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Kuroda K, Maeda R, Shinshima F, Urasaki K, Kubota K, Nobu MK, Noguchi TQP, Satoh H, Yamauchi M, Narihiro T, Yamada M. Microbiological insights into anaerobic phenol degradation mechanisms and bulking phenomenon in a mesophilic upflow anaerobic sludge blanket reactor in long-term operation. WATER RESEARCH 2024; 253:121271. [PMID: 38341972 DOI: 10.1016/j.watres.2024.121271] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Revised: 01/14/2024] [Accepted: 02/05/2024] [Indexed: 02/13/2024]
Abstract
In this study, a long-term operation of 2,747 days was conducted to evaluate the performance of the upflow anaerobic sludge blanket (UASB) reactor and investigated the degradation mechanisms of high-organic loading phenol wastewater. During the reactor operation, the maximum chemical oxygen demand (COD) removal rate of 6.1 ± 0.6 kg/m3/day under 1,680 mg/L phenol concentration was achieved in the mesophilic UASB reactor. After a significant change in the operating temperature from 24.0 ± 4.1 °C to 35.9 ± 0.6 °C, frequent observations of floating and washout of the bloated granular sludge (novel types of the bulking phenomenon) were made in the UASB reactor, suggesting that the change in operating temperature could be a trigger for the bulking phenomenon. Through the metagenomic analysis, phenol degradation mechanisms were predicted that phenol was converted to 4-hydroxybenzoate via two possible routes by Syntrophorhabdaceae and Pelotomaculaceae bacteria. Furthermore, the degradation of 4-hydroxybenzoate to benzoyl-CoA was carried out by members of Syntrophorhabdaceae and Smithellaceae. In the bulking sludge, a predominant presence of Nanobdellota, belonging to DPANN archaea, was detected. The metagenome-assembled genome of the Nanobdellota lacks many biosynthetic pathways and has several genes for the symbiotic lifestyle such as trimeric autotransporter adhesin-related protein. Furthermore, the Nanobdellota have significant correlations with several methanogenic archaea that are predominantly present in the UASB reactor. Considering the results of this study, the predominant Nanobdellota may negatively affect the growth of the methanogens through the parasitic lifestyle and change the balance of microbial interactions in the granular sludge ecosystem.
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Affiliation(s)
- Kyohei Kuroda
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 2-17-2-1 Tsukisamu-Higashi, Toyohira-ku, Sapporo, Hokkaido 062-8517 Japan.
| | - Ryota Maeda
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 2-17-2-1 Tsukisamu-Higashi, Toyohira-ku, Sapporo, Hokkaido 062-8517 Japan; Department of Chemical Science and Engineering, National Institute of Technology, Miyakonojo College, 473-1 Yoshio-cho, Miyakonojo, Miyazaki 885-8567, Japan; Department of Frontier Sciences for Advanced Environment, Graduate School of Environmental Studies, Tohoku University, 6-6-06 Aza-Aoba, Aramaki, Aoba-ku, Sendai, Miyagi 980-8579, Japan
| | - Futaba Shinshima
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 2-17-2-1 Tsukisamu-Higashi, Toyohira-ku, Sapporo, Hokkaido 062-8517 Japan; Department of Chemical Science and Engineering, National Institute of Technology, Miyakonojo College, 473-1 Yoshio-cho, Miyakonojo, Miyazaki 885-8567, Japan
| | - Kampachiro Urasaki
- Department of Civil and Environmental Engineering, Graduate School of Engineering, Tohoku University, 6-6-06 Aza-Aoba, Aramaki, Aoba-ku, Sendai, Miyagi 980-8579, Japan
| | - Kengo Kubota
- Department of Frontier Sciences for Advanced Environment, Graduate School of Environmental Studies, Tohoku University, 6-6-06 Aza-Aoba, Aramaki, Aoba-ku, Sendai, Miyagi 980-8579, Japan; Department of Civil and Environmental Engineering, Graduate School of Engineering, Tohoku University, 6-6-06 Aza-Aoba, Aramaki, Aoba-ku, Sendai, Miyagi 980-8579, Japan
| | - Masaru K Nobu
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Central 6, Higashi 1-1-1, Tsukuba, Ibaraki 305-8566, Japan
| | - Taro Q P Noguchi
- Department of Chemical Science and Engineering, National Institute of Technology, Miyakonojo College, 473-1 Yoshio-cho, Miyakonojo, Miyazaki 885-8567, Japan
| | - Hisashi Satoh
- Division of Environmental Engineering, Faculty of Engineering, Hokkaido University, North-13, West-8, Hokkaido 060-8628 Japan
| | - Masahito Yamauchi
- Department of Urban Environmental Design and Engineering, National Institute of Technology, Kagoshima College, 1460-1 Shinkou, Hayato, Kirishima, Kagoshima 899-5193, Japan
| | - Takashi Narihiro
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 2-17-2-1 Tsukisamu-Higashi, Toyohira-ku, Sapporo, Hokkaido 062-8517 Japan.
| | - Masayoshi Yamada
- Department of Urban Environmental Design and Engineering, National Institute of Technology, Kagoshima College, 1460-1 Shinkou, Hayato, Kirishima, Kagoshima 899-5193, Japan.
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Iqbal S, Begum F, Ullah I, Jalal N, Shaw P. Peeling off the layers from microbial dark matter (MDM): recent advances, future challenges, and opportunities. Crit Rev Microbiol 2024:1-21. [PMID: 38385313 DOI: 10.1080/1040841x.2024.2319669] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Accepted: 02/10/2024] [Indexed: 02/23/2024]
Abstract
Microbes represent the most common organisms on Earth; however, less than 2% of microbial species in the environment can undergo cultivation for study under laboratory conditions, and the rest of the enigmatic, microbial world remains mysterious, constituting a kind of "microbial dark matter" (MDM). In the last two decades, remarkable progress has been made in culture-dependent and culture-independent techniques. More recently, studies of MDM have relied on culture-independent techniques to recover genetic material through either unicellular genomics or shotgun metagenomics to construct single-amplified genomes (SAGs) and metagenome-assembled genomes (MAGs), respectively, which provide information about evolution and metabolism. Despite the remarkable progress made in the past decades, the functional diversity of MDM still remains uncharacterized. This review comprehensively summarizes the recently developed culture-dependent and culture-independent techniques for characterizing MDM, discussing major challenges, opportunities, and potential applications. These activities contribute to expanding our knowledge of the microbial world and have implications for various fields including Biotechnology, Bioprospecting, Functional genomics, Medicine, Evolutionary and Planetary biology. Overall, this review aims to peel off the layers from MDM, shed light on recent advancements, identify future challenges, and illuminate the exciting opportunities that lie ahead in unraveling the secrets of this intriguing microbial realm.
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Affiliation(s)
- Sajid Iqbal
- Oujiang Lab (Zhejiang Laboratory for Regenerative Medicine, Vision, and Brain Health), Wenzhou, China
- School of Pharmaceutical Science, Wenzhou Medical University, Wenzhou, China
| | - Farida Begum
- Department of Biochemistry, Abdul Wali Khan University Mardan, Mardan, Pakistan
| | - Ihsan Ullah
- College of Chemical Engineering, Fuzhou University, Fuzhou, China
| | - Nasir Jalal
- Oujiang Lab (Zhejiang Laboratory for Regenerative Medicine, Vision, and Brain Health), Wenzhou, China
| | - Peter Shaw
- Oujiang Lab (Zhejiang Laboratory for Regenerative Medicine, Vision, and Brain Health), Wenzhou, China
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3
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Göker M, Oren A. Valid publication of names of two domains and seven kingdoms of prokaryotes. Int J Syst Evol Microbiol 2024; 74. [PMID: 38252124 DOI: 10.1099/ijsem.0.006242] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2024] Open
Abstract
The International Code of Nomenclature of Prokaryotes (ICNP) now includes the categories domain and kingdom. For the purpose of the valid publication of their names under the ICNP, we consider here the two known domains, 'Bacteria' and 'Archaea', as well as a number of taxa suitable for the rank of kingdom, based on previous phylogenetic and taxonomic studies. It is proposed to subdivide the domain Bacteria into the kingdoms Bacillati, Fusobacteriati, Pseudomonadati and Thermotogati. This arrangement reflects contemporary phylogenetic hypotheses as well as previous taxonomic proposals based on cell wall structure, including 'diderms' vs. 'monoderms', Gracilicutes vs. Firmicutes, 'Negibacteria' vs. 'Unibacteria', 'Hydrobacteria' vs. 'Terrabacteria', and 'Hydrobacterida' vs. 'Terrabacterida'. The domain Archaea is proposed to include the kingdoms Methanobacteriati, Nanobdellati and Thermoproteati, reflecting the previous division into 'Euryarchaeota', 'DPANN superphylum' and 'TACK superphylum'.
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Affiliation(s)
- Markus Göker
- Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Inhoffenstrasse 7B, D-38124 Braunschweig, Germany
| | - Aharon Oren
- The Hebrew University of Jerusalem, The Institute of Life Sciences, Edmond J. Safra Campus - Givat Ram, 9190401 Jerusalem, Israel
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Sekiguchi Y, Teramoto K, Tourlousse DM, Ohashi A, Hamajima M, Miura D, Yamada Y, Iwamoto S, Tanaka K. A large-scale genomically predicted protein mass database enables rapid and broad-spectrum identification of bacterial and archaeal isolates by mass spectrometry. Genome Biol 2023; 24:257. [PMID: 38049850 PMCID: PMC10696839 DOI: 10.1186/s13059-023-03096-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Accepted: 10/24/2023] [Indexed: 12/06/2023] Open
Abstract
MALDI-TOF MS-based microbial identification relies on reference spectral libraries, which limits the screening of diverse isolates, including uncultured lineages. We present a new strategy for broad-spectrum identification of bacterial and archaeal isolates by MALDI-TOF MS using a large-scale database of protein masses predicted from nearly 200,000 publicly available genomes. We verify the ability of the database to identify microorganisms at the species level and below, achieving correct identification for > 90% of measured spectra. We further demonstrate its utility by identifying uncultured strains from mouse feces with metagenomics, allowing the identification of new strains by customizing the database with metagenome-assembled genomes.
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Affiliation(s)
- Yuji Sekiguchi
- Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), AIST Tsukuba Central 6, Ibaraki, 305-8566, Japan.
| | | | - Dieter M Tourlousse
- Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), AIST Tsukuba Central 6, Ibaraki, 305-8566, Japan
| | - Akiko Ohashi
- Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), AIST Tsukuba Central 6, Ibaraki, 305-8566, Japan
| | - Mayu Hamajima
- Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), AIST Tsukuba Central 6, Ibaraki, 305-8566, Japan
| | - Daisuke Miura
- Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), AIST Tsukuba Central 6, Ibaraki, 305-8566, Japan
| | - Yoshihiro Yamada
- Koichi Tanaka Mass Spectrometry Research Laboratory, Shimadzu Corporation, Kyoto, Japan
| | - Shinichi Iwamoto
- Koichi Tanaka Mass Spectrometry Research Laboratory, Shimadzu Corporation, Kyoto, Japan
| | - Koichi Tanaka
- Koichi Tanaka Mass Spectrometry Research Laboratory, Shimadzu Corporation, Kyoto, Japan
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5
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Oren A, Göker M. Candidatus List. Lists of names of prokaryotic Candidatus phyla. Int J Syst Evol Microbiol 2023; 73. [PMID: 37159402 DOI: 10.1099/ijsem.0.005821] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/11/2023] Open
Affiliation(s)
- Aharon Oren
- The Institute of Life Sciences, The Hebrew University of Jerusalem, The Edmond J. Safra Campus, 9190401 Jerusalem, Israel
| | - Markus Göker
- Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Inhoffenstrasse 7B, 38124 Braunschweig, Germany
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Snyder C, Centlivre JP, Bhute S, Shipman G, Friel AD, Viver T, Palmer M, Konstantinidis KT, Sun HJ, Rossello-Mora R, Nadeau J, Hedlund BP. Microbial Motility at the Bottom of North America: Digital Holographic Microscopy and Genomic Motility Signatures in Badwater Spring, Death Valley National Park. ASTROBIOLOGY 2023; 23:295-307. [PMID: 36625891 DOI: 10.1089/ast.2022.0090] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
Motility is widely distributed across the tree of life and can be recognized by microscopy regardless of phylogenetic affiliation, biochemical composition, or mechanism. Microscopy has thus been proposed as a potential tool for detection of biosignatures for extraterrestrial life; however, traditional light microscopy is poorly suited for this purpose, as it requires sample preparation, involves fragile moving parts, and has a limited volume of view. In this study, we deployed a field-portable digital holographic microscope (DHM) to explore microbial motility in Badwater Spring, a saline spring in Death Valley National Park, and complemented DHM imaging with 16S rRNA gene amplicon sequencing and shotgun metagenomics. The DHM identified diverse morphologies and distinguished run-reverse-flick and run-reverse types of flagellar motility. PICRUSt2- and literature-based predictions based on 16S rRNA gene amplicons were used to predict motility genotypes/phenotypes for 36.0-60.1% of identified taxa, with the predicted motile taxa being dominated by members of Burkholderiaceae and Spirochaetota. A shotgun metagenome confirmed the abundance of genes encoding flagellar motility, and a Ralstonia metagenome-assembled genome encoded a full flagellar gene cluster. This study demonstrates the potential of DHM for planetary life detection, presents the first microbial census of Badwater Spring and brine pool, and confirms the abundance of mobile microbial taxa in an extreme environment.
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Affiliation(s)
- Carl Snyder
- Department of Physics, Portland State University, Portland, Oregon, USA
| | - Jakob P Centlivre
- School of Life Sciences, University of Nevada, Las Vegas, Las Vegas, Nevada, USA
| | - Shrikant Bhute
- School of Life Sciences, University of Nevada, Las Vegas, Las Vegas, Nevada, USA
| | - Gözde Shipman
- School of Life Sciences, University of Nevada, Las Vegas, Las Vegas, Nevada, USA
| | - Ariel D Friel
- School of Life Sciences, University of Nevada, Las Vegas, Las Vegas, Nevada, USA
| | - Tomeu Viver
- Marine Microbiology Group, Department of Animal and Microbial Biodiversity, Mediterranean Institute for Advanced Studies (CSIC-UIB), Esporles, Illes Balears, Spain
| | - Marike Palmer
- School of Life Sciences, University of Nevada, Las Vegas, Las Vegas, Nevada, USA
| | | | - Henry J Sun
- Desert Research Institute, Las Vegas, Nevada, USA
| | - Ramon Rossello-Mora
- Marine Microbiology Group, Department of Animal and Microbial Biodiversity, Mediterranean Institute for Advanced Studies (CSIC-UIB), Esporles, Illes Balears, Spain
| | - Jay Nadeau
- Department of Physics, Portland State University, Portland, Oregon, USA
| | - Brian P Hedlund
- School of Life Sciences, University of Nevada, Las Vegas, Las Vegas, Nevada, USA
- Nevada Institute of Personalized Medicine, Las Vegas, Nevada, USA
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Zhang L, Yuan Y, Zhang Y, Liu Y. Exploring key factors in anaerobic syntrophic interactions: Biomass activity, microbial community, and morphology. BIORESOURCE TECHNOLOGY 2022; 363:127852. [PMID: 36067891 DOI: 10.1016/j.biortech.2022.127852] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Revised: 08/20/2022] [Accepted: 08/22/2022] [Indexed: 06/15/2023]
Abstract
The present work evaluated the impacts of microbial communities, biomass activity and sludge morphology on anaerobic syntrophic reactions. Experiments were conducted using mature floc sludge and granular sludge under different food/microbes ratios, and with different sludge types (floc sludge, concentrated floc sludge and granular sludge) and sludge morphology (granules, vortexed granules, and granules with different particle sizes). The results show that the intact granules achieved the most effective syntrophic reaction among all sludge types. The granule structure facilitated the enrichment of syntrophic acetate oxidation bacteria (g_Syner-01 and g_Mesotoga) and methanogens, which corresponds to their superior specific methanogenic activity and high production of communication compounds. Despite the high diffusion and substrate uptake capacities, the disintegrated granules had low H2 consumption rates, which led to poor syntrophic activities. The results underline the importance of sludge spatial structures in promoting excellent syntrophic activities and the development of diverse microbial communities.
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Affiliation(s)
- Lei Zhang
- Department of Civil and Environmental Engineering, University of Alberta, Edmonton, Canada
| | - Yiyang Yuan
- Department of Civil and Environmental Engineering, University of Alberta, Edmonton, Canada
| | - Yingdi Zhang
- Department of Civil and Environmental Engineering, University of Alberta, Edmonton, Canada
| | - Yang Liu
- Department of Civil and Environmental Engineering, University of Alberta, Edmonton, Canada.
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Abstract
Subcellular compartmentalization is a defining feature of all cells. In prokaryotes, compartmentalization is generally achieved via protein-based strategies. The two main classes of microbial protein compartments are bacterial microcompartments and encapsulin nanocompartments. Encapsulins self-assemble into proteinaceous shells with diameters between 24 and 42 nm and are defined by the viral HK97-fold of their shell protein. Encapsulins have the ability to encapsulate dedicated cargo proteins, including ferritin-like proteins, peroxidases, and desulfurases. Encapsulation is mediated by targeting sequences present in all cargo proteins. Encapsulins are found in many bacterial and archaeal phyla and have been suggested to play roles in iron storage, stress resistance, sulfur metabolism, and natural product biosynthesis. Phylogenetic analyses indicate that they share a common ancestor with viral capsid proteins. Many pathogens encode encapsulins, and recent evidence suggests that they may contribute toward pathogenicity. The existing information on encapsulin structure, biochemistry, biological function, and biomedical relevance is reviewed here.
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Affiliation(s)
- Tobias W. Giessen
- Departments of Biomedical Engineering and Biological Chemistry, University of Michigan Medical School, Ann Arbor, Michigan, USA
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9
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Mao G, Han Y, Liu X, Crittenden J, Huang N, Ahmad UM. Technology status and trends of industrial wastewater treatment: A patent analysis. CHEMOSPHERE 2022; 288:132483. [PMID: 34624344 DOI: 10.1016/j.chemosphere.2021.132483] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Revised: 09/18/2021] [Accepted: 10/04/2021] [Indexed: 06/13/2023]
Abstract
Globally, 80% of wastewater, among which 28% came from industry, returned to the ecosystem without treatment or reuse. The discharge of industrial wastewater poses public health and environmental concerns. The necessity and urgency of industrial wastewater treatment (IWT) will bring great challenges to most countries. This paper conducted the patent analysis combined with text mining to quantitatively analyze 11,840 patents related to IWT in the Derwent Innovations Index database. The results showed that: From 1973 to 2020, the number of patents related to IWT annually was increasing consistently. China ranked first in the number of patent publications. In contrast, the United States and some patent organizations, such as World Intellectual Property Organization, produced fewer patents, while they played more important roles in knowledge transfer. The core technology analysis suggested that method, device, material and related industry were hot topics. From activated sludge treatment technology, industrial wastewater treatment technology had gone through a development process from single technology treatment to combined technologies treatment. In the foreseeable future, research on devices for physical treatment, advanced oxidation processes, automated and energy-saving treatment systems were the promising directions.
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Affiliation(s)
- Guozhu Mao
- School of Environmental Science and Engineering, Tianjin University, Tianjin, 300350, China; Center for Green Buildings and Sponge Cities, Georgia Tech Tianjin University Shenzhen Institute, Shenzhen, Guangdong, 518071, China
| | - Yixin Han
- School of Environmental Science and Engineering, Tianjin University, Tianjin, 300350, China; Center for Green Buildings and Sponge Cities, Georgia Tech Tianjin University Shenzhen Institute, Shenzhen, Guangdong, 518071, China
| | - Xi Liu
- Institute of Blue and Green Development, Shandong University, Weihai, 264209, China; College of Management and Economics, Tianjin University, Tianjin, 300072, China.
| | - John Crittenden
- Brook Byers Institute for Sustainable Systems, School of Civil and Environmental Engineering, Georgia Institute of Technology, Atlanta, GA, USA
| | - Ning Huang
- School of Environmental Science and Engineering, Tianjin University, Tianjin, 300350, China; Center for Green Buildings and Sponge Cities, Georgia Tech Tianjin University Shenzhen Institute, Shenzhen, Guangdong, 518071, China
| | - Umme Marium Ahmad
- School of Environmental Science and Engineering, Tianjin University, Tianjin, 300350, China
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10
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Kagemasa S, Kuroda K, Nakai R, Li YY, Kubota K. Diversity of <i>Candidatus</i> Patescibacteria in Activated Sludge Revealed by a Size-Fractionation Approach. Microbes Environ 2022; 37. [PMID: 35676047 PMCID: PMC9530733 DOI: 10.1264/jsme2.me22027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Uncultivated members of Candidatus Patescibacteria are commonly found in activated sludge treating sewage and are widely distributed in wastewater treatment plants in different regions and countries. However, the phylogenetic diversity of Ca. Patescibacteria is difficult to examine because of their low relative abundance in the environment. Since Ca. Patescibacteria members have small cell sizes, we herein collected small microorganisms from activated sludge using a filtration-based size-fractionation approach (i.e., 0.45–0.22 μm and 0.22–0.1 μm fractions). Fractionated samples were characterized using 16S rRNA gene amplicon and shotgun metagenomic sequence analyses. The amplicon analysis revealed that the relative abundance of Ca. Patescibacteria increased to 73.5% and 52.5% in the 0.45–0.22 μm and 0.22–0.1 μm fraction samples, respectively, from 5.8% in the unfractionated sample. The members recovered from the two size-fractionated samples included Ca. Saccharimonadia, Ca. Gracilibacteria, Ca. Paceibacteria, Ca. Microgenomatia, class-level uncultured lineage ABY1, Ca. Berkelbacteria, WS6 (Ca. Dojkabacteria), and WWE3, with Ca. Saccharimonadia being predominant in both fraction samples. The number of operational taxonomic units belonging to Ca. Patescibacteria was approximately 6-fold higher in the size-fractionated samples than in the unfractionated sample. The shotgun metagenomic analysis of the 0.45–0.22 μm fractioned sample enabled the reconstruction of 24 high-quality patescibacterial bins. The bins obtained were classified into diverse clades at the family and genus levels, some of which were rarely detected in previous activated sludge studies. Collectively, the present results suggest that the overall diversity of Ca. Patescibacteria inhabiting activated sludge is higher than previously expected.
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Affiliation(s)
- Shuka Kagemasa
- Department of Civil and Environmental Engineering, Tohoku University
| | - Kyohei Kuroda
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST)
| | - Ryosuke Nakai
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST)
| | - Yu-You Li
- Department of Civil and Environmental Engineering, Tohoku University
| | - Kengo Kubota
- Department of Frontier Sciences for Advanced Environment, Tohoku University
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11
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Flood BE, Louw DC, Van der Plas AK, Bailey JV. Giant sulfur bacteria (Beggiatoaceae) from sediments underlying the Benguela upwelling system host diverse microbiomes. PLoS One 2021; 16:e0258124. [PMID: 34818329 PMCID: PMC8612568 DOI: 10.1371/journal.pone.0258124] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Accepted: 09/20/2021] [Indexed: 01/04/2023] Open
Abstract
Due to their lithotrophic metabolisms, morphological complexity and conspicuous appearance, members of the Beggiatoaceae have been extensively studied for more than 100 years. These bacteria are known to be primarily sulfur-oxidizing autotrophs that commonly occur in dense mats at redox interfaces. Their large size and the presence of a mucous sheath allows these cells to serve as sites of attachment for communities of other microorganisms. But little is known about their individual niche preferences and attached microbiomes, particularly in marine environments, due to a paucity of cultivars and their prevalence in habitats that are difficult to access and study. Therefore, in this study, we compare Beggiatoaceae strain composition, community composition, and geochemical profiles collected from sulfidic sediments at four marine stations off the coast of Namibia. To elucidate community members that were directly attached and enriched in both filamentous Beggiatoaceae, namely Ca. Marithioploca spp. and Ca. Maribeggiatoa spp., as well as non-filamentous Beggiatoaceae, Ca. Thiomargarita spp., the Beggiatoaceae were pooled by morphotype for community analysis. The Beggiatoaceae samples collected from a highly sulfidic site were enriched in strains of sulfur-oxidizing Campylobacterota, that may promote a more hospitable setting for the Beggiatoaceae, which are known to have a lower tolerance for high sulfide to oxygen ratios. We found just a few host-specific associations with the motile filamentous morphotypes. Conversely, we detected 123 host specific enrichments with non-motile chain forming Beggiatoaceae. Potential metabolisms of the enriched strains include fermentation of host sheath material, syntrophic exchange of H2 and acetate, inorganic sulfur metabolism, and nitrite oxidation. Surprisingly, we did not detect any enrichments of anaerobic ammonium oxidizing bacteria as previously suggested and postulate that less well-studied anaerobic ammonium oxidation pathways may be occurring instead.
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Affiliation(s)
- Beverly E. Flood
- Department of Earth and Environmental Sciences, University of Minnesota, Twin Cities, Minnesota, United States of America
- * E-mail:
| | - Deon C. Louw
- National Marine Information and Research Centre, Swakopmund, Namibia
| | | | - Jake V. Bailey
- Department of Earth and Environmental Sciences, University of Minnesota, Twin Cities, Minnesota, United States of America
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12
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Andreas MP, Giessen TW. Large-scale computational discovery and analysis of virus-derived microbial nanocompartments. Nat Commun 2021; 12:4748. [PMID: 34362927 PMCID: PMC8346489 DOI: 10.1038/s41467-021-25071-y] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2021] [Accepted: 07/12/2021] [Indexed: 02/06/2023] Open
Abstract
Encapsulins are a class of microbial protein compartments defined by the viral HK97-fold of their capsid protein, self-assembly into icosahedral shells, and dedicated cargo loading mechanism for sequestering specific enzymes. Encapsulins are often misannotated and traditional sequence-based searches yield many false positive hits in the form of phage capsids. Here, we develop an integrated search strategy to carry out a large-scale computational analysis of prokaryotic genomes with the goal of discovering an exhaustive and curated set of all HK97-fold encapsulin-like systems. We find over 6,000 encapsulin-like systems in 31 bacterial and four archaeal phyla, including two novel encapsulin families. We formulate hypotheses about their potential biological functions and biomedical relevance, which range from natural product biosynthesis and stress resistance to carbon metabolism and anaerobic hydrogen production. An evolutionary analysis of encapsulins and related HK97-type virus families shows that they share a common ancestor, and we conclude that encapsulins likely evolved from HK97-type bacteriophages.
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Affiliation(s)
- Michael P Andreas
- Department of Biomedical Engineering, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Tobias W Giessen
- Department of Biomedical Engineering, University of Michigan Medical School, Ann Arbor, MI, USA.
- Department of Biological Chemistry, University of Michigan Medical School, Ann Arbor, MI, USA.
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13
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Deryusheva E, Machulin A, Matyunin M, Galzitskaya O. Sequence and evolutionary analysis of bacterial ribosomal S1 proteins. Proteins 2021; 89:1111-1124. [PMID: 33843105 DOI: 10.1002/prot.26084] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2020] [Revised: 03/17/2021] [Accepted: 04/07/2021] [Indexed: 12/21/2022]
Abstract
The multi-domain bacterial S1 protein is the largest and most functionally important ribosomal protein of the 30S subunit, which interacts with both mRNA and proteins. The family of ribosomal S1 proteins differs in the classical sense from a protein with tandem repeats and has a "bead-on-string" organization, where each repeat is folded into a globular domain. Based on our recent data, the study of evolutionary relationships for the bacterial phyla will provide evidence for one of the proposed theories of the evolutionary development of proteins with structural repeats: from multiple repeats of assembles to single repeats, or vice versa. In this comparative analysis of 1333 S1 sequences that were identified in 24 different phyla, we demonstrate how such phyla can form independently/dependently during evolution. To the best of our knowledge, this work is the first study of the evolutionary history of bacterial ribosomal S1 proteins. The collected and structured data can be useful to computer biologists as a resource for determining percent identity, amino acid composition and logo motifs, as well as dN/dS ratio in bacterial S1 protein. The obtained research data indicate that the evolutionary development of bacterial ribosomal S1 proteins evolved from multiple assemblies to single repeat. The presented data are integrated into the server, which can be accessed at http://oka.protres.ru:4200.
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Affiliation(s)
- Evgeniya Deryusheva
- Institute for Biological Instrumentation, Federal Research Center "Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences", Pushchino, Russian Federation
| | - Andrey Machulin
- Skryabin Institute of Biochemistry and Physiology of Microorganisms, Russian Academy of Sciences, Federal Research Center "Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences", Pushchino, Russian Federation
| | - Maxim Matyunin
- Institute of Protein Research, Russian Academy of Sciences, Pushchino, Russian Federation
| | - Oxana Galzitskaya
- Institute of Protein Research, Russian Academy of Sciences, Pushchino, Russian Federation.,Institute of Theoretical and Experimental Biophysics, Russian Academy of Sciences, Pushchino, Russian Federation
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14
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Jiang C, McIlroy SJ, Qi R, Petriglieri F, Yashiro E, Kondrotaite Z, Nielsen PH. Identification of microorganisms responsible for foam formation in mesophilic anaerobic digesters treating surplus activated sludge. WATER RESEARCH 2021; 191:116779. [PMID: 33401166 DOI: 10.1016/j.watres.2020.116779] [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: 08/26/2020] [Revised: 12/06/2020] [Accepted: 12/20/2020] [Indexed: 06/12/2023]
Abstract
Foaming is a common operational problem in anaerobic digestion (AD) systems, where hydrophobic filamentous microorganisms are usually considered to be the major cause. However, little is known about the identity of foam-stabilising microorganisms in AD systems, and control measures are lacking. This study identified putative foam forming microorganisms in 13 full-scale mesophilic digesters located at 11 wastewater treatment plants in Denmark, using 16S rRNA gene amplicon sequencing with species-level resolution and fluorescence in situ hybridization (FISH) for visualization. A foaming potential aeration test was applied to classify the digester sludges according to their foaming propensity. A high foaming potential for sludges was linked to the abundance of species from the genus Candidatus Microthrix, immigrating with the feed stream (surplus activated sludge), but also to several novel phylotypes potentially growing in the digester. These species were classified to the genera Ca. Brevefilum (Ca. B. fermentans) and Tetrasphaera (midas_s_5), the families ST-12K33 (midas_s_22), and Rikenellaceae (midas_s_141), and the archaeal genus Methanospirillum (midas_s_2576). Application of FISH showed that these potential foam-forming organisms all had a filamentous morphology. Additionally, it was shown that concentrations of ammonium and total nitrogen correlated strongly to the presence of foam-formers. This study provided new insight into the identity of putative foam-forming microorganisms in mesophilic AD systems, allowing for the subsequent surveillance of their abundances and studies of their ecology. Such information will importantly inform the development of control measures for these problematic microorganisms.
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Affiliation(s)
- Chenjing Jiang
- Center for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University, 9220 Aalborg, Denmark; Key Laboratory of Engineering Oceanography, Second Institute of Oceanography, SOA, Hangzhou, 310012, China
| | - Simon Jon McIlroy
- Center for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University, 9220 Aalborg, Denmark; Centre for Microbiome Research, School of Biomedical Sciences, Queensland University of Technology (QUT), Translational Research Institute, Woolloongabba, Australia
| | - Rong Qi
- State Key Laboratory of Environmental Aquatic Chemistry, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 10085, China
| | - Francesca Petriglieri
- Center for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University, 9220 Aalborg, Denmark
| | - Erika Yashiro
- Center for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University, 9220 Aalborg, Denmark
| | - Zivile Kondrotaite
- Center for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University, 9220 Aalborg, Denmark
| | - Per Halkjær Nielsen
- Center for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University, 9220 Aalborg, Denmark.
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15
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Bovio-Winkler P, Cabezas A, Etchebehere C. Database Mining to Unravel the Ecology of the Phylum Chloroflexi in Methanogenic Full Scale Bioreactors. Front Microbiol 2021; 11:603234. [PMID: 33552017 PMCID: PMC7854539 DOI: 10.3389/fmicb.2020.603234] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2020] [Accepted: 12/28/2020] [Indexed: 11/13/2022] Open
Abstract
Although microbial communities of anaerobic bioreactors have been extensively studied using DNA-based tools, there are still several knowledge gaps regarding the microbiology of the process, in particular integration of all generated data is still limited. One understudied core phylum within anaerobic bioreactors is the phylum Chloroflexi, despite being one of the most abundant groups in anaerobic reactors. In order to address the abundance, diversity and phylogeny of this group in full-scale methanogenic reactors globally distributed, a compilation of 16S ribosomal RNA gene sequence data from 62 full-scale methanogenic reactors studied worldwide, fed either with wastewater treatment anaerobic reactors (WTARs) or solid-waste treatment anaerobic reactors (STARs), was performed. One of the barriers to overcome was comparing data generated using different primer sets and different sequencing platforms. The sequence analysis revealed that the average abundance of Chloroflexi in WTARs was higher than in STARs. Four genera belonging to the Anaerolineae class dominated both WTARs and STARs but the core populations were different. According to the phylogenetic analysis, most of the sequences formed clusters with no cultured representatives. The Anaerolineae class was more abundant in reactors with granular biomass than in reactors with disperse biomass supporting the hypothesis that Anaerolineae play an important role in granule formation and structure due to their filamentous morphology. Cross-study comparisons can be fruitfully used to understand the complexity of the anaerobic digestion process. However, more efforts are needed to standardize protocols and report metadata information.
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Affiliation(s)
- Patricia Bovio-Winkler
- Microbial Ecology Laboratory, Department of Microbial Biochemistry and Genomic, Biological Research Institute “Clemente Estable,” Montevideo, Uruguay
| | - Angela Cabezas
- Instituto Tecnológico Regional Centro Sur, Universidad Tecnológica, Durazno, Uruguay
| | - Claudia Etchebehere
- Microbial Ecology Laboratory, Department of Microbial Biochemistry and Genomic, Biological Research Institute “Clemente Estable,” Montevideo, Uruguay
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16
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Fujitani H, Momiuchi K, Ishii K, Nomachi M, Kikuchi S, Ushiki N, Sekiguchi Y, Tsuneda S. Genomic and Physiological Characteristics of a Novel Nitrite-Oxidizing Nitrospira Strain Isolated From a Drinking Water Treatment Plant. Front Microbiol 2020; 11:545190. [PMID: 33042056 PMCID: PMC7522533 DOI: 10.3389/fmicb.2020.545190] [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: 03/24/2020] [Accepted: 08/24/2020] [Indexed: 11/13/2022] Open
Abstract
Nitrite-oxidizing bacteria (NOB) catalyze the second step of nitrification, which is an important process of the biogeochemical nitrogen cycle and is exploited extensively as a biological nitrogen removal process. Members of the genus Nitrospira are often identified as the dominant NOB in a diverse range of natural and artificial environments. Additionally, a number of studies examining the distribution, abundance, and characterization of complete ammonia oxidation (comammox) Nitrospira support the ecological importance of the genus Nitrospira. However, niche differentiation between nitrite-oxidizing Nitrospira and comammox Nitrospira remains unknown due to a lack of pure cultures. In this study, we report the isolation, physiology, and genome of a novel nitrite-oxidizing Nitrospira strain isolated from a fixed-bed column at a drinking water treatment plant. Continuous feeding of ammonia led to the enrichment of Nitrospira-like cells, as well as members of ammonia-oxidizing genus Nitrosomonas. Subsequently, a microcolony sorting technique was used to isolate a novel nitrite-oxidizing Nitrospira strain. Sequences of strains showing the growth of microcolonies in microtiter plates were checked. Consequently, the most abundant operational taxonomic unit (OTU) exhibited high sequence similarity with Nitrospira japonica (98%) at the 16S rRNA gene level. The two other Nitrospira OTUs shared over 99% sequence similarities with N. japonica and Nitrospira sp. strain GC86. Only one strain identified as Nitrospira was successfully subcultivated and designated as Nitrospira sp. strain KM1 with high sequence similarity with N. japonica (98%). The half saturation constant for nitrite and the maximum nitrite oxidation rate of strain KM1 were orders of magnitude lower than the published data of other known Nitrospira strains; moreover, strain KM1 was more sensitive to free ammonia compared with previously isolated Nitrospira strains. Therefore, the new Nitrospira strain appears to be better adapted to oligotrophic environments compared with other known non-marine nitrite oxidizers. The complete genome of strain KM1 was 4,509,223 bp in length and contained 4,318 predicted coding sequences. Average nucleotide identities between strain KM1 and known cultured Nitrospira genome sequences are 76.7-78.4%, suggesting at least species-level novelty of the strain in the Nitrospira lineage II. These findings broaden knowledge of the ecophysiological diversity of nitrite-oxidizing Nitrospira.
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Affiliation(s)
- Hirotsugu Fujitani
- Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology, Tsukuba, Japan.,Research Organization for Nano & Life Innovation, Waseda University, Tokyo, Japan
| | - Kengo Momiuchi
- Department of Life Science and Medical Bioscience, Waseda University, Tokyo, Japan
| | - Kento Ishii
- Department of Life Science and Medical Bioscience, Waseda University, Tokyo, Japan
| | - Manami Nomachi
- Department of Life Science and Medical Bioscience, Waseda University, Tokyo, Japan
| | - Shuta Kikuchi
- Department of Life Science and Medical Bioscience, Waseda University, Tokyo, Japan
| | - Norisuke Ushiki
- Department of Life Science and Medical Bioscience, Waseda University, Tokyo, Japan
| | - Yuji Sekiguchi
- Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology, Tsukuba, Japan
| | - Satoshi Tsuneda
- Research Organization for Nano & Life Innovation, Waseda University, Tokyo, Japan.,Department of Life Science and Medical Bioscience, Waseda University, Tokyo, Japan
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17
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Oren A, Garrity GM, Parker CT, Chuvochina M, Trujillo ME. Lists of names of prokaryotic Candidatus taxa. Int J Syst Evol Microbiol 2020; 70:3956-4042. [DOI: 10.1099/ijsem.0.003789] [Citation(s) in RCA: 782] [Impact Index Per Article: 195.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
We here present annotated lists of names of Candidatus taxa of prokaryotes with ranks between subspecies and class, proposed between the mid-1990s, when the provisional status of Candidatus taxa was first established, and the end of 2018. Where necessary, corrected names are proposed that comply with the current provisions of the International Code of Nomenclature of Prokaryotes and its Orthography appendix. These lists, as well as updated lists of newly published names of Candidatus taxa with additions and corrections to the current lists to be published periodically in the International Journal of Systematic and Evolutionary Microbiology, may serve as the basis for the valid publication of the Candidatus names if and when the current proposals to expand the type material for naming of prokaryotes to also include gene sequences of yet-uncultivated taxa is accepted by the International Committee on Systematics of Prokaryotes.
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Affiliation(s)
- Aharon Oren
- The Institute of Life Sciences, The Hebrew University of Jerusalem, The Edmond J. Safra Campus, 9190401 Jerusalem, Israel
| | - George M. Garrity
- NamesforLife, LLC, PO Box 769, Okemos MI 48805-0769, USA
- Department of Microbiology & Molecular Genetics, Biomedical Physical Sciences, Michigan State University, East Lansing, MI 48824-4320, USA
| | | | - Maria Chuvochina
- Australian Centre for Ecogenomics, University of Queensland, St. Lucia QLD 4072, Brisbane, Australia
| | - Martha E. Trujillo
- Departamento de Microbiología y Genética, Campus Miguel de Unamuno, Universidad de Salamanca, 37007, Salamanca, Spain
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18
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Lam TYC, Mei R, Wu Z, Lee PKH, Liu WT, Lee PH. Superior resolution characterisation of microbial diversity in anaerobic digesters using full-length 16S rRNA gene amplicon sequencing. WATER RESEARCH 2020; 178:115815. [PMID: 32380296 DOI: 10.1016/j.watres.2020.115815] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/21/2019] [Revised: 03/18/2020] [Accepted: 04/08/2020] [Indexed: 05/24/2023]
Abstract
In the past decade, the characterisation of the microbial community in anaerobic digestion was primarily done by using high-throughput short-read amplicon sequencing. However, the short-read approach has inherent primer bias and low phylogenetic resolution. Our previous study using Illumina MiSeq suggested that the heterogeneity of AD microbiome was operation-driven. To advance our knowledge towards the complexity of the AD microbiome, we performed full-length 16S rRNA gene amplicon sequencing using PacBio Sequel for a more accurate phylogenetic identification. To this end, purified DNA samples from 19 global anaerobic digesters were sequenced. Sixteen methanogenic archaea were identified at the species level. Among them, Methanosarcina horonobensis and Methanosarcina flavescens had significant presence under specific operating conditions. Methanothrix concilii presented in all digesters sequenced. Unexpectedly, over 90% of the Smithella detected were closely related to alkane-degrading Smithella strains D17 and M82, not Smithella propionica. Using LEfSe and network analysis, the interspecies relationship between the fermentative and syntrophic bacteria was addressed. Comparison of the short- and long-read sequencing results were performed and discussed. From sample preparation to data analysis, this work characterised the digester microbiomes in a superior resolution.
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Affiliation(s)
- Theo Y C Lam
- Department of Civil and Environmental Engineering, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong.
| | - Ran Mei
- Department of Civil and Environmental Engineering, University of Illinois at Urbana-Champaign, Urbana, IL, USA.
| | - Zhuoying Wu
- Department of Civil and Environmental Engineering, Imperial College London, London, SW7 2AZ, UK
| | - Patrick K H Lee
- School of Energy and Environment, City University of Hong Kong, Kowloon, Hong Kong
| | - Wen-Tso Liu
- Department of Civil and Environmental Engineering, University of Illinois at Urbana-Champaign, Urbana, IL, USA.
| | - Po-Heng Lee
- Department of Civil and Environmental Engineering, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong; Department of Civil and Environmental Engineering, Imperial College London, London, SW7 2AZ, UK.
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19
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Puvar AC, Nathani NM, Shaikh I, Bhatt AD, Bhargava P, Joshi CG, Joshi MN. Bacterial line of defense in Dirinaria lichen from two different ecosystems: First genomic insights of its mycobiont Dirinaria sp. GBRC AP01. Microbiol Res 2019; 233:126407. [PMID: 31945518 DOI: 10.1016/j.micres.2019.126407] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2019] [Revised: 12/09/2019] [Accepted: 12/27/2019] [Indexed: 11/30/2022]
Abstract
Lichens have been widely studied for their symbiotic properties and for the secondary metabolites production by its fungal symbiont. Recent molecular studies have confirmed coexistence of bacteria along with the fungal and algal symbionts. Direct nucleic acid study by -omics approaches is providing better insights into their structural and functional dynamics. However, genomic analysis of individual members of lichen is difficult by the conventional approach. Hence, genome assembly from metagenome data needs standardization in the eukaryotic system like lichens. The present study aimed at metagenomic characterization of rock associated lichen Dirinaria collected from Kutch and Dang regions of Gujarat, followed by genome reconstruction and annotation of the mycobiont Dirinaria. The regions considered in the study are eco-geographically highly variant. The results revealed higher alpha diversity in the dry region Kutch as compared to the tropical forest associated lichen from Dang. Ascomycota was the most abundant eukaryote while Proteobacteria dominated the bacterial population. There were 23 genera observed only in the Kutch lichen (KL) and one genus viz., Candidatus Vecturithrix unique to the Dang lichen (DL). The exclusive bacterial genera in the Kutch mostly belonged to groups reported for stress tolerance and earlier isolated from lithobionts of extreme niches. The assembled data of KL & DL were further used for genome reconstruction of Dirinaria sp. using GC and tetra-pentamer parameters and reassembly that resulted into a final draft genome of 31.7 Mb and 9556 predicted genes. Twenty-eight biosynthesis gene clusters were predicted that included genes for polyketide, indole and terpene synthesis. Association analysis of bacteria and mycobiont revealed 8 pathways specific to bacteria with implications in lichen symbiosis and environment interaction. The study provides the first draft genome of the entire fungal Dirinaria genus and provides insights into the Dirinaria lichen metagenome from Gujarat region.
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Affiliation(s)
- Apurvasinh C Puvar
- Gujarat Biotechnology Research Centre (GBRC), Gandhinagar, 382011, Gujarat, India; Hemchandracharya North Gujarat University (HNGU), Patan, Gujarat, India
| | - Neelam M Nathani
- Gujarat Biotechnology Research Centre (GBRC), Gandhinagar, 382011, Gujarat, India
| | - Inayatullah Shaikh
- Gujarat Biotechnology Research Centre (GBRC), Gandhinagar, 382011, Gujarat, India
| | - Arpan D Bhatt
- Hemchandracharya North Gujarat University (HNGU), Patan, Gujarat, India
| | - Poonam Bhargava
- Gujarat Biotechnology Research Centre (GBRC), Gandhinagar, 382011, Gujarat, India
| | - Chaitanya G Joshi
- Gujarat Biotechnology Research Centre (GBRC), Gandhinagar, 382011, Gujarat, India
| | - Madhvi N Joshi
- Gujarat Biotechnology Research Centre (GBRC), Gandhinagar, 382011, Gujarat, India.
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20
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Speirs LBM, Rice DTF, Petrovski S, Seviour RJ. The Phylogeny, Biodiversity, and Ecology of the Chloroflexi in Activated Sludge. Front Microbiol 2019; 10:2015. [PMID: 31572309 PMCID: PMC6753630 DOI: 10.3389/fmicb.2019.02015] [Citation(s) in RCA: 112] [Impact Index Per Article: 22.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2019] [Accepted: 08/16/2019] [Indexed: 02/01/2023] Open
Abstract
It is now clear that several of the filamentous bacteria in activated sludge wastewater treatment plants globally, are members of the phylum Chloroflexi. They appear to be more commonly found in treatment plants designed to remove nitrogen (N) and phosphorus (P), most of which operate at long sludge ages and expose the biomass to anaerobic conditions. The Chloroflexi seem to play an important beneficial role in providing the filamentous scaffolding around which flocs are formed, to feed on the debris from lysed bacterial cells, to ferment carbohydrates and to degrade other complex polymeric organic compounds to low molecular weight substrates to support their growth and that of other bacterial populations. A few commonly extend beyond the floc surface, while others can align in bundles, which may facilitate interfloc bridging and hence generate a bulking sludge. Although several recent papers have examined the phylogeny and in situ physiology of Chloroflexi in activated sludge plants in Denmark, this review takes a wider look at what we now know about these filaments, especially their global distribution in activated sludge plants, and what their functional roles there might be. It also attempts to outline why such information might provide us with clues as to how their population levels may be manipulated, and the main research questions that need addressing to achieve these outcomes.
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Affiliation(s)
- Lachlan B. M. Speirs
- La Trobe Institute for Molecular Sciences, La Trobe University, Bendigo, VIC, Australia
| | - Daniel T. F. Rice
- Department of Physiology, Anatomy and Microbiology, La Trobe University, Bundoora, VIC, Australia
| | - Steve Petrovski
- Department of Physiology, Anatomy and Microbiology, La Trobe University, Bundoora, VIC, Australia
| | - Robert J. Seviour
- Department of Physiology, Anatomy and Microbiology, La Trobe University, Bundoora, VIC, Australia
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21
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Guermazi-Toumi S, Chouari R, Sghir A. Molecular analysis of methanogen populations and their interactions within anaerobic sludge digesters. ENVIRONMENTAL TECHNOLOGY 2019; 40:2864-2879. [PMID: 29560816 DOI: 10.1080/09593330.2018.1455747] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2017] [Accepted: 03/15/2018] [Indexed: 06/08/2023]
Abstract
Knowledge of archaeal population structure, function and interactions is of great interest for a deeper understanding of the anaerobic digestion step in wastewater treatment process, that represents a bottle neck in the optimization of digesters performance. Although culture-independent techniques have enabled the exploration of archaeal population in such systems, their population dynamics and interactions still require further investigation. In the present study, 2646 almost full archaeal 16S rRNA gene sequences retrieved from 22 anaerobic digesters located worldwide were analyzed and classified into 83 Operational Taxonomic Units (OTUs) for Euryarchaeotes and 2 OTUs for Crenarchaeotes. Among the Euryarchaeotes, Methanosarcinales represent the predominant archaeal population (47.5% of total sequences), followed by the ARC I (WSA2) lineage (25.3%), Methanomicrobiales (19.9%) and Methanobacteriales (1.9%). Theses lineages are predominant in nine, five, two and one digesters respectively. However, the remaining 5 digesters show no predominance of any methanogenic group. According to the predominance of theses lineages, 5 digester profiles were distinguished. This study revealed a clear interaction between the 4 methanogenic lineages. A core of 12 OTUs represented by five, four, two and one OTU for Methanosarcinales, Methanomicrobiales, ARC I and Methanobacteriales respectively were quantitatively abundant in at least 50% of the analyzed digesters. 16S rRNA targeted hybridization oligonucleotide probes targeting the predominant OTUs are being developed to follow their population dynamics under various parameters.
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Affiliation(s)
- Sonda Guermazi-Toumi
- a Faculté des Sciences de Gafsa, Université de Gafsa , Gafsa , Tunisie
- b Laboratoire de recherche Toxicologie-Microbiologie Environnementale et Santé (LR17ES06), Faculté des Sciences de Sfax, Université de Sfax , Sfax , Tunisie
| | - Rakia Chouari
- c Faculté des Sciences de Bizerte, UR11ES32 Plant Toxicology and Molecular Biology of Microorganims, Université de Carthage , Bizerte , Tunisie
| | - Abdelghani Sghir
- d Université d'Evry Val d'Essonne , Evry , France
- e CNRS-UMR 8030 , Evry , France
- f CEA, DRF, Institut de biologie François Jacob , Genoscope, Evry , France
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22
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Zheng Y, Saitou A, Wang CM, Toyoda A, Minakuchi Y, Sekiguchi Y, Ueda K, Takano H, Sakai Y, Abe K, Yokota A, Yabe S. Genome Features and Secondary Metabolites Biosynthetic Potential of the Class Ktedonobacteria. Front Microbiol 2019; 10:893. [PMID: 31080444 PMCID: PMC6497799 DOI: 10.3389/fmicb.2019.00893] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2019] [Accepted: 04/08/2019] [Indexed: 12/30/2022] Open
Abstract
The prevalence of antibiotic resistance and the decrease in novel antibiotic discovery in recent years necessitates the identification of potentially novel microbial resources to produce natural products. Ktedonobacteria, a class of deeply branched bacterial lineage in the ancient phylum Chloroflexi, are ubiquitous in terrestrial environments and characterized by their large genome size and complex life cycle. These characteristics indicate Ktedonobacteria as a potential active producer of bioactive compounds. In this study, we observed the existence of a putative "megaplasmid," multiple copies of ribosomal RNA operons, and high ratio of hypothetical proteins with unknown functions in the class Ktedonobacteria. Furthermore, a total of 104 antiSMASH-predicted putative biosynthetic gene clusters (BGCs) for secondary metabolites with high novelty and diversity were identified in nine Ktedonobacteria genomes. Our investigation of domain composition and organization of the non-ribosomal peptide synthetase and polyketide synthase BGCs further supports the concept that class Ktedonobacteria may produce compounds structurally different from known natural products. Furthermore, screening of bioactive compounds from representative Ktedonobacteria strains resulted in the identification of broad antimicrobial activities against both Gram-positive and Gram-negative tested bacterial strains. Based on these findings, we propose the ancient, ubiquitous, and spore-forming Ktedonobacteria as a versatile and promising microbial resource for natural product discovery.
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Affiliation(s)
- Yu Zheng
- Graduate School of Agricultural Science, Tohoku University, Sendai, Japan
| | - Ayana Saitou
- Faculty of Agriculture, Tohoku University, Sendai, Japan
| | - Chiung-Mei Wang
- Graduate School of Agricultural Science, Tohoku University, Sendai, Japan
| | - Atsushi Toyoda
- Comparative Genomics Laboratory, National Institute of Genetics, Mishima, Japan
| | - Yohei Minakuchi
- Comparative Genomics Laboratory, National Institute of Genetics, Mishima, Japan
| | - Yuji Sekiguchi
- Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology, Tsukuba, Japan
| | - Kenji Ueda
- Life Science Research Center, College of Bioresource Sciences, Nihon University, Fujisawa, Japan
| | - Hideaki Takano
- Life Science Research Center, College of Bioresource Sciences, Nihon University, Fujisawa, Japan
| | - Yasuteru Sakai
- Graduate School of Agricultural Science, Tohoku University, Sendai, Japan
| | - Keietsu Abe
- Graduate School of Agricultural Science, Tohoku University, Sendai, Japan
| | - Akira Yokota
- Graduate School of Agricultural Science, Tohoku University, Sendai, Japan
| | - Shuhei Yabe
- Graduate School of Agricultural Science, Tohoku University, Sendai, Japan
- Hazaka Plant Research Center, Kennan Eisei Kogyo Co., Ltd., Miyagi, Japan
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23
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Watanabe M, Kojima H, Umezawa K, Fukui M. Genomic Characteristics of Desulfonema ishimotonii Tokyo 01 T Implying Horizontal Gene Transfer Among Phylogenetically Dispersed Filamentous Gliding Bacteria. Front Microbiol 2019; 10:227. [PMID: 30837965 PMCID: PMC6390638 DOI: 10.3389/fmicb.2019.00227] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2018] [Accepted: 01/28/2019] [Indexed: 11/13/2022] Open
Abstract
Desulfonema ishimotonii strain Tokyo 01T is a filamentous sulfate-reducing bacterium isolated from a marine sediment. In this study, the genome of this strain was sequenced and analyzed with a focus on gene transfer from phylogenetically distant organisms. While the strain belongs to the class Deltaproteobacteria, hundreds of proteins encoded in the genome showed the highest sequence similarities to those of organisms outside of the class Deltaproteobacteria, suggesting that more than 20% of the genome is putatively of foreign origins. Many of these proteins had the highest sequence identities with proteins encoded in the genomes of filamentous bacteria, including giant sulfur oxidizers of the orders Thiotrichales, cyanobacteria of various genera, and uncultured bacteria of the candidate phylum KSB3. As mobile genetic elements transferred from phylogenetically distant organisms, putative inteins were identified in the GyrB and DnaE proteins encoded in the genome of strain Tokyo 01T. Genes involved in DNA recombination and repair were enriched in comparison to the closest relatives in the same family. Some of these genes were also related to those of organisms outside of the class Deltaproteobacteria, suggesting that they were acquired by horizontal gene transfer from diverse bacteria. The genomic data suggested significant genetic transfer among filamentous gliding bacteria in phylogenetically dispersed lineages including filamentous sulfate reducers. This study provides insights into the genomic evolution of filamentous bacteria belonging to diverse lineages, characterized by various physiological functions and different ecological roles.
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Affiliation(s)
- Miho Watanabe
- Institute of Low Temperature Science, Hokkaido University, Sapporo, Japan.,Japan Society for the Promotion of Science, Tokyo, Japan
| | - Hisaya Kojima
- Institute of Low Temperature Science, Hokkaido University, Sapporo, Japan
| | - Kazuhiro Umezawa
- Institute of Low Temperature Science, Hokkaido University, Sapporo, Japan
| | - Manabu Fukui
- Institute of Low Temperature Science, Hokkaido University, Sapporo, Japan
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Lambrechts S, Willems A, Tahon G. Uncovering the Uncultivated Majority in Antarctic Soils: Toward a Synergistic Approach. Front Microbiol 2019; 10:242. [PMID: 30828325 PMCID: PMC6385771 DOI: 10.3389/fmicb.2019.00242] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2018] [Accepted: 01/29/2019] [Indexed: 01/22/2023] Open
Abstract
Although Antarctica was once believed to be a sterile environment, it is now clear that the microbial communities inhabiting the Antarctic continent are surprisingly diverse. Until the beginning of the new millennium, little was known about the most abundant inhabitants of the continent: prokaryotes. From then on, however, the rising use of deep sequencing techniques has led to a better understanding of the Antarctic prokaryote diversity and provided insights in the composition of prokaryotic communities in different Antarctic environments. Although these cultivation-independent approaches can produce millions of sequences, linking these data to organisms is hindered by several problems. The largest difficulty is the lack of biological information on large parts of the microbial tree of life, arising from the fact that most microbial diversity on Earth has never been characterized in laboratory cultures. These unknown prokaryotes, also known as microbial dark matter, have been dominantly detected in all major environments on our planet. Laboratory cultures provide access to the complete genome and the means to experimentally verify genomic predictions and metabolic functions and to provide evidence of horizontal gene transfer. Without such well-documented reference data, microbial dark matter will remain a major blind spot in deep sequencing studies. Here, we review our current understanding of prokaryotic communities in Antarctic ice-free soils based on cultivation-dependent and cultivation-independent approaches. We discuss advantages and disadvantages of both approaches and how these strategies may be combined synergistically to strengthen each other and allow a more profound understanding of prokaryotic life on the frozen continent.
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Affiliation(s)
- Sam Lambrechts
- Laboratory of Microbiology, Department of Biochemistry and Microbiology, Ghent University, Ghent, Belgium
| | | | - Guillaume Tahon
- Laboratory of Microbiology, Department of Biochemistry and Microbiology, Ghent University, Ghent, Belgium
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25
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Vavourakis CD, Andrei AS, Mehrshad M, Ghai R, Sorokin DY, Muyzer G. A metagenomics roadmap to the uncultured genome diversity in hypersaline soda lake sediments. MICROBIOME 2018; 6:168. [PMID: 30231921 PMCID: PMC6146748 DOI: 10.1186/s40168-018-0548-7] [Citation(s) in RCA: 91] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/23/2018] [Accepted: 09/03/2018] [Indexed: 05/06/2023]
Abstract
BACKGROUND Hypersaline soda lakes are characterized by extreme high soluble carbonate alkalinity. Despite the high pH and salt content, highly diverse microbial communities are known to be present in soda lake brines but the microbiome of soda lake sediments received much less attention of microbiologists. Here, we performed metagenomic sequencing on soda lake sediments to give the first extensive overview of the taxonomic diversity found in these complex, extreme environments and to gain novel physiological insights into the most abundant, uncultured prokaryote lineages. RESULTS We sequenced five metagenomes obtained from four surface sediments of Siberian soda lakes with a pH 10 and a salt content between 70 and 400 g L-1. The recovered 16S rRNA gene sequences were mostly from Bacteria, even in the salt-saturated lakes. Most OTUs were assigned to uncultured families. We reconstructed 871 metagenome-assembled genomes (MAGs) spanning more than 45 phyla and discovered the first extremophilic members of the Candidate Phyla Radiation (CPR). Five new species of CPR were among the most dominant community members. Novel dominant lineages were found within previously well-characterized functional groups involved in carbon, sulfur, and nitrogen cycling. Moreover, key enzymes of the Wood-Ljungdahl pathway were encoded within at least four bacterial phyla never previously associated with this ancient anaerobic pathway for carbon fixation and dissimilation, including the Actinobacteria. CONCLUSIONS Our first sequencing effort of hypersaline soda lake sediment metagenomes led to two important advances. First, we showed the existence and obtained the first genomes of haloalkaliphilic members of the CPR and several hundred other novel prokaryote lineages. The soda lake CPR is a functionally diverse group, but the most abundant organisms in this study are likely fermenters with a possible role in primary carbon degradation. Second, we found evidence for the presence of the Wood-Ljungdahl pathway in many more taxonomic groups than those encompassing known homo-acetogens, sulfate-reducers, and methanogens. Since only few environmental metagenomics studies have targeted sediment microbial communities and never to this extent, we expect that our findings are relevant not only for the understanding of haloalkaline environments but can also be used to set targets for future studies on marine and freshwater sediments.
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Affiliation(s)
- Charlotte D. Vavourakis
- Microbial Systems Ecology, Department of Freshwater and Marine Ecology, Institute for Biodiversity and Ecosystem Dynamics, Faculty of Science, University of Amsterdam, Postbus 94248, 1090 GE Amsterdam, the Netherlands
| | - Adrian-Stefan Andrei
- Department of Aquatic Microbial Ecology, Institute of Hydrobiology, Biology Centre CAS, Na Sadkach 7, 370 05 Ceske Budejovice, Czech Republic
| | - Maliheh Mehrshad
- Department of Aquatic Microbial Ecology, Institute of Hydrobiology, Biology Centre CAS, Na Sadkach 7, 370 05 Ceske Budejovice, Czech Republic
| | - Rohit Ghai
- Department of Aquatic Microbial Ecology, Institute of Hydrobiology, Biology Centre CAS, Na Sadkach 7, 370 05 Ceske Budejovice, Czech Republic
| | - Dimitry Y. Sorokin
- Winogradsky Institute of Microbiology, Research Centre of Biotechnology, Russian Academy of Sciences, 60 let Oktyabrya pr-t, 7, bld. 2, Moscow, Russian Federation 117312
- Environmental Biotechnology, Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629 HZ Delft, the Netherlands
| | - Gerard Muyzer
- Microbial Systems Ecology, Department of Freshwater and Marine Ecology, Institute for Biodiversity and Ecosystem Dynamics, Faculty of Science, University of Amsterdam, Postbus 94248, 1090 GE Amsterdam, the Netherlands
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26
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Lee JZ, Everroad RC, Karaoz U, Detweiler AM, Pett-Ridge J, Weber PK, Prufert-Bebout L, Bebout BM. Metagenomics reveals niche partitioning within the phototrophic zone of a microbial mat. PLoS One 2018; 13:e0202792. [PMID: 30204767 PMCID: PMC6133358 DOI: 10.1371/journal.pone.0202792] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2018] [Accepted: 08/09/2018] [Indexed: 11/19/2022] Open
Abstract
Hypersaline photosynthetic microbial mats are stratified microbial communities known for their taxonomic and metabolic diversity and strong light-driven day-night environmental gradients. In this study of the upper photosynthetic zone of hypersaline microbial mats of Elkhorn Slough, California (USA), we show how metagenome sequencing can be used to meaningfully assess microbial ecology and genetic partitioning in these complex microbial systems. Mapping of metagenome reads to the dominant Cyanobacteria observed in the system, Coleofasciculus (Microcoleus) chthonoplastes, was used to examine strain variants within these metagenomes. Highly conserved gene subsystems indicated a core genome for the species, and a number of variant genes and subsystems suggested strain level differentiation, especially for nutrient utilization and stress response. Metagenome sequence coverage binning was used to assess ecosystem partitioning of remaining microbes to both reconstruct the model organisms in silico and identify their ecosystem functions as well as to identify novel clades and propose their role in the biogeochemical cycling of mats. Functional gene annotation of these bins (primarily of Proteobacteria, Bacteroidetes, and Cyanobacteria) recapitulated the known biogeochemical functions in microbial mats using a genetic basis, and revealed significant diversity in the Bacteroidetes, presumably in heterotrophic cycling. This analysis also revealed evidence of putative phototrophs within the Gemmatimonadetes and Gammaproteobacteria residing in microbial mats. This study shows that metagenomic analysis can produce insights into the systems biology of microbial ecosystems from a genetic perspective and to suggest further studies of novel microbes.
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Affiliation(s)
- Jackson Z. Lee
- Exobiology Branch, NASA Ames Research Center, Moffett Field, CA, United States of America
- Bay Area Environmental Research Institute, Petaluma, CA, United States of America
- * E-mail:
| | - R. Craig Everroad
- Exobiology Branch, NASA Ames Research Center, Moffett Field, CA, United States of America
| | - Ulas Karaoz
- Earth and Environmental Sciences, Lawrence Berkeley National Laboratory, Berkeley, CA, United States of America
| | - Angela M. Detweiler
- Exobiology Branch, NASA Ames Research Center, Moffett Field, CA, United States of America
- Bay Area Environmental Research Institute, Petaluma, CA, United States of America
| | - Jennifer Pett-Ridge
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, United States of America
| | - Peter K. Weber
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, United States of America
| | - Leslie Prufert-Bebout
- Exobiology Branch, NASA Ames Research Center, Moffett Field, CA, United States of America
| | - Brad M. Bebout
- Exobiology Branch, NASA Ames Research Center, Moffett Field, CA, United States of America
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27
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Momper L, Aronson HS, Amend JP. Genomic Description of ' Candidatus Abyssubacteria,' a Novel Subsurface Lineage Within the Candidate Phylum Hydrogenedentes. Front Microbiol 2018; 9:1993. [PMID: 30210471 PMCID: PMC6121073 DOI: 10.3389/fmicb.2018.01993] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2018] [Accepted: 08/08/2018] [Indexed: 12/03/2022] Open
Abstract
The subsurface biosphere is a massive repository of fixed carbon, harboring approximately 90% of Earth’s microbial biomass. These microbial communities drive transformations central to Earth’s biogeochemical cycles. However, there is still much we do not understand about how complex subterranean microbial communities survive and how they interact with these cycles. Recent metagenomic investigation of deeply circulating terrestrial subsurface fluids revealed the presence of several novel lineages of bacteria. In one particular example, phylogenomic analyses do not converge on any one previously identified taxon; here we describe the first full genomic sequences of a new bacterial lineage within the candidate phylum Hydrogenedentes, ‘Candidatus Abyssubacteria.’ A global survey revealed that members of this proposed lineage are widely distributed in both marine and terrestrial subsurface environments, but their physiological and ecological roles have remained unexplored. Two high quality metagenome assembled genomes (SURF_5: 97%, 4%; SURF_17: 91% and 4% completeness and contamination, respectively) were reconstructed from fluids collected 1.5 kilometers below surface in the former Homestake gold mine—now the Sanford Underground Research Facility (SURF)—in Lead, South Dakota, United States. Metabolic reconstruction suggests versatile metabolic capability, including possible nitrogen reduction, sulfite oxidation, sulfate reduction and homoacetogenesis. This first glimpse into the metabolic capabilities of these cosmopolitan bacteria suggests that they are involved in key geochemical processes, including sulfur, nitrogen, and carbon cycling, and that they are adapted to survival in the dark, often anoxic, subsurface biosphere.
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Affiliation(s)
- Lily Momper
- Department of Earth, Atmospheric and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, MA, United States
| | - Heidi S Aronson
- Department of Biological Sciences, University of Southern California, Los Angeles, CA, United States
| | - Jan P Amend
- Department of Biological Sciences, University of Southern California, Los Angeles, CA, United States.,Department of Earth Sciences, University of Southern California, Los Angeles, CA, United States
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28
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A standardized bacterial taxonomy based on genome phylogeny substantially revises the tree of life. Nat Biotechnol 2018; 36:996-1004. [PMID: 30148503 DOI: 10.1038/nbt.4229] [Citation(s) in RCA: 1839] [Impact Index Per Article: 306.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2017] [Accepted: 07/27/2018] [Indexed: 02/07/2023]
Abstract
Taxonomy is an organizing principle of biology and is ideally based on evolutionary relationships among organisms. Development of a robust bacterial taxonomy has been hindered by an inability to obtain most bacteria in pure culture and, to a lesser extent, by the historical use of phenotypes to guide classification. Culture-independent sequencing technologies have matured sufficiently that a comprehensive genome-based taxonomy is now possible. We used a concatenated protein phylogeny as the basis for a bacterial taxonomy that conservatively removes polyphyletic groups and normalizes taxonomic ranks on the basis of relative evolutionary divergence. Under this approach, 58% of the 94,759 genomes comprising the Genome Taxonomy Database had changes to their existing taxonomy. This result includes the description of 99 phyla, including six major monophyletic units from the subdivision of the Proteobacteria, and amalgamation of the Candidate Phyla Radiation into a single phylum. Our taxonomy should enable improved classification of uncultured bacteria and provide a sound basis for ecological and evolutionary studies.
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29
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Macarie H, Esquivel M, Laguna A, Baron O, El Mamouni R, Guiot SR, Monroy O. Strategy to identify the causes and to solve a sludge granulation problem in methanogenic reactors: application to a full-scale plant treating cheese wastewater. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2018; 25:21318-21331. [PMID: 28842799 DOI: 10.1007/s11356-017-9818-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/03/2017] [Accepted: 07/24/2017] [Indexed: 06/07/2023]
Abstract
Granulation of biomass is at the basis of the operation of the most successful anaerobic systems (UASB, EGSB and IC reactors) applied worldwide for wastewater treatment. Despite of decades of studies of the biomass granulation process, it is still not fully understood and controlled. "Degranulation/lack of granulation" is a problem that occurs sometimes in anaerobic systems resulting often in heavy loss of biomass and poor treatment efficiencies or even complete reactor failure. Such a problem occurred in Mexico in two full-scale UASB reactors treating cheese wastewater. A close follow-up of the plant was performed to try to identify the factors responsible for the phenomenon. Basically, the list of possible causes to a granulation problem that were investigated can be classified amongst nutritional, i.e. related to wastewater composition (e.g. deficiency or excess of macronutrients or micronutrients, too high COD proportion due to proteins or volatile fatty acids, high ammonium, sulphate or fat concentrations), operational (excessive loading rate, sub- or over-optimal water upflow velocity) and structural (poor hydraulic design of the plant). Despite of an intensive search, the causes of the granulation problems could not be identified. The present case remains however an example of the strategy that must be followed to identify these causes and could be used as a guide for plant operators or consultants who are confronted with a similar situation independently of the type of wastewater. According to a large literature based on successful experiments at lab scale, an attempt to artificially granulate the industrial reactor biomass through the dosage of a cationic polymer was also tested but equally failed. Instead of promoting granulation, the dosage caused a heavy sludge flotation. This shows that the scaling of such a procedure from lab to real scale cannot be advised right away unless its operability at such a scale can be demonstrated.
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Affiliation(s)
- Hervé Macarie
- Aix Marseille Univ, Univ Avignon, CNRS, IRD, IMBE, Marseille, France.
- Faculté des Sciences St-Jérôme, Aix Marseille Université, Case 421, Avenue Escadrille Normandie Niemen, 13397, Marseille Cedex 20, France.
| | - Maricela Esquivel
- Depto Biotecnología, Universidad Autónoma Metropolitana-Iztapalapa, Mexico City, Mexico
| | - Acela Laguna
- Depto Biotecnología, Universidad Autónoma Metropolitana-Iztapalapa, Mexico City, Mexico
| | | | - Rachid El Mamouni
- National Research Council Canada, Royalmount Avenue, 6100, Montréal, QC, H4P 2R2, Canada
| | - Serge R Guiot
- National Research Council Canada, Royalmount Avenue, 6100, Montréal, QC, H4P 2R2, Canada
| | - Oscar Monroy
- Depto Biotecnología, Universidad Autónoma Metropolitana-Iztapalapa, Mexico City, Mexico
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30
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Kroeger ME, Delmont TO, Eren AM, Meyer KM, Guo J, Khan K, Rodrigues JLM, Bohannan BJM, Tringe SG, Borges CD, Tiedje JM, Tsai SM, Nüsslein K. New Biological Insights Into How Deforestation in Amazonia Affects Soil Microbial Communities Using Metagenomics and Metagenome-Assembled Genomes. Front Microbiol 2018; 9:1635. [PMID: 30083144 PMCID: PMC6064768 DOI: 10.3389/fmicb.2018.01635] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2018] [Accepted: 06/30/2018] [Indexed: 11/17/2022] Open
Abstract
Deforestation in the Brazilian Amazon occurs at an alarming rate, which has broad effects on global greenhouse gas emissions, carbon storage, and biogeochemical cycles. In this study, soil metagenomes and metagenome-assembled genomes (MAGs) were analyzed for alterations to microbial community composition, functional groups, and putative physiology as it related to land-use change and tropical soil. A total of 28 MAGs were assembled encompassing 10 phyla, including both dominant and rare biosphere lineages. Amazon Acidobacteria subdivision 3, Melainabacteria, Microgenomates, and Parcubacteria were found exclusively in pasture soil samples, while Candidatus Rokubacteria was predominant in the adjacent rainforest soil. These shifts in relative abundance between land-use types were supported by the different putative physiologies and life strategies employed by the taxa. This research provides unique biological insights into candidate phyla in tropical soil and how deforestation may impact the carbon cycle and affect climate change.
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Affiliation(s)
- Marie E Kroeger
- Department of Microbiology, University of Massachusetts Amherst, Amherst, MA, United States
| | - Tom O Delmont
- Department of Medicine, University of Chicago, Chicago, IL, United States
| | - A M Eren
- Department of Medicine, University of Chicago, Chicago, IL, United States.,Josephine Bay Paul Center, Marine Biological Laboratory, Woods Hole, MA, United States
| | - Kyle M Meyer
- Institute of Ecology and Evolution, University of Oregon, Eugene, OR, United States
| | - Jiarong Guo
- Center for Microbial Ecology, Michigan State University, East Lansing, MI, United States
| | - Kiran Khan
- Department of Microbiology, University of Massachusetts Amherst, Amherst, MA, United States
| | - Jorge L M Rodrigues
- Department of Land, Air, and Water Resources, University of California, Davis, Davis, CA, United States
| | - Brendan J M Bohannan
- Institute of Ecology and Evolution, University of Oregon, Eugene, OR, United States
| | | | - Clovis D Borges
- Centro de Energia Nuclear na Agricultura, University of São Paulo, Piracicaba, Brazil
| | - James M Tiedje
- Center for Microbial Ecology, Michigan State University, East Lansing, MI, United States
| | - Siu M Tsai
- Centro de Energia Nuclear na Agricultura, University of São Paulo, Piracicaba, Brazil
| | - Klaus Nüsslein
- Department of Microbiology, University of Massachusetts Amherst, Amherst, MA, United States
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31
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Ionescu MI, Oniga O. Molecular Docking Evaluation of ( E)-5-arylidene-2-thioxothiazolidin-4-one Derivatives as Selective Bacterial Adenylate Kinase Inhibitors. Molecules 2018; 23:molecules23051076. [PMID: 29751552 PMCID: PMC6102543 DOI: 10.3390/molecules23051076] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2018] [Revised: 04/27/2018] [Accepted: 05/01/2018] [Indexed: 12/13/2022] Open
Abstract
Multi-drug resistant microorganism infections with emerging problems that require not only a prevention strategy, but also the development of new inhibitory compounds. Six previously synthesized 5-arylidene-2-thioxothiazolidin-4-one derivatives 1a–f, were screened for inhibitory activity on adenylate kinases of different origins by molecular docking. The compounds 1c and 1d were the most efficient inhibitors of bacterial and some archean adenylate kinases. Hydrogen bond interactions were observed with the residues belonging to the ATP binding site. Moreover human adenylate kinases are poor targets, suggesting that this selectivity offers promising prospectives for refining the structure of our compounds.
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Affiliation(s)
- Mihaela Ileana Ionescu
- Department of Microbiology, Iuliu Hațieganu University of Medicine and Pharmacy, 400349 Cluj-Napoca, Romania.
- Department of Microbiology, County Emergency Clinical Hospital, 400006 Cluj-Napoca, Romania.
| | - Ovidiu Oniga
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Iuliu Hațieganu University of Medicine and Pharmacy, 400012 Cluj-Napoca, Romania.
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32
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Deng Y, Li B, Zhang T. Bacteria That Make a Meal of Sulfonamide Antibiotics: Blind Spots and Emerging Opportunities. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2018; 52:3854-3868. [PMID: 29498514 DOI: 10.1021/acs.est.7b06026] [Citation(s) in RCA: 90] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
The release of sulfonamide antibiotics into the environment is alarming because the existence of these antibiotics in the environment may promote resistance in clinically relevant microorganisms, which is a potential threat to the effectiveness of antibiotic therapies. Controllable biodegradation processes are of particular significance for the inexpensive yet effective restoration of sulfonamide-contaminated environments. Cultivation-based techniques have already made great strides in successfully isolating bacteria with promising sulfonamide degradation abilities, but the implementation of these isolates in bioremediation has been limited by unknown microbial diversity, vast population responsiveness, and the impact of perturbations from open and complex environments. Advances in DNA sequencing technologies and metagenomic analyses are being used to complement the information derived from cultivation-based procedures. In this Review, we provide an overview of the growing understanding of isolated sulfonamide degraders and identify shortcomings of the prevalent literature in this field. In addition, we propose a technical paradigm that integrates experimental testing with metagenomic analysis to pave the way for improved understanding and exploitation of these ecologically important isolates. Overall, this Review aims to outline how metagenomic studies of isolated sulfonamide degraders are being applied for the advancement of bioremediation strategies for sulfonamide contamination.
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Affiliation(s)
- Yu Deng
- Environmental Biotechnology Laboratory, Department of Civil Engineering , The University of Hong Kong , Pokfulam Road , Hong Kong , PR China
| | - Bing Li
- Division of Energy & Environment, Graduate School at Shenzhen , Tsinghua University , Shenzhen 518055 , PR China
| | - Tong Zhang
- Environmental Biotechnology Laboratory, Department of Civil Engineering , The University of Hong Kong , Pokfulam Road , Hong Kong , PR China
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33
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Ushiki N, Fujitani H, Shimada Y, Morohoshi T, Sekiguchi Y, Tsuneda S. Genomic Analysis of Two Phylogenetically Distinct Nitrospira Species Reveals Their Genomic Plasticity and Functional Diversity. Front Microbiol 2018; 8:2637. [PMID: 29375506 PMCID: PMC5767232 DOI: 10.3389/fmicb.2017.02637] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2017] [Accepted: 12/18/2017] [Indexed: 02/02/2023] Open
Abstract
The genus Nitrospira represents a dominant group of nitrite-oxidizing bacteria in natural and engineered ecosystems. This genus is phylogenetically divided into six lineages, for which vast phylogenetic and functional diversity has been revealed by recent molecular ecophysiological analyses. However, the genetic basis underlying these phenotypic differences remains largely unknown because of the lack of genome sequences representing their diversity. To gain a more comprehensive understanding of Nitrospira, we performed genomic comparisons between two Nitrospira strains (ND1 and NJ1 belonging to lineages I and II, respectively) previously isolated from activated sludge. In addition, the genomes of these strains were systematically compared with previously reported six Nitrospira genomes to reveal their similarity and presence/absence of several functional genes/operons. Comparisons of Nitrospira genomes indicated that their genomic diversity reflects phenotypic differences and versatile nitrogen metabolisms. Although most genes involved in key metabolic pathways were conserved between strains ND1 and NJ1, assimilatory nitrite reduction pathways of the two Nitrospira strains were different. In addition, the genomes of both strains contain a phylogenetically different urease locus and we confirmed their ureolytic activity. During gene annotation of strain NJ1, we found a gene cluster encoding a quorum-sensing system. From the enriched supernatant of strain NJ1, we successfully identified seven types of acyl-homoserine lactones with a range of C10–C14. In addition, the genome of strain NJ1 lacks genes relevant to flagella and the clustered regularly interspaced short palindromic repeat (CRISPR)-Cas (CRISPR-associated genes) systems, whereas most nitrifying bacteria including strain ND1 possess these genomic elements. These findings enhance our understanding of genomic plasticity and functional diversity among members of the genus Nitrospira.
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Affiliation(s)
- Norisuke Ushiki
- Department of Life Science and Medical Bioscience, Waseda University, Tokyo, Japan
| | - Hirotsugu Fujitani
- Department of Life Science and Medical Bioscience, Waseda University, Tokyo, Japan
| | - Yu Shimada
- Department of Life Science and Medical Bioscience, Waseda University, Tokyo, Japan
| | - Tomohiro Morohoshi
- Department of Material and Environmental Chemistry, Graduate School of Engineering, Utsunomiya University, Tochigi, Japan
| | - Yuji Sekiguchi
- Bio-Measurement Research Group, Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology, Ibaraki, Japan
| | - Satoshi Tsuneda
- Department of Life Science and Medical Bioscience, Waseda University, Tokyo, Japan
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34
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Becraft ED, Woyke T, Jarett J, Ivanova N, Godoy-Vitorino F, Poulton N, Brown JM, Brown J, Lau MCY, Onstott T, Eisen JA, Moser D, Stepanauskas R. Rokubacteria: Genomic Giants among the Uncultured Bacterial Phyla. Front Microbiol 2017; 8:2264. [PMID: 29234309 PMCID: PMC5712423 DOI: 10.3389/fmicb.2017.02264] [Citation(s) in RCA: 63] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2017] [Accepted: 11/02/2017] [Indexed: 01/08/2023] Open
Abstract
Recent advances in single-cell genomic and metagenomic techniques have facilitated the discovery of numerous previously unknown, deep branches of the tree of life that lack cultured representatives. Many of these candidate phyla are composed of microorganisms with minimalistic, streamlined genomes lacking some core metabolic pathways, which may contribute to their resistance to growth in pure culture. Here we analyzed single-cell genomes and metagenome bins to show that the "Candidate phylum Rokubacteria," formerly known as SPAM, represents an interesting exception, by having large genomes (6-8 Mbps), high GC content (66-71%), and the potential for a versatile, mixotrophic metabolism. We also observed an unusually high genomic heterogeneity among individual Rokubacteria cells in the studied samples. These features may have contributed to the limited recovery of sequences of this candidate phylum in prior cultivation and metagenomic studies. Our analyses suggest that Rokubacteria are distributed globally in diverse terrestrial ecosystems, including soils, the rhizosphere, volcanic mud, oil wells, aquifers, and the deep subsurface, with no reports from marine environments to date.
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Affiliation(s)
- Eric D Becraft
- Bigelow Laboratory for Ocean Sciences, East Boothbay, ME, United States
| | - Tanja Woyke
- Joint Genome Institute, Walnut Creek, CA, United States
| | | | | | - Filipa Godoy-Vitorino
- Department of Natural Sciences, Inter American University of Puerto Rico, San Juan, Puerto Rico
| | - Nicole Poulton
- Bigelow Laboratory for Ocean Sciences, East Boothbay, ME, United States
| | - Julia M Brown
- Bigelow Laboratory for Ocean Sciences, East Boothbay, ME, United States
| | - Joseph Brown
- Bigelow Laboratory for Ocean Sciences, East Boothbay, ME, United States
| | - M C Y Lau
- Department of Geosciences, Princeton University, Princeton, NJ, United States
| | - Tullis Onstott
- Department of Geosciences, Princeton University, Princeton, NJ, United States
| | - Jonathan A Eisen
- College of Biological Sciences, Genome Center, University of California, Davis, Davis, CA, United States
| | - Duane Moser
- Desert Research Institute, Las Vegas, NV, United States
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Dudek NK, Sun CL, Burstein D, Kantor RS, Aliaga Goltsman DS, Bik EM, Thomas BC, Banfield JF, Relman DA. Novel Microbial Diversity and Functional Potential in the Marine Mammal Oral Microbiome. Curr Biol 2017; 27:3752-3762.e6. [PMID: 29153320 DOI: 10.1016/j.cub.2017.10.040] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2017] [Revised: 09/13/2017] [Accepted: 10/13/2017] [Indexed: 12/28/2022]
Abstract
The vast majority of bacterial diversity lies within phylum-level lineages called "candidate phyla," which lack isolated representatives and are poorly understood. These bacteria are surprisingly abundant in the oral cavity of marine mammals. We employed a genome-resolved metagenomic approach to recover and characterize genomes and functional potential from microbes in the oral gingival sulcus of two bottlenose dolphins (Tursiops truncatus). We detected organisms from 24 known bacterial phyla and one archaeal phylum. We also recovered genomes from two deep-branching, previously uncharacterized phylum-level lineages (here named "Candidatus Delphibacteria" and "Candidatus Fertabacteria"). The Delphibacteria lineage is found in both managed and wild dolphins; its metabolic profile suggests a capacity for denitrification and a possible role in dolphin health. We uncovered a rich diversity of predicted Cas9 proteins, including the two longest predicted Cas9 proteins to date. Notably, we identified the first type II CRISPR-Cas systems encoded by members of the Candidate Phyla Radiation. Using their spacer sequences, we subsequently identified and assembled a complete Saccharibacteria phage genome. These findings underscore the immense microbial diversity and functional potential that await discovery in previously unexplored environments.
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Affiliation(s)
- Natasha K Dudek
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, Santa Cruz, CA 95064, USA
| | - Christine L Sun
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - David Burstein
- Department of Earth and Planetary Science, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Rose S Kantor
- Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Daniela S Aliaga Goltsman
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Elisabeth M Bik
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Brian C Thomas
- Department of Earth and Planetary Science, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Jillian F Banfield
- Department of Earth and Planetary Science, University of California, Berkeley, Berkeley, CA 94720, USA; Earth and Environmental Science, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - David A Relman
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA; Veterans Affairs Palo Alto Health Care System, Palo Alto, CA 94304, USA.
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36
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Recovery of nearly 8,000 metagenome-assembled genomes substantially expands the tree of life. Nat Microbiol 2017; 2:1533-1542. [PMID: 28894102 DOI: 10.1038/s41564-017-0012-7] [Citation(s) in RCA: 960] [Impact Index Per Article: 137.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2017] [Accepted: 07/25/2017] [Indexed: 12/24/2022]
Abstract
Challenges in cultivating microorganisms have limited the phylogenetic diversity of currently available microbial genomes. This is being addressed by advances in sequencing throughput and computational techniques that allow for the cultivation-independent recovery of genomes from metagenomes. Here, we report the reconstruction of 7,903 bacterial and archaeal genomes from >1,500 public metagenomes. All genomes are estimated to be ≥50% complete and nearly half are ≥90% complete with ≤5% contamination. These genomes increase the phylogenetic diversity of bacterial and archaeal genome trees by >30% and provide the first representatives of 17 bacterial and three archaeal candidate phyla. We also recovered 245 genomes from the Patescibacteria superphylum (also known as the Candidate Phyla Radiation) and find that the relative diversity of this group varies substantially with different protein marker sets. The scale and quality of this data set demonstrate that recovering genomes from metagenomes provides an expedient path forward to exploring microbial dark matter.
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37
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Kirkegaard RH, McIlroy SJ, Kristensen JM, Nierychlo M, Karst SM, Dueholm MS, Albertsen M, Nielsen PH. The impact of immigration on microbial community composition in full-scale anaerobic digesters. Sci Rep 2017; 7:9343. [PMID: 28839166 PMCID: PMC5571154 DOI: 10.1038/s41598-017-09303-0] [Citation(s) in RCA: 79] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2017] [Accepted: 07/25/2017] [Indexed: 01/04/2023] Open
Abstract
Anaerobic digestion is widely applied to treat organic waste at wastewater treatment plants. Characterisation of the underlying microbiology represents a source of information to develop strategies for improved operation. Hence, we investigated microbial communities of thirty-two full-scale anaerobic digesters over a six-year period using 16S rRNA gene amplicon sequencing. Sampling of the sludge fed into these systems revealed that several of the most abundant populations were likely inactive and immigrating with the influent. This observation indicates that a failure to consider immigration will interfere with correlation analysis and give an inaccurate picture of the growing microbial community. Furthermore, several abundant OTUs could not be classified to genus level with commonly applied taxonomies, making inference of their function unreliable and comparison to other studies problematic. As such, the existing MiDAS taxonomy was updated to include these abundant phylotypes. The communities of individual digesters surveyed were remarkably similar - with only 300 OTUs representing 80% of the total reads across all plants, and 15% of these identified as non-growing and possibly inactive immigrating microbes. By identifying abundant and growing taxa in anaerobic digestion, this study paves the way for targeted characterisation of the process-important organisms towards an in-depth understanding of the microbiology.
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Affiliation(s)
- Rasmus H Kirkegaard
- Centre for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University, Fredrik Bajers Vej 7H, DK-9220, Aalborg, Denmark
| | - Simon J McIlroy
- Centre for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University, Fredrik Bajers Vej 7H, DK-9220, Aalborg, Denmark
| | - Jannie M Kristensen
- Centre for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University, Fredrik Bajers Vej 7H, DK-9220, Aalborg, Denmark
| | - Marta Nierychlo
- Centre for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University, Fredrik Bajers Vej 7H, DK-9220, Aalborg, Denmark
| | - Søren M Karst
- Centre for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University, Fredrik Bajers Vej 7H, DK-9220, Aalborg, Denmark
| | - Morten S Dueholm
- Centre for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University, Fredrik Bajers Vej 7H, DK-9220, Aalborg, Denmark
| | - Mads Albertsen
- Centre for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University, Fredrik Bajers Vej 7H, DK-9220, Aalborg, Denmark
| | - Per H Nielsen
- Centre for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University, Fredrik Bajers Vej 7H, DK-9220, Aalborg, Denmark.
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38
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Bowers RM, Kyrpides NC, Stepanauskas R, Harmon-Smith M, Doud D, Reddy TBK, Schulz F, Jarett J, Rivers AR, Eloe-Fadrosh EA, Tringe SG, Ivanova NN, Copeland A, Clum A, Becraft ED, Malmstrom RR, Birren B, Podar M, Bork P, Weinstock GM, Garrity GM, Dodsworth JA, Yooseph S, Sutton G, Glöckner FO, Gilbert JA, Nelson WC, Hallam SJ, Jungbluth SP, Ettema TJG, Tighe S, Konstantinidis KT, Liu WT, Baker BJ, Rattei T, Eisen JA, Hedlund B, McMahon KD, Fierer N, Knight R, Finn R, Cochrane G, Karsch-Mizrachi I, Tyson GW, Rinke C, Lapidus A, Meyer F, Yilmaz P, Parks DH, Eren AM, Schriml L, Banfield JF, Hugenholtz P, Woyke T. Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea. Nat Biotechnol 2017; 35:725-731. [PMID: 28787424 PMCID: PMC6436528 DOI: 10.1038/nbt.3893] [Citation(s) in RCA: 1064] [Impact Index Per Article: 152.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2016] [Accepted: 04/27/2017] [Indexed: 12/20/2022]
Abstract
Standards for sequencing the microbial 'uncultivated majority', namely bacterial and archaeal single-cell genome sequences, and genome sequences from metagenomic datasets, are proposed. We present two standards developed by the Genomic Standards Consortium (GSC) for reporting bacterial and archaeal genome sequences. Both are extensions of the Minimum Information about Any (x) Sequence (MIxS). The standards are the Minimum Information about a Single Amplified Genome (MISAG) and the Minimum Information about a Metagenome-Assembled Genome (MIMAG), including, but not limited to, assembly quality, and estimates of genome completeness and contamination. These standards can be used in combination with other GSC checklists, including the Minimum Information about a Genome Sequence (MIGS), Minimum Information about a Metagenomic Sequence (MIMS), and Minimum Information about a Marker Gene Sequence (MIMARKS). Community-wide adoption of MISAG and MIMAG will facilitate more robust comparative genomic analyses of bacterial and archaeal diversity.
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Affiliation(s)
- Robert M Bowers
- Department of Energy Joint Genome Institute, Walnut Creek, California, USA
| | - Nikos C Kyrpides
- Department of Energy Joint Genome Institute, Walnut Creek, California, USA
| | | | | | - Devin Doud
- Department of Energy Joint Genome Institute, Walnut Creek, California, USA
| | - T B K Reddy
- Department of Energy Joint Genome Institute, Walnut Creek, California, USA
| | - Frederik Schulz
- Department of Energy Joint Genome Institute, Walnut Creek, California, USA
| | - Jessica Jarett
- Department of Energy Joint Genome Institute, Walnut Creek, California, USA
| | - Adam R Rivers
- Department of Energy Joint Genome Institute, Walnut Creek, California, USA.,United States Department of Agriculture, Agricultural Research Service, Genomics and Bioinformatics Research Unit, Gainesville, Florida, USA
| | | | - Susannah G Tringe
- Department of Energy Joint Genome Institute, Walnut Creek, California, USA.,School of Natural Sciences, University of California Merced, Merced, California, USA
| | - Natalia N Ivanova
- Department of Energy Joint Genome Institute, Walnut Creek, California, USA
| | - Alex Copeland
- Department of Energy Joint Genome Institute, Walnut Creek, California, USA
| | - Alicia Clum
- Department of Energy Joint Genome Institute, Walnut Creek, California, USA
| | - Eric D Becraft
- Bigelow Laboratory for Ocean Sciences, East Boothbay, Maine, USA
| | - Rex R Malmstrom
- Department of Energy Joint Genome Institute, Walnut Creek, California, USA
| | | | - Mircea Podar
- Biosciences Division, Oak Ridge National Laboratory, Oakridge Tennessee, USA
| | - Peer Bork
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - George M Weinstock
- The Jackson Laboratory for Genomic Medicine, Farmington, Connecticut, USA
| | - George M Garrity
- Department of Microbiology &Molecular Genetics, Biomedical Physical Sciences, Michigan State University, East Lansing, Michigan, USA
| | - Jeremy A Dodsworth
- Department of Biology, California State University, San Bernardino, California, USA
| | - Shibu Yooseph
- J. Craig Venter Institute, San Diego, California, USA
| | | | - Frank O Glöckner
- Microbial Genomics and Bioinformatics Research Group, Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Jack A Gilbert
- Biosciences Division, Argonne National Laboratory, Argonne, Illinois, USA.,Department of Surgery, University of Chicago, Chicago, Illinois, USA
| | - William C Nelson
- Biological Sciences Division, Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington, USA
| | - Steven J Hallam
- Department of Microbiology &Immunology, University of British Columbia, Vancouver, British Columbia, Canada
| | - Sean P Jungbluth
- Department of Energy Joint Genome Institute, Walnut Creek, California, USA.,Center for Dark Energy Biosphere Investigation, University of Southern California, Los Angeles, California, USA
| | - Thijs J G Ettema
- Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Scott Tighe
- Advanced Genomics Lab, University of Vermont Cancer Center, Burlington Vermont, USA
| | | | - Wen-Tso Liu
- Department of Civil and Environmental Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Brett J Baker
- Department of Marine Science, University of Texas-Austin, Marine Science Institute, Austin, Texas, USA
| | - Thomas Rattei
- Department of Microbiology and Ecosystem Science, University of Vienna, Vienna, Austria
| | | | - Brian Hedlund
- School of Life Sciences, University of Nevada Las Vegas, Las Vegas, Nevada, USA.,Nevada Institute of Personalized Medicine, University of Nevada Las Vegas, Las Vegas, Nevada, USA
| | - Katherine D McMahon
- Department of Civil and Environmental Engineering, University of Wisconsin-Madison, Madison, Wisconsin, USA.,Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Noah Fierer
- Cooperative Institute for Research in Environmental Sciences, University of Colorado, Boulder, Colorado, USA.,Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, Colorado, USA
| | - Rob Knight
- Center for Microbiome Innovation, and Departments of Pediatrics and Computer Science &Engineering, University of California San Diego, La Jolla, California, USA
| | - Rob Finn
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Welcome Trust Genome Campus, Hinxton, Cambridge, UK
| | - Guy Cochrane
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Welcome Trust Genome Campus, Hinxton, Cambridge, UK
| | - Ilene Karsch-Mizrachi
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland, USA
| | - Gene W Tyson
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Queensland, Australia
| | - Christian Rinke
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Queensland, Australia
| | | | - Alla Lapidus
- Centre for Algorithmic Biotechnology, ITBM, St. Petersburg State University, St. Petersburg, Russia
| | - Folker Meyer
- Biosciences Division, Argonne National Laboratory, Argonne, Illinois, USA
| | - Pelin Yilmaz
- Microbial Genomics and Bioinformatics Research Group, Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Donovan H Parks
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Queensland, Australia
| | - A M Eren
- Knapp Center for Biomedical Discovery, Chicago, Illinois, USA
| | - Lynn Schriml
- National Cancer Institute, Frederick, Maryland, USA
| | - Jillian F Banfield
- Department of Earth and Planetary Science, University of California, Berkeley, California, USA
| | - Philip Hugenholtz
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Queensland, Australia
| | - Tanja Woyke
- Department of Energy Joint Genome Institute, Walnut Creek, California, USA.,School of Natural Sciences, University of California Merced, Merced, California, USA
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Draft Genome Sequence of Terrimicrobium sacchariphilum NM-5 T, a Facultative Anaerobic Soil Bacterium of the Class Spartobacteria. GENOME ANNOUNCEMENTS 2017; 5:5/30/e00666-17. [PMID: 28751395 PMCID: PMC5532833 DOI: 10.1128/genomea.00666-17] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
We report here a high-quality draft genome sequence of Terrimicrobium sacchariphilum strain NM-5T, a facultative anaerobic, mesophilic, fermentative bacterium belonging to the class Spartobacteria of the phylum Verrucomicrobia The genome comprises 4,751,807 bp in three contigs and has a G+C content of 60.19%. Annotation predicted 4,175 protein-coding sequences and 54 RNAs.
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40
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Draft Genome Sequence of Paludibacter jiangxiensis NM7 T, a Propionate-Producing Fermentative Bacterium. GENOME ANNOUNCEMENTS 2017; 5:5/29/e00667-17. [PMID: 28729272 PMCID: PMC5522939 DOI: 10.1128/genomea.00667-17] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
We report here a high-quality draft genome sequence of Paludibacter jiangxiensis strain NM7T, a mesophilic, anaerobic, propionate-producing fermentative bacterium within the family Porphyromonadaceae of the phylum Bacteroidetes. The genome comprises 3,664,884 bp in four contigs, has a G+C content of 42.92%, and contains 2,949 protein-coding sequences and 62 RNAs.
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41
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Mohiuddin MM, Salama Y, Schellhorn HE, Golding GB. Shotgun metagenomic sequencing reveals freshwater beach sands as reservoir of bacterial pathogens. WATER RESEARCH 2017; 115:360-369. [PMID: 28340372 DOI: 10.1016/j.watres.2017.02.057] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2016] [Revised: 02/24/2017] [Accepted: 02/25/2017] [Indexed: 05/06/2023]
Abstract
Recreational waters and adjacent beach sands harbor complex microbial communities which may contain human pathogens that cannot be detected by conventional methods. Here, we investigate the diversity of bacterial populations inhabiting four freshwater beaches of the Great Lakes region using shotgun metagenomic sequencing approach. Our analysis suggests that average taxonomic richness and alpha diversity are significantly higher (P < 0.001) in beach sands compared to the corresponding water environments. Compared to the water environments, beach sands harbored taxa from a more diverse range of phyla, including a higher proportion of sequences from unclassified phyla. Unique phyla were also identified in sand which included species from Aquificae, Candidatus Microgenomates, Latescibacteria, and Candidatus Aminicenantes. Sequences originating from pathogens were detected in both sand and water, with some pathogens enriched in both environments. Both lakes exhibited similar community composition suggesting that geographic location did not appear to have any major impact on bacterial diversity. These findings reveal the diversity of bacterial communities of freshwater beaches and highlight the importance of monitoring pathogens in recreational beaches, especially in the sand environment of these beaches.
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Affiliation(s)
- Mahi M Mohiuddin
- Department of Biology, McMaster University, Hamilton, ON, Canada
| | - Yasser Salama
- Department of Biology, McMaster University, Hamilton, ON, Canada
| | | | - G Brian Golding
- Department of Biology, McMaster University, Hamilton, ON, Canada.
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42
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Kantor RS, Huddy RJ, Iyer R, Thomas BC, Brown CT, Anantharaman K, Tringe S, Hettich RL, Harrison STL, Banfield JF. Genome-Resolved Meta-Omics Ties Microbial Dynamics to Process Performance in Biotechnology for Thiocyanate Degradation. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2017; 51:2944-2953. [PMID: 28139919 DOI: 10.1021/acs.est.6b04477] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Remediation of industrial wastewater is important for preventing environmental contamination and enabling water reuse. Biological treatment for one industrial contaminant, thiocyanate (SCN-), relies upon microbial hydrolysis, but this process is sensitive to high loadings. To examine the activity and stability of a microbial community over increasing SCN- loadings, we established and operated a continuous-flow bioreactor fed increasing loadings of SCN-. A second reactor was fed ammonium sulfate to mimic breakdown products of SCN-. Biomass was sampled from both reactors for metagenomics and metaproteomics, yielding a set of genomes for 144 bacteria and one rotifer that constituted the abundant community in both reactors. We analyzed the metabolic potential and temporal dynamics of these organisms across the increasing loadings. In the SCN- reactor, Thiobacillus strains capable of SCN- degradation were highly abundant, whereas the ammonium sulfate reactor contained nitrifiers and heterotrophs capable of nitrate reduction. Key organisms in the SCN- reactor expressed proteins involved in SCN- degradation, sulfur oxidation, carbon fixation, and nitrogen removal. Lower performance at higher loadings was linked to changes in microbial community composition. This work provides an example of how meta-omics can increase our understanding of industrial wastewater treatment and inform iterative process design and development.
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Affiliation(s)
- Rose S Kantor
- Department of Plant and Microbial Biology, University of California , Berkeley, California 94720, United States
| | - Robert J Huddy
- Centre for Bioprocess Engineering Research, Department of Chemical Engineering, University of Cape Town , Rondebosch, 7701, South Africa
| | - Ramsunder Iyer
- Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37830, United States
- Graduate School of Genome Science and Technology, University of Tennessee , Knoxville, Tennessee 37996, United States
| | - Brian C Thomas
- Department of Earth and Planetary Sciences, University of California , Berkeley, California 94720, United States
| | - Christopher T Brown
- Department of Plant and Microbial Biology, University of California , Berkeley, California 94720, United States
| | - Karthik Anantharaman
- Department of Earth and Planetary Sciences, University of California , Berkeley, California 94720, United States
| | - Susannah Tringe
- Joint Genome Institute , Walnut Creek, California 94598, United States
| | - Robert L Hettich
- Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37830, United States
| | - Susan T L Harrison
- Centre for Bioprocess Engineering Research, Department of Chemical Engineering, University of Cape Town , Rondebosch, 7701, South Africa
| | - Jillian F Banfield
- Department of Earth and Planetary Sciences, University of California , Berkeley, California 94720, United States
- Department of Environmental Science, Policy, and Management, University of California , Berkeley, California 94720, United States
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43
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Thandar SM, Ushiki N, Fujitani H, Sekiguchi Y, Tsuneda S. Ecophysiology and Comparative Genomics of Nitrosomonas mobilis Ms1 Isolated from Autotrophic Nitrifying Granules of Wastewater Treatment Bioreactor. Front Microbiol 2016; 7:1869. [PMID: 27920767 PMCID: PMC5118430 DOI: 10.3389/fmicb.2016.01869] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2016] [Accepted: 11/07/2016] [Indexed: 01/15/2023] Open
Abstract
Ammonia-oxidizing bacteria (AOB), which oxidize ammonia to nitrite in the first step of nitrification, play an important role in biological wastewater treatment systems. Nitrosomonas mobilis is an important and dominant AOB in various wastewater treatment systems. However, the detailed physiological and genomic properties of N. mobilis have not been thoroughly investigated because of limited success isolating pure cultures. This study investigated the key physiological characteristics of N. mobilis Ms1, which was previously isolated into pure culture from the nitrifying granules of wastewater treatment bioreactor. The pure culture of N. mobilis Ms1 was cultivated in liquid mineral medium with 30 mg-N L-1 (2.14 mM) of ammonium at room temperature under dark conditions. The optimum growth of N. mobilis Ms1 occurred at 27°C and pH 8, with a maximum growth rate of 0.05–0.07 h-1, which corresponded to a generation time of 10–14 h. The half saturation constant for ammonium uptake rate and the maximum ammonium uptake rate of N. mobilis Ms1 were 30.70 ± 0.51 μM NH4+ and 0.01 ± 0.002 pmol NH4+ cells-1 h-1, respectively. N. mobilis Ms1 had higher ammonia oxidation activity than N. europaea in this study. The oxygen uptake activity kinetics of N. mobilis Ms1 were Km(O2) = 21.74 ± 4.01 μM O2 and V max(O2) = 0.06 ± 0.02 pmol O2 cells-1 h-1. Ms1 grew well at ammonium and NaCl concentrations of up to 100 and 500 mM, respectively. The nitrite tolerance of N. mobilis Ms1 was extremely high (up to 300 mM) compared to AOB previously isolated from activated sludge and wastewater treatment plants. The average nucleotide identity between the genomes of N. mobilis Ms1 and other Nitrosomonas species indicated that N. mobilis Ms1 was distantly related to other Nitrosomonas species. The organization of the genes encoding protein inventory involved in ammonia oxidation and nitrifier denitrification processes were different from other Nitrosomonas species. The current study provides a needed physiological and genomic characterization of N. mobilis-like bacteria and a better understanding of their ecophysiological properties, enabling comparison of these bacteria with other AOB in wastewater treatment systems and natural ecosystems.
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Affiliation(s)
- Soe Myat Thandar
- Tsuneda Laboratory, Department of Life Science and Medical Bioscience, Waseda UniversityTokyo, Japan; Department of Biotechnology, Mandalay Technological University, Ministry of EducationMandalay, Myanmar
| | - Norisuke Ushiki
- Tsuneda Laboratory, Department of Life Science and Medical Bioscience, Waseda University Tokyo, Japan
| | - Hirotsugu Fujitani
- Tsuneda Laboratory, Department of Life Science and Medical Bioscience, Waseda University Tokyo, Japan
| | - Yuji Sekiguchi
- Advanced Biomeasurements Research Group, Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology Ibaraki, Japan
| | - Satoshi Tsuneda
- Tsuneda Laboratory, Department of Life Science and Medical Bioscience, Waseda University Tokyo, Japan
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44
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Scholes E, Verheyen V, Brook-Carter P. A review of practical tools for rapid monitoring of membrane bioreactors. WATER RESEARCH 2016; 102:252-262. [PMID: 27362445 DOI: 10.1016/j.watres.2016.06.031] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/28/2016] [Revised: 05/17/2016] [Accepted: 06/13/2016] [Indexed: 06/06/2023]
Abstract
The production of high quality effluent from membrane bioreactors (MBRs) arguably requires less supervision than conventional activated sludge (CAS) processes. Nevertheless, the use of membranes brings additional issues of activated sludge filterability, cake layer formation and membrane fouling. From a practical standpoint, process engineers and operators require simple tools which offer timely information about the biological health and filterability of the mixed liquor as well as risks of membrane fouling. To this end, a range of analytical tools and biological assays are critically reviewed from this perspective. This review recommends that Capillary Suction Time (CST) analysis along with Total Suspended and Volatile Solids (TSS/VSS) analysis is used daily. For broad characterisation, total carbon and nitrogen analysis offer significant advantages over the commonly used chemical and biological oxygen demand (COD/BOD) analyses. Of the technologies for determining the vitality of the microbial biomass the most robust and reproducible, are the second generation adenosine-5'-triphosphate (ATP) test kits. Extracellular polymer concentrations are best monitored by measurement of turbidity after centrifugation. Taken collectively these tools can be used routinely to ensure timely intervention and smoother operation of MBR systems.
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Affiliation(s)
- E Scholes
- Monash University, Faculty of Science, Victoria, Australia
| | - V Verheyen
- School of Applied and Biomedical Sciences, Federation University Australia, Northways Rd, Churchill, Victoria 3842, Australia.
| | - P Brook-Carter
- School of Applied and Biomedical Sciences, Federation University Australia, Northways Rd, Churchill, Victoria 3842, Australia
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Reis MP, Dias MF, Costa PS, Ávila MP, Leite LR, de Araújo FMG, Salim ACM, Bucciarelli-Rodriguez M, Oliveira G, Chartone-Souza E, Nascimento AMA. Metagenomic signatures of a tropical mining-impacted stream reveal complex microbial and metabolic networks. CHEMOSPHERE 2016; 161:266-273. [PMID: 27441985 DOI: 10.1016/j.chemosphere.2016.06.097] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2016] [Revised: 06/24/2016] [Accepted: 06/26/2016] [Indexed: 06/06/2023]
Abstract
Bacteria from aquatic ecosystems significantly contribute to biogeochemical cycles, but details of their community structure in tropical mining-impacted environments remain unexplored. In this study, we analyzed a bacterial community from circumneutral-pH tropical stream sediment by 16S rRNA and shotgun deep sequencing. Carrapatos stream sediment, which has been exposed to metal stress due to gold and iron mining (21 [g Fe]/kg), revealed a diverse community, with predominance of Proteobacteria (39.4%), Bacteroidetes (12.2%), and Parcubacteria (11.4%). Among Proteobacteria, the most abundant reads were assigned to neutrophilic iron-oxidizing taxa, such as Gallionella, Sideroxydans, and Mariprofundus, which are involved in Fe cycling and harbor several metal resistance genes. Functional analysis revealed a large number of genes participating in nitrogen and methane metabolic pathways despite the low concentrations of inorganic nitrogen in the Carrapatos stream. Our findings provide important insights into bacterial community interactions in a mining-impacted environment.
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Affiliation(s)
- Mariana P Reis
- Departamento de Biologia Geral, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Av. Antônio Carlos 6627, Belo Horizonte, Minas Gerais 31270-901, Brazil
| | - Marcela F Dias
- Departamento de Biologia Geral, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Av. Antônio Carlos 6627, Belo Horizonte, Minas Gerais 31270-901, Brazil
| | - Patrícia S Costa
- Departamento de Biologia Geral, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Av. Antônio Carlos 6627, Belo Horizonte, Minas Gerais 31270-901, Brazil
| | - Marcelo P Ávila
- Departamento de Biologia Geral, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Av. Antônio Carlos 6627, Belo Horizonte, Minas Gerais 31270-901, Brazil
| | - Laura R Leite
- Centro de Pesquisas René Rachou Fundação Oswaldo Cruz, Av. Augusto de Lima 1715, Belo Horizonte, Minas Gerais 30190-002, Brazil
| | - Flávio M G de Araújo
- Centro de Pesquisas René Rachou Fundação Oswaldo Cruz, Av. Augusto de Lima 1715, Belo Horizonte, Minas Gerais 30190-002, Brazil
| | - Anna C M Salim
- Centro de Pesquisas René Rachou Fundação Oswaldo Cruz, Av. Augusto de Lima 1715, Belo Horizonte, Minas Gerais 30190-002, Brazil
| | - Mônica Bucciarelli-Rodriguez
- Departamento de Biologia Geral, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Av. Antônio Carlos 6627, Belo Horizonte, Minas Gerais 31270-901, Brazil
| | - Guilherme Oliveira
- Centro de Pesquisas René Rachou Fundação Oswaldo Cruz, Av. Augusto de Lima 1715, Belo Horizonte, Minas Gerais 30190-002, Brazil; Instituto Tecnológico Vale, Rua Boaventura da Silva 955, Belém, Pará 66055-090, Brazil
| | - Edmar Chartone-Souza
- Departamento de Biologia Geral, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Av. Antônio Carlos 6627, Belo Horizonte, Minas Gerais 31270-901, Brazil
| | - Andréa M A Nascimento
- Departamento de Biologia Geral, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Av. Antônio Carlos 6627, Belo Horizonte, Minas Gerais 31270-901, Brazil.
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46
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Insights into microbial diversity in wastewater treatment systems: How far have we come? Biotechnol Adv 2016; 34:790-802. [DOI: 10.1016/j.biotechadv.2016.04.003] [Citation(s) in RCA: 91] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2015] [Revised: 02/15/2016] [Accepted: 04/07/2016] [Indexed: 11/16/2022]
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Maus I, Koeck DE, Cibis KG, Hahnke S, Kim YS, Langer T, Kreubel J, Erhard M, Bremges A, Off S, Stolze Y, Jaenicke S, Goesmann A, Sczyrba A, Scherer P, König H, Schwarz WH, Zverlov VV, Liebl W, Pühler A, Schlüter A, Klocke M. Unraveling the microbiome of a thermophilic biogas plant by metagenome and metatranscriptome analysis complemented by characterization of bacterial and archaeal isolates. BIOTECHNOLOGY FOR BIOFUELS 2016; 9:171. [PMID: 27525040 PMCID: PMC4982221 DOI: 10.1186/s13068-016-0581-3] [Citation(s) in RCA: 89] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/23/2016] [Accepted: 07/27/2016] [Indexed: 05/24/2023]
Abstract
BACKGROUND One of the most promising technologies to sustainably produce energy and to mitigate greenhouse gas emissions from combustion of fossil energy carriers is the anaerobic digestion and biomethanation of organic raw material and waste towards biogas by highly diverse microbial consortia. In this context, the microbial systems ecology of thermophilic industrial-scale biogas plants is poorly understood. RESULTS The microbial community structure of an exemplary thermophilic biogas plant was analyzed by a comprehensive approach comprising the analysis of the microbial metagenome and metatranscriptome complemented by the cultivation of hydrolytic and acido-/acetogenic Bacteria as well as methanogenic Archaea. Analysis of metagenome-derived 16S rRNA gene sequences revealed that the bacterial genera Defluviitoga (5.5 %), Halocella (3.5 %), Clostridium sensu stricto (1.9 %), Clostridium cluster III (1.5 %), and Tepidimicrobium (0.7 %) were most abundant. Among the Archaea, Methanoculleus (2.8 %) and Methanothermobacter (0.8 %) were predominant. As revealed by a metatranscriptomic 16S rRNA analysis, Defluviitoga (9.2 %), Clostridium cluster III (4.8 %), and Tepidanaerobacter (1.1 %) as well as Methanoculleus (5.7 %) mainly contributed to these sequence tags indicating their metabolic activity, whereas Hallocella (1.8 %), Tepidimicrobium (0.5 %), and Methanothermobacter (<0.1 %) were transcriptionally less active. By applying 11 different cultivation strategies, 52 taxonomically different microbial isolates representing the classes Clostridia, Bacilli, Thermotogae, Methanomicrobia and Methanobacteria were obtained. Genome analyses of isolates support the finding that, besides Clostridium thermocellum and Clostridium stercorarium, Defluviitoga tunisiensis participated in the hydrolysis of hemicellulose producing ethanol, acetate, and H2/CO2. The latter three metabolites are substrates for hydrogentrophic and acetoclastic archaeal methanogenesis. CONCLUSIONS Obtained results showed that high abundance of microorganisms as deduced from metagenome analysis does not necessarily indicate high transcriptional or metabolic activity, and vice versa. Additionally, it appeared that the microbiome of the investigated thermophilic biogas plant comprised a huge number of up to now unknown and insufficiently characterized species.
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Affiliation(s)
- Irena Maus
- Center for Biotechnology (CeBiTec), Institute for Genome Research and Systems Biology, Bielefeld University, Universitätsstr. 27, 33615 Bielefeld, Germany
| | - Daniela E. Koeck
- Department of Microbiology, Technische Universität München, Emil-Ramann-Str. 4, 85354 Freising-Weihenstephan, Germany
| | - Katharina G. Cibis
- Institute of Microbiology and Wine Research, Johannes Gutenberg-University, Becherweg 15, 55128 Mainz, Germany
| | - Sarah Hahnke
- Dept. Bioengineering, Leibniz-Institut für Agrartechnik Potsdam-Bornim e.V. (ATB), Max-Eyth-Allee 100, 14469 Potsdam, Germany
| | - Yong S. Kim
- Faculty Life Sciences/Research Center ‚‘Biomass Utilization Hamburg’, University of Applied Sciences Hamburg (HAW), Ulmenliet 20, 21033 Hamburg-Bergedorf, Germany
| | - Thomas Langer
- Dept. Bioengineering, Leibniz-Institut für Agrartechnik Potsdam-Bornim e.V. (ATB), Max-Eyth-Allee 100, 14469 Potsdam, Germany
| | - Jana Kreubel
- Institute of Microbiology and Wine Research, Johannes Gutenberg-University, Becherweg 15, 55128 Mainz, Germany
| | - Marcel Erhard
- RIPAC-LABOR GmbH, Am Mühlenberg 11, 14476 Potsdam-Golm, Germany
| | - Andreas Bremges
- Center for Biotechnology (CeBiTec), Institute for Genome Research and Systems Biology, Bielefeld University, Universitätsstr. 27, 33615 Bielefeld, Germany
- Faculty of Technology, Bielefeld University, Universitätsstr. 25, 33615 Bielefeld, Germany
| | - Sandra Off
- Faculty Life Sciences/Research Center ‚‘Biomass Utilization Hamburg’, University of Applied Sciences Hamburg (HAW), Ulmenliet 20, 21033 Hamburg-Bergedorf, Germany
| | - Yvonne Stolze
- Center for Biotechnology (CeBiTec), Institute for Genome Research and Systems Biology, Bielefeld University, Universitätsstr. 27, 33615 Bielefeld, Germany
| | - Sebastian Jaenicke
- Department of Bioinformatics and Systems Biology, Justus-Liebig University Gießen, Heinrich-Buff-Ring 58, 35392 Giessen, Germany
| | - Alexander Goesmann
- Department of Bioinformatics and Systems Biology, Justus-Liebig University Gießen, Heinrich-Buff-Ring 58, 35392 Giessen, Germany
| | - Alexander Sczyrba
- Center for Biotechnology (CeBiTec), Institute for Genome Research and Systems Biology, Bielefeld University, Universitätsstr. 27, 33615 Bielefeld, Germany
- Faculty of Technology, Bielefeld University, Universitätsstr. 25, 33615 Bielefeld, Germany
| | - Paul Scherer
- Faculty Life Sciences/Research Center ‚‘Biomass Utilization Hamburg’, University of Applied Sciences Hamburg (HAW), Ulmenliet 20, 21033 Hamburg-Bergedorf, Germany
| | - Helmut König
- Institute of Microbiology and Wine Research, Johannes Gutenberg-University, Becherweg 15, 55128 Mainz, Germany
| | - Wolfgang H. Schwarz
- Department of Microbiology, Technische Universität München, Emil-Ramann-Str. 4, 85354 Freising-Weihenstephan, Germany
| | - Vladimir V. Zverlov
- Department of Microbiology, Technische Universität München, Emil-Ramann-Str. 4, 85354 Freising-Weihenstephan, Germany
| | - Wolfgang Liebl
- Department of Microbiology, Technische Universität München, Emil-Ramann-Str. 4, 85354 Freising-Weihenstephan, Germany
| | - Alfred Pühler
- Center for Biotechnology (CeBiTec), Institute for Genome Research and Systems Biology, Bielefeld University, Universitätsstr. 27, 33615 Bielefeld, Germany
| | - Andreas Schlüter
- Center for Biotechnology (CeBiTec), Institute for Genome Research and Systems Biology, Bielefeld University, Universitätsstr. 27, 33615 Bielefeld, Germany
| | - Michael Klocke
- Dept. Bioengineering, Leibniz-Institut für Agrartechnik Potsdam-Bornim e.V. (ATB), Max-Eyth-Allee 100, 14469 Potsdam, Germany
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Vanwonterghem I, Jensen PD, Rabaey K, Tyson GW. Genome-centric resolution of microbial diversity, metabolism and interactions in anaerobic digestion. Environ Microbiol 2016; 18:3144-58. [DOI: 10.1111/1462-2920.13382] [Citation(s) in RCA: 92] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2015] [Accepted: 03/17/2016] [Indexed: 12/16/2022]
Affiliation(s)
- Inka Vanwonterghem
- Advanced Water Management Centre (AWMC), The University of Queensland; QLD 4072 St Lucia Australia
- Australian Centre for Ecogenomics (ACE); The University of Queensland; QLD 4072 St Lucia Australia
| | - Paul D. Jensen
- Advanced Water Management Centre (AWMC), The University of Queensland; QLD 4072 St Lucia Australia
| | - Korneel Rabaey
- Advanced Water Management Centre (AWMC), The University of Queensland; QLD 4072 St Lucia Australia
- Centre for Microbial Ecology and Technology (CMET); Ghent University; Coupure Links 653 Ghent 9000 Belgium
| | - Gene W. Tyson
- Advanced Water Management Centre (AWMC), The University of Queensland; QLD 4072 St Lucia Australia
- Australian Centre for Ecogenomics (ACE); The University of Queensland; QLD 4072 St Lucia Australia
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Sun L, Toyonaga M, Ohashi A, Tourlousse DM, Matsuura N, Meng XY, Tamaki H, Hanada S, Cruz R, Yamaguchi T, Sekiguchi Y. Lentimicrobium saccharophilum gen. nov., sp. nov., a strictly anaerobic bacterium representing a new family in the phylum Bacteroidetes, and proposal of Lentimicrobiaceae fam. nov. Int J Syst Evol Microbiol 2016; 66:2635-2642. [DOI: 10.1099/ijsem.0.001103] [Citation(s) in RCA: 118] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Affiliation(s)
- Liwei Sun
- Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Ibaraki 305-8566, Japan
- School of Energy & Environment, Southeast University, Nanjing, Jiangsu 210096, PR China
| | - Mayu Toyonaga
- Department of Civil and Environmental Engineering, Nagaoka University of Technology, Nagaoka, Niigata, 940-2188, Japan
| | - Akiko Ohashi
- Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Ibaraki 305-8566, Japan
| | - Dieter M. Tourlousse
- Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Ibaraki 305-8566, Japan
| | - Norihisa Matsuura
- Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Ibaraki 305-8566, Japan
| | - Xian-Ying Meng
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Ibaraki 305-8566, Japan
| | - Hideyuki Tamaki
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Ibaraki 305-8566, Japan
| | - Satoshi Hanada
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Ibaraki 305-8566, Japan
| | - Rodrigo Cruz
- EPAS International NV, Dok-Noord 4, Gent 9000, Belgium
| | - Takashi Yamaguchi
- Department of Civil and Environmental Engineering, Nagaoka University of Technology, Nagaoka, Niigata, 940-2188, Japan
| | - Yuji Sekiguchi
- Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Ibaraki 305-8566, Japan
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Moleculo Long-Read Sequencing Facilitates Assembly and Genomic Binning from Complex Soil Metagenomes. mSystems 2016; 1:mSystems00045-16. [PMID: 27822530 PMCID: PMC5069762 DOI: 10.1128/msystems.00045-16] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2016] [Accepted: 05/24/2016] [Indexed: 11/20/2022] Open
Abstract
Soil microorganisms carry out key processes for life on our planet, including cycling of carbon and other nutrients and supporting growth of plants. However, there is poor molecular-level understanding of their functional roles in ecosystem stability and responses to environmental perturbations. This knowledge gap is largely due to the difficulty in culturing the majority of soil microbes. Thus, use of culture-independent approaches, such as metagenomics, promises the direct assessment of the functional potential of soil microbiomes. Soil is, however, a challenge for metagenomic assembly due to its high microbial diversity and variable evenness, resulting in low coverage and uneven sampling of microbial genomes. Despite increasingly large soil metagenome data volumes (>200 Gbp), the majority of the data do not assemble. Here, we used the cutting-edge approach of synthetic long-read sequencing technology (Moleculo) to assemble soil metagenome sequence data into long contigs and used the assemblies for binning of genomes. Soil metagenomics has been touted as the “grand challenge” for metagenomics, as the high microbial diversity and spatial heterogeneity of soils make them unamenable to current assembly platforms. Here, we aimed to improve soil metagenomic sequence assembly by applying the Moleculo synthetic long-read sequencing technology. In total, we obtained 267 Gbp of raw sequence data from a native prairie soil; these data included 109.7 Gbp of short-read data (~100 bp) from the Joint Genome Institute (JGI), an additional 87.7 Gbp of rapid-mode read data (~250 bp), plus 69.6 Gbp (>1.5 kbp) from Moleculo sequencing. The Moleculo data alone yielded over 5,600 reads of >10 kbp in length, and over 95% of the unassembled reads mapped to contigs of >1.5 kbp. Hybrid assembly of all data resulted in more than 10,000 contigs over 10 kbp in length. We mapped three replicate metatranscriptomes derived from the same parent soil to the Moleculo subassembly and found that 95% of the predicted genes, based on their assignments to Enzyme Commission (EC) numbers, were expressed. The Moleculo subassembly also enabled binning of >100 microbial genome bins. We obtained via direct binning the first complete genome, that of “Candidatus Pseudomonas sp. strain JKJ-1” from a native soil metagenome. By mapping metatranscriptome sequence reads back to the bins, we found that several bins corresponding to low-relative-abundance Acidobacteria were highly transcriptionally active, whereas bins corresponding to high-relative-abundance Verrucomicrobia were not. These results demonstrate that Moleculo sequencing provides a significant advance for resolving complex soil microbial communities. IMPORTANCE Soil microorganisms carry out key processes for life on our planet, including cycling of carbon and other nutrients and supporting growth of plants. However, there is poor molecular-level understanding of their functional roles in ecosystem stability and responses to environmental perturbations. This knowledge gap is largely due to the difficulty in culturing the majority of soil microbes. Thus, use of culture-independent approaches, such as metagenomics, promises the direct assessment of the functional potential of soil microbiomes. Soil is, however, a challenge for metagenomic assembly due to its high microbial diversity and variable evenness, resulting in low coverage and uneven sampling of microbial genomes. Despite increasingly large soil metagenome data volumes (>200 Gbp), the majority of the data do not assemble. Here, we used the cutting-edge approach of synthetic long-read sequencing technology (Moleculo) to assemble soil metagenome sequence data into long contigs and used the assemblies for binning of genomes. Author Video: An author video summary of this article is available.
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