomic units (OTUs) dominated most samples and grouping of samples based on OTU abundances exhibited no apparent seasonal pattern. Similarities between samples regarding functional gene content were high, with all samples sharing >70% similarity in functional pathways. These community-wide patterns were further confirmed by analysis of metagenome-assembled genomes (MAGs), which showed that novel species and genera of the chemoautotrophic Campylobacterales order dominated the springs. These MAGs carried different pathways for thiosulfate or sulfide oxidation coupled to carbon fixation pathways. Overall, our study showed that even in the long term, functions of microbial communities in a moderately hot terrestrial spring remain stable, presumably driving the corresponding stability in community structure.
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Affiliation(s)
- A Meziti
- Department of Ichthyology and Aquatic Environment, University of Thessaly, Volos, 38446, Greece.,School of Civil and Environmental Engineering, Georgia Institute of Technology, Ford Environmental Science and Technology Building, 311 Ferst Drive, Atlanta, GA, 30332, USA
| | - E Nikouli
- Department of Ichthyology and Aquatic Environment, University of Thessaly, Volos, 38446, Greece.,School of Civil and Environmental Engineering, Georgia Institute of Technology, Ford Environmental Science and Technology Building, 311 Ferst Drive, Atlanta, GA, 30332, USA
| | - J K Hatt
- School of Civil and Environmental Engineering, Georgia Institute of Technology, Ford Environmental Science and Technology Building, 311 Ferst Drive, Atlanta, GA, 30332, USA
| | - K T Konstantinidis
- School of Civil and Environmental Engineering, Georgia Institute of Technology, Ford Environmental Science and Technology Building, 311 Ferst Drive, Atlanta, GA, 30332, USA.,School of Biological Sciences, Georgia Institute of Technology, Ford Environmental Sciences and Technology Building, 311 Ferst Drive, Atlanta, GA, 30332, USA
| | - K A Kormas
- Department of Ichthyology and Aquatic Environment, University of Thessaly, Volos, 38446, Greece
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228
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Gray HK, Arora-Williams KK, Young C, Bouwer E, Davis MF, Preheim SP. Contribution of Time, Taxonomy, and Selective Antimicrobials to Antibiotic and Multidrug Resistance in Wastewater Bacteria. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2020; 54:15946-15957. [PMID: 33258596 PMCID: PMC8463082 DOI: 10.1021/acs.est.0c03803] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
The use of nontherapeutic broad-spectrum antimicrobial agents triclosan (TCS) and benzalkonium chloride (BC) can contribute to bacterial resistance to clinically relevant antibiotics. Antimicrobial-resistant bacteria within wastewater may reflect the resistance burden within the human microbiome, as antibiotics and pathogens in wastewater can track with clinically relevant parameters during perturbations to the community. In this study, we monitored culturable and resistant wastewater bacteria and cross-resistance to clinically relevant antibiotics to gauge the impact of each antimicrobial and identify factors influencing cross-resistance profiles. Bacteria resistant to TCS and BC were isolated from wastewater influent over 21 months, and cross-resistance, taxonomy, and monthly changes were characterized under both antimicrobial selection regimes. Cross-resistance profiles from each antimicrobial differed within and between taxa. BC-isolated bacteria had a significantly higher prevalence of resistance to "last-resort antibiotic" colistin, while isolates resistant to TCS exhibited higher rates of multidrug resistance. Prevalence of culturable TCS-resistant bacteria decreased over time following Food and Drug Administration (FDA) TCS bans. Cross-resistance patterns varied according to sampling date, including among the most clinically important antibiotics. Correlations between strain-specific resistance profiles were largely influenced by taxonomy, with some variations associated with sampling date. The results reveal that time, taxonomy, and selection by TCS and BC impact features of cross-resistance patterns among diverse wastewater microorganisms, which could reflect the variety of factors influencing resistance patterns relevant to a community microbiome.
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Affiliation(s)
- Hannah K Gray
- Department of Environmental Health and Engineering, Whiting School of Engineering, Johns Hopkins University, 3400 North Charles Street, 313 Ames Hall, Baltimore, Maryland 21218, United States
| | - Keith K Arora-Williams
- Department of Environmental Health and Engineering, Whiting School of Engineering, Johns Hopkins University, 3400 North Charles Street, 313 Ames Hall, Baltimore, Maryland 21218, United States
| | - Charles Young
- The Johns Hopkins Applied Physics Laboratory, 11100 Johns Hopkins Road, Laurel, Maryland 20723, United States
| | - Edward Bouwer
- Department of Environmental Health and Engineering, Whiting School of Engineering, Johns Hopkins University, 3400 North Charles Street, 313 Ames Hall, Baltimore, Maryland 21218, United States
| | - Meghan F Davis
- Department of Environmental Health and Engineering, Bloomberg School of Public Health, Johns Hopkins University, 615 North Wolfe Street, E7612, Baltimore, Maryland 21205, United States
| | - Sarah P Preheim
- Department of Environmental Health and Engineering, Whiting School of Engineering, Johns Hopkins University, 3400 North Charles Street, 313 Ames Hall, Baltimore, Maryland 21218, United States
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229
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Whole-Genome Sequence Analysis of Multidrug-Resistant Enterobacter hormaechei Isolated from Imported Retail Shrimp. Microbiol Resour Announc 2020; 9:9/50/e01103-20. [PMID: 33303661 PMCID: PMC7729409 DOI: 10.1128/mra.01103-20] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Here, we announce the draft genome sequence of Enterobacter hormaechei 2B-MC1, isolated from a shrimp sample collected from a farmer's market in Atlanta, Georgia. The assembled genome sequence observed was 4,661,561 bp long with a G+C content of 55.3%. The isolate harbored sul1, sul2, qnrA1, oqxB, dfrA23, bla ACT, floR, fosA, tet(A), aph(6)-Id, and aph(3″)-Ib antibiotic resistance genes.
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230
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Nitrosophilus alvini gen. nov., sp. nov., a hydrogen-oxidizing chemolithoautotroph isolated from a deep-sea hydrothermal vent in the East Pacific Rise, inferred by a genome-based taxonomy of the phylum "Campylobacterota". PLoS One 2020; 15:e0241366. [PMID: 33301463 PMCID: PMC7728183 DOI: 10.1371/journal.pone.0241366] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Accepted: 10/13/2020] [Indexed: 12/15/2022] Open
Abstract
A novel bacterium, strain EPR55-1T, was isolated from a deep-sea hydrothermal vent on the East Pacific Rise. The cells were motile rods. Growth was observed at temperatures between 50 and 60°C (optimum, 60°C), at pH values between 5.4 and 8.6 (optimum, pH 6.6) and in the presence of 2.4–3.2% (w/v) NaCl (optimum, 2.4%). The isolate used molecular hydrogen as its sole electron donor, carbon dioxide as its sole carbon source, ammonium as its sole nitrogen source, and thiosulfate, sulfite (0.01 to 0.001%, w/v) or elemental sulfur as its sole sulfur source. Nitrate, nitrous oxide (33%, v/v), thiosulfate, molecular oxygen (0.1%, v/v) or elemental sulfur could serve as the sole electron acceptor to support growth. Phylogenetic analyses based on both 16S rRNA gene sequences and whole genome sequences indicated that strain EPR55-1T belonged to the family Nitratiruptoraceae of the class “Campylobacteria”, but it had the distinct phylogenetic relationship with the genus Nitratiruptor. On the basis of the physiological and molecular characteristics of the isolate, the name Nitrosophilus alvini gen. nov. sp. nov. is proposed, with EPR55-1T as the type strain (= JCM 32893T = KCTC 15925T). In addition, it is shown that “Nitratiruptor labii” should be transferred to the genus Nitrtosophilus; the name Nitrosophilus labii comb. nov. (JCM 34002T = DSM 111345T) is proposed for this organism. Furthermore, 16S rRNA gene-based and genome-based analyses showed that Cetia pacifica is phylogenetically associated with Caminibacter species. We therefore propose the reclassification of Cetia pacifica as Caminibacter pacificus comb. nov. (DSM 27783T = JCM 19563T). Additionally, AAI thresholds for genus classification and the reclassification of subordinate taxa within “Campylobacteria” are also evaluated, based on the analyses using publicly available genomes of all the campylobacterial species.
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231
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Hou X, Liu H, Shang Y, Mao S, Li S, Sang F, Deng H, Wang L, Kong L, Zhang C, Ding Z, Gao Y, Wei S, Chen Z. Paraflavitalea devenefica sp. nov., isolated from urban soil. Int J Syst Evol Microbiol 2020; 71. [PMID: 33275090 DOI: 10.1099/ijsem.0.004587] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-stain-negative, rod-shaped, mesophilic, milky white-pigmented, aerobic, non-spore-forming and non-flagellated bacterium, designated strain X16T, was isolated from urban soil of Zibo, Shandong, China. According to 16S rRNA gene sequence analysis, the isolate showed highest similarities with Paraflavitalea soli 5GH32-13T (97.6 %), Pseudoflavitalea soli KIS20-3T (96.2 %), Pseudobacter ginsenosidimutans Gsoil 221T (96.0 %) and Pseudoflavitalea rhizosphaerae T16R-265T (95.8 %). The neighbour-joining tree based on 16S rRNA gene sequences showed that strain X16T formed a subcluster with Paraflavitalea soli 5GH32-13T, and the subcluster was closely related to Pseudoflavitalea soli KIS20-3T, Pseudobacter ginsenosidimutans Gsoil 221T and Pseudoflavitalea rhizosphaerae T16R-265T. Strain X16T also formed a subcluster with Paraflavitalea soli 5GH32-13T in phylogenetic tree based on genomic sequences. The polar lipids are phosphatidylethanolamine, two unknown aminolipids, two unknown aminophospholipids, two unknown lipids and two unknown phospholipids. The major quinone of strain X16T is menaquinone-7 and the main fatty acids (>10 % of total fatty acids) of strain X16T are iso-C15 : 0, iso-C17 : 0 3-OH and iso-C15 : 1 G. The genome length of strain X16T is 8.7 Mb with a DNA G+C content of 47.4 %. ANI values among strain X16T and strain Paraflavitalea soli 5GH32-13T, Pseudobacter ginsenosidimutans Gsoil 221T, and Pseudoflavitalea rhizosphaerae T16R-265T are 78.1, 70.7, 70.6 %, respectively. On the basis of the results of the polyphasic characterization presented in this study, it is concluded that strain X16T represents a novel species. Besides, strain X16T can detoxify high toxicity selenite [Se(IV)] to low toxicity elemental selenium [Se(0)], for which the name Paraflavitale devenefica sp. nov. is proposed. The type strain is X16T (=KACC 21698T=GDMCC1.1757T).
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Affiliation(s)
- Xiaoxiao Hou
- School of Life Sciences, Shandong University of Technology, Zibo, 255000, Shandong Province, PR China
| | - Hongliang Liu
- School of Life Sciences, Shandong University of Technology, Zibo, 255000, Shandong Province, PR China.,Shandong Provincial Research Center for Bioinformatic Engineering and Technique, Shandong University of Technology, Zibo, 255000, Shandong, PR China
| | - Yumang Shang
- Hengshui University, Hengshui, 053000, Hebei, PR China
| | - Sidi Mao
- School of Life Sciences, Shandong University of Technology, Zibo, 255000, Shandong Province, PR China
| | - Shucheng Li
- School of Life Sciences, Shandong University of Technology, Zibo, 255000, Shandong Province, PR China
| | - Feng Sang
- School of Life Sciences, Shandong University of Technology, Zibo, 255000, Shandong Province, PR China
| | - Hongkuan Deng
- School of Life Sciences, Shandong University of Technology, Zibo, 255000, Shandong Province, PR China
| | - Lijuan Wang
- Shandong Provincial Research Center for Bioinformatic Engineering and Technique, Shandong University of Technology, Zibo, 255000, Shandong, PR China.,School of Life Sciences, Shandong University of Technology, Zibo, 255000, Shandong Province, PR China
| | - Ling Kong
- School of Life Sciences, Shandong University of Technology, Zibo, 255000, Shandong Province, PR China
| | - ChunYang Zhang
- School of Life Sciences, Shandong University of Technology, Zibo, 255000, Shandong Province, PR China
| | - Zhongfeng Ding
- School of Life Sciences, Shandong University of Technology, Zibo, 255000, Shandong Province, PR China
| | - Yan Gao
- Zibo IT & Engineering School, Zibo, 255038, Shandong, PR China
| | - Shuzhen Wei
- Hengshui University, Hengshui, 053000, Hebei, PR China
| | - Zhiwei Chen
- Institute of Food and Nutrition Science, Shandong University of Technology, Zibo, 255000, PR China
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232
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Raths R, Peta V, Bücking H. Duganella callida sp. nov., a novel addition to the Duganella genus, isolated from the soil of a cultivated maize field. Int J Syst Evol Microbiol 2020; 71. [PMID: 33269999 DOI: 10.1099/ijsem.0.004599] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-negative, rod-shaped bacterium, strain Duganella callida DN04T, was isolated from the soil of a maize field in North Carolina, USA. Based on the 16S rRNA gene sequence, the most similar Duganella species are D. sacchari Sac-22T, D. ginsengisoli DCY83T, and D. radicis Sac-41T with a 97.8, 97.6, or 96.9 % sequence similarity, respectively. We compared the biochemical phenotype of DN04T to D. sacchari Sac-22T and D. zoogloeoides 115T and other reference strains from different genera within the Oxalobacteraceae and while the biochemical profile of DN04T is most similar to D. sacchari Sac-22T and other Duganella and Massilia strains, there are also distinct differences. DN04T can for example utilize turanose, N-acetyl-d-glucosamine, inosine, and l-pyroglutamic acid. The four fatty acids found in the highest percentages were C15 : 0 iso (24.6 %), C15 : 1 isoG (19.4 %), C17 : 0 iso3-OH (16.8 %), and summed feature 3 (C16:1 ⍵7c and/or C16:1 ⍵6c) (12.5 %). We also applied whole genome sequencing to determine if DN04T is a novel species. The most similar AAI (average amino acid identity) score was 70.8 % (Massilia plicata NZ CP038026T), and the most similar ANI (average nucleotide identity) score was 84.8 % (D. radicis KCTC 22382T), which indicates that DN04T is a novel species. The genome-to-genome-distance calculation (GGDC) revealed a DDH of 28.3 % to D. radicis KCTC 22382T, which is much lower than the new species threshold. Based on the morphological, phenotypic, and genomic differences, we propose Duganella callida sp. nov. as a novel species within the Duganella genus (type strain DN04T=NRRL B-65552T=LMG 31736T).
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Affiliation(s)
- Rachel Raths
- South Dakota State University, Biology and Microbiology Department, Brookings SD 57007, USA
| | - Vincent Peta
- South Dakota State University, Biology and Microbiology Department, Brookings SD 57007, USA
| | - Heike Bücking
- South Dakota State University, Biology and Microbiology Department, Brookings SD 57007, USA
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233
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Ertekin E, Meslier V, Browning A, Treadgold J, DiRuggiero J. Rock structure drives the taxonomic and functional diversity of endolithic microbial communities in extreme environments. Environ Microbiol 2020; 23:3937-3956. [PMID: 33078515 DOI: 10.1111/1462-2920.15287] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2020] [Revised: 10/07/2020] [Accepted: 10/18/2020] [Indexed: 11/29/2022]
Abstract
Endolithic (rock-dwelling) microbial communities are ubiquitous in hyper-arid deserts around the world and the last resort for life under extreme aridity. These communities are excellent models to explore biotic and abiotic drivers of diversity because they are of low complexity. Using high-throughput amplicon and metagenome sequencing, combined with X-ray computed tomography, we investigated how water availability and substrate architecture modulated the taxonomic and functional composition of gypsum endolithic communities in the Atacama Desert, Chile. We found that communities inhabiting gypsum rocks with a more fragmented substrate architecture had higher taxonomic and functional diversity, despite having less water available. This effect was tightly linked with community connectedness and likely the result of niche differentiation. Gypsum communities were functionally similar, yet adapted to their unique micro-habitats by modulating their carbon and energy acquisition strategies and their growth modalities. Reconstructed population genomes showed that these endolithic microbial populations encoded potential pathways for anoxygenic phototrophy and atmospheric hydrogen oxidation as supplemental energy sources.
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Affiliation(s)
- Emine Ertekin
- Department of Biology, Johns Hopkins University, Baltimore, MD, USA
| | - Victoria Meslier
- Department of Biology, Johns Hopkins University, Baltimore, MD, USA.,MetaGenoPolis, Jouy-en-Josas, France
| | | | | | - Jocelyne DiRuggiero
- Department of Biology, Johns Hopkins University, Baltimore, MD, USA.,Department of Earth and Planetary Sciences, Johns Hopkins University, Baltimore, MD, USA
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234
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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.
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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
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Kallscheuer N, Jogler M, Wiegand S, Peeters SH, Heuer A, Boedeker C, Jetten MSM, Rohde M, Jogler C. Rubinisphaera italica sp. nov. isolated from a hydrothermal area in the Tyrrhenian Sea close to the volcanic island Panarea. Antonie Van Leeuwenhoek 2020; 113:1727-1736. [PMID: 31773447 PMCID: PMC7717053 DOI: 10.1007/s10482-019-01329-w] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2019] [Accepted: 09/09/2019] [Indexed: 01/09/2023]
Abstract
Planctomycetes is a fascinating phylum of mostly aquatic bacteria, not only due to the environmental importance in global carbon and nitrogen cycles, but also because of a unique cell biology. Their lifestyle and metabolic capabilities are not well explored, which motivated us to study the role of Planctomycetes in biofilms on marine biotic surfaces. Here, we describe the novel strain Pan54T which was isolated from algae in a hydrothermal area close to the volcanic island Panarea in the Tyrrhenian Sea, north of Sicily in Italy. The strain grew best at pH 9.0 and 26 °C and showed typical characteristics of planctomycetal bacteria, e.g. division by polar budding, formation of aggregates and presence of stalks and crateriform structures. Phylogenetically, the strain belongs to the genus Rubinisphaera. Our analysis suggests that Pan54T represents a novel species of this genus, for which we propose the name Rubinisphaera italica sp. nov. We suggest Pan54T (= DSM 29369 = LMG 29789) as the type strain of the novel species.
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Affiliation(s)
- Nicolai Kallscheuer
- Department of Microbiology, Radboud Universiteit Nijmegen, Nijmegen, The Netherlands
| | - Mareike Jogler
- Department of Microbiology, Radboud Universiteit Nijmegen, Nijmegen, The Netherlands
- Leibniz Institute DSMZ, Braunschweig, Germany
| | - Sandra Wiegand
- Department of Microbiology, Radboud Universiteit Nijmegen, Nijmegen, The Netherlands
| | - Stijn H Peeters
- Department of Microbiology, Radboud Universiteit Nijmegen, Nijmegen, The Netherlands
| | - Anja Heuer
- Leibniz Institute DSMZ, Braunschweig, Germany
| | | | - Mike S M Jetten
- Department of Microbiology, Radboud Universiteit Nijmegen, Nijmegen, The Netherlands
| | - Manfred Rohde
- Central Facility for Microscopy, Helmholtz Centre for Infection Research, HZI, Braunschweig, Germany
| | - Christian Jogler
- Department of Microbiology, Radboud Universiteit Nijmegen, Nijmegen, The Netherlands.
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236
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Zinke LA, Evans PN, Santos-Medellín C, Schroeder AL, Parks DH, Varner RK, Rich VI, Tyson GW, Emerson JB. Evidence for non-methanogenic metabolisms in globally distributed archaeal clades basal to the Methanomassiliicoccales. Environ Microbiol 2020; 23:340-357. [PMID: 33185945 DOI: 10.1111/1462-2920.15316] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2020] [Revised: 11/05/2020] [Accepted: 11/09/2020] [Indexed: 12/21/2022]
Abstract
Recent discoveries of mcr and mcr-like genes in genomes from diverse archaeal lineages suggest that methane metabolism is an ancient pathway with a complicated evolutionary history. One conventional view is that methanogenesis is an ancestral metabolism of the class Thermoplasmata. Through comparative genomic analysis of 12 Thermoplasmata metagenome-assembled genomes (MAGs) basal to the Methanomassiliicoccales, we show that these microorganisms do not encode the genes required for methanogenesis. Further analysis of 770 Ca. Thermoplasmatota genomes/MAGs found no evidence of mcrA homologues outside of the Methanomassiliicoccales. Together, these results suggest that methanogenesis was laterally acquired by an ancestor of the Methanomassiliicoccales. The 12 analysed MAGs include representatives from four orders basal to the Methanomassiliicoccales, including a high-quality MAG that likely represents a new order, Ca. Lunaplasma lacustris ord. nov. sp. nov. These MAGs are predicted to use diverse energy conservation pathways, including heterotrophy, sulfur and hydrogen metabolism, denitrification, and fermentation. Two lineages are widespread among anoxic, sedimentary environments, whereas Ca. Lunaplasma lacustris has thus far only been detected in alpine caves and subarctic lake sediments. These findings advance our understanding of the metabolic potential, ecology, and global distribution of the Thermoplasmata and provide insight into the evolutionary history of methanogenesis within the Ca. Thermoplasmatota.
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Affiliation(s)
- Laura A Zinke
- Department of Plant Pathology, University of California, Davis, CA, USA
| | - Paul N Evans
- The Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Qld, 4072, Australia
| | | | - Alena L Schroeder
- Department of Plant Pathology, University of California, Davis, CA, USA
| | - Donovan H Parks
- The Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Qld, 4072, Australia
| | - Ruth K Varner
- Earth Systems Research Center, Institute for the Study of Earth, Oceans and Space, University of New Hampshire, Durham, NH, USA.,Department of Earth Sciences, University of New Hampshire, Durham, NH, USA
| | - Virginia I Rich
- Department of Microbiology, The Ohio State University, Columbus, OH, USA
| | - Gene W Tyson
- Centre for Microbiome Research, School of Biomedical Sciences, Queensland University of Technology (QUT), Translational Research Institute, Brisbane, Qld, 4102, Australia
| | - Joanne B Emerson
- Department of Plant Pathology, University of California, Davis, CA, USA
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237
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Tian L, Huang C, Mazloom R, Heath LS, Vinatzer BA. LINbase: a web server for genome-based identification of prokaryotes as members of crowdsourced taxa. Nucleic Acids Res 2020; 48:W529-W537. [PMID: 32232369 PMCID: PMC7319462 DOI: 10.1093/nar/gkaa190] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2020] [Revised: 03/04/2020] [Accepted: 03/16/2020] [Indexed: 02/07/2023] Open
Abstract
High throughput DNA sequencing in combination with efficient algorithms could provide the basis for a highly resolved, genome phylogeny-based and digital prokaryotic taxonomy. However, current taxonomic practice continues to rely on cumbersome journal publications for the description of new species, which still constitute the smallest taxonomic units. In response, we introduce LINbase, a web server that allows users to genomically circumscribe any group of prokaryotes with measurable DNA similarity and that uses the individual isolate as smallest unit. Since LINbase leverages the concept of Life Identification Numbers (LINs), which are codes assigned to individual genomes based on reciprocal average nucleotide identity, we refer to groups circumscribed in LINbase as LINgroups. Users can associate with each LINgroup a name, a short description, and a URL to a peer-reviewed publication. As soon as a LINgroup is circumscribed, any user can immediately identify query genomes as members and submit comments about the LINgroup. Most genomes currently in LINbase were imported from GenBank, but users can upload their own genome sequences as well. In conclusion, LINbase combines the resolution of LINs with the power of crowdsourcing in support of a highly resolved, genome phylogeny-based digital taxonomy. LINbase is available at http://www.LINbase.org.
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Affiliation(s)
- Long Tian
- School of Plant and Environmental Sciences, Virginia Tech, Blacksburg, VA 24061, USA
| | - Chengjie Huang
- Department of Computer Science, Virginia Tech, Blacksburg, VA 24061, USA
| | - Reza Mazloom
- Department of Computer Science, Virginia Tech, Blacksburg, VA 24061, USA
| | - Lenwood S Heath
- Department of Computer Science, Virginia Tech, Blacksburg, VA 24061, USA
| | - Boris A Vinatzer
- School of Plant and Environmental Sciences, Virginia Tech, Blacksburg, VA 24061, USA
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238
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Zhou YY, Shao WL, Liu YD, Li X, Shan XY, Jin XB, Gao J, Li W. Genome-based analysis to understanding rapid resuscitation of cryopreserved anammox consortia via sequential supernatant addition. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 744:140785. [PMID: 32707413 DOI: 10.1016/j.scitotenv.2020.140785] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/21/2020] [Revised: 06/23/2020] [Accepted: 07/04/2020] [Indexed: 06/11/2023]
Abstract
Simple cryopreservation of anaerobic ammonium-oxidation (anammox) consortia has become a promising preservation technology for the fast start-up of the anammox process. Here, we use genome-resolved metagenomics and metatranscriptomics to understand of the microbial interaction in a simple and effective resuscitation process for long-term cryopreserved anammox consortia by sequential addition of anammox SBR supernatant. Performance results showed that sequential addition of anammox supernatant significantly reduced the resuscitation time of the granule-based anammox process from 40 to 20 days. Genome-centric metagenomics were used to recover 19 high-quality draft genomes of anammox and heterotrophic bacteria. Comparative metatranscriptomic analysis was conducted to examine the gene expression of Candidatus Kuenenia stuttgartiensis, the dominant anammox bacterium, and heterotrophic bacteria to better understand their potential interactions. Proteobacteria-affiliated bacteria found in the supernatant were highly active in producing the secondary metabolites molybdopterin cofactor and folate which are needed for growth of the auxotrophic anammox bacteria. In addition, the significantly higher expression levels of hzsA and CO2-fixtion genes in the Candidatus Kuenenia genome indicated the anammox bacteria were likely more active and growing faster after sequential anammox supernatant addition during the resuscitation process. The resuscitation treatment pulse assays confirmed that sequential addition of supernatant was an effective way for the rapid resuscitation of anammox consortia. Our findings offer the first evidence of cross-feeding during the rapid resuscitation of cryopreserved anammox consortia.
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Affiliation(s)
- Yuan-Yuan Zhou
- State Environmental Protection Key Laboratory of Environmental Risk Assessment and Control on Chemical Process, School of Resources and Environmental Engineering, East China University of Science and Technology, Shanghai, China; National Engineering Laboratory for Industrial Wastewater Treatment, School of Resources and Environmental Engineering, East China University of Science and Technology, Shanghai, China
| | - Wen-Li Shao
- State Environmental Protection Key Laboratory of Environmental Risk Assessment and Control on Chemical Process, School of Resources and Environmental Engineering, East China University of Science and Technology, Shanghai, China; National Engineering Laboratory for Industrial Wastewater Treatment, School of Resources and Environmental Engineering, East China University of Science and Technology, Shanghai, China
| | - Yong-di Liu
- State Environmental Protection Key Laboratory of Environmental Risk Assessment and Control on Chemical Process, School of Resources and Environmental Engineering, East China University of Science and Technology, Shanghai, China; National Engineering Laboratory for Industrial Wastewater Treatment, School of Resources and Environmental Engineering, East China University of Science and Technology, Shanghai, China; Shanghai Institute of Pollution Control and Ecological Security, Shanghai, China
| | - Xiang Li
- Suzhou University of Science and Technology, Suzhou, China
| | - Xiao-Yu Shan
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, USA
| | - Xin-Bai Jin
- State Environmental Protection Key Laboratory of Environmental Risk Assessment and Control on Chemical Process, School of Resources and Environmental Engineering, East China University of Science and Technology, Shanghai, China; National Engineering Laboratory for Industrial Wastewater Treatment, School of Resources and Environmental Engineering, East China University of Science and Technology, Shanghai, China
| | - Jie Gao
- State Environmental Protection Key Laboratory of Environmental Risk Assessment and Control on Chemical Process, School of Resources and Environmental Engineering, East China University of Science and Technology, Shanghai, China; National Engineering Laboratory for Industrial Wastewater Treatment, School of Resources and Environmental Engineering, East China University of Science and Technology, Shanghai, China
| | - Wei Li
- State Environmental Protection Key Laboratory of Environmental Risk Assessment and Control on Chemical Process, School of Resources and Environmental Engineering, East China University of Science and Technology, Shanghai, China; National Engineering Laboratory for Industrial Wastewater Treatment, School of Resources and Environmental Engineering, East China University of Science and Technology, Shanghai, China; Shanghai Institute of Pollution Control and Ecological Security, Shanghai, China.
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239
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Patin NV, Peña-Gonzalez A, Hatt JK, Moe C, Kirby A, Konstantinidis KT. The Role of the Gut Microbiome in Resisting Norovirus Infection as Revealed by a Human Challenge Study. mBio 2020; 11:e02634-20. [PMID: 33203758 PMCID: PMC7683401 DOI: 10.1128/mbio.02634-20] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2020] [Accepted: 10/16/2020] [Indexed: 12/11/2022] Open
Abstract
Norovirus infections take a heavy toll on worldwide public health. While progress has been made toward understanding host responses to infection, the role of the gut microbiome in determining infection outcome is unknown. Moreover, data are lacking on the nature and duration of the microbiome response to norovirus infection, which has important implications for diagnostics and host recovery. Here, we characterized the gut microbiomes of subjects enrolled in a norovirus challenge study. We analyzed microbiome features of asymptomatic and symptomatic individuals at the genome (population) and gene levels and assessed their response over time in symptomatic individuals. We show that the preinfection microbiomes of subjects with asymptomatic infections were enriched in Bacteroidetes and depleted in Clostridia relative to the microbiomes of symptomatic subjects. These compositional differences were accompanied by differences in genes involved in the metabolism of glycans and sphingolipids that may aid in host resilience to infection. We further show that microbiomes shifted in composition following infection and that recovery times were variable among human hosts. In particular, Firmicutes increased immediately following the challenge, while Bacteroidetes and Proteobacteria decreased over the same time. Genes enriched in the microbiomes of symptomatic subjects, including the adenylyltransferase glgC, were linked to glycan metabolism and cell-cell signaling, suggesting as-yet unknown roles for these processes in determining infection outcome. These results provide important context for understanding the gut microbiome role in host susceptibility to symptomatic norovirus infection and long-term health outcomes.IMPORTANCE The role of the human gut microbiome in determining whether an individual infected with norovirus will be symptomatic is poorly understood. This study provides important data on microbes that distinguish asymptomatic from symptomatic microbiomes and links these features to infection responses in a human challenge study. The results have implications for understanding resistance to and treatment of norovirus infections.
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Affiliation(s)
- N V Patin
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - A Peña-Gonzalez
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia, USA
- Max Planck Tandem Group in Computational Biology, Department of Biological Sciences, Universidad de los Andes, Bogotá, Colombia
| | - J K Hatt
- School of Civil and Environmental Engineering, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - C Moe
- Rollins School of Public Health, Emory University, Atlanta, Georgia, USA
| | - A Kirby
- Waterborne Disease Prevention Branch, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - K T Konstantinidis
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia, USA
- School of Civil and Environmental Engineering, Georgia Institute of Technology, Atlanta, Georgia, USA
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240
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Paranjape K, Bédard É, Shetty D, Hu M, Choon FCP, Prévost M, Faucher SP. Unravelling the importance of the eukaryotic and bacterial communities and their relationship with Legionella spp. ecology in cooling towers: a complex network. MICROBIOME 2020; 8:157. [PMID: 33183356 PMCID: PMC7664032 DOI: 10.1186/s40168-020-00926-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Accepted: 09/20/2020] [Indexed: 06/11/2023]
Abstract
BACKGROUND Cooling towers are a major source of large community-associated outbreaks of Legionnaires' disease, a severe pneumonia. This disease is contracted when inhaling aerosols that are contaminated with bacteria from the genus Legionella, most importantly Legionella pneumophila. How cooling towers support the growth of this bacterium is still not well understood. As Legionella species are intracellular parasites of protozoa, it is assumed that protozoan community in cooling towers play an important role in Legionella ecology and outbreaks. However, the exact mechanism of how the eukaryotic community contributes to Legionella ecology is still unclear. Therefore, we used 18S rRNA gene amplicon sequencing to characterize the eukaryotic communities of 18 different cooling towers. The data from the eukaryotic community was then analysed with the bacterial community of the same towers in order to understand how each community could affect Legionella spp. ecology in cooling towers. RESULTS We identified several microbial groups in the cooling tower ecosystem associated with Legionella spp. that suggest the presence of a microbial loop in these systems. Dissolved organic carbon was shown to be a major factor in shaping the eukaryotic community and may be an important factor for Legionella ecology. Network analysis, based on co-occurrence, revealed that Legionella was correlated with a number of different organisms. Out of these, the bacterial genus Brevundimonas and the ciliate class Oligohymenophorea were shown, through in vitro experiments, to stimulate the growth of L. pneumophila through direct and indirect mechanisms. CONCLUSION Our results suggest that Legionella ecology depends on the host community, including ciliates and on several groups of organisms that contribute to its survival and growth in the cooling tower ecosystem. These findings further support the idea that some cooling tower microbiomes may promote the survival and growth of Legionella better than others. Video Abstract.
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Affiliation(s)
- Kiran Paranjape
- Department of Natural Resource Sciences, Faculty of Agricultural and Environmental Sciences, McGill University, Sainte-Anne-de-Bellevue, QC, Canada
| | - Émilie Bédard
- Department of Civil Engineering, Polytechnique Montreal, Montréal, QC, Canada
| | - Deeksha Shetty
- Department of Natural Resource Sciences, Faculty of Agricultural and Environmental Sciences, McGill University, Sainte-Anne-de-Bellevue, QC, Canada
| | - Mengqi Hu
- Department of Natural Resource Sciences, Faculty of Agricultural and Environmental Sciences, McGill University, Sainte-Anne-de-Bellevue, QC, Canada
| | - Fiona Chan Pak Choon
- Department of Natural Resource Sciences, Faculty of Agricultural and Environmental Sciences, McGill University, Sainte-Anne-de-Bellevue, QC, Canada
| | - Michèle Prévost
- Department of Civil Engineering, Polytechnique Montreal, Montréal, QC, Canada
| | - Sébastien P Faucher
- Department of Natural Resource Sciences, Faculty of Agricultural and Environmental Sciences, McGill University, Sainte-Anne-de-Bellevue, QC, Canada.
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241
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Esmaeel Q, Jacquard C, Sanchez L, Clément C, Ait Barka E. The mode of action of plant associated Burkholderia against grey mould disease in grapevine revealed through traits and genomic analyses. Sci Rep 2020; 10:19393. [PMID: 33173115 PMCID: PMC7655954 DOI: 10.1038/s41598-020-76483-7] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2020] [Accepted: 10/28/2020] [Indexed: 11/09/2022] Open
Abstract
Plant-associated Burkholderia spp. have been shown to offer a promising alternative method that may address concerns with ecological issue associated with pesticide overuse in agriculture. However to date, little work has studied the role of Burkholderia species as biocontrol agents for grapevine pathogens. To this end, two Burkholderia strains, BE17 and BE24 isolated from the maize rhizosphere in France, were investigated to determine their biocontrol potential and their ability to induce systemic resistance against grey mould disease in grapevine. Results showed the capacity of both strains to inhibit spore germination and mycelium growth of Botrytis cinerea. Experimental inoculation with BE17 and BE24 showed a significant protection of bacterized-plantlets against grey mould compared to the non-bacterized control. BE17 and BE24-bacterized plants accumulated more reactive oxygen species and an increased callose deposition was observed in leaves of bacterized plantlets compared to the control plantlets. In bacterized plants, gene expression analysis subsequent to B. cinerea challenge showed that strains BE17 and BE24 significantly increased the relative transcript level of pathogenesis-related (PR) proteins PR5 and PR10, two markers involved in the Salicylic acid (SA)-signaling pathway. Furthermore, in silico analysis of strains revealed the presence of genes involved in plant growth promotion and biocontrol highlighting the attractiveness of these strains for sustainable agricultural applications.
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Affiliation(s)
- Qassim Esmaeel
- Unité de Résistance Induite et Bioprotection des Plantes EA 4707, SFR Condorcet FR CNRS 3417, University of Reims-Champagne-Ardenne, Reims, France.
| | - Cédric Jacquard
- Unité de Résistance Induite et Bioprotection des Plantes EA 4707, SFR Condorcet FR CNRS 3417, University of Reims-Champagne-Ardenne, Reims, France
| | - Lisa Sanchez
- Unité de Résistance Induite et Bioprotection des Plantes EA 4707, SFR Condorcet FR CNRS 3417, University of Reims-Champagne-Ardenne, Reims, France
| | - Christophe Clément
- Unité de Résistance Induite et Bioprotection des Plantes EA 4707, SFR Condorcet FR CNRS 3417, University of Reims-Champagne-Ardenne, Reims, France
| | - Essaid Ait Barka
- Unité de Résistance Induite et Bioprotection des Plantes EA 4707, SFR Condorcet FR CNRS 3417, University of Reims-Champagne-Ardenne, Reims, France.
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242
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Zhuang JL, Zhou YY, Liu YD, Li W. Flocs are the main source of nitrous oxide in a high-rate anammox granular sludge reactor: insights from metagenomics and fed-batch experiments. WATER RESEARCH 2020; 186:116321. [PMID: 32861184 DOI: 10.1016/j.watres.2020.116321] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/17/2020] [Revised: 07/10/2020] [Accepted: 08/19/2020] [Indexed: 06/11/2023]
Abstract
Nitrous oxide (N2O) emissions from anammox-based processes are well documented but insight into source of the N2O emission in high-rate anammox granular sludge reactors (AGSR) is limited. In this study, metagenomics and fed-batch experiments were applied to investigate the relative contributions of anammox granules and flocs to N2O production in a high-rate AGSR. Flocs, which constitute only ~10% of total biomass contributed about 60% of the total N2O production. Granules, the main contributor of nitrogen removal (~95%), were responsible for the remaining ~40% of N2O production. This result is inconsistent with reads-based analysis that found the gene encoding clade II type nitrous oxide reductase (nosZII) had similar abundances in both granules and flocs. Another notable trend observed was the relatively higher abundance of the gene for NO-producing nitrite reductase (nir) in comparison to the gene for the nitric oxide reductase gene (nor) in both granules and flocs, indicating nitric oxide (NO) may accumulate in the AGSR. This is significant since NO and N2O pulse assays demonstrated that NO could lead to N2O production from both granules and flocs. However, since anammox bacteria, which were shown to be in higher abundance in granules than in flocs, have the capacity to scavenge NO this provides a mechanism by which its inhibitory effects can be mitigated, limiting N2O release from the granules, consistent with experimental observation. These results demonstrate flocs are the main source of N2O emission in AGSR and provide lab-scale evidence that NO-dependent anammox can mitigate N2O emission.
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Affiliation(s)
- Jin-Long Zhuang
- National Engineering Laboratory for Industrial Wastewater Treatment, School of Resources and Environmental Engineering, East China University of Science and Technology, Shanghai, China; State Environmental Protection Key Laboratory of Environmental Risk Assessment and Control on Chemical Process, School of Resources and Environmental Engineering, East China University of Science and Technology, Shanghai, China
| | - Yuan-Yuan Zhou
- National Engineering Laboratory for Industrial Wastewater Treatment, School of Resources and Environmental Engineering, East China University of Science and Technology, Shanghai, China; State Environmental Protection Key Laboratory of Environmental Risk Assessment and Control on Chemical Process, School of Resources and Environmental Engineering, East China University of Science and Technology, Shanghai, China
| | - Yong-di Liu
- National Engineering Laboratory for Industrial Wastewater Treatment, School of Resources and Environmental Engineering, East China University of Science and Technology, Shanghai, China; State Environmental Protection Key Laboratory of Environmental Risk Assessment and Control on Chemical Process, School of Resources and Environmental Engineering, East China University of Science and Technology, Shanghai, China; Shanghai Institute of Pollution Control and Ecological Security, Shanghai, China
| | - Wei Li
- National Engineering Laboratory for Industrial Wastewater Treatment, School of Resources and Environmental Engineering, East China University of Science and Technology, Shanghai, China; State Environmental Protection Key Laboratory of Environmental Risk Assessment and Control on Chemical Process, School of Resources and Environmental Engineering, East China University of Science and Technology, Shanghai, China; Shanghai Institute of Pollution Control and Ecological Security, Shanghai, China.
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243
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Sphingopyxis sp. Strain OPL5, an Isoprene-Degrading Bacterium from the Sphingomonadaceae Family Isolated from Oil Palm Leaves. Microorganisms 2020; 8:microorganisms8101557. [PMID: 33050387 PMCID: PMC7600658 DOI: 10.3390/microorganisms8101557] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2020] [Revised: 09/30/2020] [Accepted: 10/07/2020] [Indexed: 11/16/2022] Open
Abstract
The volatile secondary metabolite, isoprene, is released by trees to the atmosphere in enormous quantities, where it has important effects on air quality and climate. Oil palm trees, one of the highest isoprene emitters, are increasingly dominating agroforestry over large areas of Asia, with associated uncertainties over their effects on climate. Microbes capable of using isoprene as a source of carbon for growth have been identified in soils and in the tree phyllosphere, and most are members of the Actinobacteria. Here, we used DNA stable isotope probing to identify the isoprene-degrading bacteria associated with oil palm leaves and inhabiting the surrounding soil. Among the most abundant isoprene degraders of the leaf-associated community were members of the Sphingomonadales, although no representatives of this order were previously known to degrade isoprene. Informed by these data, we obtained representatives of the most abundant isoprene degraders in enrichments, including Sphingopyxis strain OPL5 (Sphingomonadales), able to grow on isoprene as the sole source of carbon and energy. Sequencing of the genome of strain OPL5, as well as a novel Gordonia strain, confirmed their pathways of isoprene degradation and broadened our knowledge of the genetic and taxonomic diversity of this important bacterial trait.
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244
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Carroll LM, Cheng RA, Kovac J. No Assembly Required: Using BTyper3 to Assess the Congruency of a Proposed Taxonomic Framework for the Bacillus cereus Group With Historical Typing Methods. Front Microbiol 2020; 11:580691. [PMID: 33072050 PMCID: PMC7536271 DOI: 10.3389/fmicb.2020.580691] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Accepted: 08/25/2020] [Indexed: 12/19/2022] Open
Abstract
The Bacillus cereus group, also known as B. cereus sensu lato (s.l.), is a species complex comprising numerous closely related lineages, which vary in their ability to cause illness in humans and animals. The classification of B. cereus s.l. isolates into species-level taxonomic units is essential for facilitating communication between and among microbiologists, clinicians, public health officials, and industry professionals, but is not always straightforward. A recently proposed genomospecies-subspecies-biovar taxonomic framework aims to provide a standardized nomenclature for this species complex but relies heavily on whole-genome sequencing (WGS). It thus is unclear whether popular, low-cost typing methods (e.g., single- and multi-locus sequence typing) remain congruent with the proposed taxonomy. Here, we characterize 2,231 B. cereus s.l. genomes using a combination of in silico (i) average-nucleotide identity (ANI)-based genomospecies assignment, (ii) ANI-based subspecies assignment, (iii) seven-gene multi-locus sequence typing (MLST), (iv) single-locus panC group assignment, (v) rpoB allelic typing, and (vi) virulence factor detection. We show that sequence types (STs) assigned using MLST can be used for genomospecies assignment, and we provide a comprehensive list of ST/genomospecies associations. For panC group assignment, we show that an adjusted, eight-group framework is largely, albeit not perfectly, congruent with the proposed eight-genomospecies taxonomy, as panC alone may not distinguish (i) B. luti from Group II B. mosaicus and (ii) B. paramycoides from Group VI B. mycoides. We additionally provide a list of loci that capture the topology of the whole-genome B. cereus s.l. phylogeny that may be used in future sequence typing efforts. For researchers with access to WGS, MLST, and/or panC data, we showcase how our recently released software, BTyper3 (https://github.com/lmc297/BTyper3), can be used to assign B. cereus s.l. isolates to taxonomic units within this proposed framework with little-to-no user intervention or domain-specific knowledge of B. cereus s.l. taxonomy. We additionally outline a novel method for assigning B. cereus s.l. genomes to pseudo-gene flow units within proposed genomospecies. The results presented here highlight the backward-compatibility and accessibility of the recently proposed genomospecies-subspecies-biovar taxonomic framework and illustrate that WGS is not a necessity for microbiologists who want to use the proposed nomenclature effectively.
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Affiliation(s)
- Laura M. Carroll
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Rachel A. Cheng
- Department of Food Science, College of Agriculture and Life Sciences, Cornell University, Ithaca, NY, United States
| | - Jasna Kovac
- Department of Food Science, College of Agricultural Sciences, The Pennsylvania State University, University Park, PA, United States
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Sun X, Xu R, Dong Y, Li F, Tao W, Kong T, Zhang M, Qiu L, Wang X, Sun W. Investigation of the Ecological Roles of Putative Keystone Taxa during Tailing Revegetation. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2020; 54:11258-11270. [PMID: 32786562 DOI: 10.1021/acs.est.0c03031] [Citation(s) in RCA: 52] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Metal contamination released from tailings is a global environmental concern. Although phytoremediation is a promising remediation method, its practice is often impeded by the adverse tailing geochemical conditions, which suppress biological activities. The ecosystem services provided by indigenous microorganisms could alter environmental conditions and facilitate revegetation in tailings. During the process, the keystone taxa of the microbial community are assumed an essential role in regulating the community composition and functions. The identity and the environmental functions of the keystone taxa during tailing revegetation, however, remain unelucidated. The current study compared the microbial community composition and interactions of two contrasting stibnite (Sb2S3) tailings, one revegetated and one unvegetated. The microbial interaction networks and keystone taxa were significantly different in the two tailings. Similar keystone taxa were also identified in other revegetated tailings, but not in their corresponding unvegetated tailings. Metagenome-assembled genomes (MAGs) indicated that the keystone taxa in the revegetated tailing may use both organic and inorganic energy sources (e.g., sulfur, arsenic, and antimony). They could also facilitate plant growth since a number of plant-growth-promoting genes, including phosphorus solubilization and siderophore production genes, were encoded. The current study suggests that keystone taxa may play important roles in tailing revegetation by providing nutrients, such as P and Fe, and promoting plant growth.
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Affiliation(s)
- Xiaoxu Sun
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Guangdong Institute of Eco-environmental Science & Technology, Guangdong Academy of Sciences, Guangzhou 510650, China
- Guangdong-Hong Kong-Macao Joint Laboratory for Environmental Pollution and Control, Guangzhou 510650, China
| | - Rui Xu
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Guangdong Institute of Eco-environmental Science & Technology, Guangdong Academy of Sciences, Guangzhou 510650, China
- Guangdong-Hong Kong-Macao Joint Laboratory for Environmental Pollution and Control, Guangzhou 510650, China
| | - Yiran Dong
- School of Environmental Studies, China University of Geosciences (Wuhan), Wuhan 430074, China
| | - Fangbai Li
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Guangdong Institute of Eco-environmental Science & Technology, Guangdong Academy of Sciences, Guangzhou 510650, China
- Guangdong-Hong Kong-Macao Joint Laboratory for Environmental Pollution and Control, Guangzhou 510650, China
| | - Wan Tao
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Guangdong Institute of Eco-environmental Science & Technology, Guangdong Academy of Sciences, Guangzhou 510650, China
- Guangdong-Hong Kong-Macao Joint Laboratory for Environmental Pollution and Control, Guangzhou 510650, China
| | - Tianle Kong
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Guangdong Institute of Eco-environmental Science & Technology, Guangdong Academy of Sciences, Guangzhou 510650, China
- Guangdong-Hong Kong-Macao Joint Laboratory for Environmental Pollution and Control, Guangzhou 510650, China
| | - Miaomiao Zhang
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Guangdong Institute of Eco-environmental Science & Technology, Guangdong Academy of Sciences, Guangzhou 510650, China
- Guangdong-Hong Kong-Macao Joint Laboratory for Environmental Pollution and Control, Guangzhou 510650, China
| | - Lang Qiu
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Guangdong Institute of Eco-environmental Science & Technology, Guangdong Academy of Sciences, Guangzhou 510650, China
- Guangdong-Hong Kong-Macao Joint Laboratory for Environmental Pollution and Control, Guangzhou 510650, China
| | - Xiaoyu Wang
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Guangdong Institute of Eco-environmental Science & Technology, Guangdong Academy of Sciences, Guangzhou 510650, China
- Guangdong-Hong Kong-Macao Joint Laboratory for Environmental Pollution and Control, Guangzhou 510650, China
| | - Weimin Sun
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Guangdong Institute of Eco-environmental Science & Technology, Guangdong Academy of Sciences, Guangzhou 510650, China
- Guangdong-Hong Kong-Macao Joint Laboratory for Environmental Pollution and Control, Guangzhou 510650, China
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246
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Genomic analysis of facultatively oligotrophic haloarchaea of the genera Halarchaeum, Halorubrum, and Halolamina, isolated from solar salt. Arch Microbiol 2020; 203:261-268. [PMID: 32918097 DOI: 10.1007/s00203-020-02027-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2020] [Revised: 08/19/2020] [Accepted: 09/02/2020] [Indexed: 11/27/2022]
Abstract
Extremely halophilic archaea (haloarchaea) belonging to the phylum Euryarchaeota have been found in high-salinity environments. In this study, Halarchaeum sp. CBA1220, Halorubrum sp. CBA1229, and Halolamina sp. CBA1230, which are facultatively oligotrophic haloarchaea, were isolated from solar salt by culture under oligotrophic culture conditions. The complete genomes of strains CBA1220, CBA1229, and CBA1230 were sequenced and were found to contain 3,175,875, 3,582,278, and 3,465,332 bp, with a G + C content of 68.25, 67.66, and 66.75 mol %, respectively. In total, 60, 36, and 33 carbohydrate-active enzyme genes were determined in the respective strains. The strains harbored various genes encoding stress-tolerance proteins, including universal stress proteins, cold-shock proteins, and rubrerythrin and rubrerythrin-related proteins. The genome data produced in this study will facilitate further research to improve our understanding of other halophilic strains and promote their industrial application.
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247
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Bubrig LT, Sutton JM, Fierst JL. Caenorhabditis elegans dauers vary recovery in response to bacteria from natural habitat. Ecol Evol 2020; 10:9886-9895. [PMID: 33005351 PMCID: PMC7520223 DOI: 10.1002/ece3.6646] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Revised: 07/13/2020] [Accepted: 07/16/2020] [Indexed: 01/06/2023] Open
Abstract
Many species use dormant stages for habitat selection by tying recovery to informative external cues. Other species have an undiscerning strategy in which they recover randomly despite having advanced sensory systems. We investigated whether elements of a species' habitat structure and life history can bar it from developing a discerning recovery strategy. The nematode Caenorhabditis elegans has a dormant stage called the dauer larva that disperses between habitat patches. On one hand, C. elegans colonization success is profoundly influenced by the bacteria found in its habitat patches, so we might expect this to select for a discerning strategy. On the other hand, C. elegans' habitat structure and life history suggest that there is no fitness benefit to varying recovery, which might select for an undiscerning strategy. We exposed dauers of three genotypes to a range of bacteria acquired from the worms' natural habitat. We found that C. elegans dauers recover in all conditions but increase recovery on certain bacteria depending on the worm's genotype, suggesting a combination of undiscerning and discerning strategies. Additionally, the worms' responses did not match the bacteria's objective quality, suggesting that their decision is based on other characteristics.
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Affiliation(s)
- Louis T. Bubrig
- Department of Biological SciencesThe University of AlabamaTuscaloosaALUSA
| | - John M. Sutton
- Department of Biological SciencesThe University of AlabamaTuscaloosaALUSA
| | - Janna L. Fierst
- Department of Biological SciencesThe University of AlabamaTuscaloosaALUSA
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248
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Zhuge YY, Shen XY, Liu YD, Shapleigh J, Li W. Application of acidic conditions and inert-gas sparging to achieve high-efficiency nitrous oxide recovery during nitrite denitrification. WATER RESEARCH 2020; 182:116001. [PMID: 32544733 DOI: 10.1016/j.watres.2020.116001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2020] [Revised: 05/21/2020] [Accepted: 05/28/2020] [Indexed: 06/11/2023]
Abstract
Nitrogen removal with energy recovery through denitrification dependent N2O production is garnering recent attention due to its cost advantages. The most effective current method requires alternating COD and nitrite to achieve high N2O production making it incompatible with typical wastewaters and consequently difficult to use in most settings. The work described here introduces a robust and highly efficient N2O recovery approach which has the potential to work with wastewaters containing COD and nitrite simultaneously. This method relies on low pH incubation and inert gas sparging (IGS) to shift a community of mainly N2 producing nitrite denitrifiers to a community that accumulates N2O when incubated in the absence of IGS. Before experiencing IGS, samples from activated sludge incubated at a pH of 4.5 and 6.0 only achieved a maximum N2O production efficiency (PE_N2O) of ∼26%. After IGS the PE_N2O values increased to ∼97.5% and ∼80.2% for samples from these same pH 4.5 and pH 6.0 reactors, respectively. IGS did not lead to N2O production in a pH 7.5 bioreactor. Meta-omics analysis revealed that IGS resulted in an increase in bacteria utilizing the clade I nitrous oxide reductase (nosZI) relative to bacteria utilizing the clade II nitrous oxide reductase (nosZII). This likely results from IGS flushing out N2O leaving nitrite as the principal nitrogen oxide available for respiration, favoring nosZI utilizing bacteria which are more likely to be complete denitrifiers. Metatranscriptomic analysis suggested that the high PE_N2O values that occurred after stopping IGS result from the NO generated by chemodenitrification accumulating to levels that inactivate [4Fe:4S] clusters in the NosR protein essential for N2O reduction in the nosZI denitrifiers. This study provides an efficient and straightforward method for N2O recovery, widening the options for energy recovery from nitrogen-based wastes.
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Affiliation(s)
- Yang-Yang Zhuge
- National Engineering Laboratory for Industrial Wastewater Treatment, School of Resources and Environmental Engineering, East China University of Science and Technology, Shanghai, China; State Environmental Protection Key Laboratory of Environmental Risk Assessment and Control on Chemical Process, School of Resources and Environmental Engineering, East China University of Science and Technology, Shanghai, China
| | - Xun-Yu Shen
- National Engineering Laboratory for Industrial Wastewater Treatment, School of Resources and Environmental Engineering, East China University of Science and Technology, Shanghai, China; State Environmental Protection Key Laboratory of Environmental Risk Assessment and Control on Chemical Process, School of Resources and Environmental Engineering, East China University of Science and Technology, Shanghai, China
| | - Yong-di Liu
- National Engineering Laboratory for Industrial Wastewater Treatment, School of Resources and Environmental Engineering, East China University of Science and Technology, Shanghai, China; State Environmental Protection Key Laboratory of Environmental Risk Assessment and Control on Chemical Process, School of Resources and Environmental Engineering, East China University of Science and Technology, Shanghai, China; Shanghai Institute of Pollution Control and Ecological Security, Shanghai, China
| | | | - Wei Li
- National Engineering Laboratory for Industrial Wastewater Treatment, School of Resources and Environmental Engineering, East China University of Science and Technology, Shanghai, China; State Environmental Protection Key Laboratory of Environmental Risk Assessment and Control on Chemical Process, School of Resources and Environmental Engineering, East China University of Science and Technology, Shanghai, China; Shanghai Institute of Pollution Control and Ecological Security, Shanghai, China.
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249
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Håkonsholm F, Lunestad BT, Aguirre Sánchez JR, Martinez‐Urtaza J, Marathe NP, Svanevik CS. Vibrios from the Norwegian marine environment: Characterization of associated antibiotic resistance and virulence genes. Microbiologyopen 2020; 9:e1093. [PMID: 32558371 PMCID: PMC7520990 DOI: 10.1002/mbo3.1093] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2020] [Revised: 05/20/2020] [Accepted: 05/27/2020] [Indexed: 12/19/2022] Open
Abstract
A total of 116 Vibrio isolates comprising V. alginolyticus (n = 53), V. metschnikovii (n = 38), V. anguillarum (n = 21), V. antiquarius (n = 2), and V. fujianensis (n = 2) were obtained from seawater, fish, or bivalve molluscs from temperate Oceanic and Polar Oceanic area around Norway. Antibiotic sensitivity testing revealed resistance or reduced susceptibility to ampicillin (74%), oxolinic acid (33%), imipenem (21%), aztreonam (19%), and tobramycin (17%). Whole-genome sequence analysis of eighteen drug-resistant isolates revealed the presence of genes like β-lactamases, chloramphenicol-acetyltransferases, and genes conferring tetracycline and quinolone resistance. The strains also carried virulence genes like hlyA, tlh, rtxA to D and aceA, E and F. The genes for cholerae toxin (ctx), thermostable direct hemolysin (tdh), or zonula occludens toxin (zot) were not detected in any of the isolates. The present study shows low prevalence of multidrug resistance and absence of virulence genes of high global concern among environmental vibrios in Norway. However, in the light of climate change, and projected rising sea surface temperatures, even in the cold temperate areas, there is a need for frequent monitoring of resistance and virulence in vibrios to be prepared for future public health challenges.
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Affiliation(s)
| | | | | | - Jaime Martinez‐Urtaza
- Department of Genetics and MicrobiologyUniversitat Autònoma de Barcelona (UAB)BarcelonaSpain
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250
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Starke R, Morais D, Větrovský T, López Mondéjar R, Baldrian P, Brabcová V. Feeding on fungi: genomic and proteomic analysis of the enzymatic machinery of bacteria decomposing fungal biomass. Environ Microbiol 2020; 22:4604-4619. [PMID: 32743948 DOI: 10.1111/1462-2920.15183] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2019] [Revised: 07/21/2020] [Accepted: 07/31/2020] [Indexed: 11/29/2022]
Abstract
Dead fungal biomass is an abundant source of nutrition in both litter and soil of temperate forests largely decomposed by bacteria. Here, we have examined the utilization of dead fungal biomass by the five dominant bacteria isolated from the in situ decomposition of fungal mycelia using a multiOMIC approach. The genomes of the isolates encoded a broad suite of carbohydrate-active enzymes, peptidases and transporters. In the extracellular proteome, only Ewingella americana expressed chitinases while the two Pseudomonas isolates attacked chitin by lytic chitin monooxygenase, deacetylation and deamination. Variovorax sp. expressed enzymes acting on the side-chains of various glucans and the chitin backbone. Surprisingly, despite its genomic potential, Pedobacter sp. did not produce extracellular proteins to decompose fungal mycelia but presumably feeds on simple substrates. The ecological roles of the five individual strains exhibited complementary features for a fast and efficient decomposition of dead fungal biomass by the entire bacterial community.
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Affiliation(s)
- Robert Starke
- Laboratory of Environmental Microbiology, Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220 Praha 4, Czech Republic
| | - Daniel Morais
- Laboratory of Environmental Microbiology, Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220 Praha 4, Czech Republic
| | - Tomáš Větrovský
- Laboratory of Environmental Microbiology, Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220 Praha 4, Czech Republic
| | - Ruben López Mondéjar
- Laboratory of Environmental Microbiology, Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220 Praha 4, Czech Republic
| | - Petr Baldrian
- Laboratory of Environmental Microbiology, Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220 Praha 4, Czech Republic
| | - Vendula Brabcová
- Laboratory of Environmental Microbiology, Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220 Praha 4, Czech Republic
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