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Xing F, Zhang H, Zhao H, Sun B, Wang T, Guo K, Dong K, Gu S, Wang L. Novel insights into intrinsic mechanisms of magnetic field on long-term performance of anaerobic ammonium oxidation process. BIORESOURCE TECHNOLOGY 2024; 402:130839. [PMID: 38744396 DOI: 10.1016/j.biortech.2024.130839] [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: 03/05/2024] [Revised: 05/10/2024] [Accepted: 05/11/2024] [Indexed: 05/16/2024]
Abstract
The performance of an anaerobic ammonium oxidation (anammox) reactor with the magnetic field of 40 mT was systematically investigated. The total nitrogen removal rate was enhanced by 16% compared with that of the control group. The enhancing mechanism was elucidated from the improved mass transfer efficiency, the complicated symbiotic interspecific relationship and the improved levels of functional genes. The magnetic field promoted formation of the loose anammox granular sludge and the homogeneous and well-connected porous structure to enhance the mass transfer. Consequently, Candidatus Brocadia predominated in the sludge with an increase in abundance of 13%. Network analysis showed that the positive interactions between Candidatus Brocadia and heterotrophic bacteria were strengthened, which established a more complicated stable microbial community. Moreover, the magnetic field increased the levels of hdh by 26% and hzs by 35% to promote the nitrogen metabolic process. These results provided novel insights into the magnetic field-enhanced anammox process.
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Affiliation(s)
- Fanghua Xing
- Institute of Pollution Control and Environmental Health, School of Energy and Environmental Engineering, Hebei University of Technology, Tianjin 300401, PR China
| | - Hui Zhang
- Institute of Pollution Control and Environmental Health, School of Energy and Environmental Engineering, Hebei University of Technology, Tianjin 300401, PR China
| | - Haishuo Zhao
- Institute of Pollution Control and Environmental Health, School of Energy and Environmental Engineering, Hebei University of Technology, Tianjin 300401, PR China
| | - Binbin Sun
- Institute of Pollution Control and Environmental Health, School of Energy and Environmental Engineering, Hebei University of Technology, Tianjin 300401, PR China.
| | - Tao Wang
- Institute of Pollution Control and Environmental Health, School of Energy and Environmental Engineering, Hebei University of Technology, Tianjin 300401, PR China.
| | - Kaiyuan Guo
- Institute of Pollution Control and Environmental Health, School of Energy and Environmental Engineering, Hebei University of Technology, Tianjin 300401, PR China
| | - Kaidi Dong
- Institute of Pollution Control and Environmental Health, School of Energy and Environmental Engineering, Hebei University of Technology, Tianjin 300401, PR China
| | - Siqi Gu
- Institute of Pollution Control and Environmental Health, School of Energy and Environmental Engineering, Hebei University of Technology, Tianjin 300401, PR China
| | - Luyao Wang
- Institute of Pollution Control and Environmental Health, School of Energy and Environmental Engineering, Hebei University of Technology, Tianjin 300401, PR China
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2
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Zhao R, Le Moine Bauer S, Babbin AR. " Candidatus Subterrananammoxibiaceae," a New Anammox Bacterial Family in Globally Distributed Marine and Terrestrial Subsurfaces. Appl Environ Microbiol 2023; 89:e0080023. [PMID: 37470485 PMCID: PMC10467342 DOI: 10.1128/aem.00800-23] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Accepted: 06/29/2023] [Indexed: 07/21/2023] Open
Abstract
Bacteria specialized in anaerobic ammonium oxidation (anammox) are widespread in many anoxic habitats and form an important functional guild in the global nitrogen cycle by consuming bio-available nitrogen for energy rather than biomass production. Due to their slow growth rates, cultivation-independent approaches have been used to decipher their diversity across environments. However, their full diversity has not been well recognized. Here, we report a new family of putative anammox bacteria, "Candidatus Subterrananammoxibiaceae," existing in the globally distributed terrestrial and marine subsurface (groundwater and sediments of estuary, deep-sea, and hadal trenches). We recovered a high-quality metagenome-assembled genome of this family, tentatively named "Candidatus Subterrananammoxibius californiae," from a California groundwater site. The "Ca. Subterrananammoxibius californiae" genome not only contains genes for all essential components of anammox metabolism (e.g., hydrazine synthase, hydrazine oxidoreductase, nitrite reductase, and nitrite oxidoreductase) but also has the capacity for urea hydrolysis. In an Arctic ridge sediment core where redox zonation is well resolved, "Ca. Subterrananammoxibiaceae" is confined within the nitrate-ammonium transition zone where the anammox rate maximum occurs, providing environmental proof of the anammox activity of this new family. Phylogenetic analysis of nitrite oxidoreductase suggests that a horizontal transfer facilitated the spreading of the nitrite oxidation capacity between anammox bacteria (in the Planctomycetota phylum) and nitrite-oxidizing bacteria from Nitrospirota and Nitrospinota. By recognizing this new anammox family, we propose that all lineages within the "Ca. Brocadiales" order have anammox capacity. IMPORTANCE Microorganisms called anammox bacteria are efficient in removing bioavailable nitrogen from many natural and human-made environments. They exist in almost every anoxic habitat where both ammonium and nitrate/nitrite are present. However, only a few anammox bacteria have been cultured in laboratory settings, and their full phylogenetic diversity has not been recognized. Here, we present a new bacterial family whose members are present across both the terrestrial and marine subsurface. By reconstructing a high-quality genome from the groundwater environment, we demonstrate that this family has all critical enzymes of anammox metabolism and, notably, also urea utilization. This bacterium family in marine sediments is also preferably present in the niche where the anammox process occurs. These findings suggest that this novel family, named "Candidatus Subterrananammoxibiaceae," is an overlooked group of anammox bacteria, which should have impacts on nitrogen cycling in a range of environments.
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Affiliation(s)
- Rui Zhao
- Department of Earth, Atmospheric and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Sven Le Moine Bauer
- Centre for Deep Sea Research, Department of Earth Science, University of Bergen, Bergen, Norway
| | - Andrew R. Babbin
- Department of Earth, Atmospheric and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
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3
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Xiao C, Wan K, Hu J, Deng X, Liu X, Zhou F, Yu J, Chi R. Performance changes in the anammox process under the stress of rare-earth element Ce(III) and the evolution of microbial community and functional genes. BIORESOURCE TECHNOLOGY 2023:129349. [PMID: 37336455 DOI: 10.1016/j.biortech.2023.129349] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/05/2023] [Revised: 06/14/2023] [Accepted: 06/16/2023] [Indexed: 06/21/2023]
Abstract
The high Ce(III) content in ionic rare-earth tailings wastewater has hindered the application of anammox process in this field. Here, the effect of Ce(III) on the performance of anammox processes was investigated, and the evolution of microbial communities and functional genes was explored using metagenomic sequencing. The results showed that the reactor nitrogen removal rate decreased when the Ce(III) concentration reached 25 mg/L, although ammonia nitrogen removal (92.31%) and nitrogen removal efficiency (81.33%) remained at a high level; however, both showed a significant decreasing trend. The relative abundance of anammox bacteria increased continuously from P1-P5, reaching 48.81%, whereas the relative abundance of Candidatus jettenia reached 33.71% at P5, which surpassed that of Candidatus brocadia as the most abundant anammox bacteria, and further analysis of functional genes and metabolic pathways revealed that Candidatus brocadia was richer in biochemical metabolic genes, whereas Candidatus jettenia had richer efflux genes.
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Affiliation(s)
- Chunqiao Xiao
- Key Laboratory of Novel Biomass-Based Environmental and Energy Materials in Petroleum and Chemical Industry, School of Environmental Ecology and Biological Engineering, Wuhan Institute of Technology, Wuhan 430205, China; Hubei Three Gorges Laboratory, Yichang 443007, China.
| | - Kai Wan
- Key Laboratory of Novel Biomass-Based Environmental and Energy Materials in Petroleum and Chemical Industry, School of Environmental Ecology and Biological Engineering, Wuhan Institute of Technology, Wuhan 430205, China; Hubei Three Gorges Laboratory, Yichang 443007, China
| | - Jinggang Hu
- Key Laboratory of Novel Biomass-Based Environmental and Energy Materials in Petroleum and Chemical Industry, School of Environmental Ecology and Biological Engineering, Wuhan Institute of Technology, Wuhan 430205, China
| | - Xiangyi Deng
- Key Laboratory of Novel Biomass-Based Environmental and Energy Materials in Petroleum and Chemical Industry, School of Environmental Ecology and Biological Engineering, Wuhan Institute of Technology, Wuhan 430205, China
| | - Xuemei Liu
- Key Laboratory of Novel Biomass-Based Environmental and Energy Materials in Petroleum and Chemical Industry, School of Environmental Ecology and Biological Engineering, Wuhan Institute of Technology, Wuhan 430205, China
| | - Fang Zhou
- Key Laboratory of Novel Biomass-Based Environmental and Energy Materials in Petroleum and Chemical Industry, School of Environmental Ecology and Biological Engineering, Wuhan Institute of Technology, Wuhan 430205, China
| | - Junxia Yu
- Key Laboratory of Novel Biomass-Based Environmental and Energy Materials in Petroleum and Chemical Industry, School of Environmental Ecology and Biological Engineering, Wuhan Institute of Technology, Wuhan 430205, China
| | - Ruan Chi
- Key Laboratory of Novel Biomass-Based Environmental and Energy Materials in Petroleum and Chemical Industry, School of Environmental Ecology and Biological Engineering, Wuhan Institute of Technology, Wuhan 430205, China; Hubei Three Gorges Laboratory, Yichang 443007, China
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4
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Song Y, Ni J, Guo Y, Kubota K, Qi WK, Li YY. Anammox upflow hybrid reactor: Nitrogen removal performance and potential for phosphorus recovery. CHEMOSPHERE 2023; 313:137580. [PMID: 36529167 DOI: 10.1016/j.chemosphere.2022.137580] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Revised: 11/22/2022] [Accepted: 12/14/2022] [Indexed: 06/17/2023]
Abstract
Echoing to the call of recovering high-value-added chemicals from wastewater and achieving carbon-neutral operation in wastewater treatment, an anammox upflow hybrid reactor was successfully applied for nitrogen removal, and the potential for phosphorus recovery was put forward. Moreover, the spatial pattern of removal capacities, and distribution of biomass and HAP precipitates were recognized and demonstrated as height-oriented. The intensity of HAP precipitates was highly consistent with the amount of anammox biomass and the relative abundance of the Candidatus Kuenenia, indicating that HAP formation was encouraged by the anammox reaction itself and heterogeneous nucleation induced by organic matters (proteins and polysaccharides). The fixed bed also played an important role in immobilizing the anammox biomass, secreted organic matrix, and HAP precipitates. This finding also provoked the thought that in the anammox process, HAP precipitation was more achievable, effective and practicable using the fixed-carrier system.
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Affiliation(s)
- Ying Song
- Department of Civil and Environmental Engineering, Graduate School of Engineering, Tohoku University, 6-6-06 Aza-Aoba, Aramaki, Aoba-ku, Sendai, Miyagi 980-8579, Japan
| | - Jialing Ni
- Department of Civil and Environmental Engineering, Graduate School of Engineering, Tohoku University, 6-6-06 Aza-Aoba, Aramaki, Aoba-ku, Sendai, Miyagi 980-8579, Japan
| | - Yan Guo
- Department of Environmental Engineering, University of Science and Technology Beijing, 30 Xueyuan Road, Haidian District, Beijing 100083, China
| | - Kengo Kubota
- Department of Civil and Environmental Engineering, Graduate School of Engineering, Tohoku University, 6-6-06 Aza-Aoba, Aramaki, Aoba-ku, Sendai, Miyagi 980-8579, Japan; Department of Frontier Sciences for Advanced Environment, Graduate School of Environmental Studies, Tohoku University, 6-6-06 Aza-Aoba, Aramaki, Aoba-ku, Sendai, Miyagi, 980-8579, Japan
| | - Wei-Kang Qi
- National Engineering Laboratory for Advanced Municipal Wastewater Treatment and Reuse Technology, Key Laboratory of Beijing for Water Quality Science and Water Environment Recovery Engineering, Beijing University of Technology, Beijing 100124, China
| | - Yu-You Li
- Department of Civil and Environmental Engineering, Graduate School of Engineering, Tohoku University, 6-6-06 Aza-Aoba, Aramaki, Aoba-ku, Sendai, Miyagi 980-8579, Japan; Department of Frontier Sciences for Advanced Environment, Graduate School of Environmental Studies, Tohoku University, 6-6-06 Aza-Aoba, Aramaki, Aoba-ku, Sendai, Miyagi, 980-8579, Japan.
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5
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Oren A. Candidatus List No. 4: Lists of names of prokaryotic Candidatus taxa. Int J Syst Evol Microbiol 2022; 72. [PMID: 36748458 DOI: 10.1099/ijsem.0.005545] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Affiliation(s)
- Aharon Oren
- The Institute of Life Sciences, The Hebrew University of Jerusalem, The Edmond J. Safra Campus, 9190401 Jerusalem, Israel
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6
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Palomo A, Azevedo D, Touceda-Suárez M, Domingo-Félez C, Mutlu AG, Dechesne A, Wang Y, Zhang T, Smets BF. Efficient management of the nitritation-anammox microbiome through intermittent aeration: absence of the NOB guild and expansion and diversity of the NOx reducing guild suggests a highly reticulated nitrogen cycle. ENVIRONMENTAL MICROBIOME 2022; 17:39. [PMID: 35869541 PMCID: PMC9306079 DOI: 10.1186/s40793-022-00432-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/15/2022] [Accepted: 06/26/2022] [Indexed: 06/15/2023]
Abstract
Obtaining efficient autotrophic ammonia removal (aka partial nitritation-anammox, or PNA) requires a balanced microbiome with abundant aerobic and anaerobic ammonia oxidizing bacteria and scarce nitrite oxidizing bacteria. Here, we analyzed the microbiome of an efficient PNA process that was obtained by sequential feeding and periodic aeration. The genomes of the dominant community members were inferred from metagenomes obtained over a 6 month period. Three Brocadia spp. genomes and three Nitrosomonas spp. genomes dominated the autotrophic community; no NOB genomes were retrieved. Two of the Brocadia spp. genomes lacked the genomic potential for nitrite reduction. A diverse set of heterotrophic genomes was retrieved, each with genomic potential for only a fraction of the denitrification pathway. A mutual dependency in amino acid and vitamin synthesis was noted between autotrophic and heterotrophic community members. Our analysis suggests a highly-reticulated nitrogen cycle in the examined PNA microbiome with nitric oxide exchange between the heterotrophs and the anammox guild.
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Affiliation(s)
- Alejandro Palomo
- Microbial Ecology and Technology Lab, Department of Environmental Engineering, Technical University of Denmark, Kgs Lyngby, Denmark
- School of Environmental Science and Engineering, Southern University of Science and Technology, Shenzhen, Guangdong Province, China
| | - Daniela Azevedo
- Microbial Ecology and Technology Lab, Department of Environmental Engineering, Technical University of Denmark, Kgs Lyngby, Denmark
| | - María Touceda-Suárez
- Microbial Ecology and Technology Lab, Department of Environmental Engineering, Technical University of Denmark, Kgs Lyngby, Denmark
- Department of Environmental Science, University of Arizona, Tucson, AZ, USA
| | - Carlos Domingo-Félez
- Microbial Ecology and Technology Lab, Department of Environmental Engineering, Technical University of Denmark, Kgs Lyngby, Denmark
| | - A Gizem Mutlu
- Microbial Ecology and Technology Lab, Department of Environmental Engineering, Technical University of Denmark, Kgs Lyngby, Denmark
- Hydrotech - Veolia Water Technologies, Vellinge, Sweden
| | - Arnaud Dechesne
- Microbial Ecology and Technology Lab, Department of Environmental Engineering, Technical University of Denmark, Kgs Lyngby, Denmark
| | - Yulin Wang
- Environmental Microbiome Engineering and Biotechnology Laboratory, Department of Civil Engineering, The University of Hong Kong, Hong Kong SAR, People's Republic of China
| | - Tong Zhang
- Environmental Microbiome Engineering and Biotechnology Laboratory, Department of Civil Engineering, The University of Hong Kong, Hong Kong SAR, People's Republic of China
| | - Barth F Smets
- Microbial Ecology and Technology Lab, Department of Environmental Engineering, Technical University of Denmark, Kgs Lyngby, Denmark.
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7
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Oshiki M, Takaki Y, Hirai M, Nunoura T, Kamigaito A, Okabe S. Metagenomic Analysis of Five Phylogenetically Distant Anammox Bacterial Enrichment Cultures. Microbes Environ 2022; 37. [PMID: 35811137 PMCID: PMC9530715 DOI: 10.1264/jsme2.me22017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Anaerobic ammonium-oxidizing (anammox) bacteria are slow-growing and fastidious bacteria, and limited numbers of enrichment cultures have been established. A metagenomic analysis of our 5 established anammox bacterial enrichment cultures was performed in the present study. Fourteen high-quality metagenome-assembled genomes (MAGs) were obtained, including those of 5 anammox Planctomycetota (Candidatus Brocadia, Ca. Kuenenia, Ca. Jettenia, and Ca. Scalindua), 4 Bacteroidota, and 3 Chloroflexota. Based on the gene sets of metabolic pathways involved in the degradation of polymeric substances found in Chloroflexota and Bacteroidota MAGs, they are expected to be scavengers of extracellular polymeric substances and cell debris.
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Affiliation(s)
- Mamoru Oshiki
- Division of Environmental Engineering, Faculty of Engineering, Hokkaido University
| | - Yoshihiro Takaki
- Super-cutting-edge Grand and Advanced Research (SUGAR) Program, Institute for Extra-cutting-edge Science and Technology Avant-garde Research (X-STAR), Japan Agency for Marine-Earth Science and Technology (JAMSTEC)
| | - Miho Hirai
- Super-cutting-edge Grand and Advanced Research (SUGAR) Program, Institute for Extra-cutting-edge Science and Technology Avant-garde Research (X-STAR), Japan Agency for Marine-Earth Science and Technology (JAMSTEC)
| | - Takuro Nunoura
- Research Center for Bioscience and Nanoscience (CeBN), JAMSTEC
| | - Atsushi Kamigaito
- Division of Environmental Engineering, Faculty of Engineering, Hokkaido University
| | - Satoshi Okabe
- Division of Environmental Engineering, Faculty of Engineering, Hokkaido University
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8
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Zhao R, Biddle JF, Jørgensen SL. Introducing Candidatus Bathyanammoxibiaceae, a family of bacteria with the anammox potential present in both marine and terrestrial environments. ISME COMMUNICATIONS 2022; 2:42. [PMID: 37938673 PMCID: PMC9723696 DOI: 10.1038/s43705-022-00125-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Revised: 04/06/2022] [Accepted: 04/11/2022] [Indexed: 07/21/2023]
Abstract
Anaerobic ammonium oxidation (Anammox) bacteria are a group of extraordinary bacteria exerting a major impact on the global nitrogen cycle. Their phylogenetic breadth and diversity, however, are not well constrained. Here we describe a new, deep-branching family in the order of Candidatus Brocadiales, Candidatus Bathyanammoxibiaceae, members of which have genes encoding the key enzymes of the anammox metabolism. In marine sediment cores from the Arctic Mid-Ocean Ridge (AMOR), the presence of Ca. Bathyanammoxibiaceae was confined within the nitrate-ammonium transition zones with the counter gradients of nitrate and ammonium, coinciding with the predicted occurrence of the anammox process. Ca. Bathyanammoxibiaceae genomes encode the core genetic machinery for the anammox metabolism, including hydrazine synthase for converting nitric oxide and ammonium to hydrazine, and hydrazine dehydrogenase for hydrazine oxidation to dinitrogen gas, and hydroxylamine oxidoreductase for nitrite reduction to nitric oxide. Their occurrences assessed by genomes and 16S rRNA gene sequencings surveys indicate that they are present in both marine and terrestrial environments. By introducing the anammox potential of Ca. Bathyanammoxibiaceae and charactering their ideal niche in marine sediments, our findings suggest that the diversity and abundance of anammox bacteria may be higher than previously thought, and provide important insights on cultivating them in the future to not only assess their biogeochemical impacts but also constrain the emergence and evolutionary history of this functional guild on Earth.
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Affiliation(s)
- Rui Zhao
- School of Marine Science and Policy, University of Delaware, Lewes, DE, USA.
- Department of Earth, Atmospheric and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, MA, USA.
| | - Jennifer F Biddle
- School of Marine Science and Policy, University of Delaware, Lewes, DE, USA
| | - Steffen L Jørgensen
- Centre for Deep Sea Research, Department of Earth Science, University of Bergen, Bergen, Norway
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9
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Suarez C, Dalcin Martins P, Jetten M, Karačić S, Wilén BM, Modin O, Hagelia P, Hermansson M, Persson F. Metagenomic evidence of a novel family of anammox bacteria in a subsea environment. Environ Microbiol 2022; 24:2348-2360. [PMID: 35415863 PMCID: PMC9325076 DOI: 10.1111/1462-2920.16006] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Accepted: 04/07/2022] [Indexed: 12/02/2022]
Abstract
Bacteria in the order ‘Candidatus Brocadiales’ within the phylum Planctomycetes (Planctomycetota) have the remarkable ability to perform anaerobic ammonium oxidation (anammox). Two families of anammox bacteria with different biogeographical distributions have been reported, marine Ca. Scalinduaceae and freshwater Ca. Brocadiaceae. Here we report evidence of three new species within a novel genus and family of anammox bacteria, which were discovered in biofilms of a subsea road tunnel under a fjord in Norway. In this particular ecosystem, the nitrogen cycle is likely fuelled by ammonia from organic matter degradation in the fjord sediments and the rock mass above the tunnel, resulting in the growth of biofilms where anammox bacteria can thrive under oxygen limitation. We resolved several metagenome‐assembled genomes (MAGs) of anammox bacteria, including three Ca. Brocadiales MAGs that could not be classified at the family level. MAGs of this novel family had all the diagnostic genes for a full anaerobic ammonium oxidation pathway in which nitrite was probably reduced by a NirK‐like reductase. A survey of published molecular data indicated that this new family of anammox bacteria occurs in many marine sediments, where its members presumably would contribute to nitrogen loss.
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Affiliation(s)
- Carolina Suarez
- Division of Water Resources Engineering, Faculty of Engineering LTH, Lund University, Lund, Sweden.,Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden
| | - Paula Dalcin Martins
- Department of Microbiology, RIBES, Radboud Institute for Biological and Environmental Sciences, Radboud University, Nijmegen, Netherlands
| | - Mike Jetten
- Department of Microbiology, RIBES, Radboud Institute for Biological and Environmental Sciences, Radboud University, Nijmegen, Netherlands
| | - Sabina Karačić
- Division of Water Environment Technology, Department of Architecture and Civil Engineering, Chalmers University of Technology, Gothenburg, Sweden
| | - Britt Marie Wilén
- Division of Water Environment Technology, Department of Architecture and Civil Engineering, Chalmers University of Technology, Gothenburg, Sweden
| | - Oskar Modin
- Division of Water Environment Technology, Department of Architecture and Civil Engineering, Chalmers University of Technology, Gothenburg, Sweden
| | - Per Hagelia
- Construction Division, The Norwegian Public Roads Administration, Oslo, Norway
| | - Malte Hermansson
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden
| | - Frank Persson
- Division of Water Environment Technology, Department of Architecture and Civil Engineering, Chalmers University of Technology, Gothenburg, Sweden
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10
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Song Y, Ma Z, Du R, Guo Y, Qin Y, Tanno J, Qi WK, Li YY. Microbial commensalism-assisted fast acclimation of HAP-anammox granules to dewatered liquid of dry methane fermentation. BIORESOURCE TECHNOLOGY 2022; 344:126238. [PMID: 34743991 DOI: 10.1016/j.biortech.2021.126238] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/10/2021] [Revised: 10/22/2021] [Accepted: 10/23/2021] [Indexed: 06/13/2023]
Abstract
The treatment of a dewatered liquid of dry fermentation via the anammox process was investigated in the present study. Fast acclimation was established: within 2-months of operation, nitrogen removal rate reached 5 times (5.5 g-N/L/d) higher than it was at startup, which was achieved by inoculation with cold-stored HAP-anammox granules and inhibition control. The specific anammox activity of the dewatered liquid was highly improved and quite comparable to that of synthetic wastewater. Ca. Kuenenia with the relative abundance of 31.1% was revealed to be the only anammox genre and maintained its dominance throughout the operation. Simultaneously, Ca. D. denitrificans was proliferated, with its relative abundance increasing from 1.5% to 14.9%. The microbial co-occurrence network of HAP-anammox granules developed during the treatment of the dewatered liquid of dry fermentation. The experience of this work provides valuable strategies facilitating fast acclimation of the anammox process for the treatment of high-strength wastewater.
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Affiliation(s)
- Ying Song
- Department of Civil and Environmental Engineering, Graduate School of Engineering, Tohoku University, 6-6-06 Aza, Aramaki, Aoba-ku, Sendai, Miyagi 980-8579, Japan
| | - Zhen Ma
- Graduate School of Environmental Studies, Tohoku University, 6-6-06 Aramaki Aza Aoba, Aoba-ku, Sendai, Miyagi 980-8579, Japan
| | - Runda Du
- Department of Civil and Environmental Engineering, Graduate School of Engineering, Tohoku University, 6-6-06 Aza, Aramaki, Aoba-ku, Sendai, Miyagi 980-8579, Japan
| | - Yan Guo
- Department of Civil and Environmental Engineering, Graduate School of Engineering, Tohoku University, 6-6-06 Aza, Aramaki, Aoba-ku, Sendai, Miyagi 980-8579, Japan
| | - Yu Qin
- Department of Civil and Environmental Engineering, Graduate School of Engineering, Tohoku University, 6-6-06 Aza, Aramaki, Aoba-ku, Sendai, Miyagi 980-8579, Japan
| | - Jun Tanno
- Department of Civil and Environmental Engineering, Graduate School of Engineering, Tohoku University, 6-6-06 Aza, Aramaki, Aoba-ku, Sendai, Miyagi 980-8579, Japan; Department of Civil and Environmental Engineering, National Institute of Technology, Fukushima College, Fukushima 970-8034, Japan
| | - Wei-Kang Qi
- National Engineering Laboratory for Advanced Municipal Wastewater Treatment and Reuse Technology, Key Laboratory of Beijing for Water Quality Science and Water Environment Recovery Engineering, Beijing University of Technology, Beijing 100124, China
| | - Yu-You Li
- Department of Civil and Environmental Engineering, Graduate School of Engineering, Tohoku University, 6-6-06 Aza, Aramaki, Aoba-ku, Sendai, Miyagi 980-8579, Japan; Graduate School of Environmental Studies, Tohoku University, 6-6-06 Aramaki Aza Aoba, Aoba-ku, Sendai, Miyagi 980-8579, Japan.
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11
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Lodha T, Narvekar S, Karodi P. Classification of uncultivated anammox bacteria and Candidatus Uabimicrobium into new classes and provisional nomenclature as Candidatus Brocadiia classis nov. and Candidatus Uabimicrobiia classis nov. of the phylum Planctomycetes and novel family Candidatus Scalinduaceae fam. nov to accommodate the genus Candidatus Scalindua. Syst Appl Microbiol 2021; 44:126272. [PMID: 34735804 DOI: 10.1016/j.syapm.2021.126272] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2021] [Revised: 09/30/2021] [Accepted: 10/04/2021] [Indexed: 11/26/2022]
Abstract
The phylum Planctomycetes is metabolically unique group of bacteria divided in two classes Planctomycetia and Phycisphaerae. Anaerobic ammonia-oxidizing (anammox) bacteria are the uncultured representatives of the phylum Planctomycetes. Anammox bacterial genera are placed in the family Candidatus (Ca.) Brocadiaceae of the order Ca. Brocadiales, assigned to the class Planctomycetia. Phylogenetic analysis, showed that the anammox bacteria and Ca. Uabimicrobium form a divergent clade from the rest of the cultured representatives of the phylum Planctomycetes. The phylogenetic study, pairwise distance and Average Amino acid Identity (AAI) showed that anammox bacteria don't belong to the classes Planctomycetia and Phycisphaerae. Anammox bacteria and Ca. Uabimicrobium form a deep-branching third clade in the phylogenetic analysis indicating that it is the most ancient third class within the phylum Planctomycetes. Phenotypic characters also separate anammox bacteria from classes Planctomycetia and Phycisphaerae. Therefore, based on phenotypic, phylogenetic, pairwise distance, AAI and phylogenomic analysis we propose a novel class Ca. Brocadiia to accommodate the order Ca. Brocadiales of anammox bacteria except Ca. Anammoximicrobium. Genera Ca. Jettenia, Ca. Anammoxoglobus, Ca. Kuenenia and Ca. Brocadia show their phylogenetic affiliation to the family Ca. Brocadiaceae. However, Ca. Scalindua showed a distant relationship with the family Ca. Brocadiaceae. Therefore, we suggest the exclusion of the genus Ca. Scalindua from the family Ca. Brocadiaceae; and propose its inclusion under a novel family with a provisional name as Ca. Scalinduaceae fam. nov. Similarly, Ca. Uabimicrobium amporphum showed distinct phylogenetic affiliation, therefore we propose a novel class Ca. Uabimicrobiia classis nov. to accommodate the genus Ca. Uabimicrobium.
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Affiliation(s)
- Tushar Lodha
- National Centre for Microbial Resource, National Centre for Cell Science, Pune 411021, India.
| | - Simran Narvekar
- National Centre for Microbial Resource, National Centre for Cell Science, Pune 411021, India
| | - Prachi Karodi
- National Centre for Microbial Resource, National Centre for Cell Science, Pune 411021, India
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Okubo T, Takami H. Metabolic potential of the imperfect denitrifier Candidatus Desulfobacillus denitrificans in an anammox bioreactor. Microbiologyopen 2021; 10:e1227. [PMID: 34459550 PMCID: PMC8402940 DOI: 10.1002/mbo3.1227] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Revised: 07/10/2021] [Accepted: 07/16/2021] [Indexed: 11/09/2022] Open
Abstract
The imperfect denitrifier, Candidatus (Ca.) Desulfobacillus denitrificans, which lacks nitric oxide (NO) reductase, frequently appears in anammox bioreactors depending on the operating conditions. We used genomic and metatranscriptomic analyses to evaluate the metabolic potential of Ca. D. denitrificans and deduce its functional relationships to anammox bacteria (i.e., Ca. Brocadia pituitae). Although Ca. D. denitrificans is hypothesized to supply NO to Ca. B. pituitae as a byproduct of imperfect denitrification, this microbe also possesses hydroxylamine oxidoreductase, which catalyzes the oxidation of hydroxylamine to NO and potentially the reverse reaction. Ca. D. denitrificans can use a range of electron donors for denitrification, including aromatic compounds, glucose, sulfur compounds, and hydrogen, but metatranscriptomic analysis suggested that the major electron donors are aromatic compounds, which inhibit anammox activity. The interrelationship between Ca. D. denitirificans and Ca. B. pituitae via the metabolism of aromatic compounds may govern the population balance of both species. Ca. D. denitrificans also has the potential to fix CO2 via an irregular Calvin cycle and couple denitrification to the oxidation of hydrogen and sulfur compounds under chemolithoautotrophic conditions. This metabolic versatility, which suggests a mixotrophic lifestyle, would facilitate the growth of Ca. D. denitrificans in the anammox bioreactor.
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Affiliation(s)
- Takashi Okubo
- Marine Microbiology, Atmosphere and Ocean Research InstituteThe University of TokyoKashiwaJapan
| | - Hideto Takami
- Marine Microbiology, Atmosphere and Ocean Research InstituteThe University of TokyoKashiwaJapan
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Narzary D, Boro N, Borah A, Okubo T, Takami H. Community structure and metabolic potentials of the traditional rice beer starter 'emao'. Sci Rep 2021; 11:14628. [PMID: 34272462 PMCID: PMC8285430 DOI: 10.1038/s41598-021-94059-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Accepted: 07/06/2021] [Indexed: 01/02/2023] Open
Abstract
The emao, a traditional beer starter used in the North-East regions of India produces a high quality of beer from rice substrates; however, its microbial community structure and functional metabolic modules remain unknown. To address this gap, we have used shot-gun whole-metagenome sequencing technology; accordingly, we have detected several enzymes that are known to catalyze saccharification, lignocellulose degradation, and biofuel production indicating the presence of metabolic functionome in the emao. The abundance of eukaryotic microorganisms, specifically the members of Mucoromycota and Ascomycota, dominated over the prokaryotes in the emao compared to previous metagenomic studies on such traditional starters where the relative abundance of prokaryotes occurred higher than the eukaryotes. The family Rhizopodaceae (64.5%) and its genus Rhizopus (64%) were the most dominant ones, followed by Phaffomycetaceae (11.14%) and its genus Wickerhamomyces (10.03%). The family Leuconostocaceae (6.09%) represented by two genera (Leuconostoc and Weissella) was dominant over the other bacteria, and it was the third-highest in overall relative abundance in the emao. The comprehensive microbial species diversity, community structure, and metabolic modules found in the emao are of practical value in the formulation of mixed-microbial cultures for biofuel production from plant-based feedstocks.
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Affiliation(s)
- Diganta Narzary
- Microbiology and Molecular Systematics Lab, Department of Botany, Gauhati University, Guwahati, Assam, India.
- Yokohama Institute for Earth Sciences, JAMSTEC, Yokohama, 236-0001, Japan.
| | - Nitesh Boro
- Microbiology and Molecular Systematics Lab, Department of Botany, Gauhati University, Guwahati, Assam, India
| | - Ashis Borah
- Microbiology and Molecular Systematics Lab, Department of Botany, Gauhati University, Guwahati, Assam, India
| | - Takashi Okubo
- Yokohama Institute for Earth Sciences, JAMSTEC, Yokohama, 236-0001, Japan
- Macrogen Japan Corp., 2-4-32 Aomi, Koto-ku, Tokyo, 135-0064, Japan
| | - Hideto Takami
- Yokohama Institute for Earth Sciences, JAMSTEC, Yokohama, 236-0001, Japan
- Marine Microbiology, Atmosphere and Ocean Research Institute, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba, 277-8564, Japan
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Procaryotic Diversity and Hydrogenotrophic Methanogenesis in an Alkaline Spring (La Crouen, New Caledonia). Microorganisms 2021; 9:microorganisms9071360. [PMID: 34201651 PMCID: PMC8307142 DOI: 10.3390/microorganisms9071360] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Revised: 06/17/2021] [Accepted: 06/19/2021] [Indexed: 01/01/2023] Open
Abstract
(1) Background: The geothermal spring of La Crouen (New Caledonia) discharges warm (42 °C) alkaline water (pH~9) enriched in dissolved nitrogen with traces of methane, but its microbial diversity has not yet been studied. (2) Methods: Cultivation-dependent and -independent methods (e.g., Illumina sequencing and quantitative PCR based on 16S rRNA gene) were used to describe the prokaryotic diversity of this spring. (3) Results: Prokaryotes were mainly represented by Proteobacteria (57% on average), followed by Cyanobacteria, Chlorofexi, and Candidatus Gracilibacteria (GN02/BD1-5) (each > 5%). Both potential aerobes and anaerobes, as well as mesophilic and thermophilic microorganisms, were identified. Some of them had previously been detected in continental hyperalkaline springs found in serpentinizing environments (The Cedars, Samail, Voltri, and Zambales ophiolites). Gammaproteobacteria, Ca. Gracilibacteria and Thermotogae were significantly more abundant in spring water than in sediments. Potential chemolithotrophs mainly included beta- and gammaproteobacterial genera of sulfate-reducers (Ca. Desulfobacillus), methylotrophs (Methyloversatilis), sulfur-oxidizers (Thiofaba, Thiovirga), or hydrogen-oxidizers (Hydrogenophaga). Methanogens (Methanobacteriales and Methanosarcinales) were the dominant Archaea, as found in serpentinization-driven and deep subsurface ecosystems. A novel alkaliphilic hydrogenotrophic methanogen (strain CAN) belonging to the genus Methanobacterium was isolated, suggesting that hydrogenotrophic methanogenesis occurs at La Crouen.
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Gushchin I, Aleksenko VA, Orekhov P, Goncharov IM, Nazarenko VV, Semenov O, Remeeva A, Gordeliy V. Nitrate- and Nitrite-Sensing Histidine Kinases: Function, Structure, and Natural Diversity. Int J Mol Sci 2021; 22:5933. [PMID: 34072989 PMCID: PMC8199190 DOI: 10.3390/ijms22115933] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Revised: 05/27/2021] [Accepted: 05/28/2021] [Indexed: 12/18/2022] Open
Abstract
Under anaerobic conditions, bacteria may utilize nitrates and nitrites as electron acceptors. Sensitivity to nitrous compounds is achieved via several mechanisms, some of which rely on sensor histidine kinases (HKs). The best studied nitrate- and nitrite-sensing HKs (NSHKs) are NarQ and NarX from Escherichia coli. Here, we review the function of NSHKs, analyze their natural diversity, and describe the available structural information. In particular, we show that around 6000 different NSHK sequences forming several distinct clusters may now be found in genomic databases, comprising mostly the genes from Beta- and Gammaproteobacteria as well as from Bacteroidetes and Chloroflexi, including those from anaerobic ammonia oxidation (annamox) communities. We show that the architecture of NSHKs is mostly conserved, although proteins from Bacteroidetes lack the HAMP and GAF-like domains yet sometimes have PAS. We reconcile the variation of NSHK sequences with atomistic models and pinpoint the structural elements important for signal transduction from the sensor domain to the catalytic module over the transmembrane and cytoplasmic regions spanning more than 200 Å.
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Affiliation(s)
- Ivan Gushchin
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, 141700 Dolgoprudny, Russia; (V.A.A.); (P.O.); (I.M.G.); (V.V.N.); (O.S.); (A.R.)
| | - Vladimir A. Aleksenko
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, 141700 Dolgoprudny, Russia; (V.A.A.); (P.O.); (I.M.G.); (V.V.N.); (O.S.); (A.R.)
| | - Philipp Orekhov
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, 141700 Dolgoprudny, Russia; (V.A.A.); (P.O.); (I.M.G.); (V.V.N.); (O.S.); (A.R.)
- Faculty of Biology, M.V. Lomonosov Moscow State University, 119991 Moscow, Russia
| | - Ivan M. Goncharov
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, 141700 Dolgoprudny, Russia; (V.A.A.); (P.O.); (I.M.G.); (V.V.N.); (O.S.); (A.R.)
| | - Vera V. Nazarenko
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, 141700 Dolgoprudny, Russia; (V.A.A.); (P.O.); (I.M.G.); (V.V.N.); (O.S.); (A.R.)
| | - Oleg Semenov
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, 141700 Dolgoprudny, Russia; (V.A.A.); (P.O.); (I.M.G.); (V.V.N.); (O.S.); (A.R.)
| | - Alina Remeeva
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, 141700 Dolgoprudny, Russia; (V.A.A.); (P.O.); (I.M.G.); (V.V.N.); (O.S.); (A.R.)
| | - Valentin Gordeliy
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, 141700 Dolgoprudny, Russia; (V.A.A.); (P.O.); (I.M.G.); (V.V.N.); (O.S.); (A.R.)
- Institut de Biologie Structurale J.-P. Ebel, Université Grenoble Alpes-CEA-CNRS, 38000 Grenoble, France
- Institute of Biological Information Processing (IBI-7: Structural Biochemistry), Forschungszentrum Jülich, 52428 Jülich, Germany
- JuStruct: Jülich Center for Structural Biology, Forschungszentrum Jülich, 52428 Jülich, Germany
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