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Zou D, Zhang C, Liu Y, Li M. Biogeographical distribution and community assembly of Myxococcota in mangrove sediments. ENVIRONMENTAL MICROBIOME 2024; 19:47. [PMID: 39003484 PMCID: PMC11245791 DOI: 10.1186/s40793-024-00593-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/05/2024] [Accepted: 07/08/2024] [Indexed: 07/15/2024]
Abstract
BACKGROUND Myxococcota, characterized by their distinct social lifestyles, are widely distributed micro-predators in global sediments. They can feed on a wide range of bacterial, archaeal, and fungal prey. Myxococcota are capable of producing diverse secondary metabolites, playing key roles in microbial food webs, and regulating the microbial community structures in different ecosystems. However, Myxococcota are rarely pure cultured due to the challenging and stringent culturing conditions. Their natural distribution, niche differentiation, and predator-prey relationships in a specific habitat are poorly understood. RESULTS In this study, we conducted a comprehensive analysis of the 16S rRNA gene sequence data from public databases and our collection. We compared the abundance, diversity, and distribution patterns of Myxococcota in various habitats, with a specific focus on mangroves. We found that Myxococcota accounted for 1.45% of the total prokaryotes in global sediments based on the abundance of 16S rRNA genes. Myxococcota are abundant and diverse in mangrove sediments. They tend to be more generalistic in mangroves than in other habitats due to their wide niche breadth. Besides, the deterministic processes (variable selection) influenced the assembly of mangrove Myxococcota communities significantly more than stochastic processes. Further, we determined that environmental factors explained a greater amount of total community variation in mangrove Myxococcota than geographical variables (latitude and sediment depth). In the end, through the analysis of microbial co-occurrence networks, Myxococcota emerges as a key component and functions as a connector in the mangrove microbial community. CONCLUSIONS Our study enhances comprehension of mangrove Myxococcota's biogeography, assembly patterns, driving factors, and co-occurrence relationships, as well as highlights their unique niche and ecological importance in mangrove sediments.
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Affiliation(s)
- Dayu Zou
- Archaeal Biology Center, Institute for Advanced Study, Shenzhen University, Shenzhen, 518060, China
- Institute for Advanced Study, Shenzhen Key Laboratory of Marine Microbiome Engineering, Shenzhen University, Shenzhen, 518060, China
- Synthetic Biology Research Center, Shenzhen University, Shenzhen, 518060, China
| | - Cuijing Zhang
- Archaeal Biology Center, Institute for Advanced Study, Shenzhen University, Shenzhen, 518060, China
- Institute for Advanced Study, Shenzhen Key Laboratory of Marine Microbiome Engineering, Shenzhen University, Shenzhen, 518060, China
- Synthetic Biology Research Center, Shenzhen University, Shenzhen, 518060, China
| | - Yang Liu
- Archaeal Biology Center, Institute for Advanced Study, Shenzhen University, Shenzhen, 518060, China.
- Institute for Advanced Study, Shenzhen Key Laboratory of Marine Microbiome Engineering, Shenzhen University, Shenzhen, 518060, China.
- Synthetic Biology Research Center, Shenzhen University, Shenzhen, 518060, China.
| | - Meng Li
- Archaeal Biology Center, Institute for Advanced Study, Shenzhen University, Shenzhen, 518060, China.
- Institute for Advanced Study, Shenzhen Key Laboratory of Marine Microbiome Engineering, Shenzhen University, Shenzhen, 518060, China.
- Synthetic Biology Research Center, Shenzhen University, Shenzhen, 518060, China.
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Imachi H, Nobu MK, Kato S, Takaki Y, Miyazaki M, Miyata M, Ogawara M, Saito Y, Sakai S, Tahara YO, Takano Y, Tasumi E, Uematsu K, Yoshimura T, Itoh T, Ohkuma M, Takai K. Promethearchaeum syntrophicum gen. nov., sp. nov., an anaerobic, obligately syntrophic archaeon, the first isolate of the lineage 'Asgard' archaea, and proposal of the new archaeal phylum Promethearchaeota phyl. nov. and kingdom Promethearchaeati regn. nov. Int J Syst Evol Microbiol 2024; 74:006435. [PMID: 38967634 PMCID: PMC11316595 DOI: 10.1099/ijsem.0.006435] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2024] [Accepted: 06/12/2024] [Indexed: 07/06/2024] Open
Abstract
An anaerobic, mesophilic, syntrophic, archaeon strain MK-D1T, was isolated as a pure co-culture with Methanogenium sp. strain MK-MG from deep-sea methane seep sediment. This organism is, to our knowledge, the first cultured representative of 'Asgard' archaea, an archaeal group closely related to eukaryotes. Here, we describe the detailed physiology and phylogeny of MK-D1T and propose Promethearchaeum syntrophicum gen. nov., sp. nov. to accommodate this strain. Cells were non-motile, small cocci, approximately 300-750 nm in diameter and produced membrane vesicles, chains of blebs and membrane-based protrusions. MK-D1T grew at 4-30 °C with optimum growth at 20 °C. The strain grew chemoorganotrophically with amino acids, peptides and yeast extract with obligate dependence on syntrophy with H2-/formate-utilizing organisms. MK-D1T showed the fastest growth and highest maximum cell yield when grown with yeast extract as the substrate: approximately 3 months to full growth, reaching up to 6.7×106 16S rRNA gene copies ml-1. MK-D1T had a circular 4.32 Mb chromosome with a DNA G+C content of 31.1 mol%. The results of phylogenetic analyses of the 16S rRNA gene and conserved marker proteins indicated that the strain is affiliated with 'Asgard' archaea and more specifically DHVC1/DSAG/MBG-B and 'Lokiarchaeota'/'Lokiarchaeia'. On the basis of the results of 16S rRNA gene sequence analysis, the most closely related isolated relatives were Infirmifilum lucidum 3507LTT (76.09 %) and Methanothermobacter tenebrarum RMAST (77.45 %) and the closest relative in enrichment culture was Candidatus 'Lokiarchaeum ossiferum' (95.39 %). The type strain of the type species is MK-D1T (JCM 39240T and JAMSTEC no. 115508). We propose the associated family, order, class, phylum, and kingdom as Promethearchaeaceae fam. nov., Promethearchaeales ord. nov., Promethearchaeia class. nov., Promethearchaeota phyl. nov., and Promethearchaeati regn. nov., respectively. These are in accordance with ICNP Rules 8 and 22 for nomenclature, Rule 30(3)(b) for validation and maintenance of the type strain, and Rule 31a for description as a member of an unambiguous syntrophic association.
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Affiliation(s)
- Hiroyuki Imachi
- Institute for Extra-cutting-edge Science and Technology Avant-garde Research (X-star), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Japan
| | - Masaru K. Nobu
- Institute for Extra-cutting-edge Science and Technology Avant-garde Research (X-star), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Japan
| | - Shingo Kato
- Japan Collection of Microorganisms (JCM), RIKEN BioResource Research Center, Tsukuba, Japan
- Submarine Resources Research Center, JAMSTEC, Yokosuka, Japan
| | - Yoshihiro Takaki
- Institute for Extra-cutting-edge Science and Technology Avant-garde Research (X-star), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Japan
| | - Masayuki Miyazaki
- Institute for Extra-cutting-edge Science and Technology Avant-garde Research (X-star), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Japan
| | - Makoto Miyata
- Graduate School of Science, Osaka Metropolitan University, Osaka, Japan
| | - Miyuki Ogawara
- Institute for Extra-cutting-edge Science and Technology Avant-garde Research (X-star), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Japan
| | - Yumi Saito
- Institute for Extra-cutting-edge Science and Technology Avant-garde Research (X-star), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Japan
| | - Sanae Sakai
- Institute for Extra-cutting-edge Science and Technology Avant-garde Research (X-star), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Japan
| | - Yuhei O. Tahara
- Graduate School of Science, Osaka Metropolitan University, Osaka, Japan
| | | | - Eiji Tasumi
- Institute for Extra-cutting-edge Science and Technology Avant-garde Research (X-star), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Japan
| | - Katsuyuki Uematsu
- Department of Marine and Earth Sciences, Marine Work Japan, Yokosuka, Japan
| | | | - Takashi Itoh
- Japan Collection of Microorganisms (JCM), RIKEN BioResource Research Center, Tsukuba, Japan
| | - Moriya Ohkuma
- Japan Collection of Microorganisms (JCM), RIKEN BioResource Research Center, Tsukuba, Japan
| | - Ken Takai
- Institute for Extra-cutting-edge Science and Technology Avant-garde Research (X-star), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Japan
- Section for Exploration of Life in Extreme Environments, Exploratory Research Center on Life and Living Systems (ExCELLS), National Institute of Natural Sciences, Okazaki, Japan
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3
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Imachi H, Nobu MK, Miyazaki M, Tasumi E, Saito Y, Sakai S, Ogawara M, Ohashi A, Takai K. Cultivation of previously uncultured microorganisms with a continuous-flow down-flow hanging sponge (DHS) bioreactor, using a syntrophic archaeon culture obtained from deep marine sediment as a case study. Nat Protoc 2022; 17:2784-2814. [DOI: 10.1038/s41596-022-00735-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Accepted: 06/14/2022] [Indexed: 11/09/2022]
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Wegener G, Laso-Pérez R, Orphan VJ, Boetius A. Anaerobic Degradation of Alkanes by Marine Archaea. Annu Rev Microbiol 2022; 76:553-577. [PMID: 35917471 DOI: 10.1146/annurev-micro-111021-045911] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Alkanes are saturated apolar hydrocarbons that range from its simplest form, methane, to high-molecular-weight compounds. Although alkanes were once considered biologically recalcitrant under anaerobic conditions, microbiological investigations have now identified several microbial taxa that can anaerobically degrade alkanes. Here we review recent discoveries in the anaerobic oxidation of alkanes with a specific focus on archaea that use specific methyl coenzyme M reductases to activate their substrates. Our understanding of the diversity of uncultured alkane-oxidizing archaea has expanded through the use of environmental metagenomics and enrichment cultures of syntrophic methane-, ethane-, propane-, and butane-oxidizing marine archaea with sulfate-reducing bacteria. A recently cultured group of archaea directly couples long-chain alkane degradation with methane formation, expanding the range of substrates used for methanogenesis. This article summarizes the rapidly growing knowledge of the diversity, physiology, and habitat distribution of alkane-degrading archaea. Expected final online publication date for the Annual Review of Microbiology, Volume 76 is September 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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Affiliation(s)
- Gunter Wegener
- MARUM, Center for Marine Environmental Sciences, University Bremen, Bremen, Germany; , .,Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Rafael Laso-Pérez
- MARUM, Center for Marine Environmental Sciences, University Bremen, Bremen, Germany; , .,Max Planck Institute for Marine Microbiology, Bremen, Germany.,Current affiliation: Systems Biology Department, Centro Nacional de Biotecnología (CNB-CSIC), Madrid, Spain
| | - Victoria J Orphan
- MARUM, Center for Marine Environmental Sciences, University Bremen, Bremen, Germany; , .,Division of Geological and Planetary Sciences and Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California, USA;
| | - Antje Boetius
- MARUM, Center for Marine Environmental Sciences, University Bremen, Bremen, Germany; , .,Max Planck Institute for Marine Microbiology, Bremen, Germany.,Helmholtz Center for Polar and Marine Research, Bremerhaven, Germany;
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5
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Feng JC, Yan J, Wang Y, Yang Z, Zhang S, Liang S, Li XS. Methane mitigation: Learning from the natural marine environment. Innovation (N Y) 2022; 3:100297. [PMID: 36051819 PMCID: PMC9425072 DOI: 10.1016/j.xinn.2022.100297] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Accepted: 08/01/2022] [Indexed: 11/19/2022] Open
Affiliation(s)
- Jing-Chun Feng
- School of Ecology, Environment and Resources, Guangdong University of Technology, Guangzhou 510006, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 511458, China
- Corresponding author
| | - Jinyue Yan
- Future Energy Center, School of Business, Society and Engineering, Mälardalen University, SE-721 23 Västerås, Sweden
| | - Yi Wang
- Key Laboratory of Gas Hydrate, Guangzhou Institute of Energy Conversion, Chinese Academy of Sciences, Guangzhou 510640, China
- Corresponding author
| | - Zhifeng Yang
- School of Ecology, Environment and Resources, Guangdong University of Technology, Guangzhou 510006, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 511458, China
| | - Si Zhang
- School of Ecology, Environment and Resources, Guangdong University of Technology, Guangzhou 510006, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 511458, China
| | - Sai Liang
- School of Ecology, Environment and Resources, Guangdong University of Technology, Guangzhou 510006, China
| | - Xiao-Sen Li
- Key Laboratory of Gas Hydrate, Guangzhou Institute of Energy Conversion, Chinese Academy of Sciences, Guangzhou 510640, China
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6
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Community Structure and Microbial Associations in Sediment-Free Methanotrophic Enrichment Cultures from a Marine Methane Seep. Appl Environ Microbiol 2022; 88:e0210921. [PMID: 35604226 DOI: 10.1128/aem.02109-21] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Syntrophic consortia of anaerobic methanotrophic archaea (ANME) and sulfate-reducing bacteria (SRB) consume large amounts of methane and serve as the foundational microorganisms in marine methane seeps. Despite their importance in the carbon cycle, research on the physiology of ANME-SRB consortia has been hampered by the slow growth and complex physicochemical environment the consortia inhabit. Here, we report successful sediment-free enrichment of ANME-SRB consortia from deep-sea methane seep sediments in the Santa Monica Basin, California. Anoxic Percoll density gradients and size-selective filtration were used to separate ANME-SRB consortia from sediment particles and single cells to accelerate the cultivation process. Over a 3-year period, a subset of the sediment-associated ANME and SRB lineages, predominantly comprised of ANME-2a/2b ("Candidatus Methanocomedenaceae") and their syntrophic bacterial partners, SEEP-SRB1/2, adapted and grew under defined laboratory conditions. Metagenome-assembled genomes from several enrichments revealed that ANME-2a, SEEP-SRB1, and Methanococcoides in different enrichments from the same inoculum represented distinct species, whereas other coenriched microorganisms were closely related at the species level. This suggests that ANME, SRB, and Methanococcoides are more genetically diverse than other members in methane seeps. Flow cytometry sorting and sequencing of cell aggregates revealed that Methanococcoides, Anaerolineales, and SEEP-SRB1 were overrepresented in multiple ANME-2a cell aggregates relative to the bulk metagenomes, suggesting they were physically associated and possibly interacting. Overall, this study represents a successful case of selective cultivation of anaerobic slow-growing microorganisms from sediments based on their physical characteristics, introducing new opportunities for detailed genomic, physiological, biochemical, and ecological analyses. IMPORTANCE Biological anaerobic oxidation of methane (AOM) coupled with sulfate reduction represents a large methane sink in global ocean sediments. Methane consumption is carried out by syntrophic archaeal-bacterial consortia and fuels a unique ecosystem, yet the interactions in these slow-growing syntrophic consortia and with other associated community members remain poorly understood. The significance of this study is the establishment of sediment-free enrichment cultures of anaerobic methanotrophic archaea and sulfate-reducing bacteria performing AOM with sulfate using selective cultivation approaches based on size, density, and metabolism. By reconstructing microbial genomes and analyzing community composition of the enrichment cultures and cell aggregates, we shed light on the diversity of microorganisms physically associated with AOM consortia beyond the core syntrophic partners. These enrichment cultures offer simplified model systems to extend our understanding of the diversity of microbial interactions within marine methane seeps.
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7
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Watanabe M, Kojima H, Okano K, Fukui M. Mariniplasma anaerobium gen. nov., sp. nov., a novel anaerobic marine mollicute, and proposal of three novel genera to reclassify members of Acholeplasma clusters II-IV. Int J Syst Evol Microbiol 2021; 71. [PMID: 34874244 DOI: 10.1099/ijsem.0.005138] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A novel strictly anaerobic chemoorganotrophic bacterium, designated Mahy22T, was isolated from sulfidic bottom water of a shallow brackish meromictic lake in Japan. Cells of the strain were Gram-stain-negative, non-motile and coccoid in shape with diameters of about 600-800 nm. The temperature range for growth was 15-37 °C, with optimum growth at 30-32 °C. The pH range for growth was pH 6.2-8.9, with optimum growth at pH 7.2-7.4. The strain grew with NaCl concentrations of 5% or below (optimum, 2-3%). Growth of the strain was enhanced by the addition of thiosulfate. The major cellular fatty acids were C16:0 and anteiso-C15:0. Respiratory quinones were not detected. The complete genome sequence of strain Mahy22T possessed a 1 885 846 bp circular chromosome and a 12 782 bp circular genetic element. The G+C content of the genome sequence was 30.1 mol%. Phylogenetic analysis based on the 16S rRNA gene revealed that the novel strain belonged to the family Acholeplasmataceae, class Mollicutes. The closest relative of strain Mahy22T with a validly published name was Acholeplasma palmae J233T with a 16S rRNA gene sequence similarity of 90.5%. Based on the results of polyphasic analysis, the name Mariniplasma anaerobium gen. nov., sp. nov. is proposed to accommodate strain Mahy22T, along with reclassification of some Acholeplasma species into Alteracholeplasma gen. nov., Haploplasma gen. nov. and Paracholeplasma gen. nov.
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Affiliation(s)
- Miho Watanabe
- Institute of Low Temperature Science, Hokkaido University, Kita-19, Nishi-8, Kita-ku, Sapporo 060-0819, Japan.,Department of Biological Environment, Akita Prefectural University, Shimoshinjyo-Nakano, Akita 010-0195, Japan
| | - Hisaya Kojima
- Institute of Low Temperature Science, Hokkaido University, Kita-19, Nishi-8, Kita-ku, Sapporo 060-0819, Japan
| | - Kunihiro Okano
- Department of Biological Environment, Akita Prefectural University, Shimoshinjyo-Nakano, Akita 010-0195, Japan
| | - Manabu Fukui
- Institute of Low Temperature Science, Hokkaido University, Kita-19, Nishi-8, Kita-ku, Sapporo 060-0819, Japan
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8
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Li J, Chen X, Yang Z, Liu Z, Chen Y, Wang YE, Xie H. Denitrification performance and mechanism of sequencing batch reactor with a novel iron-polyurethane foam composite carrier. Biochem Eng J 2021. [DOI: 10.1016/j.bej.2021.108209] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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9
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Thorup C, Petro C, Bøggild A, Ebsen TS, Brokjær S, Nielsen LP, Schramm A, Bjerg JJ. How to grow your cable bacteria: Establishment of a stable single-strain culture in sediment and proposal of Candidatus Electronema aureum GS. Syst Appl Microbiol 2021; 44:126236. [PMID: 34332367 DOI: 10.1016/j.syapm.2021.126236] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Revised: 07/08/2021] [Accepted: 07/12/2021] [Indexed: 01/04/2023]
Abstract
Cable bacteria are multicellular filamentous bacteria within the Desulfobulbaceae that couple the oxidation of sulfide to the reduction of oxygen over centimeter distances via long distance electron transport (LDET). So far, none of the freshwater or marine cable bacteria species have been isolated into pure culture. Here we describe a method for establishing a stable single-strain cable bacterium culture in partially sterilized sediment. By repeated transfers of a single cable bacterium filament from freshwater pond sediment into autoclaved sediment, we obtained strain GS, identified by its 16S rRNA gene as a member of Ca. Electronema. This strain was further propagated by transferring sediment clumps, and has now been stable within its semi-natural microbial community for several years. Its metagenome-assembled genome was 93% complete, had a size of 2.76 Mbp, and a DNA G + C content of 52%. Average Nucleotide Identity (ANI) and Average Amino Acid Identity (AAI) suggest the affiliation of strain GS to Ca. Electronema as a novel species. Cell size, number of outer ridges, and detection of LDET in the GS culture are likewise consistent with Ca. Electronema. Based on these combined features, we therefore describe strain GS as a new cable bacterium species of the candidate genus Electronema, for which we propose the name Candidatus Electronema aureum sp.nov. Although not a pure culture, this stable single-strain culture will be useful for physiological and omics-based studies; similar approaches with single-cell or single-filament transfers into natural medium may also aid the characterization of other difficult-to-culture microbes.
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Affiliation(s)
- Casper Thorup
- Section for Microbiology, Department of Biology, Aarhus University, Denmark; Center for Electromicrobiology, Aarhus University, Denmark; Center for Geomicrobiology, Aarhus University, Denmark
| | - Caitlin Petro
- Section for Microbiology, Department of Biology, Aarhus University, Denmark; Center for Electromicrobiology, Aarhus University, Denmark; Center for Geomicrobiology, Aarhus University, Denmark
| | - Andreas Bøggild
- Department for Molecular Biology and Genetics, Aarhus University, Denmark
| | | | - Signe Brokjær
- Section for Microbiology, Department of Biology, Aarhus University, Denmark
| | - Lars Peter Nielsen
- Section for Microbiology, Department of Biology, Aarhus University, Denmark; Center for Electromicrobiology, Aarhus University, Denmark; Center for Geomicrobiology, Aarhus University, Denmark
| | - Andreas Schramm
- Section for Microbiology, Department of Biology, Aarhus University, Denmark; Center for Electromicrobiology, Aarhus University, Denmark; Center for Geomicrobiology, Aarhus University, Denmark.
| | - Jesper Jensen Bjerg
- Section for Microbiology, Department of Biology, Aarhus University, Denmark; Center for Electromicrobiology, Aarhus University, Denmark; Center for Geomicrobiology, Aarhus University, Denmark; ECOBE, Department of Biology, University of Antwerp, Belgium
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10
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Kerk D, Mattice JF, Valdés-Tresanco ME, Noskov SY, Ng KKS, Moorhead GB. The origin and radiation of the phosphoprotein phosphatase (PPP) enzymes of Eukaryotes. Sci Rep 2021; 11:13681. [PMID: 34211082 PMCID: PMC8249667 DOI: 10.1038/s41598-021-93206-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Accepted: 06/22/2021] [Indexed: 11/18/2022] Open
Abstract
Phosphoprotein phosphatase (PPP) enzymes are ubiquitous proteins involved in cellular signaling pathways and other functions. Here we have traced the origin of the PPP sequences of Eukaryotes and their radiation. Using a bacterial PPP Hidden Markov Model (HMM) we uncovered "BacterialPPP-Like" sequences in Archaea. A HMM derived from eukaryotic PPP enzymes revealed additional, unique sequences in Archaea and Bacteria that were more like the eukaryotic PPP enzymes then the bacterial PPPs. These sequences formed the basis of phylogenetic tree inference and sequence structural analysis allowing the history of these sequence types to be elucidated. Our phylogenetic tree data strongly suggest that eukaryotic PPPs ultimately arose from ancestors in the Asgard archaea. We have clarified the radiation of PPPs within Eukaryotes, substantially expanding the range of known organisms with PPP subtypes (Bsu1, PP7, PPEF/RdgC) previously thought to have a more restricted distribution. Surprisingly, sequences from the Methanosarcinaceae (Euryarchaeota) form a strongly supported sister group to eukaryotic PPPs in our phylogenetic analysis. This strongly suggests an intimate association between an Asgard ancestor and that of the Methanosarcinaceae. This is highly reminiscent of the syntrophic association recently demonstrated between the cultured Lokiarchaeal species Prometheoarchaeum and a methanogenic bacterial species.
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Affiliation(s)
- David Kerk
- Department of Biological Sciences, University of Calgary, 2500 University Dr. NW, Calgary, AB, T2N 1N4, Canada
| | - Jordan F Mattice
- Department of Biological Sciences, University of Calgary, 2500 University Dr. NW, Calgary, AB, T2N 1N4, Canada
| | - Mario E Valdés-Tresanco
- Department of Biological Sciences, University of Calgary, 2500 University Dr. NW, Calgary, AB, T2N 1N4, Canada
| | - Sergei Yu Noskov
- Department of Biological Sciences, University of Calgary, 2500 University Dr. NW, Calgary, AB, T2N 1N4, Canada
| | - Kenneth K-S Ng
- Department of Biological Sciences, University of Calgary, 2500 University Dr. NW, Calgary, AB, T2N 1N4, Canada
- Department of Chemistry and Biochemistry, University of Windsor, 401 Sunset Avenue, Windsor, ON, N9B 3P4, Canada
| | - Greg B Moorhead
- Department of Biological Sciences, University of Calgary, 2500 University Dr. NW, Calgary, AB, T2N 1N4, Canada.
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11
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Controls on Interspecies Electron Transport and Size Limitation of Anaerobically Methane-Oxidizing Microbial Consortia. mBio 2021; 12:mBio.03620-20. [PMID: 33975943 PMCID: PMC8263020 DOI: 10.1128/mbio.03620-20] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
Abstract
About 382 Tg yr−1 of methane rising through the seafloor is oxidized anaerobically (W. S. Reeburgh, Chem Rev 107:486–513, 2007, https://doi.org/10.1021/cr050362v), preventing it from reaching the atmosphere, where it acts as a strong greenhouse gas. Microbial consortia composed of anaerobic methanotrophic archaea and sulfate-reducing bacteria couple the oxidation of methane to the reduction of sulfate under anaerobic conditions via a syntrophic process. Recent experimental studies and modeling efforts indicate that direct interspecies electron transfer (DIET) is involved in this syntrophy. Here, we explore a fluorescent in situ hybridization-nanoscale secondary ion mass spectrometry data set of large, segregated anaerobic oxidation of methane (AOM) consortia that reveal a decline in metabolic activity away from the archaeal-bacterial interface and use a process-based model to identify the physiological controls on rates of AOM. Simulations reproducing the observational data reveal that ohmic resistance and activation loss are the two main factors causing the declining metabolic activity, where activation loss dominated at a distance of <8 μm. These voltage losses limit the maximum spatial distance between syntrophic partners with model simulations, indicating that sulfate-reducing bacterial cells can remain metabolically active up to ∼30 μm away from the archaeal-bacterial interface. Model simulations further predict that a hybrid metabolism that combines DIET with a small contribution of diffusive exchange of electron donors can offer energetic advantages for syntrophic consortia.
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12
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Tikhomirova TS, But SY. Laboratory scale bioreactor designs in the processes of methane bioconversion: Mini-review. Biotechnol Adv 2021; 47:107709. [PMID: 33548452 DOI: 10.1016/j.biotechadv.2021.107709] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Revised: 01/29/2021] [Accepted: 01/31/2021] [Indexed: 02/07/2023]
Abstract
Global methane emissions have been steadily increasing over the past few decades, exerting a negative effect on the environment. Biogas from landfills and sewage treatment plants is the main anthropogenic source of methane. This makes methane bioconversion one of the priority areas of biotechnology. This process involves the production of biochemical compounds from non-food sources through microbiological synthesis. Methanotrophic bacteria are a promising tool for methane bioconversion due to their ability to use this greenhouse gas and to produce protein-rich biomass, as well as a broad range of useful organic compounds. Currently, methane is used not only to produce biomass and chemical compounds, but also to increase the efficiency of water and solid waste treatment. However, the use of gaseous substrates in biotechnological processes is associated with some difficulties. The low solubility of methane in water is one of the major problems. Different approaches have been involved to encounter these challenges, including different bioreactor and gas distribution designs, solid carriers and bulk sorbents, as well as varying air/oxygen supply, the ratio of volumetric flow rate of gas mixture to its consumption rate, etc. The aim of this review was to summarize the current data on different bioreactor designs and the aspects of their applications for methane bioconversion and wastewater treatment. The bioreactors used in these processes must meet a number of requirements such as low methane emission, improved gas exchange surface, and controlled substrate supply to the reaction zone.
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Affiliation(s)
- Tatyana S Tikhomirova
- Institute for Biological Instrumentation of the Russian Academy of Sciences, Federal Research Center «Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences», Institutskaya 7, Pushchino, Moscow Region 142290, Russia.
| | - Sergey Y But
- G.K. Skryabin Institute of Biochemistry and Physiology of Microorganisms of the Russian Academy of Sciences, Federal Research Center «Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences», Prospect Nauki 5, Pushchino, Moscow Region 142290, Russia
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13
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Aoki M, Kowada T, Hirakata Y, Watari T, Yamaguchi T. Enrichment of microbial communities for hexavalent chromium removal using a biofilm reactor. JOURNAL OF ENVIRONMENTAL SCIENCE AND HEALTH. PART A, TOXIC/HAZARDOUS SUBSTANCES & ENVIRONMENTAL ENGINEERING 2020; 55:1589-1595. [PMID: 32998606 DOI: 10.1080/10934529.2020.1826791] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/09/2020] [Revised: 09/10/2020] [Accepted: 09/11/2020] [Indexed: 06/11/2023]
Abstract
Given the toxicity and widespread occurrence of hexavalent chromium [Cr(VI)] in aquatic environments, we investigated the feasibility of a down-flow hanging sponge (DHS) biofilm reactor for the enrichment of microbial communities capable of Cr(VI) removal. In the present study, a laboratory-scale DHS reactor fed with a molasses-based medium containing Cr(VI) was operated for 112 days for the investigation. The enrichment of Cr(VI)-removing microbial communities was evaluated based on water quality and prokaryotic community analyses. Once the DHS reactor began to operate, high average volumetric Cr(VI) removal rates of 1.21-1.45 mg L-sponge-1 h-1 were confirmed under varying influent Cr(VI) concentrations (approximately 20-40 mg L-1). 16S rRNA gene amplicon sequencing analysis suggested the presence of phylogenetically diverse prokaryotic lineages, including phyla that contain well-known Cr(VI)-reducing bacteria (e.g., Bacteroidetes, Firmicutes, and Proteobacteria) in the polyurethane sponge media of the DHS reactor. Therefore, our findings indicate that DHS reactors have great potential for the enrichment of Cr(VI)-removing microbial communities.
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Affiliation(s)
- Masataka Aoki
- Department of Civil Engineering, National Institute of Technology, Wakayama College, Gobo, Wakayama, Japan
| | - Taisei Kowada
- Department of Civil Engineering, National Institute of Technology, Wakayama College, Gobo, Wakayama, Japan
| | - Yuga Hirakata
- Department of Science of Technology Innovation, Nagaoka University of Technology, Nagaoka, Niigata, Japan
| | - Takahiro Watari
- Department of Civil and Environmental Engineering, Nagaoka University of Technology, Nagaoka, Niigata, Japan
| | - Takashi Yamaguchi
- Department of Science of Technology Innovation, Nagaoka University of Technology, Nagaoka, Niigata, Japan
- Department of Civil and Environmental Engineering, Nagaoka University of Technology, Nagaoka, Niigata, Japan
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14
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Tran P T, Hatamoto M, Tsuba D, Watari T, Yamaguchi T. Positive impact of a reducing agent on autotrophic nitrogen removal process and nexus of nitrous oxide emission in an anaerobic downflow hanging sponge reactor. CHEMOSPHERE 2020; 256:126952. [PMID: 32428737 DOI: 10.1016/j.chemosphere.2020.126952] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/22/2020] [Revised: 04/19/2020] [Accepted: 04/30/2020] [Indexed: 06/11/2023]
Abstract
The adjustment of hydraulic retention time (HRT) and the supplement of titanium(III) nitrilotriacetate (Ti(III)-NTA) as a reducing agent were implemented in an anaerobic downflow hanging sponge (DHS) reactor with the aims to (i) improve nitrogen removal performance and to (ii) eliminate N2O emission. A laboratory-scale DHS reactor was operated at 35 °C, under autotrophic denitrification conditions with methane gas (14.2 L d-1) as the main carbon source, NaNO3 and NaNO2 (20 mg N L-1 per compound) as nitrogen sources. The sufficient HRT for simultaneously removing nitrate and nitrite in this reactor was found at 12 h when HRT was reduced from 24 to 6 h. Then at the HRT of 12 h, the addition of Ti(III)-NTA at a final concentration of 25 μM Ti(III) boosted the reactor's nitrogen removal rates from 1.4 ± 0.6 to 4.1 ± 1.9 g NO3--N m-3 d-1 and 3.2 ± 2.8 to 6.6 ± 3.3 g NO2--N m-3 d-1. Furthermore, this study is the first to consider the N2O emission in a continuous reactor applying denitrification coupled to anaerobic methane oxidation (DAMO) process. Produced N2O in this DHS reactor was from 10.6 × 10-4% to 89.0 × 10-4% of removed NOx- without Ti(III)-NTA and from 0.7 × 10-4% to 61.4 × 10-4% of removed NOx- with Ti(III)-NTA. Overall, these findings suggested the advantage of Ti(III)-NTA as an oxygen scavenger for denitrification processes and the potential of the anaerobic DHS reactor for facilitating the DAMO processes and mitigating N2O gas.
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Affiliation(s)
- Thao Tran P
- Department of Science of Technology Innovation, Nagaoka University of Technology, Nagaoka, 940-2188, Japan.
| | - Masashi Hatamoto
- Department of Civil and Environmental Engineering, Nagaoka University of Technology, Nagaoka, 940-2188, Japan.
| | - Daisuke Tsuba
- Department of Civil and Environmental Engineering, Nagaoka University of Technology, Nagaoka, 940-2188, Japan
| | - Takahiro Watari
- Department of Civil and Environmental Engineering, Nagaoka University of Technology, Nagaoka, 940-2188, Japan.
| | - Takashi Yamaguchi
- Department of Science of Technology Innovation, Nagaoka University of Technology, Nagaoka, 940-2188, Japan.
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15
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Abstract
The anaerobic oxidation of methane (AOM) is an important sink of methane that plays a significant role in global warming. However, evidence for the AOM in freshwater habitats is rare, especially in dam and weir (small-scale dam) reservoirs. Here, the AOM process was examined in freshwater sediments of a small-scale dam reservoir located in Rzeszów, SE Poland. The AOM rate was determined in the main experiment with the addition of the 13CH4 isotope marker (He+13CH4). Sediments were collected three times: in spring (in May, 15 °C), in summer (in July, 20 °C) and in autumn (in September, 10 °C). Further analysis considers the impact on AOM rate of potential electron acceptors present in pore-water (NO2−, NO3−, SO42−, and Fe3+ ions). The work suggests that an AOM process does take place in the studied reservoir sediments, with this evidenced by the presence in the headspace of an increased 13CO2 concentration deemed to derive from 13CH4 oxidation. Rates of AOM noted were of 0.36–1.42 nmol·g−1·h−1, with the most intensive oxidation in each sediment layer occurring at 20 °C. While none of the potential electron acceptors considered individually were found to have had a statistically significant influence on the AOM rate, their significance to the dynamics of the AOM process was not precluded.
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16
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Rasool A, Nasim W, Xiao T, Ali W, Shafeeque M, Sultana SR, Fahad S, Munis MFH, Chaudhary HJ. Microbial diversity response in thallium polluted riverbank soils of the Lanmuchang. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2020; 187:109854. [PMID: 31678700 DOI: 10.1016/j.ecoenv.2019.109854] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/02/2019] [Revised: 10/19/2019] [Accepted: 10/21/2019] [Indexed: 06/10/2023]
Abstract
Thallium (Tl) is a toxic element, but little is known about microbial communities' response to TI mobilization and sequestration. Here, we characterize the microbial communities and their feedbacks to Tl-pollution in riverbank soils to understand the distribution of microbial metal tolerance. These soils have been affected by pollution sourced from a Tl-rich mineralized area in Lanmuchang, Guizhou, China. In all studied soil samples, Proteobacteria, Acidobacteria, and Actinobacteria were revealed relatively in higher abundance at the phylum level. The results indicated that a number of microbial communities including Gemmatimonadetes, and Actinobacteria were correlated with total Tl, suggesting potential roles of these microbes to Tl tolerance. The patterns of phylogenetic beta-diversity in studied samples showed a high diversity of the microbial community in soils with high Tl concentrations. Sequence analysis of microbial community indicated that most of the environmental parameters in soils were associated with the major phylogenetic groups such as Gemmobacteria, Bryobacteria, Proteobacteria, Actinobacteria, Firmicutes, and Rhodobacteria. Some species of microbes, Nocardioides (genus), Actinomycetales (Order), Ralstonia (phyla) and Sphingomonas (genus) might are tolerant of Tl. These results provide direction to the microbial communities in the presence of elevated Tl concentration in Lanmuchang and shed light on bioremediation of Tl polluted locations.
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Affiliation(s)
- Atta Rasool
- State Key Laboratory of Environmental Geochemistry, Institute of Geochemistry, Chinese Academy of Sciences, Guiyang, 550081, China; University of Chinese Academy of Sciences, Beijing, 100049, China; Department of Environmental Sciences, COMSATS University, Islamabad (CUI), Vehari, 61100, Pakistan
| | - Wajid Nasim
- Department of Environmental Sciences, COMSATS University, Islamabad (CUI), Vehari, 61100, Pakistan; CIHEAM-Institut Agronomique Méditerranéen de Montpellier (IAMM), 3191Route de Mende, Montpellier, France; CSIRO Sustainable Ecosystems, National Research Flagship, Towoomba, QLD, 4350, Australia; Department of Agronomy, University College of Agriculture and Environmental Sciences, The Islamia University of Bahawalpur (IUB), Bahawalpur, Pakistan
| | - Tangfu Xiao
- Key Laboratory for Water Quality and Conservation of the Pearl River Delta, Ministry of Education, School of Environmental Science and Engineering, Guangzhou University, Guangzhou, 510006, China.
| | - Waqar Ali
- State Key Laboratory of Environmental Geochemistry, Institute of Geochemistry, Chinese Academy of Sciences, Guiyang, 550081, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Muhammad Shafeeque
- University of Chinese Academy of Sciences, Beijing, 100049, China; Key Lab of Ecosystem Network Observation and Modelling, Institute of Geographic Sciences and Natural Resources Research, Chinese Academy of Sciences, 100101, Beijing, China
| | - Syeda Refat Sultana
- Department of Environmental Sciences, COMSATS University, Islamabad (CUI), Vehari, 61100, Pakistan
| | - Shah Fahad
- Department of Agriculture, University of Swabi, Khyber Pakhtunkhwa (KPK), Pakistan
| | | | - Hassan Javed Chaudhary
- Department of Plant Sciences, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad, 45320, Pakistan
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17
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Klasek S, Torres ME, Bartlett DH, Tyler M, Hong W, Colwell F. Microbial communities from Arctic marine sediments respond slowly to methane addition during
ex situ
enrichments. Environ Microbiol 2020; 22:1829-1846. [DOI: 10.1111/1462-2920.14895] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2019] [Revised: 11/11/2019] [Accepted: 11/30/2019] [Indexed: 11/27/2022]
Affiliation(s)
- Scott Klasek
- Department of Microbiology Oregon State University Corvallis Oregon USA
| | - Marta E. Torres
- College of Earth, Ocean, and Atmospheric Sciences Oregon State University Corvallis Oregon USA
| | - Douglas H. Bartlett
- Marine Biology Research Division, Scripps Institution of Oceanography University of California San Diego California 92093‐0202 USA
| | - Madeline Tyler
- Department of Microbiology Oregon State University Corvallis Oregon USA
| | - Wei‐Li Hong
- Centre for Arctic Gas Hydrate, Environment and Climate (CAGE), Department of Geosciences UiT The Arctic University of Norway N‐9037 Tromsø Norway
| | - Frederick Colwell
- Department of Microbiology Oregon State University Corvallis Oregon USA
- College of Earth, Ocean, and Atmospheric Sciences Oregon State University Corvallis Oregon USA
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18
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Imachi H, Nobu MK, Nakahara N, Morono Y, Ogawara M, Takaki Y, Takano Y, Uematsu K, Ikuta T, Ito M, Matsui Y, Miyazaki M, Murata K, Saito Y, Sakai S, Song C, Tasumi E, Yamanaka Y, Yamaguchi T, Kamagata Y, Tamaki H, Takai K. Isolation of an archaeon at the prokaryote-eukaryote interface. Nature 2020; 577:519-525. [PMID: 31942073 PMCID: PMC7015854 DOI: 10.1038/s41586-019-1916-6] [Citation(s) in RCA: 336] [Impact Index Per Article: 84.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2019] [Accepted: 12/05/2019] [Indexed: 12/30/2022]
Abstract
The origin of eukaryotes remains unclear1-4. Current data suggest that eukaryotes may have emerged from an archaeal lineage known as 'Asgard' archaea5,6. Despite the eukaryote-like genomic features that are found in these archaea, the evolutionary transition from archaea to eukaryotes remains unclear, owing to the lack of cultured representatives and corresponding physiological insights. Here we report the decade-long isolation of an Asgard archaeon related to Lokiarchaeota from deep marine sediment. The archaeon-'Candidatus Prometheoarchaeum syntrophicum' strain MK-D1-is an anaerobic, extremely slow-growing, small coccus (around 550 nm in diameter) that degrades amino acids through syntrophy. Although eukaryote-like intracellular complexes have been proposed for Asgard archaea6, the isolate has no visible organelle-like structure. Instead, Ca. P. syntrophicum is morphologically complex and has unique protrusions that are long and often branching. On the basis of the available data obtained from cultivation and genomics, and reasoned interpretations of the existing literature, we propose a hypothetical model for eukaryogenesis, termed the entangle-engulf-endogenize (also known as E3) model.
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Affiliation(s)
- Hiroyuki Imachi
- Institute for Extra-cutting-edge Science and Technology Avant-garde Research (X-star), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Japan.
| | - Masaru K Nobu
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Japan.
| | - Nozomi Nakahara
- Institute for Extra-cutting-edge Science and Technology Avant-garde Research (X-star), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Japan
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Japan
- Department of Civil and Environmental Engineering, Nagaoka University of Technology, Nagaoka, Japan
| | - Yuki Morono
- Kochi Institute for Core Sample Research, X-star, JAMSTEC, Nankoku, Japan
| | - Miyuki Ogawara
- Institute for Extra-cutting-edge Science and Technology Avant-garde Research (X-star), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Japan
| | - Yoshihiro Takaki
- Institute for Extra-cutting-edge Science and Technology Avant-garde Research (X-star), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Japan
| | - Yoshinori Takano
- Biogeochemistry Program, Research Institute for Marine Resources Utilization, JAMSTEC, Yokosuka, Japan
| | - Katsuyuki Uematsu
- Department of Marine and Earth Sciences, Marine Work Japan, Yokosuka, Japan
| | - Tetsuro Ikuta
- Research Institute for Global Change, JAMSTEC, Yokosuka, Japan
| | - Motoo Ito
- Kochi Institute for Core Sample Research, X-star, JAMSTEC, Nankoku, Japan
| | - Yohei Matsui
- Research Institute for Marine Resources Utilization, JAMSTEC, Yokosuka, Japan
| | - Masayuki Miyazaki
- Institute for Extra-cutting-edge Science and Technology Avant-garde Research (X-star), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Japan
| | | | - Yumi Saito
- Institute for Extra-cutting-edge Science and Technology Avant-garde Research (X-star), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Japan
| | - Sanae Sakai
- Institute for Extra-cutting-edge Science and Technology Avant-garde Research (X-star), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Japan
| | - Chihong Song
- National Institute for Physiological Sciences, Okazaki, Japan
| | - Eiji Tasumi
- Institute for Extra-cutting-edge Science and Technology Avant-garde Research (X-star), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Japan
| | - Yuko Yamanaka
- Institute for Extra-cutting-edge Science and Technology Avant-garde Research (X-star), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Japan
| | - Takashi Yamaguchi
- Department of Civil and Environmental Engineering, Nagaoka University of Technology, Nagaoka, Japan
| | - Yoichi Kamagata
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Japan
| | - Hideyuki Tamaki
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Japan
| | - Ken Takai
- Institute for Extra-cutting-edge Science and Technology Avant-garde Research (X-star), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Japan
- Section for Exploration of Life in Extreme Environments, Exploratory Research Center on Life and Living Systems (ExCELLS), National Institute of Natural Sciences, Okazaki, Japan
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19
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Cassarini C, Rene ER, Bhattarai S, Vogt C, Musat N, Lens PNL. Anaerobic methane oxidation coupled to sulfate reduction in a biotrickling filter: Reactor performance and microbial community analysis. CHEMOSPHERE 2019; 236:124290. [PMID: 31310977 DOI: 10.1016/j.chemosphere.2019.07.021] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/11/2019] [Revised: 06/28/2019] [Accepted: 07/02/2019] [Indexed: 06/10/2023]
Abstract
The aim of this work was to evaluate the performance of a biotrickling filter (BTF) packed with polyurethane foam and pall rings for the enrichment of microorganisms mediating anaerobic oxidation of methane (AOM) coupled to sulfate reduction (SR) by activity tests and microbial community analysis. A BTF was inoculated with microorganisms from a known AOM active deep sea sediment collected at a depth of 528 m below the sea level (Alpha Mound, Gulf of Cadiz). The microbial community analysis was performed by catalyzed reporter deposition - fluorescence in situ hybridization (CARD-FISH) and 16S rRNA sequence analysis. The AOM occurrence and rates in the BTF were assessed by performing batch activity assays using 13C-labelled methane (13CH4). After an estimated start-up time of ∼20 days, AOM rates of ∼0.3 mmol l-1 day-1 were observed in the BTF, values almost 20 times higher than previously reported in a polyurethane foam packed BTF. The microbial community consisted mainly of anaerobic methanotrophs (ANME-2, 22% of the total number of cells) and sulfate reducing bacteria (SRB, 47% of the total number of cells). This study showed that the BTF is a suitable reactor configuration for the enrichment of microbial communities involved in AOM coupled to SR at ambient pressure and temperature with a relatively short start-up time.
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Affiliation(s)
- Chiara Cassarini
- UNESCO-IHE, Institute for Water Education, P. O. Box 3015, 2601, DA, Delft, the Netherlands; National University of Ireland Galway, University Road, Galway, H91 TK33, Ireland.
| | - Eldon R Rene
- UNESCO-IHE, Institute for Water Education, P. O. Box 3015, 2601, DA, Delft, the Netherlands
| | - Susma Bhattarai
- UNESCO-IHE, Institute for Water Education, P. O. Box 3015, 2601, DA, Delft, the Netherlands
| | - Carsten Vogt
- Helmholtz-Centre for Environmental Research - UFZ, Department of Isotope Biogeochemistry, Permoser Strasse 15, 04318, Leipzig, Germany
| | - Niculina Musat
- Helmholtz-Centre for Environmental Research - UFZ, Department of Isotope Biogeochemistry, Permoser Strasse 15, 04318, Leipzig, Germany
| | - Piet N L Lens
- UNESCO-IHE, Institute for Water Education, P. O. Box 3015, 2601, DA, Delft, the Netherlands; National University of Ireland Galway, University Road, Galway, H91 TK33, Ireland
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20
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Bhattarai S, Cassarini C, Lens PNL. Physiology and Distribution of Archaeal Methanotrophs That Couple Anaerobic Oxidation of Methane with Sulfate Reduction. Microbiol Mol Biol Rev 2019; 83:e00074-18. [PMID: 31366606 PMCID: PMC6710461 DOI: 10.1128/mmbr.00074-18] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
In marine anaerobic environments, methane is oxidized where sulfate-rich seawater meets biogenic or thermogenic methane. In those niches, a few phylogenetically distinct microbial types, i.e., anaerobic methanotrophs (ANME), are able to grow through anaerobic oxidation of methane (AOM). Due to the relevance of methane in the global carbon cycle, ANME have drawn the attention of a broad scientific community for 4 decades. This review presents and discusses the microbiology and physiology of ANME up to the recent discoveries, revealing novel physiological types of anaerobic methane oxidizers which challenge the view of obligate syntrophy for AOM. An overview of the drivers shaping the distribution of ANME in different marine habitats, from cold seep sediments to hydrothermal vents, is given. Multivariate analyses of the abundance of ANME in various habitats identify a distribution of distinct ANME types driven by the mode of methane transport. Intriguingly, ANME have not yet been cultivated in pure culture, despite intense attempts. Further advances in understanding this microbial process are hampered by insufficient amounts of enriched cultures. This review discusses the advantages, limitations, and potential improvements for ANME laboratory-based cultivation systems.
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Affiliation(s)
- S Bhattarai
- UNESCO-IHE, Institute for Water Education, Delft, The Netherlands
| | - C Cassarini
- UNESCO-IHE, Institute for Water Education, Delft, The Netherlands
- National University of Ireland Galway, Galway, Ireland
| | - P N L Lens
- UNESCO-IHE, Institute for Water Education, Delft, The Netherlands
- National University of Ireland Galway, Galway, Ireland
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21
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Zhuang M, Sanganyado E, Li P, Liu W. Distribution of microbial communities in metal-contaminated nearshore sediment from Eastern Guangdong, China. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2019; 250:482-492. [PMID: 31026695 DOI: 10.1016/j.envpol.2019.04.041] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/14/2019] [Revised: 03/22/2019] [Accepted: 04/08/2019] [Indexed: 06/09/2023]
Abstract
Nearshore environments are a critical transitional zone that connects the marine and terrestrial/freshwater ecosystems. The release of anthropogenic chemicals into nearshore ecosystems pose a human and environmental health risk. We investigated the microbial diversity, abundance and function in metal-contaminated sediments collected from the Rongjiang, Hanjiang and Lianjiang River estuaries and adjacent coastal areas using high throughput sequencing. The concentration of nutrients (NO3-N, NO2-N, NH4-N, PO4-P) and metal (Cu, Zn, Cd, Pb, As, Hg) contaminants were higher at the mouth of the rivers compared to the coastal lines, and this was confirmed using cluster analysis. Estimates obtained using geoaccumulation index showed that about 38.9% of the sites were contaminated with Pb and the pollution load index showed that sediment from the mouth of Hanjiang River Estuary was moderately polluted with metals. In the nearshore sediment samples collected, Proteobacteria, Bacteroidetes, Planctomycetes, Chloroflexi, Acidobacteria were the dominant phylum with relative abundances of 46.6%, 8.05%, 6.47%, 5.26%, and 4.59%, respectively. There was no significant correlation between environmental variables and microbial abundance and diversity except for total organic carbon (TOC) (diversity; r = 0.569, p < 0.05) and Cr (diversity; r = 0.581, p < 0.05). At phyla level, Nitrospirae had a significant negative correlation with all metals except Cr, while OD1 had a significant positive correlation with all the metals. Overall, changes in nearshore sediment microbial communities by environmental factors were observed, and these may affect biogeochemical cycling.
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Affiliation(s)
- Mei Zhuang
- Marine Biology Institute, Shantou University, Shantou, Guangdong Province, China
| | - Edmond Sanganyado
- Marine Biology Institute, Shantou University, Shantou, Guangdong Province, China
| | - Ping Li
- Marine Biology Institute, Shantou University, Shantou, Guangdong Province, China
| | - Wenhua Liu
- Marine Biology Institute, Shantou University, Shantou, Guangdong Province, China.
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22
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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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23
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Imachi H, Tasumi E, Takaki Y, Hoshino T, Schubotz F, Gan S, Tu TH, Saito Y, Yamanaka Y, Ijiri A, Matsui Y, Miyazaki M, Morono Y, Takai K, Hinrichs KU, Inagaki F. Cultivable microbial community in 2-km-deep, 20-million-year-old subseafloor coalbeds through ~1000 days anaerobic bioreactor cultivation. Sci Rep 2019; 9:2305. [PMID: 30783143 PMCID: PMC6381156 DOI: 10.1038/s41598-019-38754-w] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2018] [Accepted: 01/09/2019] [Indexed: 11/08/2022] Open
Abstract
Recent explorations of scientific ocean drilling have revealed the presence of microbial communities persisting in sediments down to ~2.5 km below the ocean floor. However, our knowledge of these microbial populations in the deep subseafloor sedimentary biosphere remains limited. Here, we present a cultivation experiment of 2-km-deep subseafloor microbial communities in 20-million-year-old lignite coalbeds using a continuous-flow bioreactor operating at 40 °C for 1029 days with lignite particles as the major energy source. Chemical monitoring of effluent samples via fluorescence emission-excitation matrices spectroscopy and stable isotope analyses traced the transformation of coalbed-derived organic matter in the dissolved phase. Hereby, the production of acetate and 13C-depleted methane together with the increase and transformation of high molecular weight humics point to an active lignite-degrading methanogenic community present within the bioreactor. Electron microscopy revealed abundant microbial cells growing on the surface of lignite particles. Small subunit rRNA gene sequence analysis revealed that diverse microorganisms grew in the bioreactor (e.g., phyla Proteobacteria, Firmicutes, Chloroflexi, Actinobacteria, Bacteroidetes, Spirochaetes, Tenericutes, Ignavibacteriae, and SBR1093). These results indicate that activation and adaptive growth of 2-km-deep microbes was successfully accomplished using a continuous-flow bioreactor, which lays the groundwork to explore networks of microbial communities of the deep biosphere and their physiologies.
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Affiliation(s)
- Hiroyuki Imachi
- Department of Subsurface Geobiological Analysis and Research (D-SUGAR), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Kanagawa, 237-0061, Japan.
- Research and Development Center for Submarine Resources, JAMSTEC, Yokosuka, Kanagawa, 237-0061, Japan.
| | - Eiji Tasumi
- Department of Subsurface Geobiological Analysis and Research (D-SUGAR), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Kanagawa, 237-0061, Japan
| | - Yoshihiro Takaki
- Department of Subsurface Geobiological Analysis and Research (D-SUGAR), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Kanagawa, 237-0061, Japan
- Project Team for Development of New-generation Research Protocol for Submarine Resources, JAMSTEC, Yokosuka, Kanagawa, 237-0061, Japan
| | - Tatsuhiko Hoshino
- Research and Development Center for Submarine Resources, JAMSTEC, Yokosuka, Kanagawa, 237-0061, Japan
- Kochi Institute for Core Sample Research, JAMSTEC, Nankoku, Kochi, 783-8502, Japan
| | - Florence Schubotz
- MARUM Center for Marine Environmental Sciences and Department of Geosciences, University of Bremen, D-28359, Bremen, Germany
| | - Shuchai Gan
- MARUM Center for Marine Environmental Sciences and Department of Geosciences, University of Bremen, D-28359, Bremen, Germany
| | - Tzu-Hsuan Tu
- Department of Subsurface Geobiological Analysis and Research (D-SUGAR), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Kanagawa, 237-0061, Japan
- Institute of Oceanography, National Taiwan University, Taipei, 106, Taiwan
| | - Yumi Saito
- Department of Subsurface Geobiological Analysis and Research (D-SUGAR), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Kanagawa, 237-0061, Japan
| | - Yuko Yamanaka
- Department of Subsurface Geobiological Analysis and Research (D-SUGAR), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Kanagawa, 237-0061, Japan
| | - Akira Ijiri
- Research and Development Center for Submarine Resources, JAMSTEC, Yokosuka, Kanagawa, 237-0061, Japan
- Project Team for Development of New-generation Research Protocol for Submarine Resources, JAMSTEC, Yokosuka, Kanagawa, 237-0061, Japan
| | - Yohei Matsui
- Research and Development Center for Submarine Resources, JAMSTEC, Yokosuka, Kanagawa, 237-0061, Japan
- Project Team for Development of New-generation Research Protocol for Submarine Resources, JAMSTEC, Yokosuka, Kanagawa, 237-0061, Japan
| | - Masayuki Miyazaki
- Department of Subsurface Geobiological Analysis and Research (D-SUGAR), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Kanagawa, 237-0061, Japan
| | - Yuki Morono
- Research and Development Center for Submarine Resources, JAMSTEC, Yokosuka, Kanagawa, 237-0061, Japan
- Kochi Institute for Core Sample Research, JAMSTEC, Nankoku, Kochi, 783-8502, Japan
| | - Ken Takai
- Department of Subsurface Geobiological Analysis and Research (D-SUGAR), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Kanagawa, 237-0061, Japan
- Research and Development Center for Submarine Resources, JAMSTEC, Yokosuka, Kanagawa, 237-0061, Japan
| | - Kai-Uwe Hinrichs
- MARUM Center for Marine Environmental Sciences and Department of Geosciences, University of Bremen, D-28359, Bremen, Germany
| | - Fumio Inagaki
- Research and Development Center for Submarine Resources, JAMSTEC, Yokosuka, Kanagawa, 237-0061, Japan
- Kochi Institute for Core Sample Research, JAMSTEC, Nankoku, Kochi, 783-8502, Japan
- Research and Development Center for Ocean Drilling Science, JAMSTEC, Yokohama, Kanagawa, 236-0001, Japan
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24
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Nakahara N, Nobu MK, Takaki Y, Miyazaki M, Tasumi E, Sakai S, Ogawara M, Yoshida N, Tamaki H, Yamanaka Y, Katayama A, Yamaguchi T, Takai K, Imachi H. Aggregatilinea lenta gen. nov., sp. nov., a slow-growing, facultatively anaerobic bacterium isolated from subseafloor sediment, and proposal of the new order Aggregatilineales ord. nov. within the class Anaerolineae of the phylum Chloroflexi. Int J Syst Evol Microbiol 2019; 69:1185-1194. [PMID: 30775966 DOI: 10.1099/ijsem.0.003291] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A novel slow-growing, facultatively anaerobic, filamentous bacterium, strain MO-CFX2T, was isolated from a methanogenic microbial community in a continuous-flow bioreactor that was established from subseafloor sediment collected off the Shimokita Peninsula of Japan. Cells were multicellular filamentous, non-motile and Gram-stain-negative. The filaments were generally more than 20 µm (up to approximately 200 µm) long and 0.5-0.6 µm wide. Cells possessed pili-like structures on the cell surface and a multilayer structure in the cytoplasm. Growth of the strain was observed at 20-37 °C (optimum, 30 °C), pH 5.5-8.0 (pH 6.5-7.0), and 0-30 g l-1 NaCl (5 g l-1 NaCl). Under optimum growth conditions, doubling time and maximum cell density were estimated to be approximately 19 days and ~105 cells ml-1, respectively. Strain MO-CFX2T grew chemoorganotrophically on a limited range of organic substrates in anaerobic conditions. The major cellular fatty acids were saturated C16 : 0 (47.9 %) and C18 : 0 (36.9 %), and unsaturated C18 : 1ω9c (6.0 %) and C16 : 1ω7 (5.1 %). The G+C content of genomic DNA was 63.2 mol%. 16S rRNA gene-based phylogenetic analysis showed that strain MO-CFX2T shares a notably low sequence identity with its closest relatives, which were Thermanaerothrix daxensis GNS-1T and Thermomarinilinea lacunifontana SW7T (both 85.8 % sequence identity). Based on these phenotypic and genomic properties, we propose the name Aggregatilinea lenta gen. nov., sp. nov. for strain MO-CFX2T (=KCTC 15625T, =JCM 32065T). In addition, we also propose the associated family and order as Aggregatilineaceae fam. nov. and Aggregatilineales ord. nov., respectively.
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Affiliation(s)
- Nozomi Nakahara
- Department of Civil and Environmental Engineering, Nagaoka University of Technology, Nagaoka, Niigata 940-2188, Japan.,Department of Subsurface Geobiological Analysis and Research (D-SUGAR), Japan Agency for Marine-Earth Science & Technology (JAMSTEC), Yokosuka, Kanagawa 237-0061, Japan
| | - Masaru K Nobu
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Ibaraki 305-8566, Japan
| | - Yoshihiro Takaki
- Department of Subsurface Geobiological Analysis and Research (D-SUGAR), Japan Agency for Marine-Earth Science & Technology (JAMSTEC), Yokosuka, Kanagawa 237-0061, Japan.,Ecosystem Observation and Evaluation Methodology Research Unit, Project Team for Development of New-generation Research Protocol for Submarine Resources, JAMSTEC, Yokosuka, Kanagawa 237-0061, Japan
| | - Masayuki Miyazaki
- Department of Subsurface Geobiological Analysis and Research (D-SUGAR), Japan Agency for Marine-Earth Science & Technology (JAMSTEC), Yokosuka, Kanagawa 237-0061, Japan
| | - Eiji Tasumi
- Department of Subsurface Geobiological Analysis and Research (D-SUGAR), Japan Agency for Marine-Earth Science & Technology (JAMSTEC), Yokosuka, Kanagawa 237-0061, Japan
| | - Sanae Sakai
- Department of Subsurface Geobiological Analysis and Research (D-SUGAR), Japan Agency for Marine-Earth Science & Technology (JAMSTEC), Yokosuka, Kanagawa 237-0061, Japan
| | - Miyuki Ogawara
- Department of Subsurface Geobiological Analysis and Research (D-SUGAR), Japan Agency for Marine-Earth Science & Technology (JAMSTEC), Yokosuka, Kanagawa 237-0061, Japan
| | - Naoko Yoshida
- Department of Civil and Environmental Engineering, Nagoya Institute of Technology, Nagoya, Aichi 466-8555, Japan
| | - Hideyuki Tamaki
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Ibaraki 305-8566, Japan
| | - Yuko Yamanaka
- Department of Subsurface Geobiological Analysis and Research (D-SUGAR), Japan Agency for Marine-Earth Science & Technology (JAMSTEC), Yokosuka, Kanagawa 237-0061, Japan
| | - Arata Katayama
- Institute of Materials and Systems for Sustainability, Nagoya University, Nagoya, Aichi 464-8601, Japan
| | - Takashi Yamaguchi
- Department of Civil and Environmental Engineering, Nagaoka University of Technology, Nagaoka, Niigata 940-2188, Japan
| | - Ken Takai
- Department of Subsurface Geobiological Analysis and Research (D-SUGAR), Japan Agency for Marine-Earth Science & Technology (JAMSTEC), Yokosuka, Kanagawa 237-0061, Japan
| | - Hiroyuki Imachi
- Department of Subsurface Geobiological Analysis and Research (D-SUGAR), Japan Agency for Marine-Earth Science & Technology (JAMSTEC), Yokosuka, Kanagawa 237-0061, Japan
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25
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Cui H, Su X, Chen F, Holland M, Yang S, Liang J, Su P, Dong H, Hou W. Microbial diversity of two cold seep systems in gas hydrate-bearing sediments in the South China Sea. MARINE ENVIRONMENTAL RESEARCH 2019; 144:230-239. [PMID: 30732863 DOI: 10.1016/j.marenvres.2019.01.009] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2018] [Revised: 12/29/2018] [Accepted: 01/14/2019] [Indexed: 05/05/2023]
Abstract
Cold seep is a unique habitat for microorganisms in deep marine sediments, and microbial communities and biogeochemical processes are still poorly understood, especially in relation to hydrate-bearing geo-systems. In this study, two cold seep systems were sampled and microbial diversity was studied at Site GMGS2-08 in the northern part of the South China Sea (SCS) during the GMGS2 gas hydrate expedition. The current cold seep system was composed of a sulfate methane transition zone (SMTZ) and an upper gas hydrate zone (UGHZ). The buried cold seep system was composed of an authigenic carbonate zone (ACZ) and a lower gas hydrate zone (LGHZ). These drill core samples provided an excellent opportunity for analyzing the microbial abundance and diversity based on quantitative polymerase chain reaction (qPCR) and high-throughput 16S rRNA gene sequencing. Compared to previous studies, the high relative abundance of ANME-1b, a clade of anaerobic methanotrophic archaea (ANME), may perform anaerobic oxidation of methane (AOM) in collaboration with ANME-2c and Desulfobacteraceae in the SMTZ, and the high relative abundances of Hadesarchaea, ANME-1b archaea and Aerophobetes bacteria were found in the gas hydrate zone (GHZ) at Site GMGS2-08. ANME-1b, detected in the GHZ, might mainly mediate the AOM process, and the process might occur in a wide depth range within the LGHZ. Moreover, bacterial communities were significantly different between the GHZ and non-GHZ sediments. In the ACZ, archaeal communities were different between the two samples from the upper and the lower layers, while bacterial communities shared similarities. Overall, this new record of cold seep microbial diversity at Site GMGS2-08 showed the complexity of the interaction between biogeochemical reactions and environmental conditions.
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Affiliation(s)
- Hongpeng Cui
- School of Ocean Sciences, China University of Geosciences, Beijing, 100083, China; State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Beijing, 100083, China
| | - Xin Su
- School of Ocean Sciences, China University of Geosciences, Beijing, 100083, China; State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Beijing, 100083, China.
| | - Fang Chen
- Guangzhou Marine Geological Survey, Guangzhou, 510075, China
| | | | - Shengxiong Yang
- Guangzhou Marine Geological Survey, Guangzhou, 510075, China
| | - Jinqiang Liang
- Guangzhou Marine Geological Survey, Guangzhou, 510075, China.
| | - Pibo Su
- Guangzhou Marine Geological Survey, Guangzhou, 510075, China
| | - Hailiang Dong
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Beijing, 100083, China; Department of Geology and Environmental Earth Science, Miami University, OH, 45056, USA
| | - Weiguo Hou
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Beijing, 100083, China
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26
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Labrado AL, Brunner B, Bernasconi SM, Peckmann J. Formation of Large Native Sulfur Deposits Does Not Require Molecular Oxygen. Front Microbiol 2019; 10:24. [PMID: 30740094 PMCID: PMC6355691 DOI: 10.3389/fmicb.2019.00024] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2018] [Accepted: 01/09/2019] [Indexed: 01/05/2023] Open
Abstract
Large native (i.e., elemental) sulfur deposits can be part of caprock assemblages found on top of or in lateral position to salt diapirs and as stratabound mineralization in gypsum and anhydrite lithologies. Native sulfur is formed when hydrocarbons come in contact with sulfate minerals in presence of liquid water. The prevailing model for native sulfur formation in such settings is that sulfide produced by sulfate-reducing bacteria is oxidized to zero-valent sulfur in presence of molecular oxygen (O2). Although possible, such a scenario is problematic because: (1) exposure to oxygen would drastically decrease growth of microbial sulfate-reducing organisms, thereby slowing down sulfide production; (2) on geologic timescales, excess supply with oxygen would convert sulfide into sulfate rather than native sulfur; and (3) to produce large native sulfur deposits, enormous amounts of oxygenated water would need to be brought in close proximity to environments in which ample hydrocarbon supply sustains sulfate reduction. However, sulfur stable isotope data from native sulfur deposits emplaced at a stage after the formation of the host rocks indicate that the sulfur was formed in a setting with little solute exchange with the ambient environment and little supply of dissolved oxygen. We deduce that there must be a process for the formation of native sulfur in absence of an external oxidant for sulfide. We hypothesize that in systems with little solute exchange, sulfate-reducing organisms, possibly in cooperation with other anaerobic microbial partners, drive the formation of native sulfur deposits. In order to cope with sulfide stress, microbes may shift from harmful sulfide production to non-hazardous native sulfur production. We propose four possible mechanisms as a means to form native sulfur: (1) a modified sulfate reduction process that produces sulfur compounds with an intermediate oxidation state, (2) coupling of sulfide oxidation to methanogenesis that utilizes methylated compounds, acetate or carbon dioxide, (3) ammonium oxidation coupled to sulfate reduction, and (4) sulfur comproportionation of sulfate and sulfide. We show these reactions are thermodynamically favorable and especially useful in environments with multiple stressors, such as salt and dissolved sulfide, and provide evidence that microbial species functioning in such environments produce native sulfur. Integrating these insights, we argue that microbes may form large native sulfur deposits in absence of light and external oxidants such as O2, nitrate, and metal oxides. The existence of such a process would not only explain enigmatic occurrences of native sulfur in the geologic record, but also provide an explanation for cryptic sulfur and carbon cycling beneath the seabed.
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Affiliation(s)
- Amanda L. Labrado
- Department of Geological Sciences, The University of Texas at El Paso, El Paso, TX, United States
| | - Benjamin Brunner
- Department of Geological Sciences, The University of Texas at El Paso, El Paso, TX, United States
| | | | - Jörn Peckmann
- Centrum für Erdsystemforschung und Nachhaltigkeit, Universität Hamburg, Hamburg, Germany
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27
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He X, Chadwick G, Kempes C, Shi Y, McGlynn S, Orphan V, Meile C. Microbial interactions in the anaerobic oxidation of methane: model simulations constrained by process rates and activity patterns. Environ Microbiol 2019; 21:631-647. [DOI: 10.1111/1462-2920.14507] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2018] [Revised: 12/04/2018] [Accepted: 12/04/2018] [Indexed: 12/01/2022]
Affiliation(s)
- Xiaojia He
- Department of Marine Sciences University of Georgia Athens GA USA
| | - Grayson Chadwick
- Division of Geological and Planetary Sciences California Institute of Technology Pasadena CA USA
| | | | - Yimeng Shi
- Department of Marine Sciences University of Georgia Athens GA USA
| | - Shawn McGlynn
- Division of Geological and Planetary Sciences California Institute of Technology Pasadena CA USA
- Earth‐Life Science Institute Tokyo Institute of Technology Ookayama, Meguro‐ku Tokyo Japan
| | - Victoria Orphan
- Division of Geological and Planetary Sciences California Institute of Technology Pasadena CA USA
| | - Christof Meile
- Department of Marine Sciences University of Georgia Athens GA USA
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28
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Guerrero-Cruz S, Cremers G, van Alen TA, Op den Camp HJM, Jetten MSM, Rasigraf O, Vaksmaa A. Response of the Anaerobic Methanotroph " Candidatus Methanoperedens nitroreducens" to Oxygen Stress. Appl Environ Microbiol 2018; 84:e01832-18. [PMID: 30291120 PMCID: PMC6275348 DOI: 10.1128/aem.01832-18] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2018] [Accepted: 10/01/2018] [Indexed: 11/20/2022] Open
Abstract
"Candidatus Methanoperedens nitroreducens" is an archaeon that couples the anaerobic oxidation of methane to nitrate reduction. In natural and man-made ecosystems, this archaeon is often found at oxic-anoxic interfaces where nitrate, the product of aerobic nitrification, cooccurs with methane produced by methanogens. As such, populations of "Ca Methanoperedens nitroreducens" could be prone to regular oxygen exposure. Here, we investigated the effect of 5% (vol/vol) oxygen exposure in batch activity assays on a "Ca Methanoperedens nitroreducens" culture, enriched from an Italian paddy field. Metagenome sequencing of the DNA extracted from the enrichment culture revealed that 83% of 16S rRNA gene reads were assigned to a novel strain, "Candidatus Methanoperedens nitroreducens Verserenetto." RNA was extracted, and metatranscriptome sequencing upon oxygen exposure revealed that the active community changed, most notably in the appearance of aerobic methanotrophs. The gene expression of "Ca Methanoperedens nitroreducens" revealed that the key genes encoding enzymes of the methane oxidation and nitrate reduction pathways were downregulated. In contrast to this, we identified upregulation of glutaredoxin, thioredoxin family/like proteins, rubrerythrins, peroxiredoxins, peroxidase, alkyl hydroperoxidase, type A flavoproteins, FeS cluster assembly protein, and cysteine desulfurases, indicating the genomic potential of "Ca Methanoperedens nitroreducens Verserenetto" to counteract the oxidative damage and adapt in environments where they might be exposed to regular oxygen intrusion.IMPORTANCE "Candidatus Methanoperedens nitroreducens" is an anaerobic archaeon which couples the reduction of nitrate to the oxidation of methane. This microorganism is present in a wide range of aquatic environments and man-made ecosystems, such as paddy fields and wastewater treatment systems. In such environments, these archaea may experience regular oxygen exposure. However, "Ca Methanoperedens nitroreducens" is able to thrive under such conditions and could be applied for the simultaneous removal of dissolved methane and nitrogenous pollutants in oxygen-limited systems. To understand what machinery "Ca Methanoperedens nitroreducens" possesses to counteract the oxidative stress and survive, we characterized the response to oxygen exposure using a multi-omics approach.
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Affiliation(s)
- Simon Guerrero-Cruz
- Department of Microbiology, IWWR, Radboud University Nijmegen, Nijmegen, the Netherlands
| | - Geert Cremers
- Department of Microbiology, IWWR, Radboud University Nijmegen, Nijmegen, the Netherlands
| | - Theo A van Alen
- Department of Microbiology, IWWR, Radboud University Nijmegen, Nijmegen, the Netherlands
| | - Huub J M Op den Camp
- Department of Microbiology, IWWR, Radboud University Nijmegen, Nijmegen, the Netherlands
| | - Mike S M Jetten
- Department of Microbiology, IWWR, Radboud University Nijmegen, Nijmegen, the Netherlands
- Department of Biotechnology, Delft University of Technology, Delft, the Netherlands
- Soehngen Institute of Anaerobic Microbiology, Nijmegen, the Netherlands
| | - Olivia Rasigraf
- Department of Microbiology, IWWR, Radboud University Nijmegen, Nijmegen, the Netherlands
| | - Annika Vaksmaa
- Department of Microbiology, IWWR, Radboud University Nijmegen, Nijmegen, the Netherlands
- Royal Netherlands Institute for Sea Research, Texel, the Netherlands
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29
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Latif MA, Mehta CM, Batstone DJ. Enhancing soluble phosphate concentration in sludge liquor by pressurised anaerobic digestion. WATER RESEARCH 2018; 145:660-666. [PMID: 30205337 DOI: 10.1016/j.watres.2018.08.069] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2018] [Revised: 08/29/2018] [Accepted: 08/30/2018] [Indexed: 06/08/2023]
Abstract
Recovery of phosphate from wastewater is challenging, with one of the best opportunities being recovery from sludge anaerobic digestion liquor, as struvite. However, this is limited by the proportion of total phosphorous which is soluble, due to in-digester metal ion precipitation. High-pressure anaerobic digestion may enable enhanced phosphate solubility (and hence recovery potential), without the use of added acid, due to an increased liquid phase CO2 concentration. This was tested at 2, 4, and 6 bar absolute (bara) vs a 1 bara control reactor, fed with activated sludge. Increased pressure significantly (p = 0.0008), increased the fraction of phosphate that was soluble, ranging from 52% at 1 bara, to 75% at 6 bara. Model based analysis indicated that the main reason for increased solubility was pH depression (down to 6.4 at 6 bara), rather than changes in ion pairing (with carbonates) or increases in ionic activity. However, biological performance was adversely impacted, with a substantial loss in VS and COD destruction (on the order of 5%-10% absolute). No organic acid accumulation was observed. Bacterial and archaeal communities were significantly impacted (p∼0.0003-0.0005), with a shift to specific organisms, including Bacteroidales Rikenellaceae within the bacteria, and a Deep Sea Euryarchaeotal Group at 2 bara, and Methanocellaceae within the archaea at 4 and 6 bara. The work indicates that high-pressure operation is a technically viable option to improve phosphate recovery, and produce a high-methane biogas product, but that the loss of overall conversion needs to be further addressed, possibly through two-stage digestion.
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Affiliation(s)
- Muhammad A Latif
- Griffith School of Engineering and Build Environment, 170 Kessels Road, Griffith University, Nathan, Queensland, 4111, Australia; Advanced Water Management Centre (AWMC), Level 4, Gehrmann Bldg. (60), Research Road, University of Queensland, Brisbane, Queensland, 4072, Australia.
| | - Chirag M Mehta
- Advanced Water Management Centre (AWMC), Level 4, Gehrmann Bldg. (60), Research Road, University of Queensland, Brisbane, Queensland, 4072, Australia
| | - Damien J Batstone
- Advanced Water Management Centre (AWMC), Level 4, Gehrmann Bldg. (60), Research Road, University of Queensland, Brisbane, Queensland, 4072, Australia.
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30
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Characterization of downflow hanging sponge reactors with regard to structure, process function, and microbial community compositions. Appl Microbiol Biotechnol 2018; 102:10345-10352. [PMID: 30343428 DOI: 10.1007/s00253-018-9406-6] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2018] [Revised: 09/11/2018] [Accepted: 09/13/2018] [Indexed: 10/28/2022]
Abstract
The activated sludge (AS) process has been the most widely used process for wastewater treatment despite it has several limitations for its further application and adoption worldwide, owing to unsustainable properties such as high-energy consumption and the production of large amount of excess sludge. To overcome the drawbacks of the AS process, the downflow hanging sponge (DHS) has been developed as an energy-saving and easy-to-maintain alternative. To date, six types of different sponge configurations have been developed and their performances have been evaluated in practical- to full-scale DHS reactors. A large number of studies have been carried out in order to enhance the performance and expand the application fields of the DHS. Transition of this process to the deployment and diffusion stage from the research and development phase is now ongoing in India and Egypt as well as in Japan. Under this situation, concise and state-of-the art review is important for enhancing DHS research and future applications. Herein, we summarize and present the DHS concerning the history of development, the mechanism of treatment, recent studies on its use in the field of wastewater treatment, and the features of microbial community structure.
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Tortorella E, Tedesco P, Palma Esposito F, January GG, Fani R, Jaspars M, de Pascale D. Antibiotics from Deep-Sea Microorganisms: Current Discoveries and Perspectives. Mar Drugs 2018; 16:md16100355. [PMID: 30274274 PMCID: PMC6213577 DOI: 10.3390/md16100355] [Citation(s) in RCA: 72] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2018] [Revised: 09/25/2018] [Accepted: 09/27/2018] [Indexed: 12/17/2022] Open
Abstract
The increasing emergence of new forms of multidrug resistance among human pathogenic bacteria, coupled with the consequent increase of infectious diseases, urgently requires the discovery and development of novel antimicrobial drugs with new modes of action. Most of the antibiotics currently available on the market were obtained from terrestrial organisms or derived semisynthetically from fermentation products. The isolation of microorganisms from previously unexplored habitats may lead to the discovery of lead structures with antibiotic activity. The deep-sea environment is a unique habitat, and deep-sea microorganisms, because of their adaptation to this extreme environment, have the potential to produce novel secondary metabolites with potent biological activities. This review covers novel antibiotics isolated from deep-sea microorganisms. The chemical classes of the compounds, their bioactivities, and the sources of organisms are outlined. Furthermore, the authors report recent advances in techniques and strategies for the exploitation of deep-sea microorganisms.
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Affiliation(s)
- Emiliana Tortorella
- Institute of Protein Biochemistry, National Research Council, I-80131 Naples, Italy.
| | - Pietro Tedesco
- Institute of Protein Biochemistry, National Research Council, I-80131 Naples, Italy.
- Laboratoire d'Ingénierie des Systèmes Biologiques et des Procédés, INSA, 31400 Toulouse, France.
| | - Fortunato Palma Esposito
- Institute of Protein Biochemistry, National Research Council, I-80131 Naples, Italy.
- Stazione Zoologica "Anthon Dorn", Villa Comunale, I-80121 Naples, Italy.
| | - Grant Garren January
- Institute of Protein Biochemistry, National Research Council, I-80131 Naples, Italy.
| | - Renato Fani
- Department of Biology, University of Florence, Sesto Fiorentino, I-50019 Florence, Italy.
| | - Marcel Jaspars
- Marine Biodiscovery Centre, Department of Chemistry, University of Aberdeen, Aberdeen, Scotland AB24 3UE, UK.
| | - Donatella de Pascale
- Institute of Protein Biochemistry, National Research Council, I-80131 Naples, Italy.
- Stazione Zoologica "Anthon Dorn", Villa Comunale, I-80121 Naples, Italy.
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Future Directions of Marine Myxobacterial Natural Product Discovery Inferred from Metagenomics. Mar Drugs 2018; 16:md16090303. [PMID: 30158489 PMCID: PMC6163921 DOI: 10.3390/md16090303] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2018] [Revised: 08/18/2018] [Accepted: 08/23/2018] [Indexed: 11/23/2022] Open
Abstract
Over the last two decades, halophilic (organisms that thrive at high salt concentrations) and halotolerant (organisms that have adapted to high salt concentrations) myxobacteria emerged as an important source of structurally diverse secondary metabolites from the marine environment. This review explores the advance of metagenomics analysis and 16S rRNA gene phylogeny of the cultured and uncultured myxobacteria from marine and other salt-environments up to July 2018. The diversity of novel groups of myxobacteria in these environments appears unprecedented, especially in the Sorangiineae and Nannocystineae suborders. The Sandaracinaceae related clade in the Sorangiineae suborder seems more widely distributed compared to the exclusively marine myxobacterial cluster. Some of the previously identified clones from metagenomic studies were found to be related to the Nannocystineae suborder. This understanding provides the foundation for a vital, unexplored resource. Understanding the conditions required to cultivate these yet “uncultured” myxobacteria in the laboratory, while a key next step, offers a significant potential to further expand access to diverse secondary metabolites.
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33
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Establishing anaerobic hydrocarbon-degrading enrichment cultures of microorganisms under strictly anoxic conditions. Nat Protoc 2018; 13:1310-1330. [DOI: 10.1038/nprot.2018.030] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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Bhattarai S, Cassarini C, Rene ER, Kümmel S, Esposito G, Lens PNL. Enrichment of ANME-2 dominated anaerobic methanotrophy from cold seep sediment in an external ultrafiltration membrane bioreactor. Eng Life Sci 2018; 18:368-378. [PMID: 32624917 DOI: 10.1002/elsc.201700148] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2017] [Revised: 12/20/2017] [Accepted: 02/14/2018] [Indexed: 11/08/2022] Open
Abstract
Anaerobic oxidation of methane (AOM) coupled to sulfate reduction is a microbially mediated unique natural phenomenon with an ecological relevance in the global carbon balance and potential application in biotechnology. This study aimed to enrich an AOM performing microbial community with the main focus on anaerobic methanotrophic archaea (ANME) present in sediments from the Ginsburg mud volcano (Gulf of Cadiz), a known site for AOM, in a membrane bioreactor (MBR) for 726 days at 22 (± 3)°C and at ambient pressure. The MBR was equipped with a cylindrical external ultrafiltration membrane, fed a defined medium containing artificial seawater and operated at a cross flow velocity of 0.02 m/min. Sulfide production with simultaneous sulfate reduction was in equimolar ratio between days 480 and 585 of MBR operation, whereas methane consumption was in oscillating trend. At the end of the MBR operation (day 726), the enriched biomass was incubated with 13C labeled methane, 13C labeled inorganic carbon was produced and the AOM rate based on 13C-inorganic carbon was 1.2 μmol/(gdw d). Microbial analysis of the enriched biomass at 400 and 726 days of MBR operation showed that ANME-2 and Desulfosarcina type sulfate reducing bacteria were enriched in the MBR, which formed closely associated aggregates. The major relevance of this study is the enrichment of an AOM consortium in a MBR system which can assist to explore the ecophysiology of ANME and provides an opportunity to explore the potential application of AOM.
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Affiliation(s)
| | - Chiara Cassarini
- UNESCO-IHE Institute for Water Education The Netherlands.,Department of Microbiology National University of Ireland Galway Ireland
| | - Eldon R Rene
- UNESCO-IHE Institute for Water Education The Netherlands
| | - Steffen Kümmel
- Department for Isotope Biogeochemistry Helmholtz-Centre for Environmental Research (UFZ) Leipzig Germany
| | - Giovanni Esposito
- Department of Civil and Mechanical Engineering University of Cassino and Southern Lazio Cassino (FR) Italy
| | - Piet N L Lens
- UNESCO-IHE Institute for Water Education The Netherlands.,Department of Microbiology National University of Ireland Galway Ireland
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35
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Kato S, Miyazaki M, Kikuchi S, Kashiwabara T, Saito Y, Tasumi E, Suzuki K, Takai K, Cao LTT, Ohashi A, Imachi H. Biotic manganese oxidation coupled with methane oxidation using a continuous-flow bioreactor system under marine conditions. WATER SCIENCE AND TECHNOLOGY : A JOURNAL OF THE INTERNATIONAL ASSOCIATION ON WATER POLLUTION RESEARCH 2017; 76:1781-1795. [PMID: 28991793 DOI: 10.2166/wst.2017.365] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Biogenic manganese oxides (BioMnOx) can be applied for the effective removal and recovery of trace metals from wastewater because of their high adsorption capacity. Although a freshwater continuous-flow system for a nitrifier-based Mn-oxidizing microbial community for producing BioMnOx has been developed so far, a seawater continuous-flow bioreactor system for BioMnOx production has not been established. Here, we report BioMnOx production by a methanotroph-based microbial community by using a continuous-flow bioreactor system. The bioreactor system was operated using a deep-sea sediment sample as the inoculum with methane as the energy source for over 2 years. The BioMnOx production became evident after 370 days of reactor operation. The maximum Mn oxidation rate was 11.4 mg L-1 day-1. An X-ray diffraction analysis showed that the accumulated BioMnOx was birnessite. 16S rRNA gene-based clone analyses indicated that methanotrophic bacterial members were relatively abundant in the system; however, none of the known Mn-oxidizing bacteria were detected. A continuous-flow bioreactor system coupled with nitrification was also run in parallel for 636 days, but no BioMnOx production was observed in this bioreactor system. The comparative experiments indicated that the methanotroph-based microbial community, rather than the nitrifier-based community, was effective for BioMnOx production under the marine environmental conditions.
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Affiliation(s)
- Shingo Kato
- Ore Genesis Research Unit, Project Team for Development of New-generation Research Protocol for Submarine Resources, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Kanagawa 237-0061, Japan; Research and Development Center for Submarine Resources, JAMSTEC, Yokosuka, Kanagawa 237-0061, Japan E-mail:
| | - Masayuki Miyazaki
- Department of Subsurface Geobiological Analysis and Research (D-SUGAR), JAMSTEC, 2-15 Natsuhima-cho, Yokosuka, Kanagawa 237-0061, Japan
| | - Sakiko Kikuchi
- Ore Genesis Research Unit, Project Team for Development of New-generation Research Protocol for Submarine Resources, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Kanagawa 237-0061, Japan; Research and Development Center for Submarine Resources, JAMSTEC, Yokosuka, Kanagawa 237-0061, Japan E-mail:
| | - Teruhiko Kashiwabara
- Ore Genesis Research Unit, Project Team for Development of New-generation Research Protocol for Submarine Resources, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Kanagawa 237-0061, Japan; Research and Development Center for Submarine Resources, JAMSTEC, Yokosuka, Kanagawa 237-0061, Japan E-mail:
| | - Yumi Saito
- Department of Subsurface Geobiological Analysis and Research (D-SUGAR), JAMSTEC, 2-15 Natsuhima-cho, Yokosuka, Kanagawa 237-0061, Japan
| | - Eiji Tasumi
- Department of Subsurface Geobiological Analysis and Research (D-SUGAR), JAMSTEC, 2-15 Natsuhima-cho, Yokosuka, Kanagawa 237-0061, Japan
| | - Katsuhiko Suzuki
- Ore Genesis Research Unit, Project Team for Development of New-generation Research Protocol for Submarine Resources, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Kanagawa 237-0061, Japan; Research and Development Center for Submarine Resources, JAMSTEC, Yokosuka, Kanagawa 237-0061, Japan E-mail:
| | - Ken Takai
- Ore Genesis Research Unit, Project Team for Development of New-generation Research Protocol for Submarine Resources, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Kanagawa 237-0061, Japan; Research and Development Center for Submarine Resources, JAMSTEC, Yokosuka, Kanagawa 237-0061, Japan E-mail: ; Department of Subsurface Geobiological Analysis and Research (D-SUGAR), JAMSTEC, 2-15 Natsuhima-cho, Yokosuka, Kanagawa 237-0061, Japan
| | - Linh Thi Thuy Cao
- Department of Civil and Environmental Engineering, Graduate School of Engineering, Hiroshima University, Higashi-Hiroshima, Hiroshima 739-8511, Japan
| | - Akiyoshi Ohashi
- Department of Civil and Environmental Engineering, Graduate School of Engineering, Hiroshima University, Higashi-Hiroshima, Hiroshima 739-8511, Japan
| | - Hiroyuki Imachi
- Research and Development Center for Submarine Resources, JAMSTEC, Yokosuka, Kanagawa 237-0061, Japan E-mail: ; Department of Subsurface Geobiological Analysis and Research (D-SUGAR), JAMSTEC, 2-15 Natsuhima-cho, Yokosuka, Kanagawa 237-0061, Japan
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36
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Cassarini C, Rene ER, Bhattarai S, Esposito G, Lens PNL. Anaerobic oxidation of methane coupled to thiosulfate reduction in a biotrickling filter. BIORESOURCE TECHNOLOGY 2017; 240:214-222. [PMID: 28318933 DOI: 10.1016/j.biortech.2017.03.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2017] [Revised: 02/26/2017] [Accepted: 03/01/2017] [Indexed: 06/06/2023]
Abstract
Microorganisms from an anaerobic methane oxidizing sediment were enriched with methane gas as the substrate in a biotrickling filter (BTF) using thiosulfate as electron acceptor for 213days. Thiosulfate disproportionation to sulfate and sulfide were the dominating sulfur conversion process in the BTF and the sulfide production rate was 0.5mmoll-1day-1. A specific group of sulfate reducing bacteria (SRB), belonging to the Desulforsarcina/Desulfococcus group, was enriched in the BTF. The BTF biomass showed maximum sulfate reduction rate (0.38mmoll-1day-1) with methane as sole electron donor, measured in the absence of thiosulfate in the BTF. Therefore, a BTF fed with thiosulfate as electron acceptor can be used to enrich SRB of the DSS group and activate the inoculum for anaerobic oxidation of methane coupled to sulfate reduction.
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Affiliation(s)
- Chiara Cassarini
- UNESCO-IHE, Institute for Water Education, PO Box 3015, 2601 DA Delft, The Netherlands
| | - Eldon R Rene
- UNESCO-IHE, Institute for Water Education, PO Box 3015, 2601 DA Delft, The Netherlands.
| | - Susma Bhattarai
- UNESCO-IHE, Institute for Water Education, PO Box 3015, 2601 DA Delft, The Netherlands
| | - Giovanni Esposito
- University of Cassino and Southern Lazio, Department of Civil and Mechanical Engineering, via Di Biasio 43, 03043 Cassino, FR, Italy
| | - Piet N L Lens
- UNESCO-IHE, Institute for Water Education, PO Box 3015, 2601 DA Delft, The Netherlands
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37
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Sun W, Xiao E, Krumins V, Dong Y, Xiao T, Ning Z, Chen H, Xiao Q. Characterization of the microbial community composition and the distribution of Fe-metabolizing bacteria in a creek contaminated by acid mine drainage. Appl Microbiol Biotechnol 2016; 100:8523-35. [PMID: 27277134 DOI: 10.1007/s00253-016-7653-y] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2016] [Revised: 05/23/2016] [Accepted: 05/26/2016] [Indexed: 01/09/2023]
Abstract
A small watershed heavily contaminated by long-term acid mine drainage (AMD) from an upstream abandoned coal mine was selected to study the microbial community developed in such extreme system. The watershed consists of AMD-contaminated creek, adjacent contaminated soils, and a small cascade aeration unit constructed downstream, which provide an excellent contaminated site to study the microbial response in diverse extreme AMD-polluted environments. The results showed that the innate microbial communities were dominated by acidophilic bacteria, especially acidophilic Fe-metabolizing bacteria, suggesting that Fe and pH are the primary environmental factors in governing the indigenous microbial communities. The distribution of Fe-metabolizing bacteria showed distinct site-specific patterns. A pronounced shift from diverse communities in the upstream to Proteobacteria-dominated communities in the downstream was observed in the ecosystem. This location-specific trend was more apparent at genus level. In the upstream samples (sampling sites just below the coal mining adit), a number of Fe(II)-oxidizing bacteria such as Alicyclobacillus spp., Metallibacterium spp., and Acidithrix spp. were dominant, while Halomonas spp. were the major Fe(II)-oxidizing bacteria observed in downstream samples. Additionally, Acidiphilium, an Fe(III)-reducing bacterium, was enriched in the upstream samples, while Shewanella spp. were the dominant Fe(III)-reducing bacteria in downstream samples. Further investigation using linear discriminant analysis (LDA) effect size (LEfSe), principal coordinate analysis (PCoA), and unweighted pair group method with arithmetic mean (UPGMA) clustering confirmed the difference of microbial communities between upstream and downstream samples. Canonical correspondence analysis (CCA) and Spearman's rank correlation indicate that total organic carbon (TOC) content is the primary environmental parameter in structuring the indigenous microbial communities, suggesting that the microbial communities are shaped by three major environmental parameters (i.e., Fe, pH, and TOC). These findings were beneficial to a better understanding of natural attenuation of AMD.
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Affiliation(s)
- Weimin Sun
- State Key Laboratory of Environmental Geochemistry, Chinese Academy of Sciences, 99 Lincheng Road West, Guiyang, 550081, Guizhou Province, People's Republic of China.,Department of Biochemistry and Microbiology, Rutgers University, New Brunswick, NJ, 08901, USA.,Guangdong Institute of Eco-environment and Soil Sciences, Guangzhou, 510650, China
| | - Enzong Xiao
- State Key Laboratory of Environmental Geochemistry, Chinese Academy of Sciences, 99 Lincheng Road West, Guiyang, 550081, Guizhou Province, People's Republic of China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Valdis Krumins
- Department of Environmental Sciences, Rutgers University, New Brunswick, NJ, 08901, USA
| | - Yiran Dong
- Department of Geology, University of Illinois-Urbana Champaign, Urbana, IL, 61801, USA
| | - Tangfu Xiao
- State Key Laboratory of Environmental Geochemistry, Chinese Academy of Sciences, 99 Lincheng Road West, Guiyang, 550081, Guizhou Province, People's Republic of China. .,Innovation Center and Key Laboratory of Waters Safety & Protection in the Pearl River Delta, Ministry of Education, Guangzhou University, Guangzhou, 510006, China.
| | - Zengping Ning
- State Key Laboratory of Environmental Geochemistry, Chinese Academy of Sciences, 99 Lincheng Road West, Guiyang, 550081, Guizhou Province, People's Republic of China
| | - Haiyan Chen
- State Key Laboratory of Environmental Geochemistry, Chinese Academy of Sciences, 99 Lincheng Road West, Guiyang, 550081, Guizhou Province, People's Republic of China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Qingxiang Xiao
- State Key Laboratory of Environmental Geochemistry, Chinese Academy of Sciences, 99 Lincheng Road West, Guiyang, 550081, Guizhou Province, People's Republic of China.,University of Chinese Academy of Sciences, Beijing, 100049, China
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38
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Imachi H, Sakai S, Kubota T, Miyazaki M, Saito Y, Takai K. Sedimentibacter acidaminivorans sp. nov., an anaerobic, amino-acid-utilizing bacterium isolated from marine subsurface sediment. Int J Syst Evol Microbiol 2016; 66:1293-1300. [PMID: 26739306 DOI: 10.1099/ijsem.0.000878] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
A novel, anaerobic bacterium, strain MO-SEDIT, was isolated from a methanogenic microbial community, which was originally obtained from marine subsurface sediments collected from off the Shimokita Peninsula of Japan. Cells were Gram-stain-negative, non-motile, non-spore-forming rods, 0.4-1.4 μm long by 0.4-0.6 μm wide. The cells also formed long filaments of up to about 11 μm. The strain grew on amino acids (i.e. valine, leucine, isoleucine, methionine, glycine, phenylalanine, tryptophan, lysine and arginine), pyruvate and melezitose in the presence of yeast extract. Growth was observed at 4-37 °C (optimally at 30 °C), at pH 6.0 and 8.5 (optimally at 7.0-7.5) and in 0-60 g l- 1 NaCl (optimally 20 g NaCl l- 1). The G+C content of the DNA was 32.0 mol%. The polar lipids of strain MO-SEDIT were phosphatidylglycerol, phosphatidyl lipids and unknown lipids. The major cellular fatty acids (>10 % of the total) were C14 : 0, C16 : 1ω9 and C16 : 0 dimethyl aldehyde. Comparative sequence analysis of the 16S rRNA gene showed that strain MO-SEDIT was affiliated with the genus Sedimentibacter within the phylum Firmicutes. It was related most closely to the type strain of Sedimentibacter saalensis (94 % sequence similarity). Based on the phenotypic and genetic characteristics, strain MO-SEDIT is considered to represent a novel species of the genus Sedimentibacter, for which the name Sedimentibacter acidaminivorans sp. nov. is proposed. The type strain is MO-SEDIT ( = JCM 17293T = DSM 24004T).
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Affiliation(s)
- Hiroyuki Imachi
- Research and Development Center for Marine Resources,JAMSTEC, Kanagawa 237-0061,Japan.,Department of Subsurface Geobiological Analysis and Research (D-SUGAR), Japan Agency for Marine-Earth Science & Technology (JAMSTEC),Yokosuka, Kanagawa 237-0061,Japan
| | - Sanae Sakai
- Department of Subsurface Geobiological Analysis and Research (D-SUGAR), Japan Agency for Marine-Earth Science & Technology (JAMSTEC),Yokosuka, Kanagawa 237-0061,Japan
| | - Takaaki Kubota
- Marine Functional Biology Group,JAMSTEC, Yokosuka, Kanagawa 237-0061,Japan
| | - Masayuki Miyazaki
- Department of Subsurface Geobiological Analysis and Research (D-SUGAR), Japan Agency for Marine-Earth Science & Technology (JAMSTEC),Yokosuka, Kanagawa 237-0061,Japan
| | - Yayoi Saito
- Department of Subsurface Geobiological Analysis and Research (D-SUGAR), Japan Agency for Marine-Earth Science & Technology (JAMSTEC),Yokosuka, Kanagawa 237-0061,Japan.,Department of Environmental Systems Engineering, Nagaoka University of Technology,Nagaoka, Niigata 940-2188,Japan
| | - Ken Takai
- Department of Subsurface Geobiological Analysis and Research (D-SUGAR), Japan Agency for Marine-Earth Science & Technology (JAMSTEC),Yokosuka, Kanagawa 237-0061,Japan
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Aoki M, Kakiuchi R, Yamaguchi T, Takai K, Inagaki F, Imachi H. Phylogenetic Diversity of aprA Genes in Subseafloor Sediments on the Northwestern Pacific Margin off Japan. Microbes Environ 2015; 30:276-80. [PMID: 26156553 PMCID: PMC4567568 DOI: 10.1264/jsme2.me15023] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Markedly diverse sequences of the adenosine-5'-phosphosulfate reductase alpha subunit gene (aprA), which encodes a key enzyme in microbial sulfate reduction and sulfur oxidation, were detected in subseafloor sediments on the northwestern Pacific off Japan. The aprA gene sequences were grouped into 135 operational taxonomic units (90% sequence identity), including genes related to putative sulfur-oxidizing bacteria predominantly detected in sulfate-depleted deep sediments. Our results suggest that microbial ecosystems in the subseafloor biosphere have phylogenetically diverse genetic potentials to mediate cryptic sulfur cycles in sediments, even where sulfate is rarely present.
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Affiliation(s)
- Masataka Aoki
- Department of Subsurface Geobiological Analysis and Research (D-SUGAR), Japan Agency for Marine-Earth Science and Technology (JAMSTEC)
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40
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Pohlschroder M, Esquivel RN. Archaeal type IV pili and their involvement in biofilm formation. Front Microbiol 2015; 6:190. [PMID: 25852657 PMCID: PMC4371748 DOI: 10.3389/fmicb.2015.00190] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2015] [Accepted: 02/20/2015] [Indexed: 12/13/2022] Open
Abstract
Type IV pili are ancient proteinaceous structures present on the cell surface of species in nearly all bacterial and archaeal phyla. These filaments, which are required for a diverse array of important cellular processes, are assembled employing a conserved set of core components. While type IV pilins, the structural subunits of pili, share little sequence homology, their signal peptides are structurally conserved allowing for in silico prediction. Recently, in vivo studies in model archaea representing the euryarchaeal and crenarchaeal kingdoms confirmed that several of these pilins are incorporated into type IV adhesion pili. In addition to facilitating surface adhesion, these in vivo studies also showed that several predicted pilins are required for additional functions that are critical to biofilm formation. Examples include the subunits of Sulfolobus acidocaldarius Ups pili, which are induced by exposure to UV light and promote cell aggregation and conjugation, and a subset of the Haloferax volcanii adhesion pilins, which play a critical role in microcolony formation while other pilins inhibit this process. The recent discovery of novel pilin functions such as the ability of haloarchaeal adhesion pilins to regulate swimming motility may point to novel regulatory pathways conserved across prokaryotic domains. In this review, we will discuss recent advances in our understanding of the functional roles played by archaeal type IV adhesion pili and their subunits, with particular emphasis on their involvement in biofilm formation.
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Affiliation(s)
| | - Rianne N Esquivel
- Department of Biology, University of Pennsylvania Philadelphia, PA, USA
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