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Kuschke SG, Wyneken J, Miller D. Baseline Skin Microbiota of the Leatherback Sea Turtle. Microorganisms 2024; 12:925. [PMID: 38792755 PMCID: PMC11124050 DOI: 10.3390/microorganisms12050925] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2024] [Revised: 04/28/2024] [Accepted: 04/29/2024] [Indexed: 05/26/2024] Open
Abstract
The integumentary system of the leatherback sea turtle (Dermochelys coriacea) is the most visible and defining difference of the species, with its smooth and waxy carapace and finely scaled skin, distinguishing it from the other six sea turtle species. The skin is the body's largest organ and serves as a primary defense against the outside world and is thus essential to health. To date, we have begun to understand that the microorganisms located on the skin aid in these functions. However, many host-microbial interactions are not yet fully defined or understood. Prior to uncovering these crucial host-microbial interactions, we must first understand the communities of microorganisms present and how they differ through life-stage classes and across the body. Here, we present a comprehensive bacterial microbial profile on the skin of leatherbacks. Using next-generation sequencing (NGS), we identified the major groups of bacteria on the skin of neonates at emergence, neonates at 3-4 weeks of age (i.e., post-hatchlings), and nesting females. These data show that the predominant bacteria on the skin of the leatherback are different at each life-stage class sampled. This suggests that there is a shift in the microbial communities of the skin associated with life-stage class or even possibly age. We also found that different sample locations on the nesting female (i.e., carapace and front appendages = flipper) have significantly different communities of bacteria present. This is likely due to differences in the microhabitats of these anatomic locations and future studies should explore if this variation also holds true for neonates. These data define baseline skin microbiota on the leatherback and can serve as a foundation for additional work to broaden our understanding of the leatherbacks' host-microbial interactions, the impacts of environmental changes or stressors over time, and even the pathogenicity of disease processes.
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Affiliation(s)
- Samantha G. Kuschke
- Department of Biomedical and Diagnostic Services, College of Veterinary Medicine, University of Tennessee, Knoxville, TN 37996, USA;
- Department of Biological Sciences, Florida Atlantic University, Boca Raton, FL 33431, USA;
- Center for Wildlife Health, University of Tennessee, Knoxville, TN 37996, USA
- One Health Initiative, University of Tennessee, Knoxville, TN 37996, USA
- Upwell, Monterey, CA 93940, USA
| | - Jeanette Wyneken
- Department of Biological Sciences, Florida Atlantic University, Boca Raton, FL 33431, USA;
| | - Debra Miller
- Department of Biomedical and Diagnostic Services, College of Veterinary Medicine, University of Tennessee, Knoxville, TN 37996, USA;
- Center for Wildlife Health, University of Tennessee, Knoxville, TN 37996, USA
- One Health Initiative, University of Tennessee, Knoxville, TN 37996, USA
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Jitsuno K, Hoshino T, Nishikawa Y, Kogawa M, Mineta K, Strasser M, Ikehara K, Everest J, Maeda L, Inagaki F, Takeyama H. Comparative single-cell genomics of Atribacterota JS1 in the Japan Trench hadal sedimentary biosphere. mSphere 2024; 9:e0033723. [PMID: 38170974 PMCID: PMC10826368 DOI: 10.1128/msphere.00337-23] [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: 07/13/2023] [Accepted: 11/30/2023] [Indexed: 01/05/2024] Open
Abstract
Deep-sea and subseafloor sedimentary environments host heterotrophic microbial communities that contribute to Earth's carbon cycling. However, the potential metabolic functions of individual microorganisms and their biogeographical distributions in hadal ocean sediments remain largely unexplored. In this study, we conducted single-cell genome sequencing on sediment samples collected from six sites (7,445-8,023 m water depth) along an approximately 500 km transect of the Japan Trench during the International Ocean Discovery Program Expedition 386. A total of 1,886 single-cell amplified genomes (SAGs) were obtained, offering comprehensive genetic insights into sedimentary microbial communities in surface sediments (<1 m depth) above the sulfate-methane transition zone along the Japan Trench. Our genome data set included 269 SAGs from Atribacterota JS1, the predominant bacterial clade in these hadal environments. Phylogenetic analysis classified SAGs into nine distinct phylotypes, whereas metagenome-assembled genomes were categorized into only two phylotypes, advancing JS1 diversity coverage through a single cell-based approach. Comparative genomic analysis of JS1 lineages from different habitats revealed frequent detection of genes related to organic carbon utilization, such as extracellular enzymes like clostripain and α-amylase, and ABC transporters of oligopeptide from Japan Trench members. Furthermore, specific JS1 phylotypes exhibited a strong correlation with in situ methane concentrations and contained genes involved in glycine betaine metabolism. These findings suggest that the phylogenomically diverse and novel Atribacterota JS1 is widely distributed in Japan Trench sediment, playing crucial roles in carbon cycling within the hadal sedimentary biosphere.IMPORTANCEThe Japan Trench represents tectonically active hadal environments associated with Pacific plate subduction beneath the northeastern Japan arc. This study, for the first time, documented a large-scale single-cell and metagenomic survey along an approximately 500 km transect of the Japan Trench, obtaining high-quality genomic information on hadal sedimentary microbial communities. Single-cell genomics revealed the predominance of diverse JS1 lineages not recoverable through conventional metagenomic binning. Their metabolic potential includes genes related to the degradation of organic matter, which contributes to methanogenesis in the deeper layers. Our findings enhance understanding of sedimentary microbial communities at water depths exceeding 7,000 m and provide new insights into the ecological role of biogeochemical carbon cycling in the hadal sedimentary biosphere.
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Affiliation(s)
- Kana Jitsuno
- Graduate School of Advanced Science and Engineering, Waseda University, Shinjuku-ku, Tokyo, Japan
- CBBD-OIL, AIST-Waseda University, Shinjuku-ku, Tokyo, Japan
| | - Tatsuhiko Hoshino
- Kochi Institute for Core Sample Research, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Nankoku, Kochi, Japan
| | - Yohei Nishikawa
- CBBD-OIL, AIST-Waseda University, Shinjuku-ku, Tokyo, Japan
- Research organization for Nano and Life Innovation, Waseda University, Shinjuku-ku, Tokyo, Japan
| | - Masato Kogawa
- Research organization for Nano and Life Innovation, Waseda University, Shinjuku-ku, Tokyo, Japan
| | - Katsuhiko Mineta
- CBBD-OIL, AIST-Waseda University, Shinjuku-ku, Tokyo, Japan
- Research organization for Nano and Life Innovation, Waseda University, Shinjuku-ku, Tokyo, Japan
- Marine Open Innovation Institute, Shizuoka, Japan
| | - Michael Strasser
- Department of Geology, University of Innsbruck, Innsbruck, Austria
| | - Ken Ikehara
- Research Institute of Geology and Geoinformation, AIST Geological Survey of Japan, Tsukuba, Japan
| | | | - Lena Maeda
- Advanced Institute for Marine Ecosystem Change (WPI-AIMEC), JAMSTEC, Yokohama, Japan
| | - Fumio Inagaki
- Research organization for Nano and Life Innovation, Waseda University, Shinjuku-ku, Tokyo, Japan
- Advanced Institute for Marine Ecosystem Change (WPI-AIMEC), JAMSTEC, Yokohama, Japan
- Department of Earth Sciences, Graduate School of Science, Tohoku University, Sendai, Japan
| | - Haruko Takeyama
- Graduate School of Advanced Science and Engineering, Waseda University, Shinjuku-ku, Tokyo, Japan
- CBBD-OIL, AIST-Waseda University, Shinjuku-ku, Tokyo, Japan
- Research organization for Nano and Life Innovation, Waseda University, Shinjuku-ku, Tokyo, Japan
- Institute for Advanced Research of Biosystem Dynamics, Waseda Research Institute for Science and Engineering, Waseda University, Tokyo, Japan
| | - IODP Expedition 386 ScientistsBellanovaPieroBrunetMorganeCaiZhirongCattaneoAntonioHochmuthKatharinaHsiungKanhsiIshizawaTakashiItakiTakuyaJitsunoKanaJohnsonJoelKanamatsuToshiyaKeepMyraKiokaArataMaerzChristianMcHughCeciliaMicallefAaronMinLuoPandeyDhananjaiProustJean NoelRasburyTroyRiedingerNataschaBaoRuiSatoguchiYasufumiSawyerDerekSeibertChloeSilverMaxwellStraubSusanneVirtasaloJoonasWangYonghongWuTing-WeiZellersSarahKöllingMartinHuangJyh-Jaan StevenNagahashiYoshitaka
- Graduate School of Advanced Science and Engineering, Waseda University, Shinjuku-ku, Tokyo, Japan
- CBBD-OIL, AIST-Waseda University, Shinjuku-ku, Tokyo, Japan
- Kochi Institute for Core Sample Research, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Nankoku, Kochi, Japan
- Research organization for Nano and Life Innovation, Waseda University, Shinjuku-ku, Tokyo, Japan
- Marine Open Innovation Institute, Shizuoka, Japan
- Department of Geology, University of Innsbruck, Innsbruck, Austria
- Research Institute of Geology and Geoinformation, AIST Geological Survey of Japan, Tsukuba, Japan
- British Geological Survey, Edinburgh, United Kingdom
- Advanced Institute for Marine Ecosystem Change (WPI-AIMEC), JAMSTEC, Yokohama, Japan
- Department of Earth Sciences, Graduate School of Science, Tohoku University, Sendai, Japan
- Institute for Advanced Research of Biosystem Dynamics, Waseda Research Institute for Science and Engineering, Waseda University, Tokyo, Japan
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Maatouk M, Rolain JM, Bittar F. Using Genomics to Decipher the Enigmatic Properties and Survival Adaptation of Candidate Phyla Radiation. Microorganisms 2023; 11:1231. [PMID: 37317205 DOI: 10.3390/microorganisms11051231] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2023] [Revised: 04/28/2023] [Accepted: 05/05/2023] [Indexed: 06/16/2023] Open
Abstract
Microbial ecology is a critical field for understanding the composition, diversity, and functions of microorganisms in various environmental and health-related processes. The discovery of Candidate Phyla Radiation (CPR) through culture-independent methods has introduced a new division of microbes characterized by a symbiotic/parasitic lifestyle, small cell size, and small genome. Despite being poorly understood, CPRs have garnered significant attention in recent years due to their widespread detection in a variety of environmental and clinical samples. These microorganisms have been found to exhibit a high degree of genetic diversity compared to other microbes. Several studies have shed light on their potential importance in global biogeochemical cycles and their impact on various human activities. In this review, we provide a systematic overview of the discovery of CPRs. We then focus on describing how the genomic characteristics of CPRs have helped them interact with and adapt to other microbes in different ecological niches. Future works should focus on discovering the metabolic capacities of CPRs and, if possible, isolating them to obtain a better understanding of these microorganisms.
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Affiliation(s)
- Mohamad Maatouk
- Aix-Marseille Université, IRD, APHM, MEPHI, 13005 Marseille, France
- IHU Méditerranée Infection, 13005 Marseille, France
| | - Jean-Marc Rolain
- Aix-Marseille Université, IRD, APHM, MEPHI, 13005 Marseille, France
- IHU Méditerranée Infection, 13005 Marseille, France
| | - Fadi Bittar
- Aix-Marseille Université, IRD, APHM, MEPHI, 13005 Marseille, France
- IHU Méditerranée Infection, 13005 Marseille, France
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Liu T, Hu S, Yuan Z, Guo J. Microbial Stratification Affects Conversions of Nitrogen and Methane in Biofilms Coupling Anammox and n-DAMO Processes. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2023; 57:4608-4618. [PMID: 36826448 DOI: 10.1021/acs.est.2c07294] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
A methane-based membrane biofilm reactor (MBfR) has a suitable configuration to incorporate anammox and nitrite/nitrate-dependent anaerobic methane oxidation (n-DAMO) processes because of its high gas-transfer efficiency and efficient biomass retention. In this study, the spatial distribution of microorganisms along with the biofilm depth in methane-based MBfRs was experimentally revealed, showing the dominance of anammox bacteria, n-DAMO bacteria, and n-DAMO archaea in the outer layer, middle layer, and inner layer of biofilms, respectively. The long-term and short-term experimental investigations in conjunction with mathematical modeling collectively revealed that microorganisms living in the outer layer of biofilms tend to use substrates from wastewater, while microorganisms inhabiting the inner layer of biofilms tend to use substrates originating from biofilm substratum. Specifically, anammox bacteria dominating the biofilm surface preferentially removed the nitrite provided from wastewater, while n-DAMO bacteria mostly utilized the nitrite generated from n-DAMO archaea as these two methane-related populations spatially clustered together inside the biofilm. Likewise, the methane supplied from the membrane was mostly consumed by n-DAMO archaea, while the dissolved methane in wastewater would be primarily utilized by n-DAMO bacteria. This study offers novel insights into the impacts of microbial stratification in biofilm systems, not only expanding the fundamental understanding of biofilms and microbial interactions therein but also providing a rationale for the potential applications of methane-based MBfRs in sewage treatment.
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Affiliation(s)
- Tao Liu
- Australian Centre for Water and Environmental Biotechnology (ACWEB, Formerly AWMC), The University of Queensland, St. Lucia, Brisbane, Queensland 4072, Australia
| | - Shihu Hu
- Australian Centre for Water and Environmental Biotechnology (ACWEB, Formerly AWMC), The University of Queensland, St. Lucia, Brisbane, Queensland 4072, Australia
| | - Zhiguo Yuan
- Australian Centre for Water and Environmental Biotechnology (ACWEB, Formerly AWMC), The University of Queensland, St. Lucia, Brisbane, Queensland 4072, Australia
| | - Jianhua Guo
- Australian Centre for Water and Environmental Biotechnology (ACWEB, Formerly AWMC), The University of Queensland, St. Lucia, Brisbane, Queensland 4072, Australia
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Gios E, Mosley OE, Weaver L, Close M, Daughney C, Handley KM. Ultra-small bacteria and archaea exhibit genetic flexibility towards groundwater oxygen content, and adaptations for attached or planktonic lifestyles. ISME COMMUNICATIONS 2023; 3:13. [PMID: 36808147 PMCID: PMC9938205 DOI: 10.1038/s43705-023-00223-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Revised: 02/06/2023] [Accepted: 02/09/2023] [Indexed: 06/16/2023]
Abstract
Aquifers are populated by highly diverse microbial communities, including unusually small bacteria and archaea. The recently described Patescibacteria (or Candidate Phyla Radiation) and DPANN radiation are characterized by ultra-small cell and genomes sizes, resulting in limited metabolic capacities and probable dependency on other organisms to survive. We applied a multi-omics approach to characterize the ultra-small microbial communities over a wide range of aquifer groundwater chemistries. Results expand the known global range of these unusual organisms, demonstrate the wide geographical range of over 11,000 subsurface-adapted Patescibacteria, Dependentiae and DPANN archaea, and indicate that prokaryotes with ultra-small genomes and minimalistic metabolism are a characteristic feature of the terrestrial subsurface. Community composition and metabolic activities were largely shaped by water oxygen content, while highly site-specific relative abundance profiles were driven by a combination of groundwater physicochemistries (pH, nitrate-N, dissolved organic carbon). We provide insights into the activity of ultra-small prokaryotes with evidence that they are major contributors to groundwater community transcriptional activity. Ultra-small prokaryotes exhibited genetic flexibility with respect to groundwater oxygen content, and transcriptionally distinct responses, including proportionally greater transcription invested into amino acid and lipid metabolism and signal transduction in oxic groundwater, along with differences in taxa transcriptionally active. Those associated with sediments differed from planktonic counterparts in species composition and transcriptional activity, and exhibited metabolic adaptations reflecting a surface-associated lifestyle. Finally, results showed that groups of phylogenetically diverse ultra-small organisms co-occurred strongly across sites, indicating shared preferences for groundwater conditions.
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Affiliation(s)
- Emilie Gios
- School of Biological Sciences, The University of Auckland, Auckland, New Zealand
- NINA, Norwegian Institute for Nature Research, Trondheim, Norway
| | - Olivia E Mosley
- School of Biological Sciences, The University of Auckland, Auckland, New Zealand
- NatureMetrics Ltd, Surrey Research Park, Guildford, UK
| | - Louise Weaver
- Institute of Environmental Science and Research, Christchurch, New Zealand
| | - Murray Close
- Institute of Environmental Science and Research, Christchurch, New Zealand
| | - Chris Daughney
- GNS Science, Lower Hutt, New Zealand
- NIWA, National Institute of Water and Atmospheric Research, Wellington, New Zealand
| | - Kim M Handley
- School of Biological Sciences, The University of Auckland, Auckland, New Zealand.
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Vigneron A, Cruaud P, Guyoneaud R, Goñi-Urriza M. Into the darkness of the microbial dark matter in situ activities through expression profiles of Patescibacteria populations. Front Microbiol 2023; 13:1073483. [PMID: 36699594 PMCID: PMC9868632 DOI: 10.3389/fmicb.2022.1073483] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Accepted: 12/05/2022] [Indexed: 01/11/2023] Open
Abstract
Patescibacteria form a highly diverse and widespread superphylum of uncultured microorganisms representing a third of the global microbial diversity. Most of our knowledge on Patescibacteria putative physiology relies on metagenomic mining and metagenome-assembled genomes, but the in situ activities and the ecophysiology of these microorganisms have been rarely explored, leaving the role of Patescibacteria in ecosystems elusive. Using a genome-centric metatranscriptomic approach, we analyzed the diel and seasonal gene transcription profiles of 18 Patescibacteria populations in brackish microbial mats to test whether our understanding of Patescibacteria metabolism allows the extrapolation of their in situ activities. Although our results revealed a circadian cycle in Patescibacteria activities, a strong streamlined genetic expression characterized the Patescibacteria populations. This result has a major consequence for the extrapolation of their physiology and environmental function since most transcribed genes were uncharacterized, indicating that the ecophysiology of Patescibacteria cannot be yet reliably predicted from genomic data.
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Affiliation(s)
- Adrien Vigneron
- IBEAS, Université de Pau et des Pays de l'Adour, E2S UPPA, CNRS, IPREM, Pau, France
| | | | - Rémy Guyoneaud
- IBEAS, Université de Pau et des Pays de l'Adour, E2S UPPA, CNRS, IPREM, Pau, France
| | - Marisol Goñi-Urriza
- IBEAS, Université de Pau et des Pays de l'Adour, E2S UPPA, CNRS, IPREM, Pau, France
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Saedi Y, Batista JR, Britto R, Grady D. Impacts of co-contaminants and dilution on perchlorate biodegradation using various carbon sources. Biodegradation 2023; 34:301-323. [PMID: 36598629 DOI: 10.1007/s10532-022-10013-2] [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: 09/28/2021] [Accepted: 12/21/2022] [Indexed: 01/05/2023]
Abstract
This research investigates the biodegradation of perchlorate in the presence of the co-contaminants nitrate and chlorate using soluble and slow-release carbon sources. In addition, the impact of bio-augmentation and dilution, which results in lower total dissolved salts (TDS) and contaminant levels, is examined. Laboratory microcosms were conducted using actual groundwater and soils from a contaminated aquifer. The results revealed that both soluble and slow-release carbon sources support biodegradation of contaminants in the sequence nitrate > chlorate > perchlorate. Degradation rates, including and excluding lag times, revealed that the overall impact of the presence of co-contaminants depends on degradation kinetics and the relative concentrations of the contaminants. When the lag time caused by the presence of the co-contaminants is considered, the degradation rates for chlorate and perchlorate were two to three times slower. The results also show that dilution causes lower initial contaminant concentrations, and consequently, slower degradation rates, which is not desirable. On the other hand, the dilution resulting from the injection of amendments to support remediation promotes desirably lower salinity levels. However, the salinity associated with the presence of sulfate does not inhibit biodegradation. The naturally occurring bacteria were able to support the degradation of all contaminants. Bio-augmentation was effective only in diluted microcosms. Proteobacteria and Firmicutes were the dominant phyla identified in the microcosms.
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Affiliation(s)
- Yasaman Saedi
- Department of Civil and Environmental Engineering and Construction, University of Nevada Las Vegas (UNLV), 4505 Maryland Parkway, Las Vegas, NV, 89154-4015, USA
| | - Jacimaria R Batista
- Department of Civil and Environmental Engineering and Construction, University of Nevada Las Vegas (UNLV), 4505 Maryland Parkway, Las Vegas, NV, 89154-4015, USA.
| | - Ronnie Britto
- Tetra Tech Inc, 720 Coleherne Road, Collierville, TN, 38017, USA
| | - Dana Grady
- Tetra Tech Inc, 720 Coleherne Road, Collierville, TN, 38017, USA
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Occurrence, Diversity, and Genomes of " Candidatus Patescibacteria" along the Early Diagenesis of Marine Sediments. Appl Environ Microbiol 2022; 88:e0140922. [PMID: 36468881 PMCID: PMC9765117 DOI: 10.1128/aem.01409-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/07/2022] Open
Abstract
The phylum "Candidatus Patescibacteria" (or Candidate Phyla Radiation [CPR]) accounts for roughly one-quarter of microbial diversity on Earth, but the presence and diversity of these bacteria in marine sediments have been rarely charted. Here, we investigate the abundance, diversity, and metabolic capacities of CPR bacteria in three sediment sites (Mohns Ridge, North Pond, and Costa Rica Margin) with samples covering a wide range of redox zones formed during the early diagenesis of organic matter. Through metagenome sequencing, we found that all investigated sediment horizons contain "Ca. Patescibacteria" (0.4 to 28% of the total communities), which are affiliated with the classes "Ca. Paceibacteria," "Ca. Gracilibacteria," "Ca. Microgenomatia," "Ca. Saccharimonadia," "Ca. ABY1," and "Ca. WWE3." However, only a subset of the diversity of marine sediment "Ca. Patescibacteria," especially the classes "Ca. Paceibacteria" and "Ca. Gracilibacteria," can be captured by 16S rRNA gene amplicon sequencing with commonly used universal primers. We recovered 11 metagenome-assembled genomes (MAGs) of CPR from these sediments, most of which are novel at the family or genus level in the "Ca. Paceibacteria" class and are missed by the amplicon sequencing. While individual MAGs are confined to specific anoxic niches, the lack of capacities to utilize the prevailing terminal electron acceptors indicates that they may not be directly selected by the local redox conditions. These CPR bacteria lack essential biosynthesis pathways and may use a truncated glycolysis pathway to conserve energy as fermentative organotrophs. Our findings suggest that marine sediments harbor some novel yet widespread CPR bacteria during the early diagenesis of organic matter, which needs to be considered in population dynamics assessments in this vast environment. IMPORTANCE Ultrasmall-celled "Ca. Patescibacteria" have been estimated to account for one-quarter of the total microbial diversity on Earth, the parasitic lifestyle of which may exert a profound control on the overall microbial population size of the local ecosystems. However, their diversity and metabolic functions in marine sediments, one of the largest yet understudied ecosystems on Earth, remain virtually uncharacterized. By applying cultivation-independent approaches to a range of sediment redox zones, we reveal that "Ca. Patescibacteria" members are rare but widespread regardless of the prevailing geochemical conditions. These bacteria are affiliated with novel branches of "Ca. Patescibacteria" and have been largely missed in marker gene-based surveys. They do not have respiration capacity but may conserve energy by fermenting organic compounds from their episymbiotic hosts. Our findings suggest that these novel "Ca. Patescibacteria" are among the previously overlooked microbes in diverse marine sediments.
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Ji Y, Zhang P, Zhou S, Gao P, Wang B, Jiang J. Widespread but Poorly Understood Bacteria: Candidate Phyla Radiation. Microorganisms 2022; 10:2232. [PMID: 36422302 PMCID: PMC9698310 DOI: 10.3390/microorganisms10112232] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Revised: 11/09/2022] [Accepted: 11/10/2022] [Indexed: 08/15/2023] Open
Abstract
Candidate Phyla Radiation (CPR) bacteria is a bacterial division composed mainly of candidate phyla bacteria with ultra-small cell sizes, streamlined genomes, and limited metabolic capacity, which are generally considered to survive in a parasitic or symbiotic manner. Despite their wide distribution and rich diversity, CPR bacteria have received little attention until recent years, and are therefore poorly understood. This review systematically summarizes the history of CPR research, the parasitic/symbiotic lifestyle, and the ecological distribution and unique metabolic features of CPR bacteria, hoping to provide guidance for future ecological and physiological research on CPR bacteria.
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Affiliation(s)
| | | | | | | | - Baozhan Wang
- Department of Microbiology, College of Life Sciences, Nanjing Agricultural University, Key Laboratory of Agricultural and Environmental Microbiology, Ministry of Agriculture and Rural Affairs, Nanjing 210095, China
| | - Jiandong Jiang
- Department of Microbiology, College of Life Sciences, Nanjing Agricultural University, Key Laboratory of Agricultural and Environmental Microbiology, Ministry of Agriculture and Rural Affairs, Nanjing 210095, China
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Dataset for Genome Sequencing and De Novo Assembly of the Candidate Phyla Radiation in Supragingival Plaque. THE CANADIAN JOURNAL OF INFECTIOUS DISEASES & MEDICAL MICROBIOLOGY = JOURNAL CANADIEN DES MALADIES INFECTIEUSES ET DE LA MICROBIOLOGIE MEDICALE 2022; 2022:4899824. [PMID: 35345870 PMCID: PMC8957474 DOI: 10.1155/2022/4899824] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/06/2021] [Accepted: 01/26/2022] [Indexed: 11/17/2022]
Abstract
The Candidate Phyla Radiation (CPR), as a newly discovered and difficult-to-culture bacterium, accounts for the majority of the bacterial domain, which may be related to various oral diseases, including dental caries. Restricted by laboratory culture conditions, there is limited knowledge about oral CPR. Advances in metagenomics provide a new way to study CPR through molecular biology. Here, we used metagenomic assembly and binning to reconstruct more and higher quality metagenome-assembled genomes (MAGs) of CPR from oral dental plaque. These MAGs represent novel CPR species, which differed from all known CPR organisms. Relative abundance of different CPR MAGs in the caries and caries-free group was estimated by mapping metagenomic reads to newly constructed MAGs. The relative abundance of two CPR MAGs was significantly increased in the caries group, indicating that there might be a relationship with caries activity. The detection of a large number of unclassified CPR MAGs in the dataset implies that the phylogenetic diversity of CPR is enormous. The results provide a reference value for exploring the ecological distribution and function of uncultured or difficult-to-culture microorganisms.
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11
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Danczak RE, Sengupta A, Fansler SJ, Chu RK, Garayburu-Caruso VA, Renteria L, Toyoda J, Wells J, Stegen JC. Inferring the Contribution of Microbial Taxa and Organic Matter Molecular Formulas to Ecological Assembly. Front Microbiol 2022; 13:803420. [PMID: 35250925 PMCID: PMC8894727 DOI: 10.3389/fmicb.2022.803420] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2021] [Accepted: 01/14/2022] [Indexed: 11/23/2022] Open
Abstract
Understanding the mechanisms underlying the assembly of communities has long been the goal of many ecological studies. While several studies have evaluated community wide ecological assembly, fewer have focused on investigating the impacts of individual members within a community or assemblage on ecological assembly. Here, we adapted a previous null model β-nearest taxon index (βNTI) to measure the contribution of individual features within an ecological community to overall assembly. This new metric, called feature-level βNTI (βNTIfeat), enables researchers to determine whether ecological features (e.g., individual microbial taxa) contribute to divergence, convergence, or have insignificant impacts across spatiotemporally resolved metacommunities or meta-assemblages. Using βNTIfeat, we revealed that unclassified microbial lineages often contributed to community divergence while diverse groups (e.g., Crenarchaeota, Alphaproteobacteria, and Gammaproteobacteria) contributed to convergence. We also demonstrate that βNTIfeat can be extended to other ecological assemblages such as organic molecules comprising organic matter (OM) pools. OM had more inconsistent trends compared to the microbial community though CHO-containing molecular formulas often contributed to convergence, while nitrogen and phosphorus-containing formulas contributed to both convergence and divergence. A network analysis was used to relate βNTIfeat values from the putatively active microbial community and the OM assemblage and examine potentially common contributions to ecological assembly across different communities/assemblages. This analysis revealed that P-containing formulas often contributed to convergence/divergence separately from other ecological features and N-containing formulas often contributed to assembly in coordination with microorganisms. Additionally, members of Family Geobacteraceae were often observed to contribute to convergence/divergence in conjunction with both N- and P-containing formulas, suggesting a coordinated ecological role for family members and the nitrogen/phosphorus cycle. Overall, we show that βNTIfeat offers opportunities to investigate the community or assemblage members, which shape the phylogenetic or functional landscape, and demonstrate the potential to evaluate potential points of coordination across various community types.
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Affiliation(s)
- Robert E. Danczak
- Ecosystem Sciences, Pacific Northwest National Laboratory, Richland, WA, United States
- *Correspondence: Robert E. Danczak,
| | - Aditi Sengupta
- Department of Biology, California Lutheran University, Thousand Oaks, CA, United States
| | - Sarah J. Fansler
- Ecosystem Sciences, Pacific Northwest National Laboratory, Richland, WA, United States
| | - Rosalie K. Chu
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, United States
| | | | - Lupita Renteria
- Ecosystem Sciences, Pacific Northwest National Laboratory, Richland, WA, United States
| | - Jason Toyoda
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, United States
| | - Jacqueline Wells
- Ecosystem Sciences, Pacific Northwest National Laboratory, Richland, WA, United States
| | - James C. Stegen
- Ecosystem Sciences, Pacific Northwest National Laboratory, Richland, WA, United States
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12
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Liu T, Lu Y, Zheng M, Hu S, Yuan Z, Guo J. Efficient nitrogen removal from mainstream wastewater through coupling Partial Nitritation, Anammox and Methane-dependent nitrite/nitrate reduction (PNAM). WATER RESEARCH 2021; 206:117723. [PMID: 34637975 DOI: 10.1016/j.watres.2021.117723] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Revised: 08/29/2021] [Accepted: 09/26/2021] [Indexed: 06/13/2023]
Abstract
The application of partial nitritation and anammox to remove nitrogen from mainstream wastewater is of great interest because of the potential to reduce energy cost and carbon dosage. However, this process confronts a dilemma of relatively high effluent nitrogen concentration (>10 mg N/L), owning to the unwanted prevalence of nitrite-oxidizing bacteria (NOB) and the intrinsic nitrate production by anammox bacteria. Here, a novel technology, named the one-stage PNAM, that integrates Partial Nitritation, Anammox and Methane-dependent nitrite/nitrate reduction reactions, was developed in a single membrane biofilm reactor (MBfR). With feeding of synthetic mainstream wastewater containing ∼50 mg NH4+-N/L at a hydraulic retention time of 12 h, more than 95% nitrogen was removed in the established one-stage PNAM process at a practically useful rate of 0.1 kg N/m3/d. Microbial community characterization and in-situ batch tests revealed a sophisticated microbial structure consisting of ammonia-oxidizing bacteria (AOB), anammox bacteria, nitrite/nitrate-dependent anaerobic methane oxidation (n-DAMO) bacteria and archaea, and a small fraction of NOB and aerobic methanotrophs. The role of methane in removing nitrate was confirmed by switching on/off the methane supply, which relaxed the requirement for NOB suppression. In addition, the established system was relatively robust against temperature variations, evidenced by a total nitrogen removal efficiency above 80% at temperature as low as 14 ℃. The results provide a promising alternative for efficient nitrogen removal from domestic wastewater using methane as the sole carbon source.
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Affiliation(s)
- Tao Liu
- Australian Centre for Water and Environmental Biotechnology (ACWEB, formerly AWMC), The University of Queensland, St. Lucia, Queensland 4072, Australia
| | - Yan Lu
- Australian Centre for Water and Environmental Biotechnology (ACWEB, formerly AWMC), The University of Queensland, St. Lucia, Queensland 4072, Australia
| | - Min Zheng
- Australian Centre for Water and Environmental Biotechnology (ACWEB, formerly AWMC), The University of Queensland, St. Lucia, Queensland 4072, Australia
| | - Shihu Hu
- Australian Centre for Water and Environmental Biotechnology (ACWEB, formerly AWMC), The University of Queensland, St. Lucia, Queensland 4072, Australia
| | - Zhiguo Yuan
- Australian Centre for Water and Environmental Biotechnology (ACWEB, formerly AWMC), The University of Queensland, St. Lucia, Queensland 4072, Australia
| | - Jianhua Guo
- Australian Centre for Water and Environmental Biotechnology (ACWEB, formerly AWMC), The University of Queensland, St. Lucia, Queensland 4072, Australia.
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13
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Phan HV, Kurisu F, Kiba K, Furumai H. Optimized Cultivation and Syntrophic Relationship of Anaerobic Benzene-Degrading Enrichment Cultures under Methanogenic Conditions. Microbes Environ 2021; 36. [PMID: 34433738 PMCID: PMC8446749 DOI: 10.1264/jsme2.me21028] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Abstract
Current challenges in the anaerobic bioremediation of benzene are the lack of capable cultures and limited knowledge on the biodegradation pathway. Under methanogenic conditions, benzene may be mineralized by syntrophic interactions between microorganisms, which are poorly understood. The present study developed an optimized formula for anoxic medium to successfully promote the growth of the putative benzene degrader Deltaproteobacterium Hasda-A and enhance the benzene degradation activity of methanogenic enrichment cultures. Within 70 d of incubation, the benzene degradation activity and relative abundance of Hasda-A in cultures in the new defined medium increased from 0.5 to >3 mg L–1 d–1 and from 2.5% to >17%, respectively. Together with Hasda-A, we found a strong positive relationship between the abundances of superphylum OD1 bacteria, three methanogens (Methanoregula, Methanolinea, and Methanosaeta) and benzene degradation activity. The syntrophic relationship between these microbial taxa and Hasda-A was then demonstrated in a correlation analysis of longitudinal data. The involvement of methanogenesis in anaerobic benzene mineralization was confirmed by inhibition experiments. The high benzene degradation activity and growth of Hasda-A were quickly recovered in successive dilutions of enrichment cultures, proving the feasibility of using the medium developed in the present study to produce highly capable cultures. The present results will facilitate practical applications in bioremediation and research on the molecular mechanisms underlying benzene activation and syntrophic interactions in benzene mineralization.
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Affiliation(s)
- Hop V Phan
- JSPS International Research Fellow, Research Center for Water Environment Technology, The University of Tokyo
| | - Futoshi Kurisu
- Research Center for Water Environment Technology, The University of Tokyo
| | - Koichiro Kiba
- Department of Urban Engineering, Graduate School of Engineering, The University of Tokyo
| | - Hiroaki Furumai
- Research Center for Water Environment Technology, The University of Tokyo
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14
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Genome-Resolved Meta-Analysis of the Microbiome in Oil Reservoirs Worldwide. Microorganisms 2021; 9:microorganisms9091812. [PMID: 34576708 PMCID: PMC8465018 DOI: 10.3390/microorganisms9091812] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Revised: 08/18/2021] [Accepted: 08/19/2021] [Indexed: 11/30/2022] Open
Abstract
Microorganisms inhabiting subsurface petroleum reservoirs are key players in biochemical transformations. The interactions of microbial communities in these environments are highly complex and still poorly understood. This work aimed to assess publicly available metagenomes from oil reservoirs and implement a robust pipeline of genome-resolved metagenomics to decipher metabolic and taxonomic profiles of petroleum reservoirs worldwide. Analysis of 301.2 Gb of metagenomic information derived from heavily flooded petroleum reservoirs in China and Alaska to non-flooded petroleum reservoirs in Brazil enabled us to reconstruct 148 metagenome-assembled genomes (MAGs) of high and medium quality. At the phylum level, 74% of MAGs belonged to bacteria and 26% to archaea. The profiles of these MAGs were related to the physicochemical parameters and recovery management applied. The analysis of the potential functional core in the reservoirs showed that the microbiota was specialized for each site, with 31.7% of the total KEGG orthologies annotated as functions (1690 genes) common to all oil fields, while 18% of the functions were site-specific, i.e., present only in one of the oil fields. The oil reservoirs with a lower level of intervention were the most similar to the potential functional core, while the oil fields with a long history of water injection had greater variation in functional profile. These results show how key microorganisms and their functions respond to the distinct physicochemical parameters and interventions of the oil field operations such as water injection and expand the knowledge of biogeochemical transformations in these ecosystems.
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15
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Reconstruction of Metagenome-Assembled Genomes from Aquaria. Microbiol Resour Announc 2021; 10:e0055721. [PMID: 34351234 PMCID: PMC8340870 DOI: 10.1128/mra.00557-21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Here, we report 11 metagenome-assembled genomes (MAGs) reconstructed from freshwater and saltwater aquaria, including representatives of Polynucleobacter, Anaerolinea, Roseobacter, Flavobacteriia, Octadecabacter, Mycobacterium, and Candidate Phyla Radiation (CPR) members. These MAGs can serve as a resource for aquatic research and elucidating the role of CPR taxa in the built environment.
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16
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Patin NV, Dietrich ZA, Stancil A, Quinan M, Beckler JS, Hall ER, Culter J, Smith CG, Taillefert M, Stewart FJ. Gulf of Mexico blue hole harbors high levels of novel microbial lineages. THE ISME JOURNAL 2021; 15:2206-2232. [PMID: 33612832 PMCID: PMC8319197 DOI: 10.1038/s41396-021-00917-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2020] [Revised: 01/14/2021] [Accepted: 01/27/2021] [Indexed: 01/31/2023]
Abstract
Exploration of oxygen-depleted marine environments has consistently revealed novel microbial taxa and metabolic capabilities that expand our understanding of microbial evolution and ecology. Marine blue holes are shallow karst formations characterized by low oxygen and high organic matter content. They are logistically challenging to sample, and thus our understanding of their biogeochemistry and microbial ecology is limited. We present a metagenomic and geochemical characterization of Amberjack Hole on the Florida continental shelf (Gulf of Mexico). Dissolved oxygen became depleted at the hole's rim (32 m water depth), remained low but detectable in an intermediate hypoxic zone (40-75 m), and then increased to a secondary peak before falling below detection in the bottom layer (80-110 m), concomitant with increases in nutrients, dissolved iron, and a series of sequentially more reduced sulfur species. Microbial communities in the bottom layer contained heretofore undocumented levels of the recently discovered phylum Woesearchaeota (up to 58% of the community), along with lineages in the bacterial Candidate Phyla Radiation (CPR). Thirty-one high-quality metagenome-assembled genomes (MAGs) showed extensive biochemical capabilities for sulfur and nitrogen cycling, as well as for resisting and respiring arsenic. One uncharacterized gene associated with a CPR lineage differentiated hypoxic from anoxic zone communities. Overall, microbial communities and geochemical profiles were stable across two sampling dates in the spring and fall of 2019. The blue hole habitat is a natural marine laboratory that provides opportunities for sampling taxa with under-characterized but potentially important roles in redox-stratified microbial processes.
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Affiliation(s)
- N V Patin
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA.
- Center for Microbial Dynamics and Infection, Georgia Institute of Technology, Atlanta, GA, USA.
- Ocean Chemistry and Ecosystems Division, Atlantic Oceanographic and Meteorological Laboratory, National Oceanic and Atmospheric Administration, Miami, FL, USA.
- Cooperative Institute for Marine and Atmospheric Studies, Rosenstiel School of Marine and Atmospheric Science, University of Miami, Miami, FL, USA.
- Stationed at Southwest Fisheries Science Center, National Marine Fisheries Service, National Oceanic and Atmospheric Administration, La Jolla, CA, USA.
| | | | - A Stancil
- Harbor Branch Oceanographic Institute, Florida Atlantic University, Ft. Pierce, FL, USA
| | - M Quinan
- Harbor Branch Oceanographic Institute, Florida Atlantic University, Ft. Pierce, FL, USA
| | - J S Beckler
- Harbor Branch Oceanographic Institute, Florida Atlantic University, Ft. Pierce, FL, USA
| | - E R Hall
- Mote Marine Laboratory, Sarasota, FL, USA
| | - J Culter
- Mote Marine Laboratory, Sarasota, FL, USA
| | - C G Smith
- U.S. Geological Survey, St. Petersburg Coastal and Marine Science Center, St. Petersburg, FL, USA
| | - M Taillefert
- School of Earth & Atmospheric Sciences, Georgia Institute of Technology, Atlanta, GA, USA
| | - F J Stewart
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA
- Center for Microbial Dynamics and Infection, Georgia Institute of Technology, Atlanta, GA, USA
- Department of Microbiology & Immunology, Montana State University, Bozeman, MT, USA
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17
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Chen P, Zhou H, Huang Y, Xie Z, Zhang M, Wei Y, Li J, Ma Y, Luo M, Ding W, Cao J, Jiang T, Nan P, Fang J, Li X. Revealing the full biosphere structure and versatile metabolic functions in the deepest ocean sediment of the Challenger Deep. Genome Biol 2021; 22:207. [PMID: 34256809 PMCID: PMC8276468 DOI: 10.1186/s13059-021-02408-w] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2020] [Accepted: 06/10/2021] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND The full biosphere structure and functional exploration of the microbial communities of the Challenger Deep of the Mariana Trench, the deepest known hadal zone on Earth, lag far behind that of other marine realms. RESULTS We adopt a deep metagenomics approach to investigate the microbiome in the sediment of Challenger Deep, Mariana Trench. We construct 178 metagenome-assembled genomes (MAGs) representing 26 phyla, 16 of which are reported from hadal sediment for the first time. Based on the MAGs, we find the microbial community functions are marked by enrichment and prevalence of mixotrophy and facultative anaerobic metabolism. The microeukaryotic community is found to be dominated by six fungal groups that are characterized for the first time in hadal sediment to possess the assimilatory and dissimilatory nitrate/sulfate reduction, and hydrogen sulfide oxidation pathways. By metaviromic analysis, we reveal novel hadal Caudovirales clades, distinctive virus-host interactions, and specialized auxiliary metabolic genes for modulating hosts' nitrogen/sulfur metabolism. The hadal microbiome is further investigated by large-scale cultivation that cataloged 1070 bacterial and 19 fungal isolates from the Challenger Deep sediment, many of which are found to be new species specialized in the hadal habitat. CONCLUSION Our hadal MAGs and isolates increase the diversity of the Challenger Deep sediment microbial genomes and isolates present in the public. The deep metagenomics approach fills the knowledge gaps in structure and diversity of the hadal microbiome, and provides novel insight into the ecology and metabolism of eukaryotic and viral components in the deepest biosphere on earth.
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Affiliation(s)
- Ping Chen
- CAS-Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
| | - Hui Zhou
- CAS-Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Yanyan Huang
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, School of Life Sciences, Fudan University, Shanghai, China
- Chinese Ancient Books reservation and Conservation Institute, Fudan University, Shanghai, China
| | - Zhe Xie
- Shanghai Engineering Research Center of Hadal Science and Technology, College of Marine Sciences, Shanghai Ocean University, Shanghai, China
| | - Mengjie Zhang
- CAS-Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Yuli Wei
- Shanghai Engineering Research Center of Hadal Science and Technology, College of Marine Sciences, Shanghai Ocean University, Shanghai, China
| | - Jia Li
- CAS-Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Yuewei Ma
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, School of Life Sciences, Fudan University, Shanghai, China
| | - Min Luo
- Shanghai Engineering Research Center of Hadal Science and Technology, College of Marine Sciences, Shanghai Ocean University, Shanghai, China
| | - Wenmian Ding
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, School of Life Sciences, Fudan University, Shanghai, China
| | - Junwei Cao
- Shanghai Engineering Research Center of Hadal Science and Technology, College of Marine Sciences, Shanghai Ocean University, Shanghai, China
| | - Tao Jiang
- CAS-Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Peng Nan
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, School of Life Sciences, Fudan University, Shanghai, China.
| | - Jiasong Fang
- Shanghai Engineering Research Center of Hadal Science and Technology, College of Marine Sciences, Shanghai Ocean University, Shanghai, China.
| | - Xuan Li
- CAS-Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China.
- University of Chinese Academy of Sciences, Beijing, China.
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18
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Hardoim CCP, Ramaglia ACM, Lôbo-Hajdu G, Custódio MR. Community composition and functional prediction of prokaryotes associated with sympatric sponge species of southwestern Atlantic coast. Sci Rep 2021; 11:9576. [PMID: 33953214 PMCID: PMC8100286 DOI: 10.1038/s41598-021-88288-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2020] [Accepted: 04/07/2021] [Indexed: 02/03/2023] Open
Abstract
Prokaryotes contribute to the health of marine sponges. However, there is lack of data on the assembly rules of sponge-associated prokaryotic communities, especially for those inhabiting biodiversity hotspots, such as ecoregions between tropical and warm temperate southwestern Atlantic waters. The sympatric species Aplysina caissara, Axinella corrugata, and Dragmacidon reticulatum were collected along with environmental samples from the north coast of São Paulo (Brazil). Overall, 64 prokaryotic phyla were detected; 51 were associated with sponge species, and the dominant were Proteobacteria, Bacteria (unclassified), Cyanobacteria, Crenarchaeota, and Chloroflexi. Around 64% and 89% of the unclassified operational taxonomical units (OTUs) associated with Brazilian sponge species showed a sequence similarity below 97%, with sequences in the Silva and NCBI Type Strain databases, respectively, indicating the presence of a large number of unidentified taxa. The prokaryotic communities were species-specific, ranging 56%-80% of the OTUs and distinct from the environmental samples. Fifty-four lineages were responsible for the differences detected among the categories. Functional prediction demonstrated that Ap. caissara was enriched for energy metabolism and biosynthesis of secondary metabolites, whereas D. reticulatum was enhanced for metabolism of terpenoids and polyketides, as well as xenobiotics' biodegradation and metabolism. This survey revealed a high level of novelty associated with Brazilian sponge species and that distinct members responsible from the differences among Brazilian sponge species could be correlated to the predicted functions.
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Affiliation(s)
- C C P Hardoim
- Institute of Biosciences, São Paulo State University, Coastal Campus of São Vicente, São Paulo, Brazil.
| | - A C M Ramaglia
- Institute of Biosciences, São Paulo State University, Coastal Campus of São Vicente, São Paulo, Brazil
| | - G Lôbo-Hajdu
- Department of Genetic, Biology Institute Roberto Alcântara Gomes, Rio de Janeiro State University, Rio de Janeiro, Brazil
| | - M R Custódio
- Department of Physiology, Center for Marine Biology, Biosciences Institute and NP-Biomar, São Paulo University, São Paulo, Brazil
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19
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Liu C, Liu T, Zheng X, Meng J, Chen H, Yuan Z, Hu S, Guo J. Rapid formation of granules coupling n-DAMO and anammox microorganisms to remove nitrogen. WATER RESEARCH 2021; 194:116963. [PMID: 33652229 DOI: 10.1016/j.watres.2021.116963] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/05/2020] [Revised: 01/30/2021] [Accepted: 02/22/2021] [Indexed: 06/12/2023]
Abstract
Granular sludge exhibits unique features, including rapid settling velocity, high loading rate and relative insensitivity against inhibitors, thus being a favorable platform for the cultivation of slow-growing and vulnerable microorganisms, such as anaerobic ammonium oxidation (anammox) bacteria and nitrite/nitrate-dependent anaerobic methane oxidation (n-DAMO) microorganisms. While anammox granules have been widely applied, little is known about how to speed up the granulation process of n-DAMO microorganisms, which grow even slower than anammox bacteria. In this study, we used mature anammox granules as biotic carriers to embed n-DAMO microorganisms, which obtained combined anammox + n-DAMO granules within 6 months. The results of whole-granule 16S rRNA gene amplicon sequencing showed the coexistence of anammox bacteria, n-DAMO bacteria and n-DAMO archaea. The microbial stratification along granule radius was further elucidated by cryosection-16S rRNA gene amplicon sequencing, showing the dominance of n-DAMO archaea and anammox bacteria at inner and outer layers, respectively. Moreover, the images of cryosection-fluorescence in situ hybridization (FISH) verified this stratification and also indicated a shift in microbial stratification. Specifically, n-DAMO bacteria and n-DAMO archaea attached to the anammox granule surface initially, which moved to the inner layer after 4-months operation. On the basis of combined anammox + n-DAMO granules, a practically useful nitrogen removal rate (1.0 kg N/m3/d) was obtained from sidestream wastewater, which provides new avenue to remove nitrogen from wastewater using methane as carbon source.
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Affiliation(s)
- Chunshuang Liu
- The University of Queensland, Advanced Water Management Centre, St Lucia, QLD 4072, Australia; College of Chemical Engineering, China University of Petroleum, Qingdao 266580, China
| | - Tao Liu
- The University of Queensland, Advanced Water Management Centre, St Lucia, QLD 4072, Australia
| | - Xiaoying Zheng
- The University of Queensland, Advanced Water Management Centre, St Lucia, QLD 4072, Australia; Key Laboratory of Integrated Regulation and Resource Development on Shallow Lake of Ministry of Education, College of Environment, Hohai University, Nanjing 210098, China
| | - Jia Meng
- The University of Queensland, Advanced Water Management Centre, St Lucia, QLD 4072, Australia
| | - Hui Chen
- The University of Queensland, Advanced Water Management Centre, St Lucia, QLD 4072, Australia
| | - Zhiguo Yuan
- The University of Queensland, Advanced Water Management Centre, St Lucia, QLD 4072, Australia
| | - Shihu Hu
- The University of Queensland, Advanced Water Management Centre, St Lucia, QLD 4072, Australia
| | - Jianhua Guo
- The University of Queensland, Advanced Water Management Centre, St Lucia, QLD 4072, Australia.
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20
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Vickers CJ, Fraga D, Patrick WM. Quantifying the taxonomic bias in enzymology. Protein Sci 2021; 30:914-921. [PMID: 33583070 PMCID: PMC7980516 DOI: 10.1002/pro.4041] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2021] [Revised: 02/05/2021] [Accepted: 02/09/2021] [Indexed: 12/31/2022]
Abstract
The ongoing biotechnological revolution is rooted in our knowledge of enzymes. However, metagenomics is showing how little we know about Earth's enzyme repertoire. Deep sequencing has revolutionized our view of the tree of life. The genomes of newly‐discovered organisms are replete with novel sequences, emphasizing the trove of enzyme structures and functions waiting to be explored by biochemists. Here, we sought to draw attention to the vastness of the “enzymatic dark matter” within the tree of life by placing enzymological knowledge in the context of phylogeny. We used kinetic parameters from the BRaunschweig ENzyme DAtabase (BRENDA) as our proxy for enzymological knowledge. Mapping 12,677 BRENDA entries onto the phylogenetic tree revealed that 55% of these data were from eukaryotes, even though they are the least diverse part of the tree. At the next taxonomic level, only four of 18 archaeal phyla and 24 of 111 bacterial phyla are represented in the BRENDA dataset. One phylum, the Proteobacteria, accounts for over half of all bacterial entries. Similarly, the supergroup Amorphea, which includes animals and fungi, contains over half the data on eukaryotes. Many major taxonomic groups are notable for their complete absence from BRENDA, including the ultra‐diverse bacterial Candidate Phyla Radiation. At the species level, five mammals (including human) contribute 15% of BRENDA entries. The taxonomic bias in enzymology is strong, but in the era of gene synthesis we now have the tools to address it. Doing so promises to enrich our biochemical understanding of life and uncover powerful new biocatalysts.
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Affiliation(s)
- Chelsea J Vickers
- Centre for Biodiscovery, School of Biological Sciences, Victoria University of Wellington, Wellington, New Zealand
| | - Dean Fraga
- Department of Biology, The College of Wooster, Wooster, Ohio, USA
| | - Wayne M Patrick
- Centre for Biodiscovery, School of Biological Sciences, Victoria University of Wellington, Wellington, New Zealand
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21
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Alexyuk M, Bogoyavlenskiy A, Alexyuk P, Moldakhanov Y, Berezin V, Digel I. Epipelagic microbiome of the Small Aral Sea: Metagenomic structure and ecological diversity. Microbiologyopen 2021; 10:e1142. [PMID: 33305509 PMCID: PMC7882900 DOI: 10.1002/mbo3.1142] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2020] [Revised: 11/04/2020] [Accepted: 11/07/2020] [Indexed: 11/11/2022] Open
Abstract
Microbial diversity studies regarding the aquatic communities that experienced or are experiencing environmental problems are essential for the comprehension of the remediation dynamics. In this pilot study, we present data on the phylogenetic and ecological structure of microorganisms from epipelagic water samples collected in the Small Aral Sea (SAS). The raw data were generated by massive parallel sequencing using the shotgun approach. As expected, most of the identified DNA sequences belonged to Terrabacteria and Actinobacteria (40% and 37% of the total reads, respectively). The occurrence of Deinococcus-Thermus, Armatimonadetes, Chloroflexi in the epipelagic SAS waters was less anticipated. Surprising was also the detection of sequences, which are characteristic for strict anaerobes-Ignavibacteria, hydrogen-oxidizing bacteria, and archaeal methanogenic species. We suppose that the observed very broad range of phylogenetic and ecological features displayed by the SAS reads demonstrates a more intensive mixing of water masses originating from diverse ecological niches of the Aral-Syr Darya River basin than presumed before.
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Affiliation(s)
- Madina Alexyuk
- Research and Production Center for Microbiology and VirologyAlmatyKazakhstan
| | | | - Pavel Alexyuk
- Research and Production Center for Microbiology and VirologyAlmatyKazakhstan
| | - Yergali Moldakhanov
- Research and Production Center for Microbiology and VirologyAlmatyKazakhstan
| | - Vladimir Berezin
- Research and Production Center for Microbiology and VirologyAlmatyKazakhstan
| | - Ilya Digel
- Institute for BioengineeringAachen University of Applied SciencesJülichGermany
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22
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Cui G, Zhou Y, Li W, Gao Z, Huang J, Wang Y. A novel bacterial phylum that participates in carbon and osmolyte cycling in the Challenger Deep sediments. Environ Microbiol 2020; 23:3758-3772. [PMID: 33331063 DOI: 10.1111/1462-2920.15363] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2019] [Revised: 08/18/2020] [Accepted: 09/23/2020] [Indexed: 11/24/2022]
Abstract
Large amounts of detrital organic matter and osmolytes accumulate in the sediments of hadal trenches (>6000 m depth) due to the funnelling effect. It is still unknown whether there are novel active microbes that depend on specific carbon sources in extreme and isolated environments. In this study, we present a novel active bacterial phylum, Candidatus Tianyabacteria in the FCB superphylum, which was enriched in sediments collected from the Challenger Deep. Genome binning resulted in high-quality Ca. Tianyabacteria genomes representing two Ca. Tianyabacteria lineages (L1 and L2) in sediments 0-21 cm below the surface (cmbsf); L1 tends to be abundant in the upper layers (0-9 cmbsf), and L2 seems to be more prevalent in the deeper layers (12-21 cmbsf). Gene annotation and transcriptomics results indicate that the two lineages might import and catalyse amino acids and myo-inositol into central carbon metabolism for a heterotrophic lifestyle. Probably due to differences in environmental oxygen levels, the L2 genomes harbour gene clusters responsible for denitrification and fermentation, while the L1 genomes encode octahaem cytochrome c and multicopper oxidase using unknown substrates. The Ca. Tianyabacteria are thus novel heterotrophic organisms that participate in processes of carbon, nitrogen and organic osmolyte cycling in hadal sediments.
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Affiliation(s)
- Guojie Cui
- Institute of Deep-Sea Science and Engineering, Chinese Academy of Sciences, Sanya, China.,Faculty of Marine Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Yingli Zhou
- Institute of Deep-Sea Science and Engineering, Chinese Academy of Sciences, Sanya, China.,Faculty of Marine Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Wenli Li
- Institute of Deep-Sea Science and Engineering, Chinese Academy of Sciences, Sanya, China.,Faculty of Marine Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Zhaoming Gao
- Institute of Deep-Sea Science and Engineering, Chinese Academy of Sciences, Sanya, China
| | - Jiaomei Huang
- Institute of Deep-Sea Science and Engineering, Chinese Academy of Sciences, Sanya, China.,Faculty of Marine Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Yong Wang
- Institute of Deep-Sea Science and Engineering, Chinese Academy of Sciences, Sanya, China
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23
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Microbial single-cell omics: the crux of the matter. Appl Microbiol Biotechnol 2020; 104:8209-8220. [PMID: 32845367 PMCID: PMC7471194 DOI: 10.1007/s00253-020-10844-0] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Revised: 08/08/2020] [Accepted: 08/17/2020] [Indexed: 01/10/2023]
Abstract
Abstract Single-cell genomics and transcriptomics can provide reliable context for assembled genome fragments and gene expression activity on the level of individual prokaryotic genomes. These methods are rapidly emerging as an essential complement to cultivation-based, metagenomics, metatranscriptomics, and microbial community-focused research approaches by allowing direct access to information from individual microorganisms, even from deep-branching phylogenetic groups that currently lack cultured representatives. Their integration and binning with environmental ‘omics data already provides unprecedented insights into microbial diversity and metabolic potential, enabling us to provide information on individual organisms and the structure and dynamics of natural microbial populations in complex environments. This review highlights the pitfalls and recent advances in the field of single-cell omics and its importance in microbiological and biotechnological studies. Key points • Single-cell omics expands the tree of life through the discovery of novel organisms, genes, and metabolic pathways. • Disadvantages of metagenome-assembled genomes are overcome by single-cell omics. • Functional analysis of single cells explores the heterogeneity of gene expression. • Technical challenges still limit this field, thus prompting new method developments.
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24
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Beam JP, Becraft ED, Brown JM, Schulz F, Jarett JK, Bezuidt O, Poulton NJ, Clark K, Dunfield PF, Ravin NV, Spear JR, Hedlund BP, Kormas KA, Sievert SM, Elshahed MS, Barton HA, Stott MB, Eisen JA, Moser DP, Onstott TC, Woyke T, Stepanauskas R. Ancestral Absence of Electron Transport Chains in Patescibacteria and DPANN. Front Microbiol 2020; 11:1848. [PMID: 33013724 PMCID: PMC7507113 DOI: 10.3389/fmicb.2020.01848] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2020] [Accepted: 07/15/2020] [Indexed: 12/21/2022] Open
Abstract
Recent discoveries suggest that the candidate superphyla Patescibacteria and DPANN constitute a large fraction of the phylogenetic diversity of Bacteria and Archaea. Their small genomes and limited coding potential have been hypothesized to be ancestral adaptations to obligate symbiotic lifestyles. To test this hypothesis, we performed cell-cell association, genomic, and phylogenetic analyses on 4,829 individual cells of Bacteria and Archaea from 46 globally distributed surface and subsurface field samples. This confirmed the ubiquity and abundance of Patescibacteria and DPANN in subsurface environments, the small size of their genomes and cells, and the divergence of their gene content from other Bacteria and Archaea. Our analyses suggest that most Patescibacteria and DPANN in the studied subsurface environments do not form specific physical associations with other microorganisms. These data also suggest that their unusual genomic features and prevalent auxotrophies may be a result of ancestral, minimal cellular energy transduction mechanisms that lack respiration, thus relying solely on fermentation for energy conservation.
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Affiliation(s)
- Jacob P Beam
- Bigelow Laboratory for Ocean Sciences, East Boothbay, ME, United States
| | - Eric D Becraft
- Bigelow Laboratory for Ocean Sciences, East Boothbay, ME, United States
| | - Julia M Brown
- Bigelow Laboratory for Ocean Sciences, East Boothbay, ME, United States
| | - Frederik Schulz
- Department of Energy Joint Genome Institute, Berkeley, CA, United States
| | - Jessica K Jarett
- Department of Energy Joint Genome Institute, Berkeley, CA, United States
| | - Oliver Bezuidt
- Bigelow Laboratory for Ocean Sciences, East Boothbay, ME, United States
| | - Nicole J Poulton
- Bigelow Laboratory for Ocean Sciences, East Boothbay, ME, United States
| | - Kayla Clark
- Bigelow Laboratory for Ocean Sciences, East Boothbay, ME, United States
| | - Peter F Dunfield
- Department of Biological Sciences, University of Calgary, Calgary, AB, Canada
| | - Nikolai V Ravin
- Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, Moscow, Russia
| | - John R Spear
- Civil and Environmental Engineering, Colorado School of Mines, Golden, CO, United States
| | - Brian P Hedlund
- School of Life Sciences - Nevada Institute of Personalized Medicine, University of Nevada, Las Vegas, Las Vegas, NV, United States
| | - Konstantinos A Kormas
- Department of Ichthyology and Aquatic Environment, University of Thessaly, Volos, Greece
| | - Stefan M Sievert
- Biology Department, Woods Hole Oceanographic Institution, Woods Hole, MA, United States
| | - Mostafa S Elshahed
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK, United States
| | - Hazel A Barton
- Department of Biology, University of Akron, Akron, OH, United States
| | - Matthew B Stott
- School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
| | - Jonathan A Eisen
- Department of Evolution and Ecology, Department of Medical Microbiology and Immunology, Genome Center, University of California, Davis, Davis, CA, United States
| | - Duane P Moser
- Desert Research Institute, Las Vegas, NV, United States
| | - Tullis C Onstott
- Department of Geosciences, Princeton University, Princeton, NJ, United States
| | - Tanja Woyke
- Department of Energy Joint Genome Institute, Berkeley, CA, United States
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25
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Dam HT, Vollmers J, Sobol MS, Cabezas A, Kaster AK. Targeted Cell Sorting Combined With Single Cell Genomics Captures Low Abundant Microbial Dark Matter With Higher Sensitivity Than Metagenomics. Front Microbiol 2020; 11:1377. [PMID: 32793124 PMCID: PMC7387413 DOI: 10.3389/fmicb.2020.01377] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2019] [Accepted: 05/28/2020] [Indexed: 11/13/2022] Open
Abstract
Rare members of environmental microbial communities are often overlooked and unexplored, primarily due to the lack of techniques capable of acquiring their genomes. Chloroflexi belong to one of the most understudied phyla, even though many of its members are ubiquitous in the environment and some play important roles in biochemical cycles or biotechnological applications. We here used a targeted cell-sorting approach, which enables the selection of specific taxa by fluorescent labeling and is compatible with subsequent single-cell genomics, to enrich for rare Chloroflexi species from a wastewater-treatment plant and obtain their genomes. The combined workflow was able to retrieve a substantially higher number of novel Chloroflexi draft genomes with much greater phylogenetical diversity when compared to a metagenomics approach from the same sample. The method offers an opportunity to access genetic information from rare biosphere members which would have otherwise stayed hidden as microbial dark matter and can therefore serve as an essential complement to cultivation-based, metagenomics, and microbial community-focused research approaches.
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Affiliation(s)
- Hang T Dam
- Institute for Biological Interfaces 5, Karlsruhe Institute of Technology, Eggenstein-Leopoldshafen, Germany.,Leibniz Institute DSMZ, Brunswick, Germany
| | - John Vollmers
- Institute for Biological Interfaces 5, Karlsruhe Institute of Technology, Eggenstein-Leopoldshafen, Germany.,Leibniz Institute DSMZ, Brunswick, Germany
| | - Morgan S Sobol
- Institute for Biological Interfaces 5, Karlsruhe Institute of Technology, Eggenstein-Leopoldshafen, Germany
| | - Angela Cabezas
- Instituto Tecnológico Regional Centro Sur, Universidad Tecnológica, Durazno, Uruguay
| | - Anne-Kristin Kaster
- Institute for Biological Interfaces 5, Karlsruhe Institute of Technology, Eggenstein-Leopoldshafen, Germany.,Leibniz Institute DSMZ, Brunswick, Germany
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26
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Zhong S, Chen Q, Hu J, Liu S, Qiao S, Ni J, Sun W. Vertical distribution of microbial communities and their response to metal(loid)s along the vadose zone-aquifer sediments. J Appl Microbiol 2020; 129:1657-1673. [PMID: 32533753 DOI: 10.1111/jam.14742] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2020] [Revised: 05/20/2020] [Accepted: 06/03/2020] [Indexed: 01/30/2023]
Abstract
AIMS This study attempted to demonstrate the vertical shift in bacterial, archaeal and fungal communities along the vadose zone-aquifer sediments and their respective responses to environmental factors. METHODS AND RESULTS We collected samples from the vadose zone and three aquifer sediments along a 42·5 m bore of a typical agricultural land. The results showed that the bacterial community shifted greatly with depth. The classes of Actinobacteria (19·5%) and NC10 (11·0%) were abundant in the vadose zone while Alphaproteobacteria (22·3%) and Gammaproteobacteria (20·1%) were enriched in the aquifer. Archaeal and fungal communities were relatively more homogeneous with no significant trend as a function of depth. Process analyses further indicated that selection dominated in the bacterial community, whereas stochastic processes governed archaeal and fungal communities. Moreover environment-bacteria interaction analysis showed that metal(loid)s, especially alkali metal, had a closer correlation with the bacterial community than physicochemical variables. CONCLUSIONS Depth strongly affected bacterial rather than archaeal and fungal communities. Metal(loid)s prevailed over physicochemical variables in shaping the bacterial community in the vadose zone-aquifer continuum. SIGNIFICANCE AND IMPACT OF THE STUDY Our study provides a new perspective on the structure of microbial communities from the vadose zone to the deep aquifers.
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Affiliation(s)
- S Zhong
- College of Environmental Sciences and Engineering, The Key Laboratory of Water and Sediment Sciences, Ministry of Education, Peking University, Beijing, China
| | - Q Chen
- College of Environmental Sciences and Engineering, The Key Laboratory of Water and Sediment Sciences, Ministry of Education, Peking University, Beijing, China
| | - J Hu
- College of Environmental Sciences and Engineering, The Key Laboratory of Water and Sediment Sciences, Ministry of Education, Peking University, Beijing, China
| | - S Liu
- College of Environmental Sciences and Engineering, The Key Laboratory of Water and Sediment Sciences, Ministry of Education, Peking University, Beijing, China
| | - S Qiao
- College of Environmental Sciences and Engineering, The Key Laboratory of Water and Sediment Sciences, Ministry of Education, Peking University, Beijing, China
| | - J Ni
- College of Environmental Sciences and Engineering, The Key Laboratory of Water and Sediment Sciences, Ministry of Education, Peking University, Beijing, China
| | - W Sun
- State Key Lab Plateau Ecology and Agriculture, Qinghai University, Xining, Qinghai, People's Republic of China
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27
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Liu T, Li J, Khai Lim Z, Chen H, Hu S, Yuan Z, Guo J. Simultaneous Removal of Dissolved Methane and Nitrogen from Synthetic Mainstream Anaerobic Effluent. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2020; 54:7629-7638. [PMID: 32432469 DOI: 10.1021/acs.est.0c00912] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Anaerobic technologies have been proposed as a promising solution to enhance bioenergy recovery and to transform a wastewater treatment plant (WWTP) from an energy consumer to an energy exporter. However, 20-60% of the methane produced remains dissolved in the anaerobically treated effluent, which is a potent greenhouse gas and is easily stripped out in the aeration tank. This study aims to develop a solution using dissolved methane to support denitrification, thus simultaneously enhancing nitrogen removal and achieving beneficial use of dissolved methane. By coupling anaerobic ammonium oxidation (anammox) with nitrite/nitrate-dependent anaerobic methane oxidation (n-DAMO), up to 85% of dissolved methane and more than 99% of nitrogen were removed in parallel in a biofilm system. Mass balance was conducted during both long-term operation and short-term batch tests, which indicated that n-DAMO bacteria and n-DAMO archaea indeed contributed jointly to the methane removal. The 16S rRNA gene amplicon sequencing further showed the co-presence of n-DAMO bacteria and n-DAMO archaea, while anammox bacteria were detected with a low relative abundance. This proposed technology can potentially be applied to reduce the carbon footprint and to save the organic carbon consumption in WWTPs.
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Affiliation(s)
- Tao Liu
- Advanced Water Management Centre, The University of Queensland, St. Lucia, Queensland 4072, Australia
| | - Jie Li
- Advanced Water Management Centre, The University of Queensland, St. Lucia, Queensland 4072, Australia
| | - Zhuan Khai Lim
- Advanced Water Management Centre, The University of Queensland, St. Lucia, Queensland 4072, Australia
| | - Hui Chen
- Advanced Water Management Centre, The University of Queensland, St. Lucia, Queensland 4072, Australia
| | - Shihu Hu
- Advanced Water Management Centre, The University of Queensland, St. Lucia, Queensland 4072, Australia
| | - Zhiguo Yuan
- Advanced Water Management Centre, The University of Queensland, St. Lucia, Queensland 4072, Australia
| | - Jianhua Guo
- Advanced Water Management Centre, The University of Queensland, St. Lucia, Queensland 4072, Australia
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28
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Ding X, Liu K, Gong G, Tian L, Ma J. Volatile organic compounds in the salt-lake sediments of the Tibet Plateau influence prokaryotic diversity and community assembly. Extremophiles 2020; 24:307-318. [PMID: 32025854 DOI: 10.1007/s00792-020-01155-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2019] [Accepted: 01/06/2020] [Indexed: 11/30/2022]
Abstract
Volatile organic compounds (VOCs) are important environmental factors because they supply nutrients for microbial cells and mediate intercellular interactions. However, few studies have focused on the effects of VOCs on prokaryotic diversity and community composition. In this study, we examined the relationship between prokaryotic diversity and community composition and the content of VOCs in salt-lake sediments from the Tibet Plateau using amplicon sequencing of the 16S rRNA gene. Results showed that the alpha-diversity indices (Chao1, Shannon, and Simpson) were generally negatively correlated with the content of 36 VOCs (P < 0.05). The prokaryotic communities were significantly driven by multiple VOCs at the lineage-dependent pattern (P < 0.05). Further analysis indicated that VOCs, including 3-methylpyruvate, biuret, isocitric acid, and stearic acid, jointly explained 37.3% of the variations in prokaryotic communities. Supplemental VOCs-pyruvate, biuret, alanine, and aspartic acid-notably decreased the Chao1 and Shannon indices and significantly assembled co-occurrence networks for the bacterial communities in the saline sediments. Together, these results demonstrated that VOCs play a critical role in the regulation of the diversity, compositions, and network structures of prokaryotic communities in saline sediments.
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Affiliation(s)
- Xiaowei Ding
- School of Food and Biological Engineering, Shaanxi University of Science and Technology, Xi'an, 710021, China
| | - Kaihui Liu
- School of Food and Biological Engineering, Shaanxi University of Science and Technology, Xi'an, 710021, China.
| | - Guoli Gong
- School of Food and Biological Engineering, Shaanxi University of Science and Technology, Xi'an, 710021, China
| | - Lu Tian
- School of Food and Biological Engineering, Shaanxi University of Science and Technology, Xi'an, 710021, China
| | - Jun Ma
- School of Food and Biological Engineering, Shaanxi University of Science and Technology, Xi'an, 710021, China
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29
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Biosynthetic capacity, metabolic variety and unusual biology in the CPR and DPANN radiations. Nat Rev Microbiol 2019; 16:629-645. [PMID: 30181663 DOI: 10.1038/s41579-018-0076-2] [Citation(s) in RCA: 205] [Impact Index Per Article: 41.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Candidate phyla radiation (CPR) bacteria and DPANN (an acronym of the names of the first included phyla) archaea are massive radiations of organisms that are widely distributed across Earth's environments, yet we know little about them. Initial indications are that they are consistently distinct from essentially all other bacteria and archaea owing to their small cell and genome sizes, limited metabolic capacities and often episymbiotic associations with other bacteria and archaea. In this Analysis, we investigate their biology and variations in metabolic capacities by analysis of approximately 1,000 genomes reconstructed from several metagenomics-based studies. We find that they are not monolithic in terms of metabolism but rather harbour a diversity of capacities consistent with a range of lifestyles and degrees of dependence on other organisms. Notably, however, certain CPR and DPANN groups seem to have exceedingly minimal biosynthetic capacities, whereas others could potentially be free living. Understanding of these microorganisms is important from the perspective of evolutionary studies and because their interactions with other organisms are likely to shape natural microbiome function.
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30
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Gao ZM, Huang JM, Cui GJ, Li WL, Li J, Wei ZF, Chen J, Xin YZ, Cai DS, Zhang AQ, Wang Y. In situ meta-omic insights into the community compositions and ecological roles of hadal microbes in the Mariana Trench. Environ Microbiol 2019; 21:4092-4108. [PMID: 31344308 DOI: 10.1111/1462-2920.14759] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2018] [Revised: 07/06/2019] [Accepted: 07/22/2019] [Indexed: 01/25/2023]
Abstract
The low temperature and elevated hydrostatic pressure in hadal trenches at water depths below 6000 m render sample collection difficult. Here, in situ hadal water microbial samples were collected from the Mariana Trench and analysed. The hadal microbial communities at different depths were revealed to be consistent and were dominated by heterotrophic Marinimicrobia. Thirty high-quality metagenome-assembled genomes (MAGs) were retrieved to represent the major hadal microbes affiliated with 12 prokaryotic phyla. Most of the MAGs were newly reported and probably derived from novel hadal inhabitants as exemplified by a potentially new candidate archaeal phylum in the DPANN superphylum. Metabolic reconstruction indicated that a great number of the MAGs participated in nitrogen and sulfur cycling, in which the nitrification process was driven sequentially by Thaumarchaeota and Nitrospirae and sulfur oxidization by Rhodospirillales in the Alphaproteobacteria class. Moreover, several groups of hadal microbes were revealed to be potential carbon monoxide oxidizers. Metatranscriptomic result highlighted the contribution of Chloroflexi in degrading recalcitrant dissolved organic matter and Marinimicrobia in extracellular protein decomposition. The present work provides an in-depth view on the hadal microbial communities regarding their endemism and element cycles.
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Affiliation(s)
- Zhao-Ming Gao
- Deep-sea Microbial Genomics Laboratory, Institute of Deep-sea Science and Engineering, Chinese Academy of Sciences, Sanya, Hai Nan, People's Republic of China.,Key Laboratory for Experimental Study under Deep-sea Extreme Conditions, Institute of Deep-sea Science and Engineering, Chinese Academy of Sciences, Sanya, Hai Nan, People's Republic of China
| | - Jiao-Mei Huang
- Deep-sea Microbial Genomics Laboratory, Institute of Deep-sea Science and Engineering, Chinese Academy of Sciences, Sanya, Hai Nan, People's Republic of China.,University of Chinese Academy of Sciences, Beijing, People's Republic of China
| | - Guo-Jie Cui
- Deep-sea Microbial Genomics Laboratory, Institute of Deep-sea Science and Engineering, Chinese Academy of Sciences, Sanya, Hai Nan, People's Republic of China.,University of Chinese Academy of Sciences, Beijing, People's Republic of China
| | - Wen-Li Li
- Deep-sea Microbial Genomics Laboratory, Institute of Deep-sea Science and Engineering, Chinese Academy of Sciences, Sanya, Hai Nan, People's Republic of China.,University of Chinese Academy of Sciences, Beijing, People's Republic of China
| | - Jun Li
- Deep-sea Microbial Genomics Laboratory, Institute of Deep-sea Science and Engineering, Chinese Academy of Sciences, Sanya, Hai Nan, People's Republic of China
| | - Zhan-Fei Wei
- Deep-sea Microbial Genomics Laboratory, Institute of Deep-sea Science and Engineering, Chinese Academy of Sciences, Sanya, Hai Nan, People's Republic of China.,University of Chinese Academy of Sciences, Beijing, People's Republic of China
| | - Jun Chen
- Deep-sea Microbial Genomics Laboratory, Institute of Deep-sea Science and Engineering, Chinese Academy of Sciences, Sanya, Hai Nan, People's Republic of China.,University of Chinese Academy of Sciences, Beijing, People's Republic of China
| | - Yong-Zhi Xin
- Deep-sea Microbial Genomics Laboratory, Institute of Deep-sea Science and Engineering, Chinese Academy of Sciences, Sanya, Hai Nan, People's Republic of China
| | - Du-Si Cai
- Deep-sea Microbial Genomics Laboratory, Institute of Deep-sea Science and Engineering, Chinese Academy of Sciences, Sanya, Hai Nan, People's Republic of China
| | - Ai-Qun Zhang
- Deep-sea Microbial Genomics Laboratory, Institute of Deep-sea Science and Engineering, Chinese Academy of Sciences, Sanya, Hai Nan, People's Republic of China
| | - Yong Wang
- Deep-sea Microbial Genomics Laboratory, Institute of Deep-sea Science and Engineering, Chinese Academy of Sciences, Sanya, Hai Nan, People's Republic of China.,Key Laboratory for Experimental Study under Deep-sea Extreme Conditions, Institute of Deep-sea Science and Engineering, Chinese Academy of Sciences, Sanya, Hai Nan, People's Republic of China.,HKUST-CAS Sanya Joint Laboratory of Marine Science Research, Chinese Academy of Sciences, Sanya, Hai Nan, People's Republic of China
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31
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Gavrilov SN, Korzhenkov AA, Kublanov IV, Bargiela R, Zamana LV, Popova AA, Toshchakov SV, Golyshin PN, Golyshina OV. Microbial Communities of Polymetallic Deposits' Acidic Ecosystems of Continental Climatic Zone With High Temperature Contrasts. Front Microbiol 2019; 10:1573. [PMID: 31379766 PMCID: PMC6650587 DOI: 10.3389/fmicb.2019.01573] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2019] [Accepted: 06/24/2019] [Indexed: 12/26/2022] Open
Abstract
Acid mine drainage (AMD) systems are globally widespread and are an important source of metal pollution in riverine and coastal systems. Microbial AMD communities have been extensively studied for their ability to thrive under extremely acidic conditions and for their immense contribution to the dissolution of metal ores. However, little is known on microbial inhabitants of AMD systems subjected to extremely contrasting continental seasonal temperature patterns as opposed to maritime climate zones, experiencing much weaker annual temperature variations. Here, we investigated three types of AMD sites in Eastern Transbaikalia (Russia). In this region, all surface water bodies undergo a deep and long (up to 6 months) freezing, with seasonal temperatures varying between -33 and +24°C, which starkly contrasts the common well-studied AMD environments. We sampled acidic pit lake (Sherlovaya Gora site) located in the area of a polymetallic deposit, acidic drainage water from Bugdaya gold-molybdenum-tungsten deposit and Ulan-Bulak natural acidic spring. These systems showed the abundance of bacteria-derived reads mostly affiliated with Actinobacteria, Acidobacteria, Alpha- and Gammaproteobacteria, chloroplasts, Chloroflexi, Bacteroidetes, and Firmicutes. Furthermore, candidate taxa "Ca. Saccharibacteria" (previously known as TM7), "Ca. Parcubacteria" (OD1) and WPS-2 were represented in substantial quantities (10-20%). Heterotrophy and iron redox cycling can be considered as central processes of carbon and energy flow for majority of detected bacterial taxa. Archaea were detected in low numbers, with Terrestrial Miscellaneous Euryarchaeal Group (TMEG), to be most abundant (3%) in acidic spring Ulan-Bulak. Composition of these communities was found to be typical in comparison to other AMD sites; however, certain groups (as Ignavibacteriae) could be specifically associated with this area. This study provides insight into the microbial diversity patterns in acidic ecosystems formed in areas of polymetallic deposits in extreme continental climate zone with contrasting temperature parameters.
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Affiliation(s)
- Sergey N. Gavrilov
- Laboratory of Metabolism of Extremophiles, Winogradsky Institute of Microbiology, FRC Biotechnology, RAS, Moscow, Russia
| | - Aleksei A. Korzhenkov
- Laboratory of Bioinformatics, Genomics and Genome Editing, NRC Kurchatov Institute, Moscow, Russia
| | - Ilya V. Kublanov
- Laboratory of Metabolism of Extremophiles, Winogradsky Institute of Microbiology, FRC Biotechnology, RAS, Moscow, Russia
| | - Rafael Bargiela
- School of Natural Sciences, Bangor University, Bangor, United Kingdom
| | - Leonid V. Zamana
- Laboratory of Geoecology and Hydrogeochemistry, Institute of Natural Resources, Ecology and Cryology, SB RAS, Chita, Russia
| | - Alexandra A. Popova
- Laboratory of Metabolism of Extremophiles, Winogradsky Institute of Microbiology, FRC Biotechnology, RAS, Moscow, Russia
| | - Stepan V. Toshchakov
- Laboratory of Metabolism of Extremophiles, Winogradsky Institute of Microbiology, FRC Biotechnology, RAS, Moscow, Russia
| | - Peter N. Golyshin
- School of Natural Sciences, Bangor University, Bangor, United Kingdom
- Centre for Environmental Biotechnology, Bangor University, Bangor, United Kingdom
| | - Olga V. Golyshina
- School of Natural Sciences, Bangor University, Bangor, United Kingdom
- Centre for Environmental Biotechnology, Bangor University, Bangor, United Kingdom
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32
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Bomberg M, Claesson Liljedahl L, Lamminmäki T, Kontula A. Highly Diverse Aquatic Microbial Communities Separated by Permafrost in Greenland Show Distinct Features According to Environmental Niches. Front Microbiol 2019; 10:1583. [PMID: 31354674 PMCID: PMC6637822 DOI: 10.3389/fmicb.2019.01583] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2019] [Accepted: 06/25/2019] [Indexed: 11/13/2022] Open
Abstract
The Greenland Analog Project (GAP) study area in the vicinity of Kangarlussuaq, Western Greenland, was sampled for surface water and deep groundwater in order to determine the composition and estimate the metabolic features of the microbial communities in water bodies separated by permafrost. The sampling sites comprised a freshwater pond, talik lake, deep anoxic groundwater, glacier ice and supraglacial river, meltwater river and melting permafrost active layer. The microbial communities were characterized by amplicon sequencing of the bacterial and archaeal 16S rRNA genes and fungal ITS1 spacer. In addition, bacterial, archaeal and fungal numbers were determined by qPCR and plate counts, and the utilization pattern of carbon and nitrogen substrates was determined with Biolog AN plates and metabolic functions were predicted with FAPROTAX. Different sample types were clearly distinguishable from each other based on community composition, microbial numbers, and substrate utilization patterns, forming four groups, (1) pond/lake, (2) deep groundwater, (3) glacial ice, and (4) meltwater. Bacteria were the most abundant microbial domain, ranging from 0.2–1.4 × 107 16S rRNA gene copies mL-1 in pond/lake and meltwater, 0.1-7.8 × 106 copies mL-1 in groundwater and less than 104 copies mL-1 in ice. The number of archaeal 16S and fungal 5.8S rRNA genes was generally less than 6.0 × 103 and 1.5 × 103, respectively. N2-fixing and methane-oxidizing Actinomycetes, Bacteroidetes and Verrucomicrobia were the dominant microorganisms in the pond/lake samples, whereas iron reducing Desulfosporosinus sp. dominated the deep anaerobic groundwater. The glacial ice was inhabited by Cyanobacteria, which were mostly Chloroplast-like. The meltwater contained methano- and methylotrophic Proteobacteria, but had also high relative abundances of the nano-sized Parcubacteria. The archaea composed approximately 1% of the 16S rRNA gene pool in the pond/lake samples with nano-sized Woesearchaeota as the dominating taxon, while in the other sample types archaea were almost negligent. Fungi were also most common in the pond/lake communities, were zoospore-forming Chytridiomycetes dominated. Our results show highly diverse microbial communities inhabiting the different cold Greenlandic aqueous environments and show clear segregation of the microbial communities according to habitat, with distinctive dominating metabolic features specifically inhabiting defined environmental niches and a high relative abundance of putatively parasitic or symbiotic nano-sized taxa.
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Affiliation(s)
- Malin Bomberg
- VTT Technical Research Centre of Finland Ltd., Espoo, Finland
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Herrmann M, Wegner CE, Taubert M, Geesink P, Lehmann K, Yan L, Lehmann R, Totsche KU, Küsel K. Predominance of Cand. Patescibacteria in Groundwater Is Caused by Their Preferential Mobilization From Soils and Flourishing Under Oligotrophic Conditions. Front Microbiol 2019; 10:1407. [PMID: 31281301 PMCID: PMC6596338 DOI: 10.3389/fmicb.2019.01407] [Citation(s) in RCA: 104] [Impact Index Per Article: 20.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2019] [Accepted: 06/04/2019] [Indexed: 11/13/2022] Open
Abstract
Despite the widely observed predominance of Cand. Patescibacteria in subsurface communities, their input source and ecophysiology are poorly understood. Here we study mechanisms of the formation of a groundwater microbiome and the subsequent differentiation of Cand. Patescibacteria. In the Hainich Critical Zone Exploratory, Germany, we trace the input of microorganisms from forested soils of preferential recharge areas through fractured aquifers along a 5.4 km hillslope well transect. Cand. Patescibacteria were preferentially mobilized from soils and constituted 66% of species-level OTUs shared between seepage and shallow groundwater. These OTUs, mostly related to Cand. Kaiserbacteraceae, Cand. Nomurabacteraceae, and unclassified UBA9983 at the family level, represented a relative abundance of 71.4% of the Cand. Patescibacteria community at the shallowest groundwater well, and still 44.4% at the end of the transect. Several Cand. Patescibacteria subclass-level groups exhibited preferences for different conditions in the two aquifer assemblages investigated: Cand. Kaiserbacteraceae surprisingly showed positive correlations with oxygen concentrations, while Cand. Nomurabacteraceae were negatively correlated. Co-occurrence network analysis revealed a central role of Cand. Patescibacteria in the groundwater microbial communities and pointed to potential associations with specific organisms, including abundant autotrophic taxa involved in nitrogen, sulfur and iron cycling. Strong associations among Cand. Patescibacteria themselves further suggested that for many groups within this phylum, distribution was mainly driven by conditions commonly supporting a fermentative life style without direct dependence on specific hosts. We propose that import from soil, and community differentiation driven by hydrochemical conditions, including the availability of organic resources and potential hosts, determine the success of Cand. Patescibacteria in groundwater environments.
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Affiliation(s)
- Martina Herrmann
- Aquatic Geomicrobiology, Institute of Biodiversity, Friedrich Schiller University Jena, Jena, Germany.,German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany
| | - Carl-Eric Wegner
- Aquatic Geomicrobiology, Institute of Biodiversity, Friedrich Schiller University Jena, Jena, Germany
| | - Martin Taubert
- Aquatic Geomicrobiology, Institute of Biodiversity, Friedrich Schiller University Jena, Jena, Germany
| | - Patricia Geesink
- Aquatic Geomicrobiology, Institute of Biodiversity, Friedrich Schiller University Jena, Jena, Germany
| | - Katharina Lehmann
- Hydrogeology, Institute of Geosciences, Friedrich Schiller University Jena, Jena, Germany
| | - Lijuan Yan
- Aquatic Geomicrobiology, Institute of Biodiversity, Friedrich Schiller University Jena, Jena, Germany.,German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany
| | - Robert Lehmann
- Hydrogeology, Institute of Geosciences, Friedrich Schiller University Jena, Jena, Germany
| | - Kai Uwe Totsche
- Hydrogeology, Institute of Geosciences, Friedrich Schiller University Jena, Jena, Germany
| | - Kirsten Küsel
- Aquatic Geomicrobiology, Institute of Biodiversity, Friedrich Schiller University Jena, Jena, Germany.,German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany
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Lu C, Li C, Gan Q, Zhao Y, Liu C, Gu Q, Zhu T, Zhang G, Che Q, Li D. Phomanones A-C From Phoma sp. HDN16-618: A Mariana Trench Fungus. Nat Prod Commun 2019. [DOI: 10.1177/1934578x19858813] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Three new compounds, phomanones A-C (1-3), and a known compound, 2-hydroxymethyl-3-methylcyclopent-2-enone (4), were isolated from Phoma sp. HDN16-618, a fungus derived from a sea water sample collected from Mariana Trench. Their structures, including absolute configurations, were elucidated by extensive Nuclear Magnetic Resonance (NMR), Mass Spectrometry (MS), and electronic circular dichroism analyses. None of the compounds showed significant cytotoxic activity against a panel of cancer cell lines.
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Affiliation(s)
- Changjun Lu
- School of Medicine and Pharmacy, Ocean University of China, Qingdao, People’s Republic of China
| | - Changlong Li
- School of Medicine and Pharmacy, Ocean University of China, Qingdao, People’s Republic of China
| | - Qi Gan
- School of Medicine and Pharmacy, Ocean University of China, Qingdao, People’s Republic of China
| | - Yi Zhao
- School of Medicine and Pharmacy, Ocean University of China, Qingdao, People’s Republic of China
| | - Congcong Liu
- School of Medicine and Pharmacy, Ocean University of China, Qingdao, People’s Republic of China
| | - Qianqun Gu
- School of Medicine and Pharmacy, Ocean University of China, Qingdao, People’s Republic of China
| | - Tianjiao Zhu
- School of Medicine and Pharmacy, Ocean University of China, Qingdao, People’s Republic of China
| | - Guojian Zhang
- School of Medicine and Pharmacy, Ocean University of China, Qingdao, People’s Republic of China
- Laboratory for Marine Drugs and Bioproducts of Qingdao National Laboratory for Marine Science and Technology, Qingdao, People’s Republic of China
| | - Qian Che
- School of Medicine and Pharmacy, Ocean University of China, Qingdao, People’s Republic of China
| | - Dehai Li
- School of Medicine and Pharmacy, Ocean University of China, Qingdao, People’s Republic of China
- Laboratory for Marine Drugs and Bioproducts of Qingdao National Laboratory for Marine Science and Technology, Qingdao, People’s Republic of China
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Peoples LM, Grammatopoulou E, Pombrol M, Xu X, Osuntokun O, Blanton J, Allen EE, Nunnally CC, Drazen JC, Mayor DJ, Bartlett DH. Microbial Community Diversity Within Sediments from Two Geographically Separated Hadal Trenches. Front Microbiol 2019; 10:347. [PMID: 30930856 PMCID: PMC6428765 DOI: 10.3389/fmicb.2019.00347] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2018] [Accepted: 02/11/2019] [Indexed: 11/13/2022] Open
Abstract
Hadal ocean sediments, found at sites deeper than 6,000 m water depth, are thought to contain microbial communities distinct from those at shallower depths due to high hydrostatic pressures and higher abundances of organic matter. These communities may also differ from one other as a result of geographical isolation. Here we compare microbial community composition in surficial sediments of two hadal environments—the Mariana and Kermadec trenches—to evaluate microbial biogeography at hadal depths. Sediment microbial consortia were distinct between trenches, with higher relative sequence abundances of taxa previously correlated with organic matter degradation present in the Kermadec Trench. In contrast, the Mariana Trench, and deeper sediments in both trenches, were enriched in taxa predicted to break down recalcitrant material and contained other uncharacterized lineages. At the 97% similarity level, sequence-abundant taxa were not trench-specific and were related to those found in other hadal and abyssal habitats, indicating potential connectivity between geographically isolated sediments. Despite the diversity of microorganisms identified using culture-independent techniques, most isolates obtained under in situ pressures were related to previously identified piezophiles. Members related to these same taxa also became dominant community members when native sediments were incubated under static, long-term, unamended high-pressure conditions. Our results support the hypothesis that there is connectivity between sediment microbial populations inhabiting the Mariana and Kermadec trenches while showing that both whole communities and specific microbial lineages vary between trench of collection and sediment horizon depth. This in situ biodiversity is largely missed when incubating samples within pressure vessels and highlights the need for revised protocols for high-pressure incubations.
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Affiliation(s)
- Logan M Peoples
- Marine Biology Research Division, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, United States
| | - Eleanna Grammatopoulou
- Oceanlab, The Institute of Biological and Environmental Sciences, King's College, The University of Aberdeen, Aberdeen, United Kingdom
| | - Michelle Pombrol
- Marine Biology Research Division, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, United States
| | - Xiaoxiong Xu
- Marine Biology Research Division, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, United States
| | - Oladayo Osuntokun
- Marine Biology Research Division, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, United States
| | - Jessica Blanton
- Marine Biology Research Division, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, United States
| | - Eric E Allen
- Marine Biology Research Division, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, United States
| | - Clifton C Nunnally
- Louisiana Universities Marine Consortium (LUMCON), Chauvin, LA, United States
| | - Jeffrey C Drazen
- Department of Oceanography, University of Hawai'i at Ma-noa, Honolulu, HI, United States
| | - Daniel J Mayor
- Oceanlab, The Institute of Biological and Environmental Sciences, King's College, The University of Aberdeen, Aberdeen, United Kingdom.,National Oceanography Centre, University of Southampton Waterfront Campus European Way, Southampton, United Kingdom
| | - Douglas H Bartlett
- Marine Biology Research Division, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, United States
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Song M, Luo C, Jiang L, Peng K, Zhang D, Zhang R, Li Y, Zhang G. The presence of in situ sulphamethoxazole degraders and their interactions with other microbes in activated sludge as revealed by DNA stable isotope probing and molecular ecological network analysis. ENVIRONMENT INTERNATIONAL 2019; 124:121-129. [PMID: 30641255 DOI: 10.1016/j.envint.2018.12.039] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/19/2018] [Revised: 12/15/2018] [Accepted: 12/17/2018] [Indexed: 06/09/2023]
Abstract
Wastewater treatment plants (WWTPs) are the main hotspots for the release of antibiotics, including the widely used sulphonamides. Microbes play important roles in eliminating sulphonamides in WWTPs, and knowledge about these degraders and their interactions within the microbial community is crucial for operating and optimising WWTPs. In the present study, stable isotope probing (SIP) coupled with high-throughput sequencing as culture-independent approach revealed four operational taxonomic units (OTUs) involved in sulphamethoxazole (SMX) degradation in activated sludge. Except for the OTU affiliated with Gammaproteobacteria, the others have not been previously reported to possess the ability to metabolise SMX. The isolated SMX degrader by culture-dependent method did not participate in SMX biodegradation in situ according to the SIP analysis, and showed weak correlations with other members in the activated sludge. The complex interactions between in situ active SMX degraders and non-degrading microbes might explain our failure to isolate these degraders. In addition, sul1 genes associated with SMX resistance were also labelled with 13C, suggesting that they might benefit from SMX degradation and/or originate from the active SMX degraders. These findings broaden our understanding of the diversity of SMX-degrading microbes and their associated characteristics in WWTPs.
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Affiliation(s)
- Mengke Song
- College of Natural Resources and Environment, South China Agricultural University, Guangzhou 510642, China; Joint Institute for Environmental Research and Education, South China Agricultural University, Guangzhou 510642, China
| | - Chunling Luo
- Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou 510640, China; Joint Institute for Environmental Research and Education, South China Agricultural University, Guangzhou 510642, China.
| | - Longfei Jiang
- Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou 510640, China
| | - Ke Peng
- College of Natural Resources and Environment, South China Agricultural University, Guangzhou 510642, China
| | - Dayi Zhang
- School of Environment, Tsinghua University, Beijing 100084, China
| | - Ruijie Zhang
- School of Marine Sciences, Guangxi University, Nanning 530004, China
| | - Yongtao Li
- College of Natural Resources and Environment, South China Agricultural University, Guangzhou 510642, China; Joint Institute for Environmental Research and Education, South China Agricultural University, Guangzhou 510642, China
| | - Gan Zhang
- Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou 510640, China
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37
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Zhang X, Xu W, Liu Y, Cai M, Luo Z, Li M. Metagenomics Reveals Microbial Diversity and Metabolic Potentials of Seawater and Surface Sediment From a Hadal Biosphere at the Yap Trench. Front Microbiol 2018; 9:2402. [PMID: 30369913 PMCID: PMC6194347 DOI: 10.3389/fmicb.2018.02402] [Citation(s) in RCA: 58] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2018] [Accepted: 09/19/2018] [Indexed: 11/13/2022] Open
Abstract
Hadal biosphere represents the deepest part of the ocean with water depth >6,000 m. Accumulating evidence suggests the existence of unique microbial communities dominated by heterotrophic processes in this environment. However, investigations of the microbial diversity and their metabolic potentials are limited because of technical constraints for sample collection. Here, we provide a detailed metagenomic analysis of three seawater samples at water depths 5,000-6,000 m below sea level (mbsl) and three surface sediment samples at water depths 4,435-6,578 mbsl at the Yap Trench of the western Pacific. Distinct microbial community compositions were observed with the dominance of Gammaproteobacteria in seawater and Thaumarchaeota in surface sediment. Comparative analysis of the genes involved in carbon, nitrogen and sulfur metabolisms revealed that heterotrophic processes (i.e., degradation of carbohydrates, hydrocarbons, and aromatics) are the most common microbial metabolisms in the seawater, while chemolithoautotrophic metabolisms such as ammonia oxidation with the HP/HB cycle for CO2 fixation probably dominated the surface sediment communities of the Yap Trench. Furthermore, abundant genes involved in stress response and metal resistance were both detected in the seawater and sediments, thus the enrichment of metal resistance genes is further hypothesized to be characteristic of the hadal microbial communities. Overall, this study sheds light on the metabolic versatility of microorganisms in the Yap Trench, their roles in carbon, nitrogen, and sulfur biogeochemical cycles, and how they have adapted to this unique hadal environment.
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Affiliation(s)
- Xinxu Zhang
- Institute for Advanced Study, Shenzhen University, Shenzhen, China
| | - Wei Xu
- Key Laboratory of Marine Biogenetic Resources, Third Institute of Oceanography, State Oceanic Administration, Xiamen, China
| | - Yang Liu
- Institute for Advanced Study, Shenzhen University, Shenzhen, China
| | - Mingwei Cai
- Institute for Advanced Study, Shenzhen University, Shenzhen, China
| | - Zhuhua Luo
- Key Laboratory of Marine Biogenetic Resources, Third Institute of Oceanography, State Oceanic Administration, Xiamen, China
| | - Meng Li
- Institute for Advanced Study, Shenzhen University, Shenzhen, China
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38
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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: 81] [Impact Index Per Article: 13.5] [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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Nunoura T, Nishizawa M, Hirai M, Shimamura S, Harnvoravongchai P, Koide O, Morono Y, Fukui T, Inagaki F, Miyazaki J, Takaki Y, Takai K. Microbial Diversity in Sediments from the Bottom of the Challenger Deep, the Mariana Trench. Microbes Environ 2018; 33:186-194. [PMID: 29806625 PMCID: PMC6031389 DOI: 10.1264/jsme2.me17194] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
The Challenger Deep is the deepest ocean on Earth. The present study investigated microbial community structures and geochemical cycles associated with the trench bottom sediments of the Challenger Deep, the Mariana Trench. The SSU rRNA gene communities found in trench bottom sediments were dominated by the bacteria Chloroflexi (SAR202 and other lineages), Bacteroidetes, Planctomycetes, "Ca. Marinimicrobia" (SAR406), and Gemmatimonadetes and by the archaeal α subgroup of MGI Thaumarchaeota and "Ca. Woesearchaeota" (Deep-sea Hydrothermal Vent Euryarchaeotic Group 6). The SSU rRNA gene sequencing analysis indicated that the dominant populations of the thaumarchaeal α group in hadal water and sediments were similar to each other at the species or genus level. In addition, the co-occurrence of nitrification and denitrification was revealed by the combination of pore water geochemical analyses and quantitative PCR for nitrifiers.
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Affiliation(s)
- Takuro Nunoura
- Research and Development Center for Marine Biosciences, Japan Agency for Marine-Earth Science and Technology (JAMSTEC)
| | - Manabu Nishizawa
- Department of Subsurface Geobiological Analysis and Research, Japan Agency for Marine-Earth Science and Technology (JAMSTEC)
| | - Miho Hirai
- Research and Development Center for Marine Biosciences, Japan Agency for Marine-Earth Science and Technology (JAMSTEC)
| | - Shigeru Shimamura
- Department of Subsurface Geobiological Analysis and Research, Japan Agency for Marine-Earth Science and Technology (JAMSTEC)
| | | | - Osamu Koide
- Research and Development Center for Marine Biosciences, Japan Agency for Marine-Earth Science and Technology (JAMSTEC)
| | - Yuki Morono
- Geomicrobiology Group, Kochi Institute for Core Sample Research, Japan Agency for Marine-Earth Science Technology (JAMSTEC).,Geobiotechnology Group, Research and Development Center for Submarine Resources, Japan Agency for Marine-Earth Science Technology (JAMSTEC)
| | - Toshiaki Fukui
- School of Life Science and Technology, Tokyo Institute of Technology
| | - Fumio Inagaki
- Geomicrobiology Group, Kochi Institute for Core Sample Research, Japan Agency for Marine-Earth Science Technology (JAMSTEC).,Geobiotechnology Group, Research and Development Center for Submarine Resources, Japan Agency for Marine-Earth Science Technology (JAMSTEC).,Research and Development Center for Ocean Drilling Science, Japan Agency for Marine-Earth Science Technology (JAMSTEC)
| | - Junichi Miyazaki
- Department of Subsurface Geobiological Analysis and Research, Japan Agency for Marine-Earth Science and Technology (JAMSTEC)
| | - Yoshihiro Takaki
- Research and Development Center for Marine Biosciences, Japan Agency for Marine-Earth Science and Technology (JAMSTEC).,Department of Subsurface Geobiological Analysis and Research, Japan Agency for Marine-Earth Science and Technology (JAMSTEC)
| | - Ken Takai
- Department of Subsurface Geobiological Analysis and Research, Japan Agency for Marine-Earth Science and Technology (JAMSTEC)
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40
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Danczak RE, Johnston MD, Kenah C, Slattery M, Wrighton KC, Wilkins MJ. Members of the Candidate Phyla Radiation are functionally differentiated by carbon- and nitrogen-cycling capabilities. MICROBIOME 2017; 5:112. [PMID: 28865481 PMCID: PMC5581439 DOI: 10.1186/s40168-017-0331-1] [Citation(s) in RCA: 74] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/11/2017] [Accepted: 08/23/2017] [Indexed: 05/20/2023]
Abstract
BACKGROUND The Candidate Phyla Radiation (CPR) is a recently described expansion of the tree of life that represents more than 15% of all bacterial diversity and potentially contains over 70 different phyla. Despite this broad phylogenetic variation, these microorganisms appear to feature little functional diversity, with members generally characterized as obligate fermenters. Additionally, much of the data describing CPR phyla has been generated from a limited number of environments, constraining our knowledge of their functional roles and biogeographical distribution. To expand our understanding of subsurface CPR microorganisms, we sampled four separate groundwater wells over 2 years across three Ohio counties. RESULTS Samples were analyzed using 16S rRNA gene amplicon and shotgun metagenomic sequencing. Amplicon results indicated that CPR members comprised between 2 and 20% of the microbial communities with relative abundances stable through time in Athens and Greene samples but dynamic in Licking groundwater. Shotgun metagenomic analyses generated 71 putative CPR genomes, representing roughly 32 known phyla and 2 putative new phyla, Candidatus Brownbacteria and Candidatus Hugbacteria. While these genomes largely mirrored metabolic characteristics of known CPR members, some features were previously uncharacterized. For instance, nitrite reductase, encoded by nirK, was found in four of our Parcubacteria genomes and multiple CPR genomes from other studies, indicating a potentially undescribed role for these microorganisms in denitrification. Additionally, glycoside hydrolase (GH) family profiles for our 71 genomes and over 2000 other CPR genomes were analyzed to characterize their carbon-processing potential. Although common trends were present throughout the radiation, differences highlighted potential mechanisms that could allow microorganisms across the CPR to occupy various subsurface niches. For example, members of the Microgenomates superphylum appear to potentially degrade a wider range of carbon substrates than other CPR phyla. CONCLUSIONS CPR members are present across a range of environments and often constitute a significant fraction of the microbial population in groundwater systems, particularly. Further sampling of such environments will resolve this portion of the tree of life at finer taxonomic levels, which is essential to solidify functional differences between members that populate this phylogenetically broad region of the tree of life.
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Affiliation(s)
- R E Danczak
- Department of Microbiology, The Ohio State University, Columbus, OH, USA
| | - M D Johnston
- School of Earth Sciences, The Ohio State University, Columbus, OH, USA
| | - C Kenah
- Ohio Environmental Protection Agency, Columbus, OH, USA
| | - M Slattery
- Ohio Environmental Protection Agency, Columbus, OH, USA
| | - K C Wrighton
- Department of Microbiology, The Ohio State University, Columbus, OH, USA
| | - M J Wilkins
- Department of Microbiology, The Ohio State University, Columbus, OH, USA.
- School of Earth Sciences, The Ohio State University, Columbus, OH, USA.
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