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Xu T, Wang G, Yin Q, Zhou Z, Deng N. Sulfur/zinc co-doped biochar for stabilization remediation of mercury-contaminated soil: Performance, mechanism and ecological risk. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2024; 281:116601. [PMID: 38896905 DOI: 10.1016/j.ecoenv.2024.116601] [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: 04/07/2024] [Revised: 06/11/2024] [Accepted: 06/13/2024] [Indexed: 06/21/2024]
Abstract
In this study, a novel sulfur/zinc co-doped biochar (SZ-BC) stabilizer was successfully developed for the remediation of mercury-contaminated soil. Results from SEM, TEM, FTIR and XRD revealed that biochar (BC) was successfully modified by sulfur and zinc. In the batch adsorption experiments, the sulfur-zinc co-pyrolysis biochar displayed excellent Hg(II) adsorption performance, with the maximum adsorption capacity of SZ-BC (261.074 mg/g) being approximately 16.5 times that of BC (15.855 mg/g). Laboratory-scale static incubation, column leaching, and plant pot experiments were conducted using biochar-based materials. At an additional dosage of 5 % mass ratio, the SZ-BC exhibits the most effective stabilization of mercury in soil, leading to a significant reduction in leaching loss compared to the control group (CK) by 51.30 %. Following 4 weeks of incubation and 2 weeks of leaching with SZ-BC, the residual mercury in the soil increased by 27.84 %. As a result, potential ecological risk index of mercury decreased by 92 % compared to the CK group. In the pot experiment, SZ-BC significantly enhanced the growth of Chinese cabbage, with biomass and root dry weight reaching 3.20 and 2.80 times that of the CK group, respectively. Additionally, the Translocation Factor (TF) and Bioconcentration Factor (BF) were reduced by 44.86 % and 74.43 %, respectively, in the SZ-BC group compared to the CK group. Moreover, SZ-BC can effectively improve enzyme activities and increase microbial communities in mercury-contaminated soils. The mechanisms of adsorption and stabilization were elucidated through electrostatic adsorption, ion exchange, surface complexation, and precipitation. These findings provide a potentially effective material for stabilizing soils contaminated with mercury.
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Affiliation(s)
- Tianrui Xu
- School of Water Resources & Environmental Engineering, East China University of, Technology, Nanchang 330013, China
| | - Guanghui Wang
- School of Water Resources & Environmental Engineering, East China University of, Technology, Nanchang 330013, China; Jiangxi Provincial Key Laboratory of Genesis and Remediation of Groundwater Pollution, Nanchang 330013, China.
| | - Qiuling Yin
- School of Water Resources & Environmental Engineering, East China University of, Technology, Nanchang 330013, China
| | - Zhongkui Zhou
- School of Water Resources & Environmental Engineering, East China University of, Technology, Nanchang 330013, China; Jiangxi Provincial Key Laboratory of Genesis and Remediation of Groundwater Pollution, Nanchang 330013, China
| | - Nansheng Deng
- School of Resources and Environmental Science, Wuhan University, Wuhan 430079, China
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Hao H, Yue Y, Wang Q, Xiao T, Zhao Z, Zhang J, Chen H. Effects of the rice-mushroom rotation pattern on soil properties and microbial community succession in paddy fields. Front Microbiol 2024; 15:1449922. [PMID: 39113843 PMCID: PMC11303333 DOI: 10.3389/fmicb.2024.1449922] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2024] [Accepted: 07/11/2024] [Indexed: 08/10/2024] Open
Abstract
Introduction Currently, straw biodegradation and soil improvement in rice-mushroom rotation systems have attracted much attention. However, there is still a lack of studies on the effects of rice-mushroom rotation on yield, soil properties and microbial succession. Methods In this study, no treatment (CK), green manure return (GM) and rice straw return (RS) were used as controls to fully evaluate the effect of Stropharia rugosoannulata cultivation substrate return (SRS) on soil properties and microorganisms. Results The results indicated that rice yield, soil nutrient (organic matter, organic carbon, total nitrogen, available nitrogen and available potassium) and soil enzyme (urease, saccharase, lignin peroxidase and laccase) activities had positive responses to the rice-mushroom rotation. At the interannual level, microbial diversity varied significantly among treatments, with the rice-mushroom rotation significantly increasing the relative alpha diversity index of soil bacteria and enriching beneficial microbial communities such as Rhizobium, Bacillus and Trichoderma for rice growth. Soil nutrients and enzymatic activities were significantly correlated with microbial communities during rice-mushroom rotation. The fungal-bacterial co-occurrence networks were modular, and Latescibacterota, Chloroflexi, Gemmatimonadota and Patescibacteria were closely related to the accumulation of nutrients in the soil. The structural equation model (SEM) showed that fungal diversity responded more to changes in soil nutrients than did bacterial diversity. Discussion Overall, the rice-mushroom rotation model improved soil nutrients and rice yields, enriched beneficial microorganisms and maintained microbial diversity. This study provides new insights into the use of S. rugosoannulata cultivation substrates in the sustainable development of agroecosystems.
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Affiliation(s)
- Haibo Hao
- National Research Center for Edible Fungi Biotechnology and Engineering, Key Laboratory of Applied Mycological Resources and Utilization, Shanghai Key Laboratory of Agricultural Genetics and Breeding, Ministry of Agriculture, Institute of Edible Fungi, Shanghai Academy of Agricultural Sciences, Shanghai, China
- State Key Laboratory of Genetic Engineering and Fudan Center for Genetic Diversity and Designing Agriculture, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai, China
| | - Yihong Yue
- National Research Center for Edible Fungi Biotechnology and Engineering, Key Laboratory of Applied Mycological Resources and Utilization, Shanghai Key Laboratory of Agricultural Genetics and Breeding, Ministry of Agriculture, Institute of Edible Fungi, Shanghai Academy of Agricultural Sciences, Shanghai, China
| | - Qian Wang
- National Research Center for Edible Fungi Biotechnology and Engineering, Key Laboratory of Applied Mycological Resources and Utilization, Shanghai Key Laboratory of Agricultural Genetics and Breeding, Ministry of Agriculture, Institute of Edible Fungi, Shanghai Academy of Agricultural Sciences, Shanghai, China
| | - Tingting Xiao
- National Research Center for Edible Fungi Biotechnology and Engineering, Key Laboratory of Applied Mycological Resources and Utilization, Shanghai Key Laboratory of Agricultural Genetics and Breeding, Ministry of Agriculture, Institute of Edible Fungi, Shanghai Academy of Agricultural Sciences, Shanghai, China
| | - Zelong Zhao
- Shanghai Biozeron Biotechnology Co., Ltd., Shanghai, China
| | - Jinjing Zhang
- National Research Center for Edible Fungi Biotechnology and Engineering, Key Laboratory of Applied Mycological Resources and Utilization, Shanghai Key Laboratory of Agricultural Genetics and Breeding, Ministry of Agriculture, Institute of Edible Fungi, Shanghai Academy of Agricultural Sciences, Shanghai, China
| | - Hui Chen
- National Research Center for Edible Fungi Biotechnology and Engineering, Key Laboratory of Applied Mycological Resources and Utilization, Shanghai Key Laboratory of Agricultural Genetics and Breeding, Ministry of Agriculture, Institute of Edible Fungi, Shanghai Academy of Agricultural Sciences, Shanghai, China
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Wan Q, Li X, Wang F, Yang G, Ju K, Jing H, Li K, He P, Zhang X. Study on the transformation of nitrate nitrogen by manganese-catalyzed iron-carbon micro-electrolysis and microbial coupling. RSC Adv 2024; 14:10905-10919. [PMID: 38577425 PMCID: PMC10993045 DOI: 10.1039/d4ra00377b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2024] [Accepted: 03/15/2024] [Indexed: 04/06/2024] Open
Abstract
Nitrate-nitrogen pertains to the nitrogen component of the overall nitrate present in a given sample in order to reduce nitrate nitrogen pollution in water, nitrate nitrogen removal methods based on iron-carbon micro-electrolysis have become a key research focus. The process and mechanism of nitrate nitrogen removal by microbial coupling was comprehensively explored in a novel iron-carbon micro-electrolysis (ICME) system. In order to establish the transformation pathway of nitrate nitrogen in water, the transformation paths of nitrate nitrogen in water before and after coupling microorganisms in three groups of continuous flow reaction devices, namely sponge iron (s-Fe0), sponge iron + biochar (s-Fe0/BC) and sponge iron + biochar + manganese sand (s-Fe0/BC/MS), were studied. The morphology and composition changes of sponge iron were analyzed by means of characterization, and the microbial population changes in the three groups were analyzed by high-throughput sequencing. Results showed that the nitrate conversion rate in the s-Fe0, s-Fe0/BC and s-Fe0/BC/MS systems reached 99.48%, 99.57% and 99.36%, respectively, with corresponding ammonia nitrogen generation, rates of 3.77%, 9.34% and 11.24% and nitrogen generation rates of 95.71%, 90.23% and 88.12%. Scanning electron microscopy imaging showed that in the s-Fe0/BC and s-Fe0/BC/MS systems the surface of sponge iron was highly corroded, with granular substances in the corrosion product clusters. X-ray photoelectron spectroscopy analysis found that the relative contents of Fe2O3 in the surface oxides of sponge iron after microbial coupling were 38.02% and 71.27% in the s-Fe0/BC and s-Fe0/BC/MS systems, while the relative Fe3O4 contents were 61.98% and 28.72%, respectively. Microbial high-throughput sequencing analysis revealed that the Chao and Ace index values in the s-Fe0 system were 871.89 and 880.78, while in the s-Fe0/BC system they were 1012.05 and 1017.29, and in the s-Fe0/BC/MS system were 1241.09 and 1198.29, respectively. The relative proportion of Thauera in the s-Fe0, s-Fe0/BC, and s-Fe0/BC/MS systems was 16.76%,14.25% and 10.01%, while the proportion of Acetoanaerobium was 15.36%, 13.27% and 11.11%, and the proportion of Chloroflexi was 0%, 1.11% and 2.18%, respectively. Furthermore, FAPROTAX function annotation found that the expression levels of chemoheterotrophs in the s-Fe0, s-Fe0/BC and s-Fe0/BC/MS systems were 43 316 OTU, 37 289 OTU and 34 205 OTU, while nitrate respiration expression levels were 16 230 OTU, 15 483 OTU and 9149 OTU, with nitrogen respiration expression levels of 16 328 OTU, 15 493 OTU and 9154 OTU, respectively. These findings suggest that nitrate is converted into nitrogen gas and ammonia nitrogen through the actions of the coupled system of sponge iron/biochar/manganese sand and microorganisms. The catalytic effect of MnO2 promotes the conversion of Fe2+ to Fe3+, generating more electrons, allowing denitrifying bacteria to reduce more nitrate nitrogen, effectively coupling the manganese-catalyzed ICME reaction and microbial denitrification. The micro-electrolysis system and the addition of manganese sand enhanced biodiversity within the s-Fe0/BC/MS system. The heterotrophic bacteria Thauera and Acetoanaerobium were the dominant microorganisms in all three systems, although the micro-electrolysis system with added manganese sand significantly reduced the proportion of facultative bacteria Thauera and Acetoanaerobium and promoted the growth of autotrophic Chloroflexi bacteria. The ecological functions of the three systems were mainly nitrate respiration and nitrogen respiration. By comparing the expression levels of nitrate respiration and nitrogen respiration in s-Fe0/BC and s-Fe0/BC/MS systems, it can be seen that the addition of manganese sand reduced microbial activity.
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Affiliation(s)
- Qiong Wan
- School of Architecture and Civil Engineering, Xi'an University of Science and Technology Xi'an 710054 China
| | - Xiayin Li
- School of Architecture and Civil Engineering, Xi'an University of Science and Technology Xi'an 710054 China
| | - Feng Wang
- Shaanxi Water Group Water Ecology Comprehensive Development Co., Ltd 2206 Hongqi Road, Weiyang District Xi'an 710018 China
| | - Guohong Yang
- School of Architecture and Civil Engineering, Xi'an University of Science and Technology Xi'an 710054 China
| | - Kai Ju
- School of Architecture and Civil Engineering, Xi'an University of Science and Technology Xi'an 710054 China
| | - Hongbin Jing
- Shaanxi Water Group Water Ecology Comprehensive Development Co., Ltd 2206 Hongqi Road, Weiyang District Xi'an 710018 China
| | - Kun Li
- School of Architecture and Civil Engineering, Xi'an University of Science and Technology Xi'an 710054 China
| | - Peng He
- Shaanxi Water Group Water Ecology Comprehensive Development Co., Ltd 2206 Hongqi Road, Weiyang District Xi'an 710018 China
| | - Xinyan Zhang
- School of Architecture and Civil Engineering, Xi'an University of Science and Technology Xi'an 710054 China
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Mousa WK, Abu-Izneid T, Salah-Tantawy A. High-throughput sequencing reveals the structure and metabolic resilience of desert microbiome confronting climate change. FRONTIERS IN PLANT SCIENCE 2024; 15:1294173. [PMID: 38510442 PMCID: PMC10953687 DOI: 10.3389/fpls.2024.1294173] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Accepted: 02/06/2024] [Indexed: 03/22/2024]
Abstract
Introduction Desert ecosystems harbor a unique microbial diversity that is crucial for ecological stability and biogeochemical cycles. An in-depth understanding of the biodiversity, compositions, and functions of these microbial communities is imperative to navigate global changes and confront potential threats and opportunities applicable to agricultural ecosystems amid climate change. Methods This study explores microbial communities in the rhizosphere and endosphere of desert plants native to the Arabian Peninsula using next-generation sequencing of the 16S rRNA gene (V3-V4 hypervariable region). Results Our results reveal that each microbial community has a diverse and unique microbial composition. Based on alpha and beta diversity indices, the rhizosphere microbiome is significantly diverse and richer in microbial taxa compared to the endosphere. The data reveals a shift towards fast-growing microbes with active metabolism, involvement in nutrient cycling, nitrogen fixation, and defense pathways. Our data reveals the presence of habitat-specific microbial communities in the desert, highlighting their remarkable resilience and adaptability to extreme environmental conditions. Notably, we observed the existence of radiation-resistant microbes such as Deinococcus radiotolerans, Kocuria sp., and Rubrobacter radiotolerans which can tolerate high levels of ionizing radiation. Additionally, examples of microbes exhibiting tolerance to challenging conditions include Nocardioides halotolerans, thriving in high-salinity environments, and hyperthermophilic microbes such as Quasibacillus thermotolerans. Moreover, functional analysis reveals enrichment in chaperon biosynthesis pathways associated with correct protein folding under heat stress conditions. Discussion Our research sheds light on the unique diversity of desert microbes and underscores their potential applications to increase the resilience of agriculture ecosystems, offering a promising strategy to fortify crops against the challenges posed by climate change, ultimately supporting sustainable food production for our ever-expanding global population.
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Affiliation(s)
- Walaa K. Mousa
- College of Pharmacy, Al Ain University, Abu Dhabi, United Arab Emirates
- Al Ain University (AAU) Health and Biomedical Research Center, Al Ain University, Abu Dhabi, United Arab Emirates
- College of Pharmacy, Mansoura University, Mansoura, Egypt
| | - Tareq Abu-Izneid
- College of Pharmacy, Al Ain University, Abu Dhabi, United Arab Emirates
- Al Ain University (AAU) Health and Biomedical Research Center, Al Ain University, Abu Dhabi, United Arab Emirates
| | - Ahmed Salah-Tantawy
- Institute of Analytical and Environmental Sciences, College of Nuclear Science, National Tsing Hua University, Hsinchu, Taiwan
- Department of Zoology, Marine Science Division, College of Science, Al-Azhar University, Assiut, Egypt
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He Y, Liu Y, Li X, Guo H, Zhu T, Liu Y. Polyvinyl Chloride Microplastics Facilitate Nitrous Oxide Production in Partial Nitritation Systems. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2024; 58:1954-1965. [PMID: 38239129 DOI: 10.1021/acs.est.3c09280] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/31/2024]
Abstract
Partial nitritation (PN) is an important partner with anammox in the sidestream line treating high-strength wastewater and primarily contributes to nitrous oxide (N2O) emissions in such a hybrid system, which also suffers from ubiquitous microplastics because of the growing usage and disposal levels of plastics. In this study, the influences of polyvinyl chloride microplastics (PVC-MPs) on N2O-contributing pathways were experimentally revealed to fill the knowledge gap on N2O emission from the PN system under microplastics stress. The long-term results showed that the overall PN performance was hardly affected by the low-dose PVC-MPs (0.5 mg/L) while obviously deteriorated by the high dose (5 mg/L). According to the batch tests, PVC-MPs reduced biomass-specific ammonia oxidation rates (AORs) by 5.78-21.94% and stimulated aerobic N2O production by 9.22-88.36%. Further, upon increasing dissolved oxygen concentrations from 0.3 to 0.9 mg O2/L, the degree of AOR inhibition increased but that of N2O stimulation was lightened. Site preference analysis in combination with metabolic inhibitors demonstrated that the contributions of hydroxylamine oxidation and heterotrophic denitrification to N2O production at 0.3 mg O2/L were enhanced by 18.84 and 10.34%, respectively, accompanied by a corresponding decreased contribution of nitrifier denitrification. Finally, the underlying mechanisms proposed for negative influences of PVC-MPs were bisphenol A leaching and reactive oxygen species production, which led to more cell death, altered sludge properties, and reshaped microbial communities, further resulting in enhanced N2O emission. Overall, this work implied that the ubiquitous microplastics are a hidden danger that cannot be ignored in the PN system.
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Affiliation(s)
- Yanying He
- School of Environmental Science and Engineering, Tianjin University, Tianjin 300072, P. R. China
| | - Yingrui Liu
- School of Environmental Science and Engineering, Tianjin University, Tianjin 300072, P. R. China
| | - Xuecheng Li
- School of Environmental Science and Engineering, Tianjin University, Tianjin 300072, P. R. China
| | - Haixiao Guo
- School of Environmental Science and Engineering, Tianjin University, Tianjin 300072, P. R. China
| | - Tingting Zhu
- School of Environmental Science and Engineering, Tianjin University, Tianjin 300072, P. R. China
| | - Yiwen Liu
- School of Environmental Science and Engineering, Tianjin University, Tianjin 300072, P. R. China
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Kop LFM, Koch H, Jetten MSM, Daims H, Lücker S. Metabolic and phylogenetic diversity in the phylum Nitrospinota revealed by comparative genome analyses. ISME COMMUNICATIONS 2024; 4:ycad017. [PMID: 38317822 PMCID: PMC10839748 DOI: 10.1093/ismeco/ycad017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Revised: 12/22/2023] [Accepted: 12/22/2023] [Indexed: 02/07/2024]
Abstract
The most abundant known nitrite-oxidizing bacteria in the marine water column belong to the phylum Nitrospinota. Despite their importance in marine nitrogen cycling and primary production, there are only few cultured representatives that all belong to the class Nitrospinia. Moreover, although Nitrospinota were traditionally thought to be restricted to marine environments, metagenome-assembled genomes have also been recovered from groundwater. Over the recent years, metagenomic sequencing has led to the discovery of several novel classes of Nitrospinota (UBA9942, UBA7883, 2-12-FULL-45-22, JACRGO01, JADGAW01), which remain uncultivated and have not been analyzed in detail. Here, we analyzed a nonredundant set of 98 Nitrospinota genomes with focus on these understudied Nitrospinota classes and compared their metabolic profiles to get insights into their potential role in biogeochemical element cycling. Based on phylogenomic analysis and average amino acid identities, the highly diverse phylum Nitrospinota could be divided into at least 33 different genera, partly with quite distinct metabolic capacities. Our analysis shows that not all Nitrospinota are nitrite oxidizers and that members of this phylum have the genomic potential to use sulfide and hydrogen for energy conservation. This study expands our knowledge of the phylogeny and potential ecophysiology of the phylum Nitrospinota and offers new avenues for the isolation and cultivation of these elusive bacteria.
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Affiliation(s)
- Linnea F M Kop
- Department of Microbiology, Radboud Institute for Biological and Environmental Sciences, Radboud University, Heyendaalseweg 135, Nijmegen 6525 AJ, The Netherlands
- Division of Microbial Ecology, Centre for Microbiology and Environmental Systems Science, University of Vienna, Djerassiplatz 1, Vienna 1030, Austria
| | - Hanna Koch
- Department of Microbiology, Radboud Institute for Biological and Environmental Sciences, Radboud University, Heyendaalseweg 135, Nijmegen 6525 AJ, The Netherlands
- Bioresources Unit, Center for Health & Bioresources, AIT Austrian Institute of Technology GmbH, Konrad-Lorenz-Straße 24, Tulln an der Donau 3430, Austria
| | - Mike S M Jetten
- Department of Microbiology, Radboud Institute for Biological and Environmental Sciences, Radboud University, Heyendaalseweg 135, Nijmegen 6525 AJ, The Netherlands
| | - Holger Daims
- Division of Microbial Ecology, Centre for Microbiology and Environmental Systems Science, University of Vienna, Djerassiplatz 1, Vienna 1030, Austria
| | - Sebastian Lücker
- Department of Microbiology, Radboud Institute for Biological and Environmental Sciences, Radboud University, Heyendaalseweg 135, Nijmegen 6525 AJ, The Netherlands
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Petriglieri F, Kondrotaite Z, Singleton C, Nierychlo M, Dueholm MKD, Nielsen PH. A comprehensive overview of the Chloroflexota community in wastewater treatment plants worldwide. mSystems 2023; 8:e0066723. [PMID: 37992299 PMCID: PMC10746286 DOI: 10.1128/msystems.00667-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Accepted: 10/09/2023] [Indexed: 11/24/2023] Open
Abstract
IMPORTANCE Chloroflexota are often abundant members of the biomass in wastewater treatment plants (WWTPs) worldwide, typically with a filamentous morphology, forming the backbones of the activated sludge floc. However, their overgrowth can often cause operational issues connected to poor settling or foaming, impairing effluent quality and increasing operational costs. Despite their importance, few Chloroflexota genera have been characterized so far. Here, we present a comprehensive overview of Chloroflexota abundant in WWTPs worldwide and an in-depth characterization of their morphology, phylogeny, and ecophysiology, obtaining a broad understanding of their ecological role in activated sludge.
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Affiliation(s)
- Francesca Petriglieri
- Center for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
| | - Zivile Kondrotaite
- Center for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
| | - Caitlin Singleton
- Center for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
| | - Marta Nierychlo
- Center for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
| | - Morten K. D. Dueholm
- Center for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
| | - Per H. Nielsen
- Center for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
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Hu M, Liu X, Liu S, Ya T, Zhang M, Zhang T, Gao X, Wang X. Responses of microbial interactions and functional genes to sulfamethoxazole in anammox consortia. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2023; 348:119408. [PMID: 37879180 DOI: 10.1016/j.jenvman.2023.119408] [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: 08/16/2023] [Revised: 10/06/2023] [Accepted: 10/12/2023] [Indexed: 10/27/2023]
Abstract
Sulfamethoxazole (SMX) has been widely detected in various environments and its potential environmental risks have caused great concerns. However, the impact mechanism of SMX on microbial interactions among anammox consortia remain unknown. A long-term exposure experiments (140 d) was carried out to systematically examine the influence of SMX (0-1000 μg/L) on the anammox system, especially microbial network dynamics and variations of key metabolic genes. Results showed that anammox system could adapt to SMX below 500 μg/L and maintain a high nitrogen removal efficiency (NRE) of 85.35 ± 2.42%, while 1000 μg/L SMX significantly decreased the abundance of functional microbes and deteriorated denitrification performance with NRE dropped to 36.92 ± 15.01%. Co-occurrence network analysis indicated that 1000 μg/L SMX decreased the interactions between Proteobacteria and Chloroflexi and limited AnAOB from playing an important role as central nodes in the subnetwork of Planctomycetes. Metagenomics analysis found that genes associated with nitrogen removal (i.e., hdh, hzs, nirS, and hao) showed lower expression level after addition of SMX, while SMX-related ARGs (sul1 and sul2) increased by 1.22 and 2.68 times. This study provided us a relatively comprehensive perspective in response of microbial interactions and metabolic activity to various SMX concentrations.
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Affiliation(s)
- Meina Hu
- Beijing Engineering Research Center of Environmental Material for Water Purification, College of Chemical Engineering, Beijing University of Chemical Technology, Beijing, 100029, China
| | - Xiaojing Liu
- Beijing Engineering Research Center of Environmental Material for Water Purification, College of Chemical Engineering, Beijing University of Chemical Technology, Beijing, 100029, China
| | - Shidi Liu
- Beijing Engineering Research Center of Environmental Material for Water Purification, College of Chemical Engineering, Beijing University of Chemical Technology, Beijing, 100029, China; Fuzhou Planning Design Research Institute, Fuzhou, 350108, China
| | - Tao Ya
- Beijing Engineering Research Center of Environmental Material for Water Purification, College of Chemical Engineering, Beijing University of Chemical Technology, Beijing, 100029, China
| | - Minglu Zhang
- Key Laboratory of Cleaner Production and Integrated Resource Utilization of China National Light Industry, Beijing Technology and Business University, Beijing, 100048, China
| | - Tingting Zhang
- Beijing Engineering Research Center of Environmental Material for Water Purification, College of Chemical Engineering, Beijing University of Chemical Technology, Beijing, 100029, China
| | - Xiaoping Gao
- Fuzhou Planning Design Research Institute, Fuzhou, 350108, China.
| | - Xiaohui Wang
- Beijing Engineering Research Center of Environmental Material for Water Purification, College of Chemical Engineering, Beijing University of Chemical Technology, Beijing, 100029, China.
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Li D, Qu C, Cheng X, Chen Y, Yan H, Wu Q. Effect of different fertilization strategies on the yield, quality of Euryales Semen and soil microbial community. Front Microbiol 2023; 14:1310366. [PMID: 38098669 PMCID: PMC10719947 DOI: 10.3389/fmicb.2023.1310366] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Accepted: 11/14/2023] [Indexed: 12/17/2023] Open
Abstract
Introduction Euryales Semen, a medicinal herb widely utilized in Asia, faces a critical constraint in its production, primarily attributed to fertilizer utilization. Understanding the impact of different fertilization schemes on Euryales Semen (ES) planting and exploring the supporting mechanism are crucial for achieving high yield and sustainable development of the ES planting industry. Methods In this study, a field plot experiment was conducted to evaluate the effects of four different fertilization treatments on the yield and quality of ES using morphological characteristics and metabolomic changes. These treatments included a control group and three groups with different organic fertilizer to chemical fertilizer ratios (3:7, 5:5, and 7:3). The results of this study revealed the mechanisms underlying the effect of the different treatments on the yield and quality of Euryales Semen. These insights were achieved through analyses of soil physicochemical properties, soil enzyme activity, and soil microbial structure. Results We found that the quality and yield of ES were the best at a ratio of organic fertilizer to chemical fertilizer of 7:3. The optimality of this treatment was reflected in the yield, soil available nitrogen, soil available phosphorus, and soil enzyme activity of ES. This ratio also increased soil microbial diversity, resulting in an increase and decrease in Proteobacteria and Firmicutes abundances, respectively. In addition, linear discriminant analysis showed that Chloroflexi, Gammaproteobacteria, and Hypocreales-incertae-sedis were significantly enriched in the ratio of organic fertilizer to chemical fertilizer of 7:3. Variance partitioning analysis showed that the soil properties, enzyme activities, and their interactions cumulatively can explain 90.80% of the differences in Euryales Semen yield and metabolome. In general, blending organic and chemical fertilizers at a 7:3 ratio can enhance soil fertility, boost Euryales Semen yield and quality, and bring forth conditions that are agriculturally beneficial to microbial (bacteria and fungi) dynamics. Discussion This study initially revealed the scientific connotation of the effects of different fertilization patterns on the planting of Euryales Semen and laid a theoretical foundation for the study of green planting patterns of Euryales Semen with high quality and yield.
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Affiliation(s)
- Dishuai Li
- School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, China
| | - Cheng Qu
- School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, China
- Jiangsu Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, Nanjing, China
- National and Local Collaborative Engineering Center of Chinese Medicinal Resources Industrialization and Formulae Innovative Medicine, Nanjing, China
| | - Xuemei Cheng
- School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, China
| | - Yexing Chen
- School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, China
| | - Hui Yan
- School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, China
- Jiangsu Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, Nanjing, China
- National and Local Collaborative Engineering Center of Chinese Medicinal Resources Industrialization and Formulae Innovative Medicine, Nanjing, China
| | - Qinan Wu
- School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, China
- Jiangsu Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, Nanjing, China
- National and Local Collaborative Engineering Center of Chinese Medicinal Resources Industrialization and Formulae Innovative Medicine, Nanjing, China
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Zhang L, Gao X, Li Y, Li G, Luo W, Xu Z. Optimization of free air space to regulate bacterial succession and functions for alleviating gaseous emissions during kitchen waste composting. BIORESOURCE TECHNOLOGY 2023; 387:129682. [PMID: 37586431 DOI: 10.1016/j.biortech.2023.129682] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Revised: 08/11/2023] [Accepted: 08/12/2023] [Indexed: 08/18/2023]
Abstract
This study investigated the effects of free air space (FAS) (45%, 55%, 65%) on bacterial dynamics for gaseous emissions during kitchen waste composting. Results show that FAS increase from 45% to 65% elevated oxygen diffusivity to inhibit bacteria for fermentation (e.g. Caldicoprobacter and Ruminofilibacter) to reduce methane emission by 51%. Moreover, the increased FAS accelerated heat loss to reduce temperature and the abundance of thermophiles (e.g. Thermobifida and Thermobacillus) for aerobic chemoheterotrophy to mitigate ammonia emission by 32%. Nevertheless, the reduced temperature induced the growth of Desulfitibacter and Desulfobulbus for sulfate/sulfite respiration to boost hydrogen sulphide emission. By contrast, FAS at 55% achieved the highest germination index and favored the proliferation of nitrifiers and denitrifiers (e.g. Roseiflexus and Steroidobacter) to improve nitrate availability, thus slightly enhancing nitrous oxide emission. Thus, FAS at 55% exhibits the optimal performance for gaseous emission reduction and maturity enhancement in kitchen waste composting.
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Affiliation(s)
- Lanxia Zhang
- Beijing Key Laboratory of Farmland Soil Pollution Prevention and Remediation, College of Resources and Environmental Sciences, China Agricultural University, Beijing 100193, China
| | - Xingzu Gao
- Beijing Key Laboratory of Farmland Soil Pollution Prevention and Remediation, College of Resources and Environmental Sciences, China Agricultural University, Beijing 100193, China
| | - Yanming Li
- Beijing Key Laboratory of Farmland Soil Pollution Prevention and Remediation, College of Resources and Environmental Sciences, China Agricultural University, Beijing 100193, China
| | - Guoxue Li
- Beijing Key Laboratory of Farmland Soil Pollution Prevention and Remediation, College of Resources and Environmental Sciences, China Agricultural University, Beijing 100193, China; Organic Recycling Institute (Suzhou) of China Agricultural University, Wuzhong District, Suzhou 215128, China
| | - Wenhai Luo
- Beijing Key Laboratory of Farmland Soil Pollution Prevention and Remediation, College of Resources and Environmental Sciences, China Agricultural University, Beijing 100193, China; Key Laboratory of Low-carbon Green Agriculture, Ministry of Agriculture and Rural Affairs, China Agricultural University, Beijing 100193, China
| | - Zhicheng Xu
- Beijing Key Laboratory of Farmland Soil Pollution Prevention and Remediation, College of Resources and Environmental Sciences, China Agricultural University, Beijing 100193, China.
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11
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Li C, Fan M, Wang X, Li X, Zhao G, Liu G, Zhao J. Effects of nitrogen fertilizers on the bacterial community diversity and the weathering of purple mudstone in Southwest China. Front Microbiol 2023; 14:1164826. [PMID: 37455726 PMCID: PMC10341161 DOI: 10.3389/fmicb.2023.1164826] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Accepted: 06/05/2023] [Indexed: 07/18/2023] Open
Abstract
Introduction Rock weathering is crucial in the development of soil. Yet the role of bacteria in the fine particle-forming process of purple mudstone is not fully understood, especially under nitrogen fertilization. Methods In this study, the particles (0.25 mm to 1 mm) of purple mudstone from Penglai Group (J3p) were selected as the test material. Two nitrogen fertilizers, i.e., urea (U) and ammonium bicarbonate (AB), and four application levels (0, 280, 560, and 840 N kg∙ha-1) with 18 replications were designed in an incubation experiment. The weathering indices and bacterial community structure of the purple mudstone particles were investigated after 120 days of incubation. Results The results showed that the weathering indices of purple mudstone particles in the AB treatment were higher than that in the U treatment at the same fertilization levels and a reducing trend was observed with increasing nitrogen fertilizer levels under the same nitrogen fertilizer application types. The diversities of the bacterial community were extremely significantly altered by nitrogen fertilizer application (p < 0.01). The effect of the nitrogen fertilizer application level on the beta diversity of the bacterial community (R2 = 0.34) was greater than that of the nitrogen fertilizer application type (R2 = 0.20). Through stepwise regression analysis, the positive effects of nitrification of Nitrobacter (Nitrolancea) (R2 = 0.36), the Phosphorous-dissolving bacteria (Massilia) (R2 = 0.12), and N-NO3- (R2 = 0.35) on the weathering indices of J3p purple mudstone particles could be observed. Structural equation modelling indicated that nitrogen fertilizer application level affects the abundance of the dominant species at the genus level (Nitrolancea and Massilia), and key environmental factor (N-NO3-), which in turn accelerated the weathering indices (59%). Discussion and Conclusion Our findings imply that the enhancements of nitrification of Nitrobacter (Nitrolancea) and of phosphorus solubilization of Phosphorous-dissolving bacteria (Massilia) by nitrogen fertilization are the key factors affecting the weathering indices of J3p purple mudstone particles.
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Affiliation(s)
- Chunpei Li
- College of Resources and Environment, Yunnan Agricultural University, Kunming, China
| | - Maopan Fan
- College of Resources and Environment, Yunnan Agricultural University, Kunming, China
| | - Xuan Wang
- Key Laboratory of Mountain Surface Processes and Ecological Regulation, Chinese Academy of Sciences, Institute of Mountain Hazards and Environment, Chinese Academy of Sciences, and Ministry of Water Conservancy, Chengdu, China
- University of the Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing, China
| | - Xue Li
- College of Resources and Environment, Yunnan Agricultural University, Kunming, China
| | - Guang Zhao
- Key Laboratory of Ecosystem Network Observation and Modeling, Institute of Geographic Sciences and Natural Resources Research, Chinese Academy of Sciences, Beijing, China
| | - Gangcai Liu
- Key Laboratory of Mountain Surface Processes and Ecological Regulation, Chinese Academy of Sciences, Institute of Mountain Hazards and Environment, Chinese Academy of Sciences, and Ministry of Water Conservancy, Chengdu, China
| | - Jixia Zhao
- College of Resources and Environment, Yunnan Agricultural University, Kunming, China
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12
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Palmer M, Covington JK, Zhou EM, Thomas SC, Habib N, Seymour CO, Lai D, Johnston J, Hashimi A, Jiao JY, Muok AR, Liu L, Xian WD, Zhi XY, Li MM, Silva LP, Bowen BP, Louie K, Briegel A, Pett-Ridge J, Weber PK, Tocheva EI, Woyke T, Northen TR, Mayali X, Li WJ, Hedlund BP. Thermophilic Dehalococcoidia with unusual traits shed light on an unexpected past. THE ISME JOURNAL 2023:10.1038/s41396-023-01405-0. [PMID: 37041326 DOI: 10.1038/s41396-023-01405-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Revised: 03/22/2023] [Accepted: 03/27/2023] [Indexed: 04/13/2023]
Abstract
Although the phylum Chloroflexota is ubiquitous, its biology and evolution are poorly understood due to limited cultivability. Here, we isolated two motile, thermophilic bacteria from hot spring sediments belonging to the genus Tepidiforma and class Dehalococcoidia within the phylum Chloroflexota. A combination of cryo-electron tomography, exometabolomics, and cultivation experiments using stable isotopes of carbon revealed three unusual traits: flagellar motility, a peptidoglycan-containing cell envelope, and heterotrophic activity on aromatics and plant-associated compounds. Outside of this genus, flagellar motility has not been observed in Chloroflexota, and peptidoglycan-containing cell envelopes have not been described in Dehalococcoidia. Although these traits are unusual among cultivated Chloroflexota and Dehalococcoidia, ancestral character state reconstructions showed flagellar motility and peptidoglycan-containing cell envelopes were ancestral within the Dehalococcoidia, and subsequently lost prior to a major adaptive radiation of Dehalococcoidia into marine environments. However, despite the predominantly vertical evolutionary histories of flagellar motility and peptidoglycan biosynthesis, the evolution of enzymes for degradation of aromatics and plant-associated compounds was predominantly horizontal and complex. Together, the presence of these unusual traits in Dehalococcoidia and their evolutionary histories raise new questions about the timing and selective forces driving their successful niche expansion into global oceans.
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Affiliation(s)
- Marike Palmer
- School of Life Sciences, University of Nevada Las Vegas, Las Vegas, NV, 89154, USA.
| | - Jonathan K Covington
- School of Life Sciences, University of Nevada Las Vegas, Las Vegas, NV, 89154, USA
| | - En-Min Zhou
- School of Life Sciences, University of Nevada Las Vegas, Las Vegas, NV, 89154, USA
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-Sen University, 510275, Guangzhou, People's Republic of China
- Key Laboratory of Microbial Diversity in Southwest China of Ministry of Education, Yunnan Institute of Microbiology, School of Life Sciences, Yunnan University, 650091, Kunming, People's Republic of China
| | - Scott C Thomas
- School of Life Sciences, University of Nevada Las Vegas, Las Vegas, NV, 89154, USA
- Department of Molecular Pathobiology, New York University College of Dentistry, New York, NY, 10010, USA
| | - Neeli Habib
- Key Laboratory of Microbial Diversity in Southwest China of Ministry of Education, Yunnan Institute of Microbiology, School of Life Sciences, Yunnan University, 650091, Kunming, People's Republic of China
- Department of Microbiology, Shaheed Benazir Bhutto Women University, Peshawar, Khyber Pakhtunkhwa (KPK), Pakistan
| | - Cale O Seymour
- School of Life Sciences, University of Nevada Las Vegas, Las Vegas, NV, 89154, USA
| | - Dengxun Lai
- School of Life Sciences, University of Nevada Las Vegas, Las Vegas, NV, 89154, USA
| | - Juliet Johnston
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, USA
| | - Ameena Hashimi
- Department of Microbiology and Immunology, Life Sciences Institute, The University of British Columbia, Vancouver, BC, Canada
| | - Jian-Yu Jiao
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-Sen University, 510275, Guangzhou, People's Republic of China
| | - Alise R Muok
- Institute of Biology, Centre for Microbial Cell Biology, Leiden University, Leiden, The Netherlands
| | - Lan Liu
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-Sen University, 510275, Guangzhou, People's Republic of China
| | - Wen-Dong Xian
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-Sen University, 510275, Guangzhou, People's Republic of China
| | - Xiao-Yang Zhi
- Key Laboratory of Microbial Diversity in Southwest China of Ministry of Education, Yunnan Institute of Microbiology, School of Life Sciences, Yunnan University, 650091, Kunming, People's Republic of China
| | - Meng-Meng Li
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-Sen University, 510275, Guangzhou, People's Republic of China
| | - Leslie P Silva
- The Department of Energy Joint Genome Institute, Berkeley, CA, 94720, USA
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Benjamin P Bowen
- The Department of Energy Joint Genome Institute, Berkeley, CA, 94720, USA
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Katherine Louie
- The Department of Energy Joint Genome Institute, Berkeley, CA, 94720, USA
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Ariane Briegel
- Institute of Biology, Centre for Microbial Cell Biology, Leiden University, Leiden, The Netherlands
| | - Jennifer Pett-Ridge
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, USA
- Life and Environmental Sciences, University of California Merced, Merced, CA, 95343, USA
- Innovative Genomics Institute, University of California Berkeley, Berkeley, CA, 94720, USA
| | - Peter K Weber
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, USA
| | - Elitza I Tocheva
- Department of Microbiology and Immunology, Life Sciences Institute, The University of British Columbia, Vancouver, BC, Canada
| | - Tanja Woyke
- The Department of Energy Joint Genome Institute, Berkeley, CA, 94720, USA
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
- Life and Environmental Sciences, University of California Merced, Merced, CA, 95343, USA
| | - Trent R Northen
- The Department of Energy Joint Genome Institute, Berkeley, CA, 94720, USA
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Xavier Mayali
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, USA
| | - Wen-Jun Li
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-Sen University, 510275, Guangzhou, People's Republic of China
| | - Brian P Hedlund
- School of Life Sciences, University of Nevada Las Vegas, Las Vegas, NV, 89154, USA.
- Nevada Institute of Personalized Medicine, University of Nevada Las Vegas, Las Vegas, NV, 89154, USA.
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13
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Perrone MR, Romano S, De Maria G, Tundo P, Bruno AR, Tagliaferro L, Maffia M, Fragola M. Simultaneous monitoring of SARS-CoV-2 and bacterial profiles from the air of hospital environments with COVID-19-affected patients. AEROBIOLOGIA 2022; 38:391-412. [PMID: 36097443 PMCID: PMC9453715 DOI: 10.1007/s10453-022-09754-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Accepted: 08/01/2022] [Indexed: 06/15/2023]
Abstract
UNLABELLED The SARS-CoV-2 presence and the bacterial community profile in air samples collected at the Intensive Care Unit (ICU) of the Operational Unit of Infectious Diseases of Santa Caterina Novella Hospital in Galatina (Lecce, Italy) have been evaluated in this study. Air samplings were performed in different rooms of the ICU ward with and without COVID-19 patients. No sample was found positive to SARS-CoV-2, according to Allplex 2019-nCoV Assay. The airborne bacterial community profiles determined by the 16S rRNA gene metabarcoding approach up to the species level were characterized by richness and biodiversity indices, Spearman correlation coefficients, and Principal Coordinate Analysis. Pathogenic and non-pathogenic bacterial species, also detected in outdoor air samples, were found in all collected indoor samples. Staphylococcus pettenkoferi, Corynebacterium tuberculostearicum, and others coagulase-negative staphylococci, detected at high relative abundances in all the patients' rooms, were the most abundant pathogenic species. The highest mean relative abundance of S. pettenkoferi and C. tuberculostearicum suggested that they were likely the main pathogens of COVID-19 patients at the ICU ward of this study. The identification of nosocomial pathogens representing potential patients' risks in ICU COVID-19 rooms and the still controversial airborne transmission of the SARS-CoV-2 are the main contributions of this study. SUPPLEMENTARY INFORMATION The online version contains supplementary material available at 10.1007/s10453-022-09754-7.
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Affiliation(s)
- Maria Rita Perrone
- Department of Mathematics and Physics, University of Salento, 73100 Lecce, Italy
| | - Salvatore Romano
- Department of Mathematics and Physics, University of Salento, 73100 Lecce, Italy
| | - Giuseppe De Maria
- Presidio Ospedaliero Santa Caterina Novella, Azienda Sanitaria Locale Lecce, 73013 Galatina, Lecce, Italy
| | - Paolo Tundo
- Presidio Ospedaliero Santa Caterina Novella, Azienda Sanitaria Locale Lecce, 73013 Galatina, Lecce, Italy
| | - Anna Rita Bruno
- Presidio Ospedaliero Santa Caterina Novella, Azienda Sanitaria Locale Lecce, 73013 Galatina, Lecce, Italy
| | - Luigi Tagliaferro
- Presidio Ospedaliero Santa Caterina Novella, Azienda Sanitaria Locale Lecce, 73013 Galatina, Lecce, Italy
| | - Michele Maffia
- Department of Biological and Environmental Sciences and Technologies, University of Salento, 73100 Lecce, Italy
| | - Mattia Fragola
- Department of Mathematics and Physics, University of Salento, 73100 Lecce, Italy
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14
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Zou Z, Yang H, Zhang S, Chi W, Wang X, Liu Z. Nitrogen removal performance and microbial community analysis of immobilized biological fillers in rare earth mine wastewater. Biochem Eng J 2022. [DOI: 10.1016/j.bej.2022.108559] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
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15
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Wang Y, Cheng X, Wang H, Zhou J, Liu X, Tuovinen OH. The Characterization of Microbiome and Interactions on Weathered Rocks in a Subsurface Karst Cave, Central China. Front Microbiol 2022; 13:909494. [PMID: 35847118 PMCID: PMC9277220 DOI: 10.3389/fmicb.2022.909494] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Accepted: 05/19/2022] [Indexed: 11/13/2022] Open
Abstract
Karst caves are a natural oligotrophic subsurface biosphere widely distributed in southern China. Despite the progress in bacterial and fungal diversity, the knowledge about interactions between bacteria, fungi, and minerals is still limited in caves. Hence, for the first time, we investigated the interaction between bacteria and fungi living on weathered rocks in the Heshang Cave via high-throughput sequencing of 16S rRNA and ITS1 genes, and co-occurrence analysis. The mineral compositions of weathered rocks were analyzed by X-ray diffraction. Bacterial communities were dominated by Actinobacteria (33.68%), followed by Alphaproteobacteria (8.78%), and Planctomycetia (8.73%). In contrast, fungal communities were dominated by Sordariomycetes (21.08%) and Dothideomycetes (14.06%). Mineral substrata, particularly phosphorus-bearing minerals, significantly impacted bacterial (hydroxyapatite) and fungal (fluorapatite) communities as indicated by the redundancy analysis. In comparison with fungi, the development of bacterial communities was more controlled by the environmental selection indicated by the overwhelming contribution of deterministic processes. Co-occurrence network analysis showed that all nodes were positively linked, indicating ubiquitous cooperation within bacterial groups and fungal groups, as well as between bacteria and fungi under oligotrophic conditions in the subsurface biosphere. In total, 19 bacterial ASVs and 34 fungal OTUs were identified as keystone taxa, suggesting the fundamental role of fungi in maintaining the microbial ecosystem on weathered rocks. Ascomycota was most dominant in keystone taxa, accounting for 26.42%, followed by Actinobacteria in bacteria (24.53%). Collectively, our results confirmed the highly diverse bacterial and fungal communities on weathered rocks, and their close cooperation to sustain the subsurface ecosystem. Phosphorus-bearing minerals were of significance in shaping epipetreous bacterial and fungal communities. These observations provide new knowledge about microbial interactions between bacteria, fungi, and minerals in the subterranean biosphere.
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Affiliation(s)
- Yiheng Wang
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan, China.,School of Environmental Studies, China University of Geosciences, Wuhan, China
| | - Xiaoyu Cheng
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan, China.,School of Environmental Studies, China University of Geosciences, Wuhan, China
| | - Hongmei Wang
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan, China.,School of Environmental Studies, China University of Geosciences, Wuhan, China
| | - Jianping Zhou
- School of Environmental Studies, China University of Geosciences, Wuhan, China
| | - Xiaoyan Liu
- School of Environmental Studies, China University of Geosciences, Wuhan, China
| | - Olli H Tuovinen
- Department of Microbiology, The Ohio State University, Columbus, OH, United States
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16
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Huo D, Dang Y, Sun D, Holmes DE. Efficient nitrogen removal from leachate by coupling Anammox and sulfur-siderite-driven denitrification. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 829:154683. [PMID: 35314225 DOI: 10.1016/j.scitotenv.2022.154683] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/28/2021] [Revised: 02/26/2022] [Accepted: 03/15/2022] [Indexed: 06/14/2023]
Abstract
High concentrations of nitrate can be generated during anaerobic ammonium oxidation (Anammox) wastewater treatment processes. Addition of sulfur to Anammox reactors stimulates the growth of sulfur-driven denitrifying (SADN) bacteria that can reduce nitrate to nitrogen gas. However, protons released during the SADN process lower the pH of the system and inhibit Anammox activity. The system will keep stable when pH is in the range of 7.5-8.5. This study showed that addition of siderite stabilized the reactor system and significantly improved the nitrogen removal process. In fact, even when concentrations of total nitrogen were 477.15 ± 16.84 mg/L, the sulfur/siderite reactor maintained nitrogen removal efficiencies >90%, while efficiencies in the sulfur reactor were < 80%. Anammox accounted for 31% of the bacterial sequences in the sulfur/siderite reactor compared to only 14% in the sulfur reactor with the majority of sequences clustering with Ca. Brocadia. An abundance of c-type cytochromes in anammox aggregates in the sulfur-siderite reactor also indicated that anammox activity was higher in this system.
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Affiliation(s)
- Da Huo
- Beijing Key Laboratory for Source Control Technology of Water Pollution, Engineering Research Center for Water Pollution Source Control and Eco-remediation, College of Environmental Science and Engineering, Beijing Forestry University, Beijing 100083, China
| | - Yan Dang
- Beijing Key Laboratory for Source Control Technology of Water Pollution, Engineering Research Center for Water Pollution Source Control and Eco-remediation, College of Environmental Science and Engineering, Beijing Forestry University, Beijing 100083, China
| | - Dezhi Sun
- Beijing Key Laboratory for Source Control Technology of Water Pollution, Engineering Research Center for Water Pollution Source Control and Eco-remediation, College of Environmental Science and Engineering, Beijing Forestry University, Beijing 100083, China.
| | - Dawn E Holmes
- Department of Physical and Biological Sciences, Western New England University, 1215 Wilbraham Rd, Springfield, MA 01119, USA
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17
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Narsing Rao MP, Luo ZH, Dong ZY, Li Q, Liu BB, Guo SX, Nie GX, Li WJ. Metagenomic analysis further extends the role of Chloroflexi in fundamental biogeochemical cycles. ENVIRONMENTAL RESEARCH 2022; 209:112888. [PMID: 35143804 DOI: 10.1016/j.envres.2022.112888] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Revised: 01/02/2022] [Accepted: 02/01/2022] [Indexed: 06/14/2023]
Abstract
Chloroflexi members are ubiquitous and have been extensively studied; however, the evolution and metabolic pathways of Chloroflexi members have long been debated. In the present study, the evolution and the metabolic potentials of 17 newly obtained Chloroflexi metagenome-assembled genomes (MAGs) were evaluated using genome and horizontal gene transfer (HGT) analysis. Taxonomic analysis suggests that the MAGs of the present study might be novel. One MAG encodes genes for anoxygenic phototrophy. The HGT analysis suggest that genes responsible for anoxygenic phototrophy in the MAG might have been transferred from Proteobacteria/Chlorobi. The evolution of anaerobic photosynthesis, which has long been questioned, has now been shown to be the result of HGT events. An incomplete Wood-Ljungdahl pathway (with missing genes metF, acsE, fdh, and acsA) was reported in Dehalococcoidetes members. In the present study, MAGs that were not the Dehalococcoidetes members encode genes acsA, acsB, metF and acsE. The genes responsible for sulfate reduction (sat, cysC and sir), dissimilatory sulfite reductase (dsrA and dsrB), and aerobic and anaerobic carbon monoxide oxidation (coxSML and cooSF) were detected in the present study MAGs. The present study expands our knowledge of the possible metabolic potentials of the phylum Chloroflexi and clarifies the evolution of anaerobic photosynthesis.
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Affiliation(s)
- Manik Prabhu Narsing Rao
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, PR China
| | - Zhen-Hao Luo
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, PR China
| | - Zhou-Yan Dong
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, PR China; Department of Pathogenic Biology, Binzhou Medical University, Yantai, 264003, PR China
| | - Qi Li
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, PR China
| | - Bing-Bing Liu
- Henan Key Laboratory of Industrial Microbial Resources and Fermentation Technology, College of Biological and Chemical Engineering, Nanyang Institute of Technology, Nanyang, 473004, PR China
| | - Shu-Xian Guo
- Henan Key Laboratory of Industrial Microbial Resources and Fermentation Technology, College of Biological and Chemical Engineering, Nanyang Institute of Technology, Nanyang, 473004, PR China
| | - Guo-Xin Nie
- College of Fisheries, Henan Normal University, Xinxiang, 453007, PR China.
| | - Wen-Jun Li
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, PR China.
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18
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Li Y, Dong S, Gao Q, Fan C, Fayiah M, Ganjurjav H, Hu G, Wang X, Yan Y, Gao X, Li S. Grazing Changed Plant Community Composition and Reduced Stochasticity of Soil Microbial Community Assembly of Alpine Grasslands on the Qinghai-Tibetan Plateau. FRONTIERS IN PLANT SCIENCE 2022; 13:864085. [PMID: 35677251 PMCID: PMC9168915 DOI: 10.3389/fpls.2022.864085] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Accepted: 04/26/2022] [Indexed: 05/25/2023]
Abstract
Grazing is a substantial threat to the sustainability of grassland ecosystems, while it is uncertain about the variety of plant and soil microbial community and the linkages between them limit the comprehensive understanding of grazing ecology. We conducted an experiment on the effects of the grazing regimes rotational grazing (RG), continuous grazing (CG), and grazing exclusion (GE) on an alpine meadow in Qinghai-Tibetan Plateau. The differences of plant community composition, soil microbial community assembly mechanism, and taxonomic and functional composition between grazing regimes were examined, and the relationship between plant species and the soil microbes was assessed by constructing a co-occurrence network. The results showed that the plant community composition varied with the grazing regimes, while the soil microbial community composition did not vary with the grazing regimes. The soil bacterial functional composition was similar under RG and CG, while the soil fungal functional composition was similar under GE and RG. The soil microbial community under all grazing regimes was assembled mainly according to stochastic rather than deterministic mechanisms, and RG and CG reduced the relative importance of the stochastic ratio. At the microbial phylum level, CG and GE increased the relative abundance of Acidobacteria and Armatimonadetes and CG and RG increased the relative abundance of Elusimicrobia. In the network of plant species and soil microbial classes, plants and bacteria themselves were mainly positively linked (symbiosis and promotion), while plants and soil microbes were mainly negatively linked (competition). There were five microbial generalists in the network, which connected with many microbes, and four showed no difference in their abundance among the grazing regimes. Overall, the stable key microbes in the network and the fact that many of the plants are unconnected with microbes weakened the impact of grazing-induced changes in the plant community on soil microbes, probably resulting in the stable soil microbial community composition. Moreover, there was still a dominant and tolerant plant species, Kobresia pygmaea, that connected the plant and microbial communities, implying that the dominant plant species not only played a crucial role in the plant community but also acted as a bridge between the plants and soil microbes; thus, its tolerance and dominance might stabilize the soil microbial community.
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Affiliation(s)
- Yu Li
- School of Public Administration, Chongqing Technology and Business University, Chongqing, China
| | - Shikui Dong
- School of Grassland Science, Beijing Forestry University, Beijing, China
- Department of Natural Resources, Cornell University, Ithaca, NY, United States
| | - Qingzhu Gao
- Institute of Environment and Sustainable Development in Agriculture, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Chun Fan
- School of Public Administration, Chongqing Technology and Business University, Chongqing, China
| | - Moses Fayiah
- Department of Forestry, School of Natural Resources Management, Njala University, Njala, Sierra Leone
| | - Hasbagan Ganjurjav
- Institute of Environment and Sustainable Development in Agriculture, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Guozheng Hu
- Institute of Environment and Sustainable Development in Agriculture, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xuexia Wang
- Beijing Academy of Agricultural and Forestry Sciences, Beijing, China
| | - Yulong Yan
- China New Era Group Corporation, Beijing, China
| | - Xiaoxia Gao
- State Key Laboratory of Water Environment Simulation, School of Environment, Beijing Normal University, Beijing, China
| | - Shuai Li
- State Key Laboratory of Water Environment Simulation, School of Environment, Beijing Normal University, Beijing, China
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19
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Noell SE, Baptista MS, Smith E, McDonald IR, Lee CK, Stott MB, Amend JP, Cary SC. Unique Geothermal Chemistry Shapes Microbial Communities on Mt. Erebus, Antarctica. Front Microbiol 2022; 13:836943. [PMID: 35591982 PMCID: PMC9111169 DOI: 10.3389/fmicb.2022.836943] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Accepted: 04/18/2022] [Indexed: 11/13/2022] Open
Abstract
Mt. Erebus, Antarctica, is the world's southernmost active volcano and is unique in its isolation from other major active volcanic systems and its distinctive geothermal systems. Using 16S rRNA gene amplicon sequencing and physicochemical analyses, we compared samples collected at two contrasting high-temperature (50°C-65°C) sites on Mt. Erebus: Tramway Ridge, a weather-protected high biomass site, and Western Crater, an extremely exposed low biomass site. Samples were collected along three thermal gradients, one from Western Crater and two within Tramway Ridge, which allowed an examination of the heterogeneity present at Tramway Ridge. We found distinct soil compositions between the two sites, and to a lesser extent within Tramway Ridge, correlated with disparate microbial communities. Notably, pH, not temperature, showed the strongest correlation with these differences. The abundance profiles of several microbial groups were different between the two sites; class Nitrososphaeria amplicon sequence variants (ASVs) dominated the community profiles at Tramway Ridge, whereas Acidobacteriotal ASVs were only found at Western Crater. A co-occurrence network, paired with physicochemical analyses, allowed for finer scale analysis of parameters correlated with differential abundance profiles, with various parameters (total carbon, total nitrogen, soil moisture, soil conductivity, sulfur, phosphorous, and iron) showing significant correlations. ASVs assigned to Chloroflexi classes Ktedonobacteria and Chloroflexia were detected at both sites. Based on the known metabolic capabilities of previously studied members of these groups, we predict that chemolithotrophy is a common strategy in this system. These analyses highlight the importance of conducting broader-scale metagenomics and cultivation efforts at Mt. Erebus to better understand this unique environment.
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Affiliation(s)
- Stephen E Noell
- Te Aka Mātuatua-School of Science, Te Whare Wānanga o Waikato-University of Waikato, Hamilton, New Zealand.,International Centre for Terrestrial Antarctic Research, University of Waikato, Hamilton, New Zealand
| | - Mafalda S Baptista
- International Centre for Terrestrial Antarctic Research, University of Waikato, Hamilton, New Zealand.,Interdisciplinary Centre of Marine and Environmental Research (CIIMAR/CIMAR), University of Porto, Matosinhos, Portugal.,Faculty of Sciences, University of Porto, Porto, Portugal
| | - Emily Smith
- Te Aka Mātuatua-School of Science, Te Whare Wānanga o Waikato-University of Waikato, Hamilton, New Zealand.,International Centre for Terrestrial Antarctic Research, University of Waikato, Hamilton, New Zealand
| | - Ian R McDonald
- Te Aka Mātuatua-School of Science, Te Whare Wānanga o Waikato-University of Waikato, Hamilton, New Zealand.,International Centre for Terrestrial Antarctic Research, University of Waikato, Hamilton, New Zealand
| | - Charles K Lee
- Te Aka Mātuatua-School of Science, Te Whare Wānanga o Waikato-University of Waikato, Hamilton, New Zealand.,International Centre for Terrestrial Antarctic Research, University of Waikato, Hamilton, New Zealand
| | - Matthew B Stott
- School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
| | - Jan P Amend
- Department of Earth Sciences, University of Southern California, Los Angeles, CA, United States.,Department of Biological Sciences, University of Southern California, Los Angeles, CA, United States
| | - S Craig Cary
- Te Aka Mātuatua-School of Science, Te Whare Wānanga o Waikato-University of Waikato, Hamilton, New Zealand.,International Centre for Terrestrial Antarctic Research, University of Waikato, Hamilton, New Zealand
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20
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Yang N, Zhan G, Luo H, Xiong X, Li D. Integrated simultaneous nitrification/denitrification and comammox consortia as efficient biocatalysts enhance treatment of domestic wastewater in different up-flow bioelectrochemical reactors. BIORESOURCE TECHNOLOGY 2021; 339:125604. [PMID: 34303104 DOI: 10.1016/j.biortech.2021.125604] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Revised: 07/14/2021] [Accepted: 07/15/2021] [Indexed: 06/13/2023]
Abstract
Simultaneous nitrification/denitrification (SND) can efficiently deplete NH4+ by using air-exposed biocathode (AEB) in bioelectrochemical reactors. However, the fluctuation of wastewater adversely affects the functional biofilms and therefore the performance. In this work, four up-flow bioelectrochemical reactors (UBERs) with some novel inocula were investigated to improve domestic wastewater treatment. The UBERs exhibited favorable removal of chemical oxygen demand (COD, 95%), NH4+-N (99%), and total nitrogen (TN, 99%). The maximum of current (2.7 A/m3), power density (136 mW/m3) and coulombic efficiency (20.5%) were obtained. Cyclic voltammetry analysis showed all the electrodes were of diversified catalytic reactions. Illumina pyrosequencing showed the predominant Ignavibacterium, Thauera, Nitrosomonas, Geminicoccus and Nitrospira were in all electrodes, contributing functional biofilms performing SND, comammox, and bioelectrochemical reactions. FAPROTAX analysis confirmed twenty-one functional groups with obvious changes related to chemoheterotrophy, respiration/oxidation/denitrification of nitrite and nitrate. Comfortingly, such novel diversified consortia in UBERs enhance the microbial metabolisms to treat domestic wastewater.
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Affiliation(s)
- Nuan Yang
- Key Laboratory of Development and Application of Rural Renewable Energy, Ministry of Agriculture and Rural Affairs, Biogas Institute of Ministry of Agriculture and Rural Affairs (BIOMA), Chengdu 610041, China; CAS Key Laboratory of Environmental and Applied Microbiology, Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, China.
| | - Guoqiang Zhan
- CAS Key Laboratory of Environmental and Applied Microbiology, Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, China
| | - Huiqin Luo
- CAS Key Laboratory of Environmental and Applied Microbiology, Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, China
| | - Xia Xiong
- Key Laboratory of Development and Application of Rural Renewable Energy, Ministry of Agriculture and Rural Affairs, Biogas Institute of Ministry of Agriculture and Rural Affairs (BIOMA), Chengdu 610041, China
| | - Daping Li
- CAS Key Laboratory of Environmental and Applied Microbiology, Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, China
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21
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Jiang H, Yang P, Wang Z, Ren S, Qiu J, Liang H, Peng Y, Li X, Zhang Q. Novel insights into overcoming nitrite oxidation bacteria acclimatization problem in treatment of high-ammonia wastewater through partial nitrification. BIORESOURCE TECHNOLOGY 2021; 336:125254. [PMID: 34030062 DOI: 10.1016/j.biortech.2021.125254] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/27/2021] [Revised: 04/29/2021] [Accepted: 04/30/2021] [Indexed: 06/12/2023]
Abstract
A partial nitrification sequencing batch reactor was operated to reveal mechanisms behind nitrite oxidation bacteria (NOB) acclimatization in high-ammonia wastewater treatment. The influent NH4+-N increased stepwise from 499.7 ± 4.2 mg/L to 6994.5 ± 7.5 mg/L with initial free ammonia (FA) concentration rising from 37.9 ± 3.2 mg NH3-N/L to 715.3 ± 47.3 mg NH3-N/L, respectively. NOB acclimatized this FA range with NO3--N production increasing from 29.2 ± 2.6 mg/L to 144.1 ± 31.0 mg/L in a cycle, which was caused by the shift of dominant NOB genus from Nitrospira to Nitrolencea. Nitrosomonas as ammonia oxidation bacteria, could sustain its activity of 62.1 ± 0.1 mg NH4+-N/(gVSS∙L∙h) under the same condition. Hydroxylamine addition could be implemented as an emergency measure to alleviate NOB acclimatization in short-term operation. The findings expanded knowledge about NOB acclimatization types and provided novel insights for addressing this problem in a targeted way.
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Affiliation(s)
- Hao Jiang
- National Engineering Laboratory for Advanced Municipal Wastewater Treatment and Reuse Technology, Engineering Research Center of Beijing, Beijing University of Technology, Beijing 100124, PR China
| | - Pei Yang
- State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, Harbin 150090, PR China; Engineering Technology Research Center of Beijing MSW Comprehensive Treatment and Utilization, Environmental Engineering Technology Co, Ltd., Beijing, PR China
| | - Zhong Wang
- State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, Harbin 150090, PR China
| | - Shang Ren
- National Engineering Laboratory for Advanced Municipal Wastewater Treatment and Reuse Technology, Engineering Research Center of Beijing, Beijing University of Technology, Beijing 100124, PR China
| | - Jingang Qiu
- National Engineering Laboratory for Advanced Municipal Wastewater Treatment and Reuse Technology, Engineering Research Center of Beijing, Beijing University of Technology, Beijing 100124, PR China
| | - Haoran Liang
- National Engineering Laboratory for Advanced Municipal Wastewater Treatment and Reuse Technology, Engineering Research Center of Beijing, Beijing University of Technology, Beijing 100124, PR China
| | - Yongzhen Peng
- National Engineering Laboratory for Advanced Municipal Wastewater Treatment and Reuse Technology, Engineering Research Center of Beijing, Beijing University of Technology, Beijing 100124, PR China.
| | - Xiyao Li
- National Engineering Laboratory for Advanced Municipal Wastewater Treatment and Reuse Technology, Engineering Research Center of Beijing, Beijing University of Technology, Beijing 100124, PR China
| | - Qiong Zhang
- National Engineering Laboratory for Advanced Municipal Wastewater Treatment and Reuse Technology, Engineering Research Center of Beijing, Beijing University of Technology, Beijing 100124, PR China
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22
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Yan W, Wang N, Wei D, Liang C, Chen X, Liu L, Shi J. Bacterial community compositions and nitrogen metabolism function in a cattle farm wastewater treatment plant revealed by Illumina high-throughput sequencing. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2021; 28:40895-40907. [PMID: 33772473 DOI: 10.1007/s11356-021-13570-w] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/28/2020] [Accepted: 03/16/2021] [Indexed: 06/12/2023]
Abstract
Bacteria play an important role in pollutant transformation in activated sludge-based wastewater treatment plants (WWTPs). Exploring the microbial community structure and diversity is essential to improving the performance of wastewater treatment processes. This study employed Illumina MiSeq high-throughput sequencing to investigate the microbial community composition and diversity in a cattle farm wastewater treatment plant (Cf-WWTP). The results showed that the dominant phyla in the whole process were Proteobacteria, Bacteroidetes, and Firmicutes. The principal coordinate analysis (PCoA) indicated that the different stages had a significant impact on the microbial community structure; Bacteroidetes was the dominant phylum in the anearobic stage and Proteobacteria was the dominant phylum in the anoxic-oxic stage. Redundancy analysis (RDA) revealed that total phosphorus (TP) was the most significant factor that regulated the microbial community composition, followed by chemical oxygen demand (COD), total nitrogen (TN), and pH. Proteobacteria, Patescibacteria, and Chloroflexi were simultaneously negatively correlated with TN, COD, and TP. Nitrogen metabolic pathway and transformation mechanism was elucidated by a complete denitrification function predicted with phylogenetic investigation of communities with reconstruction of unobserved states (PICRUSt), as well as detection of ammonia-oxidizing bacteria (AOB) and nitrite-oxidizing bacteria (NOB). These results provide new insights into our understanding of microbial community and metabolic functions of Cf-WWTP.
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Affiliation(s)
- Weizhi Yan
- Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai, 201210, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Na Wang
- Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai, 201210, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Dong Wei
- Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai, 201210, China
- Shanghai Engineering Research Center of Biotransformation of Organic Solid Waste, Shanghai, 200241, China
| | - Chengyu Liang
- Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai, 201210, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xiaomiao Chen
- Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai, 201210, China
- School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China
| | - Li Liu
- Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai, 201210, China.
- Shanghai Engineering Research Center of Biotransformation of Organic Solid Waste, Shanghai, 200241, China.
| | - Jiping Shi
- Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai, 201210, China.
- School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China.
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23
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Mueller AJ, Jung MY, Strachan CR, Herbold CW, Kirkegaard RH, Wagner M, Daims H. Genomic and kinetic analysis of novel Nitrospinae enriched by cell sorting. THE ISME JOURNAL 2021; 15:732-745. [PMID: 33067588 PMCID: PMC8026999 DOI: 10.1038/s41396-020-00809-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Revised: 09/23/2020] [Accepted: 10/05/2020] [Indexed: 12/18/2022]
Abstract
Chemolithoautotrophic nitrite-oxidizing bacteria (NOB) are key players in global nitrogen and carbon cycling. Members of the phylum Nitrospinae are the most abundant, known NOB in the oceans. To date, only two closely affiliated Nitrospinae species have been isolated, which are only distantly related to the environmentally abundant uncultured Nitrospinae clades. Here, we applied live cell sorting, activity screening, and subcultivation on marine nitrite-oxidizing enrichments to obtain novel marine Nitrospinae. Two binary cultures were obtained, each containing one Nitrospinae strain and one alphaproteobacterial heterotroph. The Nitrospinae strains represent two new genera, and one strain is more closely related to environmentally abundant Nitrospinae than previously cultured NOB. With an apparent half-saturation constant of 8.7 ± 2.5 µM, this strain has the highest affinity for nitrite among characterized marine NOB, while the other strain (16.2 ± 1.6 µM) and Nitrospina gracilis (20.1 ± 2.1 µM) displayed slightly lower nitrite affinities. The new strains and N. gracilis share core metabolic pathways for nitrite oxidation and CO2 fixation but differ remarkably in their genomic repertoires of terminal oxidases, use of organic N sources, alternative energy metabolisms, osmotic stress and phage defense. The new strains, tentatively named "Candidatus Nitrohelix vancouverensis" and "Candidatus Nitronauta litoralis", shed light on the niche differentiation and potential ecological roles of Nitrospinae.
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Affiliation(s)
- Anna J Mueller
- University of Vienna, Division of Microbial Ecology, Centre for Microbiology and Environmental Systems Science, Althanstrasse 14, 1090, Vienna, Austria
| | - Man-Young Jung
- University of Vienna, Division of Microbial Ecology, Centre for Microbiology and Environmental Systems Science, Althanstrasse 14, 1090, Vienna, Austria
- Department of Science Education, Jeju National University, 102 Jejudaehak-ro, Jeju, 63243, Republic of Korea
| | - Cameron R Strachan
- Department for Farm Animals and Public Health, Food Technology and Veterinary Public Health, University of Veterinary Medicine Vienna, Veterinärplatz 1, 1210, Vienna, Austria
- FFoQSI GmbH, Technopark 1C, 3430, Tulln, Austria
| | - Craig W Herbold
- University of Vienna, Division of Microbial Ecology, Centre for Microbiology and Environmental Systems Science, Althanstrasse 14, 1090, Vienna, Austria
| | - Rasmus H Kirkegaard
- Department of Chemistry and Bioscience, Center for Microbial Communities, Aalborg University, Fredrik Bajers Vej 7H, 9220, Aalborg, Denmark
| | - Michael Wagner
- University of Vienna, Division of Microbial Ecology, Centre for Microbiology and Environmental Systems Science, Althanstrasse 14, 1090, Vienna, Austria
- Department of Chemistry and Bioscience, Center for Microbial Communities, Aalborg University, Fredrik Bajers Vej 7H, 9220, Aalborg, Denmark
- University of Vienna, The Comammox Research Platform, Vienna, Austria
| | - Holger Daims
- University of Vienna, Division of Microbial Ecology, Centre for Microbiology and Environmental Systems Science, Althanstrasse 14, 1090, Vienna, Austria.
- University of Vienna, The Comammox Research Platform, Vienna, Austria.
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24
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Wang Y, Liu Y, Li X, Han X, Zhang Z, Ma X, Li J. Potentilla anserina L. developmental changes affect the rhizosphere prokaryotic community. Sci Rep 2021; 11:2838. [PMID: 33531629 PMCID: PMC7854623 DOI: 10.1038/s41598-021-82610-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2020] [Accepted: 01/22/2021] [Indexed: 11/23/2022] Open
Abstract
Plant roots and soil prokaryotes primarily interact with each other in the rhizosphere. Changes in the rhizosphere prokaryotic structure are influenced by several factors. In this study, the community structure of the Potentilla anserina L. rhizosphere prokaryotes was identified and evaluated by high-throughput sequencing technology in different continuous cropping fields and developmental stages of the plant. In total, 2 archaeal (Euryarchaeota and Thaumarchaeota) and 26 bacterial phyla were identified in the P. anserina rhizosphere. The bacterial community was mainly composed of Acidobacteria, Actinobacteria, Bacteroidetes, Chloroflexi, Gemmatimonadetes, Planctomycetes, Proteobacteria, and Verrucomicrobia. Moreover, the prokaryotic community structure of the rhizosphere varied significantly during plant development. Our results provide new insights into the dynamics of the P. anserina rhizosphere prokaryotic community and may provide useful information for enhancing the growth and development of P. anserina through artificial control of the soil prokaryotes.
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Affiliation(s)
- Yaqiong Wang
- School of Ecology, Environment and Resources, Qinghai Nationalities University, Bayi Road, Xining, 810007, Qinghai, China. .,Qinghai Provincial Key Laboratory of High-Value Utilization of Characteristic Economic Plants, Xining, 810007, China. .,Qinghai Provincial Biotechnology and Analytical Test Key Laboratory, Tibetan Plateau Juema Research Centre, Xining, 810007, China.
| | - Yuxi Liu
- School of Ecology, Environment and Resources, Qinghai Nationalities University, Bayi Road, Xining, 810007, Qinghai, China
| | - Xue Li
- School of Ecology, Environment and Resources, Qinghai Nationalities University, Bayi Road, Xining, 810007, Qinghai, China
| | - Xiaoyan Han
- School of Ecology, Environment and Resources, Qinghai Nationalities University, Bayi Road, Xining, 810007, Qinghai, China
| | - Zhen Zhang
- School of Ecology, Environment and Resources, Qinghai Nationalities University, Bayi Road, Xining, 810007, Qinghai, China
| | - Xiaoling Ma
- School of Ecology, Environment and Resources, Qinghai Nationalities University, Bayi Road, Xining, 810007, Qinghai, China
| | - Junqiao Li
- School of Ecology, Environment and Resources, Qinghai Nationalities University, Bayi Road, Xining, 810007, Qinghai, China. .,Qinghai Provincial Key Laboratory of High-Value Utilization of Characteristic Economic Plants, Xining, 810007, China. .,Qinghai Provincial Biotechnology and Analytical Test Key Laboratory, Tibetan Plateau Juema Research Centre, Xining, 810007, China.
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25
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26
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Activated sludge under free ammonia treatment using gel immobilization technology for long-term partial nitrification with different initial biomass. Process Biochem 2020. [DOI: 10.1016/j.procbio.2020.07.025] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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27
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Zhang X, Bian F, Zhong Z, Gai X, Yang C. Deciphering the rhizosphere microbiome of a bamboo plant in response to different chromium contamination levels. JOURNAL OF HAZARDOUS MATERIALS 2020; 399:123107. [PMID: 32937721 DOI: 10.1016/j.jhazmat.2020.123107] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/09/2020] [Revised: 05/13/2020] [Accepted: 06/01/2020] [Indexed: 06/11/2023]
Abstract
Bamboo has been considered a potential plant species for phytoremediation due to its high biomass and heavy metal (HM) resistance. However, little is known about the interactions between bamboo and soil microbial activities in HM-contaminated soils. Here, we investigated the characteristics of microbial communities in the rhizosphere soil of Lei bamboo (Phyllostachys praecox) along a chromium (Cr) gradient. We found that the soil Cr content was positively correlated with the total organic carbon (TOC) and HCl-extractable Cr but negatively correlated with the pH and bacterial and fungal Shannon indices. Proteobacteria and Ascomycota predominated in the bamboo rhizosphere under Cr pollution. A co-occurrence network showed that two of the most Cr-sensitive bacterial genera and keystone taxa were from the Acidobacteria, indicating that this phylum can be as an indicator for the studied Cr-polluted soils. Redundancy analysis revealed that both the soil bacterial and fungal community compositions were significantly correlated (p < 0.05) with Cr, pH, TOC, alkali-hydrolysable N (AN), and available phosphorus (AP). The increase in TOC as the Cr content increased can be ascribed to an adverse Cr effect on the soil microflora, probably because the microbial biomass was less effective in mineralizing soil C under Cr-polluted conditions.
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Affiliation(s)
- Xiaoping Zhang
- China National Bamboo Research Center, Key Laboratory of Resources and Utilization of Bamboo of State Forestry Administration, Hangzhou, Zhejiang 310012, PR China
| | - Fangyuan Bian
- China National Bamboo Research Center, Key Laboratory of Resources and Utilization of Bamboo of State Forestry Administration, Hangzhou, Zhejiang 310012, PR China
| | - Zheke Zhong
- China National Bamboo Research Center, Key Laboratory of Resources and Utilization of Bamboo of State Forestry Administration, Hangzhou, Zhejiang 310012, PR China.
| | - Xu Gai
- China National Bamboo Research Center, Key Laboratory of Resources and Utilization of Bamboo of State Forestry Administration, Hangzhou, Zhejiang 310012, PR China
| | - Chuanbao Yang
- China National Bamboo Research Center, Key Laboratory of Resources and Utilization of Bamboo of State Forestry Administration, Hangzhou, Zhejiang 310012, PR China
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28
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Park SJ, Andrei AŞ, Bulzu PA, Kavagutti VS, Ghai R, Mosier AC. Expanded Diversity and Metabolic Versatility of Marine Nitrite-Oxidizing Bacteria Revealed by Cultivation- and Genomics-Based Approaches. Appl Environ Microbiol 2020; 86:e01667-20. [PMID: 32917751 PMCID: PMC7642081 DOI: 10.1128/aem.01667-20] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Accepted: 09/03/2020] [Indexed: 12/30/2022] Open
Abstract
Nitrite-oxidizing bacteria (NOB) are ubiquitous and abundant microorganisms that play key roles in global nitrogen and carbon biogeochemical cycling. Despite recent advances in understanding NOB physiology and taxonomy, currently very few cultured NOB or representative NOB genome sequences from marine environments exist. In this study, we employed enrichment culturing and genomic approaches to shed light on the phylogeny and metabolic capacity of marine NOB. We successfully enriched two marine NOB (designated MSP and DJ) and obtained a high-quality metagenome-assembled genome (MAG) from each organism. The maximum nitrite oxidation rates of the MSP and DJ enrichment cultures were 13.8 and 30.0 μM nitrite per day, respectively, with these optimum rates occurring at 0.1 mM and 0.3 mM nitrite, respectively. Each enrichment culture exhibited a different tolerance to various nitrite and salt concentrations. Based on phylogenomic position and overall genome relatedness indices, both NOB MAGs were proposed as novel taxa within the Nitrospinota and Nitrospirota phyla. Functional predictions indicated that both NOB MAGs shared many highly conserved metabolic features with other NOB. Both NOB MAGs encoded proteins for hydrogen and organic compound metabolism and defense mechanisms for oxidative stress. Additionally, these organisms may have the genetic potential to produce cobalamin (an essential enzyme cofactor that is limiting in many environments) and, thus, may play an important role in recycling cobalamin in marine sediment. Overall, this study appreciably expands our understanding of the Nitrospinota and Nitrospirota phyla and suggests that these NOB play important biogeochemical roles in marine habitats.IMPORTANCE Nitrification is a key process in the biogeochemical and global nitrogen cycle. Nitrite-oxidizing bacteria (NOB) perform the second step of aerobic nitrification (converting nitrite to nitrate), which is critical for transferring nitrogen to other organisms for assimilation or energy. Despite their ecological importance, there are few cultured or genomic representatives from marine systems. Here, we obtained two NOB (designated MSP and DJ) enriched from marine sediments and estimated the physiological and genomic traits of these marine microbes. Both NOB enrichment cultures exhibit distinct responses to various nitrite and salt concentrations. Genomic analyses suggest that these NOB are metabolically flexible (similar to other previously described NOB) yet also have individual genomic differences that likely support distinct niche distribution. In conclusion, this study provides more insights into the ecological roles of NOB in marine environments.
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Affiliation(s)
- Soo-Je Park
- Department of Biology, Jeju National University, Jeju, Republic of Korea
| | - Adrian-Ştefan Andrei
- Department of Aquatic Microbial Ecology, Institute of Hydrobiology, Biology Centre of the Academy of Sciences of the Czech Republic, České Budějovice, Czech Republic
| | - Paul-Adrian Bulzu
- Department of Aquatic Microbial Ecology, Institute of Hydrobiology, Biology Centre of the Academy of Sciences of the Czech Republic, České Budějovice, Czech Republic
| | - Vinicius S Kavagutti
- Department of Aquatic Microbial Ecology, Institute of Hydrobiology, Biology Centre of the Academy of Sciences of the Czech Republic, České Budějovice, Czech Republic
- Department of Ecosystem Biology, Faculty of Science, University of South Bohemia, České Budějovice, Czech Republic
| | - Rohit Ghai
- Department of Aquatic Microbial Ecology, Institute of Hydrobiology, Biology Centre of the Academy of Sciences of the Czech Republic, České Budějovice, Czech Republic
| | - Annika C Mosier
- Department of Integrative Biology, University of Colorado Denver, Denver, Colorado, USA
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29
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Spieck E, Sass K, Keuter S, Hirschmann S, Spohn M, Indenbirken D, Kop LFM, Lücker S, Giaveno A. Defining Culture Conditions for the Hidden Nitrite-Oxidizing Bacterium Nitrolancea. Front Microbiol 2020; 11:1522. [PMID: 32849321 PMCID: PMC7365893 DOI: 10.3389/fmicb.2020.01522] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2020] [Accepted: 06/12/2020] [Indexed: 12/26/2022] Open
Abstract
Nitrification is a key process for N-removal in engineered and natural environments, but recent findings of novel nitrifying microorganisms with surprising features revealed that our knowledge of this functional guild is still incomplete. Especially nitrite oxidation - the second step of nitrification - is catalyzed by a phylogenetically diverse bacterial group, and only recently bacteria of the phylum Chloroflexi have been identified as thermophilic nitrite-oxidizing bacteria (NOB). Among these, Nitrolancea hollandica was isolated from a laboratory-scale nitrifying bioreactor operated at 35°C with a high load of ammonium bicarbonate. However, its distribution remains cryptic as very few closely related environmental 16S rRNA gene sequences have been retrieved so far. In this study, we demonstrate how such thermophilic NOB can be enriched using modified mineral media inoculated with samples from a wastewater side-stream reactor operated at 39.5°C. Distinct cultivation conditions resulted in quick and reproducible high enrichment of two different strains of Nitrolancea, closely related to Nl. hollandica. The same cultivation approach was applied to a complex nitrite-oxidizing pre-enrichment at 42°C inoculated with biomass from a geothermal spring in the Copahue volcano area in Neuquen, Argentina. Here, an additional distinct representative of the genus Nitrolancea was obtained. This novel species had 16S rRNA and nitrite oxidoreductase alpha subunit (nxrA) gene sequence identities to Nl. hollandica of 98.5% and 97.2%, respectively. A genomic average nucleotide identity between the Argentinian strain and Nl. hollandica of 91.9% indicates that it indeed represents a distinct species. All Nitrolancea cultures formed lancet-shaped cells identical to Nl. hollandica and revealed similar physiological features, including the capability to grow at high nitrite concentrations. Growth was optimal at temperatures of 35-37°C and was strongly enhanced by ammonium supplementation. Genomic comparisons revealed that the four Nitrolancea strains share 2399 out of 3387 orthologous gene clusters and encode similar key functions. Our results define general growth conditions that enable the selective enrichment of Nitrolancea from artificial and natural environments. In most natural habitats these NOB apparently are of low abundance and their proliferation depends on the balanced presence of nitrite and ammonium, with an optimal incubation temperature of 37°C.
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Affiliation(s)
- Eva Spieck
- Department of Microbiology and Biotechnology, Universität Hamburg, Hamburg, Germany
| | - Katharina Sass
- Department of Microbiology and Biotechnology, Universität Hamburg, Hamburg, Germany
| | - Sabine Keuter
- Department of Microbiology and Biotechnology, Universität Hamburg, Hamburg, Germany
| | - Sophia Hirschmann
- Department of Microbiology and Biotechnology, Universität Hamburg, Hamburg, Germany
| | - Michael Spohn
- Technology Platform Next Generation Sequencing, Heinrich Pette Institut, Hamburg, Germany
| | - Daniela Indenbirken
- Technology Platform Next Generation Sequencing, Heinrich Pette Institut, Hamburg, Germany
| | - Linnea F. M. Kop
- Department of Microbiology, IWWR, Radboud University, Nijmegen, Netherlands
| | - Sebastian Lücker
- Department of Microbiology, IWWR, Radboud University, Nijmegen, Netherlands
| | - Alejandra Giaveno
- PROBIEN (CONICET-UNCo), Departamento de Química, Facultad de Ingeniería, Universidad Nacional del Comahue, Neuquén, Argentina
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30
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Mills JG, Bissett A, Gellie NJC, Lowe AJ, Selway CA, Thomas T, Weinstein P, Weyrich LS, Breed MF. Revegetation of urban green space rewilds soil microbiotas with implications for human health and urban design. Restor Ecol 2020. [DOI: 10.1111/rec.13175] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Jacob G. Mills
- School of Biological Sciences and Environment Institute The University of Adelaide Adelaide South Australia 5005 Australia
| | - Andrew Bissett
- Oceans and Atmosphere, CSIRO Hobart Tasmania 7004 Australia
| | - Nicholas J. C. Gellie
- School of Biological Sciences and Environment Institute The University of Adelaide Adelaide South Australia 5005 Australia
| | - Andrew J. Lowe
- School of Biological Sciences and Environment Institute The University of Adelaide Adelaide South Australia 5005 Australia
| | - Caitlin A. Selway
- Australian Centre for Ancient DNA, School of Biological Sciences The University of Adelaide Adelaide South Australia 5005 Australia
| | - Torsten Thomas
- Centre for Marine Science and Innovation, School of Biological, Environmental and Earth Sciences University of New South Wales Sydney New South Wales 2052 Australia
| | - Philip Weinstein
- School of Biological Sciences and Environment Institute The University of Adelaide Adelaide South Australia 5005 Australia
| | - Laura S. Weyrich
- Australian Centre for Ancient DNA, School of Biological Sciences The University of Adelaide Adelaide South Australia 5005 Australia
- Department of Anthropology The Pennsylvania State University University Park Pennsylvania 16802 USA
| | - Martin F. Breed
- School of Biological Sciences and Environment Institute The University of Adelaide Adelaide South Australia 5005 Australia
- College of Science and Engineering Flinders University Adelaide South Australia 5042 Australia
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31
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Li X, Li Y, Li Y, Wu J. Myriophyllum elatinoides growth and rhizosphere bacterial community structure under different nitrogen concentrations in swine wastewater. BIORESOURCE TECHNOLOGY 2020; 301:122776. [PMID: 31958692 DOI: 10.1016/j.biortech.2020.122776] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Revised: 01/06/2020] [Accepted: 01/07/2020] [Indexed: 06/10/2023]
Abstract
In this study, Myriophyllum elatinoides growth under different nitrogen (N) concentrations (2, 250, 300, 350 and 400 mg L-1) and changes in rhizosphere bacterial community structure were investigated. High N (>300 mg L-1) concentrations caused reduction in M. elatinoides biomass. Growth tended to stabilize at 49 days. N concentration in roots were higher than that in stems and leaves under high N conditions. TN and NH4+ removal efficiencies reached 84.0% and 87.2%, respectively, in M. elatinoides surface flow constructed wetlands (SFCWs). Rhizosphere bacterial diversity increased over time. Proteobacteria, Firmicutes, Cyanobacteria, and Bacteroidetes dominated at the phylum level. Genera Turicibacter, Allochromatium, and Methylocystis increased at low N (<300 mg L-1) concentrations, while Pseudomonas increased at high N concentrations over the experimental period. Redundancy analysis showed that pH was strongly correlated with changes in rhizosphere bacterial community structure. These findings helped to insight into N removal mechanism in M. elatinoides.
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Affiliation(s)
- Xi Li
- Key Laboratory of Agro-ecological Processes in Subtropical Regions, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Hunan 410125, PR China; Changsha Research Station for Agricultural & Environmental Monitoring, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Hunan 410125, PR China
| | - Yuyuan Li
- Key Laboratory of Agro-ecological Processes in Subtropical Regions, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Hunan 410125, PR China; Changsha Research Station for Agricultural & Environmental Monitoring, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Hunan 410125, PR China.
| | - Yong Li
- Key Laboratory of Agro-ecological Processes in Subtropical Regions, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Hunan 410125, PR China; Changsha Research Station for Agricultural & Environmental Monitoring, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Hunan 410125, PR China
| | - Jinshui Wu
- Key Laboratory of Agro-ecological Processes in Subtropical Regions, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Hunan 410125, PR China; Changsha Research Station for Agricultural & Environmental Monitoring, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Hunan 410125, PR China; University of Chinese Academy of Sciences, Beijing 100049, PR China
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32
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Herber J, Klotz F, Frommeyer B, Weis S, Straile D, Kolar A, Sikorski J, Egert M, Dannenmann M, Pester M. A single Thaumarchaeon drives nitrification in deep oligotrophic Lake Constance. Environ Microbiol 2019; 22:212-228. [PMID: 31657089 DOI: 10.1111/1462-2920.14840] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2019] [Revised: 08/30/2019] [Accepted: 08/30/2019] [Indexed: 12/15/2022]
Abstract
Ammonia released during organic matter mineralization is converted during nitrification to nitrate. We followed spatiotemporal dynamics of the nitrifying microbial community in deep oligotrophic Lake Constance. Depth-dependent decrease of total ammonium (0.01-0.84 μM) indicated the hypolimnion as the major place of nitrification with 15 N-isotope dilution measurements indicating a threefold daily turnover of hypolimnetic total ammonium. This was mirrored by a strong increase of ammonia-oxidizing Thaumarchaeota towards the hypolimnion (13%-21% of bacterioplankton) throughout spring to autumn as revealed by amplicon sequencing and quantitative polymerase chain reaction. Ammonia-oxidizing bacteria were typically two orders of magnitude less abundant and completely ammonia-oxidizing (comammox) bacteria were not detected. Both, 16S rRNA gene and amoA (encoding ammonia monooxygenase subunit B) analyses identified only one major species-level operational taxonomic unit (OTU) of Thaumarchaeota (99% of all ammonia oxidizers in the hypolimnion), which was affiliated to Nitrosopumilus spp. The relative abundance distribution of the single Thaumarchaeon strongly correlated to an equally abundant Chloroflexi clade CL500-11 OTU and a Nitrospira OTU that was one order of magnitude less abundant. The latter dominated among recognized nitrite oxidizers. This extremely low diversity of nitrifiers shows how vulnerable the ecosystem process of nitrification may be in Lake Constance as Central Europe's third largest lake.
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Affiliation(s)
- Janina Herber
- Department of Biology, University of Konstanz, Universitätsstrasse 10, Constance, 78457, Germany
| | - Franziska Klotz
- Department of Biology, University of Konstanz, Universitätsstrasse 10, Constance, 78457, Germany
| | - Benjamin Frommeyer
- Department of Biology, University of Konstanz, Universitätsstrasse 10, Constance, 78457, Germany
| | - Severin Weis
- Faculty of Medical and Life Sciences, Institute of Precision Medicine, Furtwangen University, Jakob-Kienzle-Str. 17, Villingen-Schwenningen, 78054, Germany
| | - Dietmar Straile
- Limnological Institute, University of Konstanz, Mainaustraße 252, Constance, 78464, Germany
| | - Allison Kolar
- Karlsruhe Institute of Technology, Institute for Meteorology and Climate Research, Atmospheric Environmental Research (IMK-IFU), Kreuzeckbahnstr. 19, 82467, Garmisch-Partenkirchen, Germany
| | - Johannes Sikorski
- Department of Microorganisms, Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Inhoffenstr. 7B, 38124, Braunschweig, Germany
| | - Markus Egert
- Faculty of Medical and Life Sciences, Institute of Precision Medicine, Furtwangen University, Jakob-Kienzle-Str. 17, Villingen-Schwenningen, 78054, Germany
| | - Michael Dannenmann
- Karlsruhe Institute of Technology, Institute for Meteorology and Climate Research, Atmospheric Environmental Research (IMK-IFU), Kreuzeckbahnstr. 19, 82467, Garmisch-Partenkirchen, Germany
| | - Michael Pester
- Department of Biology, University of Konstanz, Universitätsstrasse 10, Constance, 78457, Germany.,Department of Microorganisms, Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Inhoffenstr. 7B, 38124, Braunschweig, Germany.,Technical University of Braunschweig, Institute for Microbiology, Spielmannstrasse 7, Braunschweig, 38106, Germany
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Zorz JK, Sharp C, Kleiner M, Gordon PMK, Pon RT, Dong X, Strous M. A shared core microbiome in soda lakes separated by large distances. Nat Commun 2019; 10:4230. [PMID: 31530813 PMCID: PMC6748926 DOI: 10.1038/s41467-019-12195-5] [Citation(s) in RCA: 48] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2019] [Accepted: 08/16/2019] [Indexed: 11/25/2022] Open
Abstract
In alkaline soda lakes, concentrated dissolved carbonates establish productive phototrophic microbial mats. Here we show how microbial phototrophs and autotrophs contribute to this exceptional productivity. Amplicon and shotgun DNA sequencing data of microbial mats from four Canadian soda lakes indicate the presence of > 2,000 species of Bacteria and Eukaryotes. We recover metagenome-assembled-genomes for a core microbiome of < 100 abundant bacteria, present in all four lakes. Most of these are related to microbes previously detected in sediments of Asian alkaline lakes, showing that common selection principles drive community assembly from a globally distributed reservoir of alkaliphile biodiversity. Detection of > 7,000 proteins show how phototrophic populations allocate resources to specific processes and occupy complementary niches. Carbon fixation proceeds by the Calvin-Benson-Bassham cycle, in Cyanobacteria, Gammaproteobacteria, and, surprisingly, Gemmatimonadetes. Our study provides insight into soda lake ecology, as well as a template to guide efforts to engineer biotechnology for carbon dioxide conversion.
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Affiliation(s)
- Jackie K Zorz
- Department of Geoscience, University of Calgary, Calgary, AB, T2N 1N4, Canada.
| | - Christine Sharp
- Department of Geoscience, University of Calgary, Calgary, AB, T2N 1N4, Canada
| | - Manuel Kleiner
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC, 27695, USA
| | - Paul M K Gordon
- Centre for Health Genomics and Informatics, University of Calgary, Calgary, AB, T2N 2T9, Canada
| | - Richard T Pon
- Centre for Health Genomics and Informatics, University of Calgary, Calgary, AB, T2N 2T9, Canada
| | - Xiaoli Dong
- Department of Geoscience, University of Calgary, Calgary, AB, T2N 1N4, Canada
| | - Marc Strous
- Department of Geoscience, University of Calgary, Calgary, AB, T2N 1N4, Canada
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34
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Speirs LBM, Rice DTF, Petrovski S, Seviour RJ. The Phylogeny, Biodiversity, and Ecology of the Chloroflexi in Activated Sludge. Front Microbiol 2019; 10:2015. [PMID: 31572309 PMCID: PMC6753630 DOI: 10.3389/fmicb.2019.02015] [Citation(s) in RCA: 112] [Impact Index Per Article: 22.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2019] [Accepted: 08/16/2019] [Indexed: 02/01/2023] Open
Abstract
It is now clear that several of the filamentous bacteria in activated sludge wastewater treatment plants globally, are members of the phylum Chloroflexi. They appear to be more commonly found in treatment plants designed to remove nitrogen (N) and phosphorus (P), most of which operate at long sludge ages and expose the biomass to anaerobic conditions. The Chloroflexi seem to play an important beneficial role in providing the filamentous scaffolding around which flocs are formed, to feed on the debris from lysed bacterial cells, to ferment carbohydrates and to degrade other complex polymeric organic compounds to low molecular weight substrates to support their growth and that of other bacterial populations. A few commonly extend beyond the floc surface, while others can align in bundles, which may facilitate interfloc bridging and hence generate a bulking sludge. Although several recent papers have examined the phylogeny and in situ physiology of Chloroflexi in activated sludge plants in Denmark, this review takes a wider look at what we now know about these filaments, especially their global distribution in activated sludge plants, and what their functional roles there might be. It also attempts to outline why such information might provide us with clues as to how their population levels may be manipulated, and the main research questions that need addressing to achieve these outcomes.
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Affiliation(s)
- Lachlan B. M. Speirs
- La Trobe Institute for Molecular Sciences, La Trobe University, Bendigo, VIC, Australia
| | - Daniel T. F. Rice
- Department of Physiology, Anatomy and Microbiology, La Trobe University, Bundoora, VIC, Australia
| | - Steve Petrovski
- Department of Physiology, Anatomy and Microbiology, La Trobe University, Bundoora, VIC, Australia
| | - Robert J. Seviour
- Department of Physiology, Anatomy and Microbiology, La Trobe University, Bundoora, VIC, Australia
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35
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Zheng Z, Huang S, Bian W, Liang D, Wang X, Zhang K, Ma X, Li J. Enhanced nitrogen removal of the simultaneous partial nitrification, anammox and denitrification (SNAD) biofilm reactor for treating mainstream wastewater under low dissolved oxygen (DO) concentration. BIORESOURCE TECHNOLOGY 2019; 283:213-220. [PMID: 30908986 DOI: 10.1016/j.biortech.2019.01.148] [Citation(s) in RCA: 59] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/25/2018] [Revised: 01/03/2019] [Accepted: 01/07/2019] [Indexed: 06/09/2023]
Abstract
The simultaneous partial nitrification, anammox and denitrification (SNAD) process for treating mainstream wastewater was investigated under different intermittent aeration modes. By controlling the aeration time of 20, 60 and 180 min during the intermittent modes, the oxygen concentration remained 3.50, 1.45 and 0.70 mg·L-1. Correspondingly, the reactor achieved the nitrogen removal rate of 0.17, 0.29 and 0.30 kg N·m-3·d-1. Meanwhile, the average total inorganic nitrogen (TIN) removal efficiency reached 93.4%, 87.5% and 92.7%. The effluent NO3--N concentration was very low. High-throughput sequencing analysis indicated that the proportion of nitrite oxidization bacteria (NOB), anammox bacteria and denitrification bacteria was 0.15%, 0.33% and 8.78%. Candidatus Anammoxoglobus was the abundant anammox bacteria genus. Further study on the unclassified sequences revealed the possibility of the high relative abundance of Nitrosomonas-related genus and Candidatus Kuenenia-related genus on the SNAD biofilm.
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Affiliation(s)
- Zhaoming Zheng
- The College of Architecture and Civil Engineering, Beijing University of Technology, Beijing 100124, China
| | - Shan Huang
- Department of Civil and Environmental Engineering, Princeton University, Princeton, NJ 08544, USA
| | - Wei Bian
- The College of Architecture and Civil Engineering, Beijing University of Technology, Beijing 100124, China
| | - Dongbo Liang
- The College of Architecture and Civil Engineering, Beijing University of Technology, Beijing 100124, China
| | - Xiujie Wang
- The College of Architecture and Civil Engineering, Beijing University of Technology, Beijing 100124, China
| | - Kai Zhang
- The College of Architecture and Civil Engineering, Beijing University of Technology, Beijing 100124, China
| | - Xiaoran Ma
- The College of Architecture and Civil Engineering, Beijing University of Technology, Beijing 100124, China
| | - Jun Li
- The College of Architecture and Civil Engineering, Beijing University of Technology, Beijing 100124, China.
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36
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Wang K, Hu H, Yan H, Hou D, Wang Y, Dong P, Zhang D. Archaeal biogeography and interactions with microbial community across complex subtropical coastal waters. Mol Ecol 2019; 28:3101-3118. [PMID: 30993759 DOI: 10.1111/mec.15105] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2018] [Revised: 04/03/2019] [Accepted: 04/10/2019] [Indexed: 01/21/2023]
Abstract
Marine Archaea are crucial in biogeochemical cycles, but their horizontal spatial variability, assembly processes, and microbial associations across complex coastal waters still lack characterizations at high coverage. Using a dense sampling strategy, we investigated horizontal variability in total archaeal, Thaumarchaeota Marine Group (MG) I, and Euryarchaeota MGII communities and associations of MGI/MGII with other microbes in surface waters with contrasting environmental characteristics across ~200 km by 16S rRNA gene amplicon sequencing. Total archaeal communities were extremely dominated by MGI and/or MGII (98.9% in average relative abundance). Niche partitioning between MGI and MGII or within each group was found across multiple environmental gradients. "Selection" was more important than "dispersal limitation" in governing biogeographic patterns of total archaeal, MGI, and MGII communities, and basic abiotic parameters (such as salinity) and inorganic/organic resources as a whole could be the main driver of "selection". While "homogenizing dispersal" also considerably governed their biogeography. MGI-Nitrospira assemblages were speculatively responsible for complete nitrification. MGI taxa commonly had negative correlations with members of Synechococcus but positive correlations with members of eukaryotic phytoplankton, suggesting that competition or synergy between MGI and phytoplankton depends on specific MGI-phytoplankton assemblages. MGII taxa showed common associations with presumed (photo)heterotrophs including members of SAR11, SAR86, SAR406, and Candidatus Actinomarina. This study sheds light on ecological processes and drivers shaping archaeal biogeography and many strong MGI/MGII-bacterial associations across complex subtropical coastal waters. Future efforts should be made on seasonality of archaeal biogeography and biological, environmental, or ecological mechanisms underlying these statistical microbial associations.
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Affiliation(s)
- Kai Wang
- School of Marine Sciences, Ningbo University, Ningbo, China.,Collaborative Innovation Center for Zhejiang Marine High-efficiency and Healthy Aquaculture, Ningbo, China
| | - Hanjing Hu
- School of Marine Sciences, Ningbo University, Ningbo, China.,Collaborative Innovation Center for Zhejiang Marine High-efficiency and Healthy Aquaculture, Ningbo, China
| | - Huizhen Yan
- School of Marine Sciences, Ningbo University, Ningbo, China
| | - Dandi Hou
- School of Marine Sciences, Ningbo University, Ningbo, China
| | - Yanting Wang
- School of Marine Sciences, Ningbo University, Ningbo, China
| | - Pengsheng Dong
- School of Marine Sciences, Ningbo University, Ningbo, China
| | - Demin Zhang
- School of Marine Sciences, Ningbo University, Ningbo, China.,Collaborative Innovation Center for Zhejiang Marine High-efficiency and Healthy Aquaculture, Ningbo, China
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37
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Vandekerckhove TGL, Kerckhof FM, De Mulder C, Vlaeminck SE, Boon N. Determining stoichiometry and kinetics of two thermophilic nitrifying communities as a crucial step in the development of thermophilic nitrogen removal. WATER RESEARCH 2019; 156:34-45. [PMID: 30904709 DOI: 10.1016/j.watres.2019.03.008] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2018] [Revised: 03/08/2019] [Accepted: 03/09/2019] [Indexed: 06/09/2023]
Abstract
Nitrification and denitrification, the key biological processes for thermophilic nitrogen removal, have separately been established in bioreactors at 50 °C. A well-characterized set of kinetic parameters is essential to integrate these processes while safeguarding the autotrophs performing nitrification. Knowledge on thermophilic nitrifying kinetics is restricted to isolated or highly enriched batch cultures, which do not represent bioreactor conditions. This study characterized the stoichiometry and kinetics of two thermophilic (50 °C) nitrifying communities. The most abundant ammonia oxidizing archaea (AOA) were related to the Nitrososphaera genus, clustering relatively far from known species Nitrososphaera gargensis (95.5% 16S rRNA gene sequence identity). The most abundant nitrite oxidizing bacteria (NOB) were related to Nitrospira calida (97% 16S rRNA gene sequence identity). The nitrification biomass yield was 0.20-0.24 g VSS g-1 N, resulting mainly from a high AOA yield (0.16-0.20 g VSS g-1 N), which was reflected in a high AOA abundance in the community (57-76%) compared to NOB (5-11%). Batch-wise determination of decay rates (AOA: 0.23-0.29 d-1; NOB: 0.32-0.43 d-1) rendered an overestimation compared to in situ estimations of overall decay rate (0.026-0.078 d-1). Possibly, the inactivation rate rather than the actual decay rate was determined in batch experiments. Maximum growth rates of AOA and NOB were 0.12-0.15 d-1 and 0.13-0.33 d-1 respectively. NOB were susceptible to nitrite, opening up opportunities for shortcut nitrogen removal. However, NOB had a similar growth rate and oxygen affinity (0.15-0.55 mg O2 L-1) as AOA and were resilient towards free ammonia (IC50 > 16 mg NH3-N L-1). This might complicate NOB outselection using common practices to establish shortcut nitrogen removal (SRT control; aeration control; free ammonia shocks). Overall, the obtained insights can assist in integrating thermophilic conversions and facilitate single-sludge nitrification/denitrification.
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Affiliation(s)
- Tom G L Vandekerckhove
- Center for Microbial Ecology and Technology (CMET), Ghent University, Coupure Links 653, 9000, Gent, Belgium
| | - Frederiek-Maarten Kerckhof
- Center for Microbial Ecology and Technology (CMET), Ghent University, Coupure Links 653, 9000, Gent, Belgium
| | - Chaïm De Mulder
- BIOMATH, Department of Mathematical Modelling, Statistics and Bioinformatics, Ghent University, Coupure Links 653, 9000, Gent, Belgium
| | - Siegfried E Vlaeminck
- Center for Microbial Ecology and Technology (CMET), Ghent University, Coupure Links 653, 9000, Gent, Belgium; Research Group of Sustainable Energy, Air and Water Technology, University of Antwerp, Groenenborgerlaan 171, 2020, Antwerpen, Belgium
| | - Nico Boon
- Center for Microbial Ecology and Technology (CMET), Ghent University, Coupure Links 653, 9000, Gent, Belgium.
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38
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Low Temperature and Neutral pH Define " Candidatus Nitrotoga sp." as a Competitive Nitrite Oxidizer in Coculture with Nitrospira defluvii. Appl Environ Microbiol 2019; 85:AEM.02569-18. [PMID: 30824434 DOI: 10.1128/aem.02569-18] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2018] [Accepted: 02/07/2019] [Indexed: 11/20/2022] Open
Abstract
Nitrification is an essential process for N removal in activated sludge to avoid toxicity of ammonium and nitrite. Besides Nitrospira, "Candidatus Nitrotoga" has been identified as a key nitrite-oxidizing bacterium (NOB) performing the second step of nitrification, nitrite oxidation to nitrate, in wastewater treatment plants (WWTPs). However, the driving forces for the dominance of Nitrotoga in certain plants have often remained unclear and could not be explained solely by temperature effects. In this study, we characterized the physiology of the ammonium-dependent Nitrotoga sp. BS with regard to temperature and pH variations and evaluated its competitiveness against Nitrospira defluvii Both NOB originated from the same WWTP and shared a comparable pH optimum of 7.3. Based on these results, coculturing experiments with these NOB were performed in batch reactors operated at either 17°C or 22°C to compare their abundances under optimal (pH 7.4) or suboptimal (pH 6.4) conditions using 1 mM nitrite. As revealed by quantitative PCR (qPCR), fluorescence in situ hybridization (FISH), and 16S amplicon sequencing, Nitrotoga sp. BS was clearly favored by its optimal growth parameters and dominated over Ns. defluvii at pH 7.4 and 17°C, whereas a pH of 6.4 was more selective for Ns. defluvii Our synthetic communities revealed that niche differentiation of NOB is influenced by a complex interaction of environmental parameters and has to be evaluated for single species.IMPORTANCE "Ca. Nitrotoga" is a NOB of high environmental relevance, but physiological data exist for only a few representatives. Initially, it was detected in specialized niches of low temperature and low nitrite concentrations, but later on, its ubiquitous distribution revealed its critical role for N removal in engineered systems like WWTPs. In this study, we analyzed the competition between Nitrotoga and Nitrospira in bioreactors and identified conditions where the K strategist Ns. defluvii was almost replaced by Nitrotoga sp. BS. We show that the pH value is an important factor that regulates the composition of the nitrite-oxidizing enrichment with a dominance of Nitrotoga sp. BS versus Ns. defluvii at a neutral pH of 7.4 in combination with a temperature of 17°C. The physiological diversity of novel Nitrotoga cultures improves our knowledge about niche differentiation of NOB with regard to functional nitrification under suboptimal conditions.
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39
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Two Chloroflexi classes independently evolved the ability to persist on atmospheric hydrogen and carbon monoxide. ISME JOURNAL 2019; 13:1801-1813. [PMID: 30872805 PMCID: PMC6776052 DOI: 10.1038/s41396-019-0393-0] [Citation(s) in RCA: 75] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/30/2018] [Revised: 01/21/2019] [Accepted: 02/20/2019] [Indexed: 11/29/2022]
Abstract
Most aerobic bacteria exist in dormant states within natural environments. In these states, they endure adverse environmental conditions such as nutrient starvation by decreasing metabolic expenditure and using alternative energy sources. In this study, we investigated the energy sources that support persistence of two aerobic thermophilic strains of the environmentally widespread but understudied phylum Chloroflexi. A transcriptome study revealed that Thermomicrobium roseum (class Chloroflexia) extensively remodels its respiratory chain upon entry into stationary phase due to nutrient limitation. Whereas primary dehydrogenases associated with heterotrophic respiration were downregulated, putative operons encoding enzymes involved in molecular hydrogen (H2), carbon monoxide (CO), and sulfur compound oxidation were significantly upregulated. Gas chromatography and microsensor experiments showed that T. roseum aerobically respires H2 and CO at a range of environmentally relevant concentrations to sub-atmospheric levels. Phylogenetic analysis suggests that the hydrogenases and carbon monoxide dehydrogenases mediating these processes are widely distributed in Chloroflexi genomes and have probably been horizontally acquired on more than one occasion. Consistently, we confirmed that the sporulating isolate Thermogemmatispora sp. T81 (class Ktedonobacteria) also oxidises atmospheric H2 and CO during persistence, though further studies are required to determine if these findings extend to mesophilic strains. This study provides axenic culture evidence that atmospheric CO supports bacterial persistence and reports the third phylum, following Actinobacteria and Acidobacteria, to be experimentally shown to mediate the biogeochemically and ecologically important process of atmospheric H2 oxidation. This adds to the growing body of evidence that atmospheric trace gases are dependable energy sources for bacterial persistence.
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Meng J, Li J, He J, Li J, Deng K, Nan J. Nutrient removal from high ammonium swine wastewater in upflow microaerobic biofilm reactor suffered high hydraulic load. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2019; 233:69-75. [PMID: 30557752 DOI: 10.1016/j.jenvman.2018.12.027] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/09/2018] [Revised: 11/07/2018] [Accepted: 12/09/2018] [Indexed: 06/09/2023]
Abstract
To understand the ability of an upflow microaerobic biofilm reactor (UMBR) to remove nutrient from manure-free swine wastewater rich in NH4+ with a COD/TN ratio less than 1.00, effect of hydraulic loading rate (HLR) on the microaerobic process was evaluated with a constant reflux ratio of 25 at 25 °C. The results showed that changes in HLR had a remarkable effect on the performance of the UMBR in nutrient removal from the wastewater. With the favorable HLR 3.0 m3/(m3·d) (Hydraulic Retention Time (HRT) 8 h), average removal of COD, NH4+ and TN in the microaerobic process reached 59.3%, 87.7% and 84.7%, respectively, though the COD/TN ratio was as low as 0.84. With an over HLR of 4.0 m3/(m3·d) (HRT decreased to 6 h), bad performance of the UMBR was observed with an average removal of COD, NH4+ and TN as low as 45.0%, 59.0% and 57.5%, respectively. Since the HLR was decreased to 2.4 m3/(m3·d) (HRT 10 h), the microaerobic process regained the efficiency in nutrient removal with a removal of COD, NH4+ and TN averaged 59.0%, 95.3% and 87.8%, respectively. The microaerobic condition allowed anammox bacteria, ammonia-oxidizing bacteria and archaea, nitrite-oxidizing bacteria and denitrifiers to all thrive in the UMBR, resulting in the efficient synchronous removal of organic carbon and nitrogen. As the dominant approach to nitrogen removal, anaerobic ammonium oxidation (anammox) pathway contributing to the TN removal in the microaerobic process exceeded 59.5% at HLR 3.0 m3/(m3·d). The results demonstrated that the UMBR can remove nitrogen and carbon from swine wastewater, with a suitable HLR.
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Affiliation(s)
- Jia Meng
- State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, 73 Huanghe Road, Harbin, 150090, PR China; Advanced Water Management Centre, The University of Queensland, St Lucia, Brisbane, QLD, 4072, Australia.
| | - Jiuling Li
- Advanced Water Management Centre, The University of Queensland, St Lucia, Brisbane, QLD, 4072, Australia
| | - Jiamin He
- State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, 73 Huanghe Road, Harbin, 150090, PR China
| | - Jianzheng Li
- State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, 73 Huanghe Road, Harbin, 150090, PR China.
| | - Kaiwen Deng
- State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, 73 Huanghe Road, Harbin, 150090, PR China
| | - Jun Nan
- State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, 73 Huanghe Road, Harbin, 150090, PR China
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Meng J, Li J, Li J, Nan J, Deng K, Antwi P. Effect of temperature on nitrogen removal and biological mechanism in an up-flow microaerobic sludge reactor treating wastewater rich in ammonium and lack in carbon source. CHEMOSPHERE 2019; 216:186-194. [PMID: 30368083 DOI: 10.1016/j.chemosphere.2018.10.132] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/25/2018] [Revised: 09/25/2018] [Accepted: 10/17/2018] [Indexed: 06/08/2023]
Abstract
Previous study has demonstrated that microaerobic process is effective in nitrogen removal from the wastewater with high ammonium and low carbon to nitrogen ratio. In the microaerobic system, synergistic action of anammox, ammonia oxidizing bacteria (AOB), nitrite oxidizing bacteria (NOB) and denitrifiers was the key issues to remove nitrogen from the wastewater rich in ammonium. Temperature has a significant effect on specific growth rate and activity of various nitrogen removal functional bacteria. In this study, the effect of temperature (35 °C-15 °C) on nitrogen removal were investigated in an up-flow microaerobic sludge reactor (UMSR) at the HRT of 8 h and reflux ratio of 45. Above 71.2% of total nitrogen (TN) and 80.7% of NH4+ removal efficiencies were observed at the temperature no less than 17 °C. With the temperature further decreasing to 15 °C, denitrifiers still dominant the UMSR, but AOB, NOB and Candidatus Brocadia as the predominant anammox bacteria were inhibited revealed by high throughput sequencing, resulting in the decrease of TN and NH4+ removal to 39.7% and 61.8%, respectively. Fortunately, when the temperature rebounded to 20 °C, a higher TN and NH4+ removal of 81.2% and 97.3% were obtained again in the UMSR.
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Affiliation(s)
- Jia Meng
- State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, 73 Huanghe Road, Harbin 150090, PR China; Advanced Water Management Centre, The University of Queensland, St Lucia, Brisbane, QLD, 4072, Australia.
| | - Jiuling Li
- Advanced Water Management Centre, The University of Queensland, St Lucia, Brisbane, QLD, 4072, Australia.
| | - Jianzheng Li
- State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, 73 Huanghe Road, Harbin 150090, PR China.
| | - Jun Nan
- State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, 73 Huanghe Road, Harbin 150090, PR China.
| | - Kaiwen Deng
- State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, 73 Huanghe Road, Harbin 150090, PR China.
| | - Philip Antwi
- School of Resources and Environmental Engineering, Jiangxi University of Science and Technology, Ganzhou 341000, PR China; State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, 73 Huanghe Road, Harbin 150090, PR China.
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Holmes DE, Dang Y, Smith JA. Nitrogen cycling during wastewater treatment. ADVANCES IN APPLIED MICROBIOLOGY 2019; 106:113-192. [PMID: 30798802 DOI: 10.1016/bs.aambs.2018.10.003] [Citation(s) in RCA: 55] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Many wastewater treatment plants in the world do not remove reactive nitrogen from wastewater prior to release into the environment. Excess reactive nitrogen not only has a negative impact on human health, it also contributes to air and water pollution, and can cause complex ecosystems to collapse. In order to avoid the deleterious effects of excess reactive nitrogen in the environment, tertiary wastewater treatment practices that ensure the removal of reactive nitrogen species need to be implemented. Many wastewater treatment facilities rely on chemicals for tertiary treatment, however, biological nitrogen removal practices are much more environmentally friendly and cost effective. Therefore, interest in biological treatment is increasing. Biological approaches take advantage of specific groups of microorganisms involved in nitrogen cycling to remove reactive nitrogen from reactor systems by converting ammonia to nitrogen gas. Organisms known to be involved in this process include autotrophic ammonia-oxidizing bacteria, heterotrophic ammonia-oxidizing bacteria, ammonia-oxidizing archaea, anaerobic ammonia oxidizing bacteria (anammox), nitrite-oxidizing bacteria, complete ammonia oxidizers, and dissimilatory nitrate reducing microorganisms. For example, in nitrifying-denitrifying reactors, ammonia- and nitrite-oxidizing bacteria convert ammonia to nitrate and then denitrifying microorganisms reduce nitrate to nonreactive dinitrogen gas. Other nitrogen removal systems (anammox reactors) take advantage of anammox bacteria to convert ammonia to nitrogen gas using NO as an oxidant. A number of promising new biological treatment technologies are emerging and it is hoped that as the cost of these practices goes down more wastewater treatment plants will start to include a tertiary treatment step.
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Tomazini A, Lal S, Munir R, Stott M, Henrissat B, Polikarpov I, Sparling R, Levin DB. Analysis of carbohydrate-active enzymes in Thermogemmatispora sp. strain T81 reveals carbohydrate degradation ability. Can J Microbiol 2018; 64:992-1003. [PMID: 30338698 DOI: 10.1139/cjm-2018-0336] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The phylum Chloroflexi is phylogenetically diverse and is a deeply branching lineage of bacteria that express a broad spectrum of physiological and metabolic capabilities. Members of the order Ktedonobacteriales, including the families Ktedonobacteriaceae, Thermosporotrichaceae, and Thermogemmatisporaceae, all have flexible aerobic metabolisms capable of utilizing a wide range of carbohydrates. A number of species within these families are considered cellulolytic and are capable of using cellulose as a sole carbon and energy source. In contrast, Ktedonobacter racemifer, the type strain of the order, does not appear to possess this cellulolytic phenotype. In this study, we confirmed the ability of Thermogemmatispora sp. strain T81 to hydrolyze cellulose, determined the whole-genome sequence of Thermogemmatispora sp. T81, and using comparative bioinformatics analyses, identified genes encoding putative carbohydrate-active enzymes (CAZymes) in the Thermogemmatispora sp. T81, Thermogemmatispora onikobensis, and Ktedonobacter racemifer genomes. Analyses of the Thermogemmatispora sp. T81 genome identified 64 CAZyme gene sequences belonging to 57 glycoside hydrolase families. The genome of Thermogemmatispora sp. T81 encodes 19 genes for putative extracellular CAZymes, similar to the number of putative extracellular CAZymes identified in T. onikobensis (17) and K. racemifer (17), despite K. racemifer not possessing a cellulolytic phenotype. These results suggest that these members of the order Ktedonobacteriales may use a broader range of carbohydrate polymers than currently described.
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Affiliation(s)
- Atilio Tomazini
- a São Carlos Institute of Physics, University of São Paulo, São Carlos 13566-590, São Paulo, Brazil
| | - Sadhana Lal
- b Department of Biosystems Engineering, University of Manitoba, Winnipeg, MB R3T 5V6, Canada
| | - Riffat Munir
- b Department of Biosystems Engineering, University of Manitoba, Winnipeg, MB R3T 5V6, Canada
| | - Matthew Stott
- c School of Biological Sciences, University of Canterbury, Christchurch 8140, New Zealand
| | - Bernard Henrissat
- d Architecture et fonction des macromolécules biologiques (AFMB), CNRS-INRA, Aix-Marseille Université, Marseille, France USC1408
| | - Igor Polikarpov
- a São Carlos Institute of Physics, University of São Paulo, São Carlos 13566-590, São Paulo, Brazil
| | - Richard Sparling
- e Department of Microbiology, University of Manitoba, Winnipeg, MB R3T 2N2, Canada
| | - David B Levin
- b Department of Biosystems Engineering, University of Manitoba, Winnipeg, MB R3T 5V6, Canada
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Mehrshad M, Rodriguez-Valera F, Amoozegar MA, López-García P, Ghai R. The enigmatic SAR202 cluster up close: shedding light on a globally distributed dark ocean lineage involved in sulfur cycling. THE ISME JOURNAL 2018; 12:655-668. [PMID: 29208946 PMCID: PMC5864207 DOI: 10.1038/s41396-017-0009-5] [Citation(s) in RCA: 57] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/09/2017] [Revised: 06/21/2017] [Accepted: 07/24/2017] [Indexed: 11/09/2022]
Abstract
The dark ocean microbiota represents the unknown majority in the global ocean waters. The SAR202 cluster belonging to the phylum Chloroflexi was the first microbial lineage discovered to specifically inhabit the aphotic realm, where they are abundant and globally distributed. The absence of SAR202 cultured representatives is a significant bottleneck towards understanding their metabolic capacities and role in the marine environment. In this work, we use a combination of metagenome-assembled genomes from deep-sea datasets and publicly available single-cell genomes to construct a genomic perspective of SAR202 phylogeny, metabolism and biogeography. Our results suggest that SAR202 cluster members are medium sized, free-living cells with a heterotrophic lifestyle, broadly divided into two distinct clades. We present the first evidence of vertical stratification of these microbes along the meso- and bathypelagic ocean layers. Remarkably, two distinct species of SAR202 cluster are highly abundant in nearly all deep bathypelagic metagenomic datasets available so far. SAR202 members metabolize multiple organosulfur compounds, many appear to be sulfite-oxidizers and are predicted to play a major role in sulfur turnover in the dark water column. This concomitantly suggests an unsuspected availability of these nutrient sources to allow for the high abundance of these microbes in the deep sea.
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Affiliation(s)
- Maliheh Mehrshad
- Institute of Hydrobiology, Department of Aquatic Microbial Ecology, Biology Centre of the Academy of Sciences of the Czech Republic, České Budějovice, Czech Republic
| | | | - Mohammad Ali Amoozegar
- Extremophiles Laboratory, Department of Microbiology, Faculty of Biology and Center of Excellence in Phylogeny of Living Organisms, College of Science, University of Tehran, Tehran, Iran
| | - Purificación López-García
- Ecologie, Systématique, Evolution, CNRS, Université Paris-Sud, Université Paris-Saclay, AgroParisTech, Orsay, France
| | - Rohit Ghai
- Institute of Hydrobiology, Department of Aquatic Microbial Ecology, Biology Centre of the Academy of Sciences of the Czech Republic, České Budějovice, Czech Republic.
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Microbial communities in the native habitats of Agaricus sinodeliciosus from Xinjiang Province revealed by amplicon sequencing. Sci Rep 2017; 7:15719. [PMID: 29146962 PMCID: PMC5691072 DOI: 10.1038/s41598-017-16082-1] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2017] [Accepted: 11/07/2017] [Indexed: 11/22/2022] Open
Abstract
Agaricus sinodeliciosus is an edible species described from China and has been successfully cultivated. However, no studies have yet reported the influence factors implicated in the process of fructification. To better know abiotic and biotic factors, physiochemical characteristics and microbial communities were investigated in five different soil samples collected in the native habitats of specimens from northern Xinjiang, southern Xinjiang, and Zhejiang Province, respectively. There are major differences in texture and morphology among different specimens of A. sinodeliciosus from Xinjiang Province. A. sinodeliciosus from southern Xinjiang was the largest. Concentrations of DOC and TN and C/N ratio are not the main reason for the differences. Microbial communities were analyzed to find out mushroom growth promoting microbes (MGPM), which may lead to the differences. Functional microbes were picked out and can be divided into two categories. Microbes in the first category may belong to MGPM. There may be symbiotic relationships between microbes in the second category and A. sinodeliciosus. Certain analyses of microbial communities support the hypothesis that interactions between microbes and mushrooms would be implicated in morphological variation of the collected mushrooms. Redundancy analysis results indicate that high DOC/NH4+-N ratio and NH4+-N concentration can improve the yield of A. sinodeliciosus.
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Yasuda T, Waki M, Fukumoto Y, Hanajima D, Kuroda K, Suzuki K, Matsumoto T, Uenishi H. Community structure of denitrifying and total bacteria during nitrogen accumulation in an ammonia‐loaded biofilter. J Appl Microbiol 2017; 123:1498-1511. [DOI: 10.1111/jam.13603] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2016] [Revised: 09/26/2017] [Accepted: 09/30/2017] [Indexed: 11/29/2022]
Affiliation(s)
- T. Yasuda
- Institute of Livestock and Grassland Science National Agriculture and Food Research Organization Tsukuba Ibaraki Japan
| | - M. Waki
- Institute of Livestock and Grassland Science National Agriculture and Food Research Organization Tsukuba Ibaraki Japan
| | - Y. Fukumoto
- Institute of Livestock and Grassland Science National Agriculture and Food Research Organization Tsukuba Ibaraki Japan
| | - D. Hanajima
- Hokkaido Agricultural Research Center National Agriculture and Food Research Organization Sapporo Hokkaido Japan
| | - K. Kuroda
- Kyushu Okinawa Agricultural Research Center National Agriculture and Food Research Organization Koshi Kumamoto Japan
| | - K. Suzuki
- Institute of Livestock and Grassland Science National Agriculture and Food Research Organization Tsukuba Ibaraki Japan
| | - T. Matsumoto
- Institute of Crop Science National Agricultural and Food Research Organization Tsukuba Ibaraki Japan
| | - H. Uenishi
- Institute of Agrobiological Sciences National Agriculture and Food Research Organization Tsukuba Ibaraki Japan
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Ushiki N, Jinno M, Fujitani H, Suenaga T, Terada A, Tsuneda S. Nitrite oxidation kinetics of two Nitrospira strains: The quest for competition and ecological niche differentiation. J Biosci Bioeng 2017; 123:581-589. [DOI: 10.1016/j.jbiosc.2016.12.016] [Citation(s) in RCA: 61] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2016] [Revised: 12/27/2016] [Accepted: 12/28/2016] [Indexed: 10/20/2022]
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A robust nitrifying community in a bioreactor at 50 °C opens up the path for thermophilic nitrogen removal. ISME JOURNAL 2016; 10:2293-303. [PMID: 26894446 DOI: 10.1038/ismej.2016.8] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/09/2015] [Revised: 01/03/2016] [Accepted: 01/04/2016] [Indexed: 11/08/2022]
Abstract
The increasing production of nitrogen-containing fertilizers is crucial to meet the global food demand, yet high losses of reactive nitrogen associated with the food production/consumption chain progressively deteriorate the natural environment. Currently, mesophilic nitrogen-removing microbes eliminate nitrogen from wastewaters. Although thermophilic nitrifiers have been separately enriched from natural environments, no bioreactors are described that couple these processes for the treatment of nitrogen in hot wastewaters. Samples from composting facilities were used as inoculum for the batch-wise enrichment of thermophilic nitrifiers (350 days). Subsequently, the enrichments were transferred to a bioreactor to obtain a stable, high-rate nitrifying process (560 days). The community contained up to 17% ammonia-oxidizing archaea (AOAs) closely related to 'Candidatus Nitrososphaera gargensis', and 25% nitrite-oxidizing bacteria (NOBs) related to Nitrospira calida. Incorporation of (13)C-derived bicarbonate into the respective characteristic membrane lipids during nitrification supported their activity as autotrophs. Specific activities up to 198±10 and 894±81 mg N g(-1) VSS per day for AOAs and NOBs were measured, where NOBs were 33% more sensitive to free ammonia. The NOBs were extremely sensitive to free nitrous acid, whereas the AOAs could only be inhibited by high nitrite concentrations, independent of the free nitrous acid concentration. The observed difference in product/substrate inhibition could facilitate the development of NOB inhibition strategies to achieve more cost-effective processes such as deammonification. This study describes the enrichment of autotrophic thermophilic nitrifiers from a nutrient-rich environment and the successful operation of a thermophilic nitrifying bioreactor for the first time, facilitating opportunities for thermophilic nitrogen removal biotechnology.
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Houghton KM, Morgan XC, Lagutin K, MacKenzie AD, Vyssotskii M, Mitchell KA, McDonald IR, Morgan HW, Power JF, Moreau JW, Hanssen E, Stott MB. Thermorudis pharmacophila sp. nov., a novel member of the class Thermomicrobia isolated from geothermal soil, and emended descriptions of Thermomicrobium roseum, Thermomicrobium carboxidum, Thermorudis peleae and Sphaerobacter thermophilus. Int J Syst Evol Microbiol 2015; 65:4479-4487. [PMID: 26374291 DOI: 10.1099/ijsem.0.000598] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
An aerobic, thermophilic and cellulolytic bacterium, designated strain WKT50.2T, was isolated from geothermal soil at Waikite, New Zealand. Strain WKT50.2T grew at 53-76 °C and at pH 5.9-8.2. The DNA G+C content was 58.4 mol%. The major fatty acids were 12-methyl C18 : 0 and C18 : 0. Polar lipids were all linked to long-chain 1,2-diols, and comprised 2-acylalkyldiol-1-O-phosphoinositol (diolPI), 2-acylalkyldiol-1-O-phosphoacylmannoside (diolP-acylMan), 2-acylalkyldiol-1-O-phosphoinositol acylmannoside (diolPI-acylMan) and 2-acylalkyldiol-1-O-phosphoinositol mannoside (diolPI-Man). Strain WKT50.2T utilized a range of cellulosic substrates, alcohols and organic acids for growth, but was unable to utilize monosaccharides. Robust growth of WKT50.2T was observed on protein derivatives. WKT50.2T was sensitive to ampicillin, chloramphenicol, kanamycin, neomycin, polymyxin B, streptomycin and vancomycin. Metronidazole, lasalocid A and trimethoprim stimulated growth. Phylogenetic analysis of 16S rRNA gene sequences showed that WKT50.2T belonged to the class Thermomicrobia within the phylum Chloroflexi, and was most closely related to Thermorudis peleae KI4T (99.6% similarity). DNA-DNA hybridization between WKT50.2T and Thermorudis peleae DSM 27169T was 18.0%. Physiological and biochemical tests confirmed the phenotypic and genotypic differentiation of strain WKT50.2T from Thermorudis peleae KI4T and other members of the Thermomicrobia. On the basis of its phylogenetic position and phenotypic characteristics, we propose that strain WKT50.2T represents a novel species, for which the name Thermorudis pharmacophila sp. nov. is proposed, with the type strain WKT50.2T ( = DSM 26011T = ICMP 20042T). Emended descriptions of Thermomicrobium roseum, Thermomicrobium carboxidum, Thermorudis peleae and Sphaerobacter thermophilus are also proposed, and include the description of a novel respiratory quinone, MK-8 2,3-epoxide (23%), in Thermomicrobium roseum.
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Affiliation(s)
- Karen M Houghton
- GNS Science, Extremophiles Research Group, Private Bag 2000, Taupo¯ 3352, New Zealand.,School of Science, University of Waikato, Private Bag 3105, Hamilton 3240, New Zealand
| | - Xochitl C Morgan
- Department of Biostatistics, Harvard T. H. Chan School of Public Health, 655 Huntington Ave, Boston, MA 02115, USA
| | - Kirill Lagutin
- Callaghan Innovation, PO Box 31310, Lower Hutt 5040, New Zealand
| | | | | | - Kevin A Mitchell
- Callaghan Innovation, PO Box 31310, Lower Hutt 5040, New Zealand
| | - Ian R McDonald
- School of Science, University of Waikato, Private Bag 3105, Hamilton 3240, New Zealand
| | - Hugh W Morgan
- School of Science, University of Waikato, Private Bag 3105, Hamilton 3240, New Zealand
| | - Jean F Power
- GNS Science, Extremophiles Research Group, Private Bag 2000, Taupo¯ 3352, New Zealand
| | - John W Moreau
- University of Melbourne, 30 Flemington Road, Victoria 3010, Australia
| | - Eric Hanssen
- University of Melbourne, 30 Flemington Road, Victoria 3010, Australia
| | - Matthew B Stott
- GNS Science, Extremophiles Research Group, Private Bag 2000, Taupo¯ 3352, New Zealand
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50
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Novel Long-Chain Diol Phospholipids from Some Bacteria Belonging to the ClassThermomicrobia. Lipids 2014; 50:303-11. [DOI: 10.1007/s11745-014-3979-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2014] [Accepted: 12/01/2014] [Indexed: 10/24/2022]
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