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Mills S, Trego AC, Prevedello M, De Vrieze J, O’Flaherty V, Lens PN, Collins G. Unifying concepts in methanogenic, aerobic, and anammox sludge granulation. ENVIRONMENTAL SCIENCE AND ECOTECHNOLOGY 2024; 17:100310. [PMID: 37705860 PMCID: PMC10495608 DOI: 10.1016/j.ese.2023.100310] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/19/2022] [Revised: 06/17/2023] [Accepted: 08/05/2023] [Indexed: 09/15/2023]
Abstract
The retention of dense and well-functioning microbial biomass is crucial for effective pollutant removal in several biological wastewater treatment technologies. High solids retention is often achieved through aggregation of microbial communities into dense, spherical aggregates known as granules, which were initially discovered in the 1980s. These granules have since been widely applied in upflow anaerobic digesters for waste-to-energy conversions. Furthermore, granular biomass has been applied in aerobic wastewater treatment and anaerobic ammonium oxidation (anammox) technologies. The mechanisms underpinning the formation of methanogenic, aerobic, and anammox granules are the subject of ongoing research. Although each granule type has been extensively studied in isolation, there has been a lack of comparative studies among these granulation processes. It is likely that there are some unifying concepts that are shared by all three sludge types. Identifying these unifying concepts could allow a unified theory of granulation to be formed. Here, we review the granulation mechanisms of methanogenic, aerobic, and anammox granular sludge, highlighting several common concepts, such as the role of extracellular polymeric substances, cations, and operational parameters like upflow velocity and shear force. We have then identified some unique features of each granule type, such as different internal structures, microbial compositions, and quorum sensing systems. Finally, we propose that future research should prioritize aspects of microbial ecology, such as community assembly or interspecies interactions in individual granules during their formation and growth.
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Affiliation(s)
- Simon Mills
- Microbial Communities Laboratory, School of Biological and Chemical Sciences, National University of Ireland Galway, University Road, Galway, H91 TK33, Ireland
| | - Anna Christine Trego
- Microbial Ecology Laboratory School of Biological and Chemical Sciences, University of Galway, University Road, Galway, H91 TK33, Ireland
| | - Marco Prevedello
- Microbial Communities Laboratory, School of Biological and Chemical Sciences, National University of Ireland Galway, University Road, Galway, H91 TK33, Ireland
| | - Jo De Vrieze
- Center for Microbial Ecology and Technology (CMET), Ghent University, Coupure Links 653, B-9000, Gent, Belgium
| | - Vincent O’Flaherty
- Microbial Ecology Laboratory School of Biological and Chemical Sciences, University of Galway, University Road, Galway, H91 TK33, Ireland
| | - Piet N.L. Lens
- University of Galway, University Road, Galway, H91 TK33, Ireland
| | - Gavin Collins
- Microbial Communities Laboratory, School of Biological and Chemical Sciences, National University of Ireland Galway, University Road, Galway, H91 TK33, Ireland
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2
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Hirakata Y, Mei R, Morinaga K, Katayama T, Tamaki H, Meng XY, Watari T, Yamaguchi T, Hatamoto M, Nobu MK. Identification and cultivation of anaerobic bacterial scavengers of dead cells. THE ISME JOURNAL 2023; 17:2279-2289. [PMID: 37872273 PMCID: PMC10689501 DOI: 10.1038/s41396-023-01538-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Revised: 10/06/2023] [Accepted: 10/09/2023] [Indexed: 10/25/2023]
Abstract
The cycle of life and death and Earth's carbon cycle(s) are intimately linked, yet how bacterial cells, one of the largest pools of biomass on Earth, are recycled back into the carbon cycle remains enigmatic. In particular, no bacteria capable of scavenging dead cells in oxygen-depleted environments have been reported thus far. In this study, we discover the first anaerobes that scavenge dead cells and the two isolated strains use distinct strategies. Based on live-cell imaging, transmission electron microscopy, and hydrolytic enzyme assays, one strain (designated CYCD) relied on cell-to-cell contact and cell invagination for degrading dead food bacteria where as the other strain (MGCD) degraded dead food bacteria via excretion of lytic extracellular enzymes. Both strains could degrade dead cells of differing taxonomy (bacteria and archaea) and differing extents of cell damage, including those without artificially inflicted physical damage. In addition, both depended on symbiotic metabolic interactions for maximizing cell degradation, representing the first cultured syntrophic Bacteroidota. We collectively revealed multiple symbiotic bacterial decomposition routes of dead prokaryotic cells, providing novel insight into the last step of the carbon cycle.
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Affiliation(s)
- Yuga Hirakata
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, 305-8566, Japan.
| | - Ran Mei
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, 305-8566, Japan
| | - Kana Morinaga
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, 305-8566, Japan
| | - Taiki Katayama
- Geomicrobiology Research Group, Research Institute for Geo-Resources and Environment, Geological Survey of Japan (GSJ), National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, 305-8567, Japan
| | - Hideyuki Tamaki
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, 305-8566, Japan
| | - Xian-Ying Meng
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, 305-8566, Japan
| | - Takahiro Watari
- Department of Civil and Environmental Engineering, Nagaoka University of Technology, Nagaoka, 940-2188, Japan
| | - Takashi Yamaguchi
- Department of Civil and Environmental Engineering, Nagaoka University of Technology, Nagaoka, 940-2188, Japan
- 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
| | - Masaru K Nobu
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, 305-8566, Japan.
- Institute for Extra-Cutting-Edge Science and Technology Avant-Garde Research (X-star), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, 237-0061, Japan.
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3
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Costas-Selas C, Martínez-García S, Logares R, Hernández-Ruiz M, Teira E. Role of Bacterial Community Composition as a Driver of the Small-Sized Phytoplankton Community Structure in a Productive Coastal System. MICROBIAL ECOLOGY 2022:10.1007/s00248-022-02125-2. [PMID: 36305941 DOI: 10.1007/s00248-022-02125-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Accepted: 10/12/2022] [Indexed: 06/16/2023]
Abstract
We present here the first detailed description of the seasonal patterns in bacterial community composition (BCC) in shelf waters off the Ría de Vigo (Spain), based on monthly samplings during 2 years. Moreover, we studied the relationship between bacterial and small-sized eukaryotic community composition to identify potential biotic interactions among components of these two communities. Bacterial operational taxonomic unit (OTU) richness and diversity systematically peaked in autumn-winter, likely related to low resource availability during this period. BCC showed seasonal and vertical patterns, with Rhodobacteraceae and Flavobacteriaceae families dominating in surface waters, and SAR11 clade dominating at the base of the photic zone (30 m depth). BCC variability was significantly explained by environmental variables (e.g., temperature of water, solar radiation, or dissolved organic matter). Interestingly, a strong and significant correlation was found between BCC and small-sized eukaryotic community composition (ECC), which suggests that biotic interactions may play a major role as structuring factors of the microbial plankton in this productive area. In addition, co-occurrence network analyses revealed strong and significant, mostly positive, associations between bacteria and small-sized phytoplankton. Positive associations likely result from mutualistic relationships (e.g., between Dinophyceae and Rhodobacteraceae), while some negative correlations suggest antagonistic interactions (e.g., between Pseudo-nitzchia sp. and SAR11). These results support the key role of biotic interactions as structuring factors of the small-sized eukaryotic community, mostly driven by positive associations between small-sized phytoplankton and bacteria.
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Affiliation(s)
- Cecilia Costas-Selas
- Centro de Investigación Mariña, Universidade de Vigo, Departamento de Ecoloxía e Bioloxía Animal, 36310, Vigo, Spain.
| | - Sandra Martínez-García
- Centro de Investigación Mariña, Universidade de Vigo, Departamento de Ecoloxía e Bioloxía Animal, 36310, Vigo, Spain
| | - Ramiro Logares
- Departament de Biologia Marina I Oceanografia, Institut de Ciéncies del Mar (ICM), CSIC, Catalonia, Barcelona, Spain
| | - Marta Hernández-Ruiz
- Centro de Investigación Mariña, Universidade de Vigo, Departamento de Ecoloxía e Bioloxía Animal, 36310, Vigo, Spain
| | - Eva Teira
- Centro de Investigación Mariña, Universidade de Vigo, Departamento de Ecoloxía e Bioloxía Animal, 36310, Vigo, Spain
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Bourland W, Pomahač O, Čepička I. Morphology and phylogeny of two anaerobic freshwater ciliates: Brachonella comma sp. nov. and the widely-distributed but little-known caenomorphid, Ludio parvulus Penard, 1922. J Eukaryot Microbiol 2022; 69:e12892. [PMID: 35113477 DOI: 10.1111/jeu.12892] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2021] [Revised: 12/16/2021] [Accepted: 01/27/2022] [Indexed: 11/26/2022]
Abstract
Hypoxic, sulfidic freshwater sediments typically support a diffuse consortium of distinctive ciliated protists, including caenomorphids, metopids, and odontostomatids among others. A recent resurgence of interest in these important members of sapropelic food webs has resulted in the description of many new species and an effort, still in its infancy, to characterize them from a morphologic, molecular, and metabolic standpoint and to determine their phylogenetic relationships. Their seemingly invariable association with prokaryotic endosymbionts and, less commonly, ectosymbionts, has become a focus for many researchers. In this report, based on morphologic and molecular data we describe a Brachonella species (Ciliophora, Metopida) new to science and analyze its phylogeny. We also provide a morphologic and molecular characterization of the smallest representative of the Caenomorphidae Poche, 1913, Ludio parvulus Penard, 1922. The phylogenetic analysis confirms the inclusion of this species in the Caenomorphidae.
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Affiliation(s)
- William Bourland
- Department of Zoology, Faculty of Science, Charles University, Prague, Czech Republic
| | - Ondřej Pomahač
- Department of Zoology, Faculty of Science, Charles University, Prague, Czech Republic
| | - Ivan Čepička
- Department of Zoology, Faculty of Science, Charles University, Prague, Czech Republic
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5
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Abstract
Wastewater treatment plants are engineering technologies used worldwide to protect the environment and human health. Microbial communities sustain these plants, so it is crucial to know the key factors responsible for the community assembly. We show, in contrast to existing understanding, that microbial immigration largely controls the community structure in these plants and that the fate (growth or death) of immigrating species in the plants is controlled by local factors. The community structure was quantitatively predicted by the immigrating microbial community, highlighting the need to revise the way we today understand, design, and manage microbial communities in wastewater treatment plants. The assembly of bacterial communities in wastewater treatment plants (WWTPs) is affected by immigration via wastewater streams, but the impact and extent of bacterial immigrants are still unknown. Here, we quantify the effect of immigration at the species level in 11 Danish full-scale activated sludge (AS) plants. All plants have different source communities but have very similar process design, defining the same overall environmental growth conditions. The AS community composition in each plant was strongly reflected by the corresponding influent wastewater (IWW) microbial composition. Most species in AS across the plants were detected and quantified in the corresponding IWW, allowing us to identify their fate in the AS: growing, disappearing, or surviving. Most of the abundant species in IWW disappeared in AS, so their presence in the AS biomass was only due to continuous mass-immigration. In AS, most of the abundant growing species were present in the IWW at very low abundances. We predicted the AS species abundances from their abundance in IWW by using a partial least square regression model. Some species in AS were predicted by their own abundance in IWW, while others by multiple species abundances. Detailed analyses of functional guilds revealed different prediction patterns for different species. We show, in contrast to the present understanding, that the AS microbial communities were strongly controlled by the IWW source community and could be quantitatively predicted by taking into account immigration. This highlights a need to revise the way we understand, design, and manage the microbial communities in WWTPs.
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Tian L, Wang L. Multi-omics analysis reveals structure and function of biofilm microbial communities in a pre-denitrification biofilter. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 757:143908. [PMID: 33316516 DOI: 10.1016/j.scitotenv.2020.143908] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Revised: 11/16/2020] [Accepted: 11/17/2020] [Indexed: 06/12/2023]
Abstract
The highly complex microbial communities in biofilm play crucial roles in the pollutant removal performance of wastewater treatment plants (WWTPs). In the present study, using multi-omics analysis, we studied microbial structure, key enzymes, functional traits, and key metabolic pathways of pre-denitrification biofilter in an urban WWTP in China. The analysis results of metagenomic and metaproteomic showed that Betaproteobacteria and Flavobacteriia were dominant in biofilms. The integrated metagenomic and metaproteomic data showed that the expression of nitrogen metabolism genes was high, and the high proportion of denitrification module indicating that denitrification was the main nitrogen removal pathway. The most abundant denitrifying bacterial genera were: Dechloromonas, Acidovorax, Bosea, Polaromonas, and Chryseobacterium. And microorganisms with denitrification potential may not be able to denitrify in the actual operation of the filter. The integrated analysis of metaproteomic and metabolomic showed that there was a correlation between biofilm microorganisms and metabolites. Metabolomic analysis indicated that metabolic profiles of biofilms varied with layer height. This study provides the first detailed microbial communities and metabolic profiles in a full-scale pre-denitrification biofilter and clarifies the mechanism of denitrification.
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Affiliation(s)
- Lu Tian
- College of Environmental Science and Engineering, Ocean University of China, Qingdao 266100, China
| | - Lin Wang
- College of Environmental Science and Engineering, Ocean University of China, Qingdao 266100, China.
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7
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Hirakata Y, Hatamoto M, Oshiki M, Watari T, Araki N, Yamaguchi T. Food selectivity of anaerobic protists and direct evidence for methane production using carbon from prey bacteria by endosymbiotic methanogen. ISME JOURNAL 2020; 14:1873-1885. [PMID: 32341474 DOI: 10.1038/s41396-020-0660-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Revised: 04/05/2020] [Accepted: 04/07/2020] [Indexed: 01/28/2023]
Abstract
Anaerobic protists are major predators of prokaryotes in anaerobic ecosystems. However, little is known about the predation behavior of anaerobic protists because almost none have been cultured. In particular, these characteristics of anaerobic protists in the phyla Metamonada and Cercozoa have not been reported previously. In this study, we isolated three anaerobic protists, Cyclidium sp., Trichomitus sp., and Paracercomonas sp., from anaerobic granular sludge in an up-flow anaerobic sludge blanket reactor used to treat domestic sewage. Ingestion and digestion of food bacteria by anaerobic protists with or without endosymbiotic methanogens were demonstrated using tracer experiments with green fluorescent protein and a stable carbon isotope. These tracer experiments also demonstrated that Cyclidium sp. supplied CO2 and hydrogen to endosymbiotic methanogens. While Cyclidium sp. and Trichomitus sp. ingested both Gram-negative and -positive bacteria, Paracercomonas sp. could only take up Gram-negative bacteria. Archaeal cells such as Methanobacterium beijingense and Methanospirillum hungatei did not support the growth of these protists. Metabolite patterns of all three protists differed and were influenced by food bacterial species. These reported growth rates, ingestion rates, food selectivity, and metabolite patterns provide important insights into the ecological roles of these protists in anaerobic ecosystems.
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Affiliation(s)
- Yuga Hirakata
- Department of Science of Technology Innovation, Nagaoka University of Technology, Nagaoka, Niigata, Japan
| | - Masashi Hatamoto
- Department of Civil and Environmental Systems Engineering, Nagaoka University of Technology, Nagaoka, Niigata, Japan.
| | - Mamoru Oshiki
- Department of Civil Engineering, Nagaoka College, National Institute of Technology, Nagaoka, Niigata, Japan
| | - Takahiro Watari
- Department of Civil and Environmental Systems Engineering, Nagaoka University of Technology, Nagaoka, Niigata, Japan
| | - Nobuo Araki
- Department of Civil Engineering, Nagaoka College, National Institute 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 Systems Engineering, Nagaoka University of Technology, Nagaoka, Niigata, Japan
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8
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Bock C, Jensen M, Forster D, Marks S, Nuy J, Psenner R, Beisser D, Boenigk J. Factors shaping community patterns of protists and bacteria on a European scale. Environ Microbiol 2020; 22:2243-2260. [PMID: 32202362 DOI: 10.1111/1462-2920.14992] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2018] [Accepted: 03/18/2020] [Indexed: 01/19/2023]
Abstract
Factors shaping community patterns of microorganisms are controversially discussed. Physical and chemical factors certainly limit the survival of individual taxa and maintenance of diversity. In recent years, a contribution of geographic distance and dispersal barriers to distribution patterns of protists and bacteria has been demonstrated. Organismic interactions such as competition, predation and mutualism further modify community structure and maintenance of distinct taxa. Here, we address the relative importance of these different factors in shaping protists and bacterial communities on a European scale using high-throughput sequencing data obtained from lentic freshwater ecosystems. We show that community patterns of protists are similar to those of bacteria. Our results indicate that cross-domain organismic factors are important variables with a higher influence on protists as compared with bacteria. Abiotic physical and chemical factors also contributed significantly to community patterns. The contribution of these latter factors was higher for bacteria, which may reflect a stronger biogeochemical coupling. The contribution of geographical distance was similar for both microbial groups.
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Affiliation(s)
- Christina Bock
- Biodiversity, University of Duisburg-Essen, Universitätsstr. 5, 45141, Essen, Germany
| | - Manfred Jensen
- Biodiversity, University of Duisburg-Essen, Universitätsstr. 5, 45141, Essen, Germany
| | - Dominik Forster
- Department of Ecology, University of Kaiserslautern, Erwin-Schrödinger-Str. 14, 67663, Kaiserslautern, Germany
| | - Sabina Marks
- Biodiversity, University of Duisburg-Essen, Universitätsstr. 5, 45141, Essen, Germany
| | - Julia Nuy
- Biodiversity, University of Duisburg-Essen, Universitätsstr. 5, 45141, Essen, Germany
| | - Roland Psenner
- Lake and Glacier Research, Institute of Ecology, University of Innsbruck, Technikerstrasse 25, 6020, Innsbruck, Austria
| | - Daniela Beisser
- Biodiversity, University of Duisburg-Essen, Universitätsstr. 5, 45141, Essen, Germany
| | - Jens Boenigk
- Biodiversity, University of Duisburg-Essen, Universitätsstr. 5, 45141, Essen, Germany
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Oshiki M, Fukushima T, Kawano S, Kasahara Y, Nakagawa J. Thiocyanate Degradation by a Highly Enriched Culture of the Neutrophilic Halophile Thiohalobacter sp. Strain FOKN1 from Activated Sludge and Genomic Insights into Thiocyanate Metabolism. Microbes Environ 2019; 34:402-412. [PMID: 31631078 PMCID: PMC6934394 DOI: 10.1264/jsme2.me19068] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
Thiocyanate (SCN-) is harmful to a wide range of organisms, and its removal is essential for environmental protection. A neutrophilic halophile capable of thiocyanate degradation, Thiohalobacter sp. strain FOKN1, was highly enriched (relative abundance; 98.4%) from activated sludge collected from a bioreactor receiving thiocyanate-rich wastewater. The enrichment culture degraded 3.38 mM thiocyanate within 140 h, with maximum activity at pH 8.8, 37°C, and 0.18 M sodium chloride. Thiocyanate degradation was inhibited by 30 mg L-1 phenol, but not by thiosulfate. Microbial thiocyanate degradation is catalyzed by thiocyanate dehydrogenase, while limited information is currently available on the molecular mechanisms underlying thiocyanate degradation by the thiocyanate dehydrogenase of neutrophilic halophiles. Therefore, (meta)genomic and proteomic analyses of enrichment cultures were performed to elucidate the whole genome sequence and proteome of Thiohalobacter sp. strain FOKN1. The 3.23-Mb circular Thiohalobacter sp. strain FOKN1 genome was elucidated using a PacBio RSII sequencer, and the expression of 914 proteins was identified by tandem mass spectrometry. The Thiohalobacter sp. strain FOKN1 genome had a gene encoding thiocyanate dehydrogenase, which was abundant in the proteome, suggesting that thiocyanate is degraded by thiocyanate dehydrogenase to sulfur and cyanate. The sulfur formed may be oxidized to sulfate by the sequential oxidation reactions of dissimilatory sulfite reductase, adenosine-5'-phosphosulfate reductase, and dissimilatory ATP sulfurylase. Although the Thiohalobacter sp. strain FOKN1 genome carried a gene encoding cyanate lyase, its protein expression was not detectable. The present study advances the understanding of the molecular mechanisms underlying thiocyanate degradation by the thiocyanate dehydrogenase of neutrophilic halophiles.
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Affiliation(s)
- Mamoru Oshiki
- Department of Civil Engineering, National Institute of Technology, Nagaoka College
| | - Toshikazu Fukushima
- Advanced Technology Research Laboratories, Research & Development, Nippon Steel Corporation
| | - Shuichi Kawano
- Department of Computer and Network Engineering Graduate School of Informatics and Engineering, The University of Electro-Communications
| | | | - Junichi Nakagawa
- Advanced Technology Research Laboratories, Research & Development, Nippon Steel Corporation
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10
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Hirakata Y, Hatamoto M, Oshiki M, Watari T, Kuroda K, Araki N, Yamaguchi T. Temporal variation of eukaryotic community structures in UASB reactor treating domestic sewage as revealed by 18S rRNA gene sequencing. Sci Rep 2019; 9:12783. [PMID: 31484981 PMCID: PMC6726610 DOI: 10.1038/s41598-019-49290-y] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2019] [Accepted: 08/22/2019] [Indexed: 11/09/2022] Open
Abstract
Eukaryotes are important components of ecosystems in wastewater treatment processes. However, little is known about eukaryotic community in anaerobic wastewater treatment systems. In this study, eukaryotic communities in an up flow anaerobic sludge blanket (UASB) reactor treating domestic sewage during two years of operation were investigated using V4 and V9 regions of 18S rRNA gene for amplicon sequencing. In addition, activated sludge and influent sewage samples were also analyzed and used as the references for aerobic eukaryotic community to characterize anaerobic eukaryotes. The amplicon sequence V4 and V9 libraries detected different taxonomic groups, especially from the UASB samples, suggesting that commonly used V4 and V9 primer pairs could produce a bias for eukaryotic communities analysis. Eukaryotic community structures in the UASB reactor were influenced by the immigration of eukaryotes via influent sewage but were clearly different from the influent sewage and activated sludge. Multivariate statistics indicated that protist genera Cyclidium, Platyophrya and Subulatomonas correlated with chemical oxygen demand and suspended solid concentration, and could be used as bioindicators of treatment performance. Uncultured eukaryotes groups were dominant in the UASB reactor, and their physiological roles need to be examined to understand their contributions to anaerobic processes in future studies.
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Affiliation(s)
- Yuga Hirakata
- Department of Science of Technology Innovation, Nagaoka University of Technology, 1603-1 Kamitomioka, Nagaoka, Niigata, 940-2188, Japan
| | - Masashi Hatamoto
- Department of Civil and Environmental Engineering, Nagaoka University of Technology, 1603-1 Kamitomioka, Nagaoka, Niigata, 940-2188, Japan.
| | - Mamoru Oshiki
- Department of Civil Engineering, National institute of Technology, Nagaoka College, 888 Nishikatakaimachi, Nagaoka, Niigata, 940-0834, Japan
| | - Takahiro Watari
- Department of Civil and Environmental Engineering, Nagaoka University of Technology, 1603-1 Kamitomioka, Nagaoka, Niigata, 940-2188, Japan
| | - Kyohei Kuroda
- Department of Chemical Science and Engineering, National Institute of Technology, Miyakonojo College, 473-1 Yoshio-cho, Miyakonojo, Miyazaki, 885-8567, Japan
| | - Nobuo Araki
- Department of Civil Engineering, National institute of Technology, Nagaoka College, 888 Nishikatakaimachi, Nagaoka, Niigata, 940-0834, Japan
| | - Takashi Yamaguchi
- Department of Science of Technology Innovation, Nagaoka University of Technology, 1603-1 Kamitomioka, Nagaoka, Niigata, 940-2188, Japan.,Department of Civil and Environmental Engineering, Nagaoka University of Technology, 1603-1 Kamitomioka, Nagaoka, Niigata, 940-2188, Japan
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11
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Oshiki M, Masuda Y, Yamaguchi T, Araki N. Synergistic inhibition of anaerobic ammonium oxidation (anammox) activity by phenol and thiocyanate. CHEMOSPHERE 2018; 213:498-506. [PMID: 30245226 DOI: 10.1016/j.chemosphere.2018.09.055] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2018] [Revised: 08/29/2018] [Accepted: 09/09/2018] [Indexed: 06/08/2023]
Abstract
Coke-oven wastewater discharged from the steel-manufacturing process is phenol and thiocyanate (SCN)-rich wastewater, which inhibits microbial activities in biological wastewater treatment processes. In the present study, synergistic inhibition of anaerobic ammonium oxidation (anammox) activity by phenol and SCN was examined by batch incubation and continuous operation of an anammox reactor. The comparison of anammox activities determined in the batch incubation, in which the anammox biomass was anoxically incubated with 10-250 mg L-1 of i) phenol, ii) SCN, or iii) both phenol and SCN, showed that synergistic inhibition by phenol and SCN was greater than the inhibitions by phenol or SCN alone. The synergistic inhibition by phenol and SCN was further investigated by operating an up-flow column anammox reactor for 262 d. The removal efficiencies of NH4+ and NO2- deteriorated when phenol and SCN concentrations in the influent increased to 16 and 32 mg L-1, respectively, and the inhibition of anammox activity was further investigated by a15NO2- tracer experiment. Addition of phenol and SCN resulted in a population shift of anammox bacteria, and the dominant species changed from "Candidatus Kuenenia stuttgartiensis" to "Ca. Brocadia sinica". The relative abundance of Azoarcus and Thiobacillus 16S rRNA gene reads increased during the operation, suggesting that they were responsible for the anaerobic phenol and SCN degradation. The present study is the first to document the synergistic inhibition of anammox activity by phenol and SCN and the microbial consortia involved in the nitrogen removal as well as the phenol and SCN degradations.
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Affiliation(s)
- Mamoru Oshiki
- Department of Civil Engineering, National Institute of Technology, Nagaoka College, Nagaoka, Japan.
| | - Yoshiko Masuda
- Department of Civil Engineering, National Institute of Technology, Nagaoka College, Nagaoka, Japan
| | - Takashi Yamaguchi
- Department of Science of Technology Innovation, Nagaoka University of Technology, Nagaoka, Japan
| | - Nobuo Araki
- Department of Civil Engineering, National Institute of Technology, Nagaoka College, Nagaoka, Japan
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12
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Oshiki M, Araki M, Hirakata Y, Hatamoto M, Yamaguchi T, Araki N. Ureolytic Prokaryotes in Soil: Community Abundance and Diversity. Microbes Environ 2018; 33:230-233. [PMID: 29709896 PMCID: PMC6031400 DOI: 10.1264/jsme2.me17188] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
Although the turnover of urea is a crucial process in nitrogen transformation in soil, limited information is currently available on the abundance and diversity of ureolytic prokaryotes. The abundance and diversity of the soil 16S rRNA gene and ureC (encoding a urease catalytic subunit) were examined in seven soil types using quantitative PCR and amplicon sequencing with Illumina MiSeq. The amplicon sequencing of ureC revealed that the ureolytic community was composed of phylogenetically varied prokaryotes, and we detected 363 to 1,685 species-level ureC operational taxonomic units (OTUs) per soil sample, whereas 5,984 OTUs were site-specific OTUs found in only one of the seven soil types.
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Affiliation(s)
- Mamoru Oshiki
- Department of Civil Engineering, National Institute of Technology, Nagaoka College
| | - Mitsuru Araki
- Department of Civil Engineering, National Institute of Technology, Nagaoka College
| | - Yuga Hirakata
- Department of Science of Technology Innovation, Nagaoka University of Technology
| | - Masashi Hatamoto
- Department of Environmental Systems Engineering, Nagaoka University of Technology
| | - Takashi Yamaguchi
- Department of Science of Technology Innovation, Nagaoka University of Technology
| | - Nobuo Araki
- Department of Civil Engineering, National Institute of Technology, Nagaoka College
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13
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Nitrogen Cycle Evaluation (NiCE) Chip for Simultaneous Analysis of Multiple N Cycle-Associated Genes. Appl Environ Microbiol 2018. [PMID: 29427421 DOI: 10.1128/aem.02615‐17] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Various microorganisms play key roles in the nitrogen (N) cycle. Quantitative PCR (qPCR) and PCR amplicon sequencing of N cycle functional genes allow us to analyze the abundance and diversity of microbes responsible for N-transforming reactions in various environmental samples. However, analysis of multiple target genes can be cumbersome and expensive. PCR-independent analysis, such as metagenomics and metatranscriptomics, is useful but expensive, especially when we analyze multiple samples and try to detect N cycle functional genes present at a relatively low abundance. Here, we present the application of microfluidic qPCR chip technology to simultaneously quantify and prepare amplicon sequence libraries for multiple N cycle functional genes as well as taxon-specific 16S rRNA gene markers for many samples. This approach, named the nitrogen cycle evaluation (NiCE) chip, was evaluated by using DNA from pure and artificially mixed bacterial cultures and by comparing the results with those obtained by conventional qPCR and amplicon sequencing methods. Quantitative results obtained by the NiCE chip were comparable to those obtained by conventional qPCR. In addition, the NiCE chip was successfully applied to examine the abundance and diversity of N cycle functional genes in wastewater samples. Although nonspecific amplification was detected on the NiCE chip, this can be overcome by optimizing the primer sequences in the future. As the NiCE chip can provide a high-throughput format to quantify and prepare sequence libraries for multiple N cycle functional genes, this tool should advance our ability to explore N cycling in various samples.IMPORTANCE We report a novel approach, namely, the nitrogen cycle evaluation (NiCE) chip, by using microfluidic qPCR chip technology. By sequencing the amplicons recovered from the NiCE chip, we can assess the diversities of N cycle functional genes. The NiCE chip technology is applicable to analysis of the temporal dynamics of N cycle gene transcription in wastewater treatment bioreactors. The NiCE chip can provide a high-throughput format to quantify and prepare sequence libraries for multiple N cycle functional genes. While there is room for future improvement, this tool should significantly advance our ability to explore the N cycle in various environmental samples.
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14
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Nitrogen Cycle Evaluation (NiCE) Chip for Simultaneous Analysis of Multiple N Cycle-Associated Genes. Appl Environ Microbiol 2018; 84:AEM.02615-17. [PMID: 29427421 DOI: 10.1128/aem.02615-17] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2017] [Accepted: 01/28/2018] [Indexed: 01/20/2023] Open
Abstract
Various microorganisms play key roles in the nitrogen (N) cycle. Quantitative PCR (qPCR) and PCR amplicon sequencing of N cycle functional genes allow us to analyze the abundance and diversity of microbes responsible for N-transforming reactions in various environmental samples. However, analysis of multiple target genes can be cumbersome and expensive. PCR-independent analysis, such as metagenomics and metatranscriptomics, is useful but expensive, especially when we analyze multiple samples and try to detect N cycle functional genes present at a relatively low abundance. Here, we present the application of microfluidic qPCR chip technology to simultaneously quantify and prepare amplicon sequence libraries for multiple N cycle functional genes as well as taxon-specific 16S rRNA gene markers for many samples. This approach, named the nitrogen cycle evaluation (NiCE) chip, was evaluated by using DNA from pure and artificially mixed bacterial cultures and by comparing the results with those obtained by conventional qPCR and amplicon sequencing methods. Quantitative results obtained by the NiCE chip were comparable to those obtained by conventional qPCR. In addition, the NiCE chip was successfully applied to examine the abundance and diversity of N cycle functional genes in wastewater samples. Although nonspecific amplification was detected on the NiCE chip, this can be overcome by optimizing the primer sequences in the future. As the NiCE chip can provide a high-throughput format to quantify and prepare sequence libraries for multiple N cycle functional genes, this tool should advance our ability to explore N cycling in various samples.IMPORTANCE We report a novel approach, namely, the nitrogen cycle evaluation (NiCE) chip, by using microfluidic qPCR chip technology. By sequencing the amplicons recovered from the NiCE chip, we can assess the diversities of N cycle functional genes. The NiCE chip technology is applicable to analysis of the temporal dynamics of N cycle gene transcription in wastewater treatment bioreactors. The NiCE chip can provide a high-throughput format to quantify and prepare sequence libraries for multiple N cycle functional genes. While there is room for future improvement, this tool should significantly advance our ability to explore the N cycle in various environmental samples.
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15
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Affiliation(s)
- Hiroyuki Imachi
- Department of Subsurface Geobiological Analysis and Research, Japan Agency for Marine-Earth Science and Technology (JAMSTEC)
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16
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Angell IL, Hanssen JF, Rudi K. Prokaryote species richness is positively correlated with eukaryote abundance in wastewater treatment biofilms. Lett Appl Microbiol 2017; 65:66-72. [PMID: 28418627 DOI: 10.1111/lam.12746] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2017] [Revised: 04/10/2017] [Accepted: 04/11/2017] [Indexed: 12/13/2022]
Abstract
Biological treatment represents a key step in nutrient removal from wastewater. Until now these process has mainly been considered prokaryotic, with the interactions between prokaryotes and eukaryotes not being properly explored. We therefore investigated the co-occurrence of eukaryotes and prokaryotes in biological nitrogen removal biofilms. We found that biofilms in the nitrifying reactor contained the highest diversity and abundance of both prokaryotes and eukaryotes, with nearly three times higher prokaryote species richness than for the denitrifying reactor. The positive associations between eukaryote abundance and prokaryote diversity could potentially be explained by mutualism - and/or predator/prey interactions. Further mechanistic insight, however, is needed to determine the main diversifying mechanisms. In summary, eukaryote and prokaryote interactions seem to play a fundamental yet underexplored role in biological wastewater treatment. SIGNIFICANCE AND IMPACT OF THE STUDY Eukaryote and prokaryote interactions may play an important role in wastewater treatment. This study found that prokaryote species richness was nearly three times higher in the aerobe nitrification than in an anaerobe denitrification reactor, coinciding with the highest level of eukaryotes. This knowledge can be important in process control, and potentially in the development of novel approaches based on nitrate accumulating denitrifying eukaryotes.
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Affiliation(s)
- I L Angell
- Department of Chemistry, Biotechnology and Food Science, Norweigan University of Life Sciences, Ås, Norway
| | - J F Hanssen
- Department of Chemistry, Biotechnology and Food Science, Norweigan University of Life Sciences, Ås, Norway
| | - K Rudi
- Department of Chemistry, Biotechnology and Food Science, Norweigan University of Life Sciences, Ås, Norway
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17
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Affiliation(s)
- Jun Murase
- Graduate School of Bioagricultural Sciences, Nagoya University
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