1
|
Akita Y, Ueki A, Tonouchi A, Sugawara Y, Honma S, Kaku N, Ueki K. Brooklawnia propionicigenes sp. nov., a facultatively anaerobic, propionate-producing bacterium isolated from a methanogenic reactor treating waste from cattle farms. Int J Syst Evol Microbiol 2024; 74. [PMID: 38573743 DOI: 10.1099/ijsem.0.006320] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/05/2024] Open
Abstract
Facultatively anaerobic bacterial strains were isolated from samples of a methanogenic reactor and, based on 16S rRNA gene sequences, found to be affiliated with the family Propionibacteriaceae in the phylum Actinomycetota. Four strains with almost-identical 16S rRNA gene sequences were comprehensively characterized. The most closely related species to the strains was Brooklawnia cerclae BL-34T (96.4 % sequence similarity). Although most of the phenotypic characteristics of the four strains were identical, distinct differences in some cellular and physiological properties were also detected. Cells of the strains were Gram-stain-positive, non-spore-forming, pleomorphic rods. The strains utilized carbohydrates and organic acids. The strains produced acetate, propionate and lactate from glucose, but the molar ratios of the products were variable depending on the strains. The strains grew at 10-40 °C (optimum at 35 °C) and pH 5.3-8.8 (optimum at pH 6.8-7.5.) The major cellular fatty acids of the strains were anteiso-C15 : 0, C15 : 0 and C15 : 0 dimethylacetal (as a summed feature). The major respiratory quinone was menaquinone MK-9(H4) and the diagnostic diamino acid in the peptidoglycan was meso-diaminopimelic acid. The genome size of the type strain (SH051T) was 3.21 Mb and the genome DNA G+C content was 65.7 mol%. Genes responsible for propionate production through the Wood-Werkman pathway were detected in the genome of strain SH051T. Based on the results of phylogenetic, genomic and phenotypic analyses of the novel strains, the name Brooklawnia propionicigenes sp. nov. is proposed to accommodate the four strains. The type strain of the novel species is SH051T (=NBRC 116195T=DSM 116141T).
Collapse
Affiliation(s)
- Yasumitsu Akita
- Faculty of Agriculture, Yamagata University, Wakaba-machi 1-23, Tsuruoka 997-8555, Japan
| | - Atsuko Ueki
- Faculty of Agriculture, Yamagata University, Wakaba-machi 1-23, Tsuruoka 997-8555, Japan
| | - Akio Tonouchi
- Faculty of Agriculture and Life Science, Hirosaki University, Bunkyo-cho 3, Hirosaki, Aomori 036-8561, Japan
| | - Yoshimichi Sugawara
- Faculty of Agriculture, Yamagata University, Wakaba-machi 1-23, Tsuruoka 997-8555, Japan
| | - Sachi Honma
- Faculty of Agriculture, Yamagata University, Wakaba-machi 1-23, Tsuruoka 997-8555, Japan
| | - Nobuo Kaku
- Faculty of Agriculture, Yamagata University, Wakaba-machi 1-23, Tsuruoka 997-8555, Japan
| | - Katsuji Ueki
- Faculty of Agriculture, Yamagata University, Wakaba-machi 1-23, Tsuruoka 997-8555, Japan
| |
Collapse
|
2
|
Karunakaran E, Battarbee R, Tait S, Brentan BM, Berney C, Grinham J, Herrero MA, Omolo R, Douterelo I. Integrating molecular microbial methods to improve faecal pollution management in rivers with designated bathing waters. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 912:168565. [PMID: 37979848 DOI: 10.1016/j.scitotenv.2023.168565] [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: 08/13/2023] [Revised: 10/23/2023] [Accepted: 11/11/2023] [Indexed: 11/20/2023]
Abstract
Rivers are at risk from a variety of pollution sources. Faecal pollution is of particular concern since it disperses pathogenic microorganisms in the aquatic environment. Currently, faecal pollution levels in rivers is monitored using faecal indicator bacteria (FIB) that do not offer information about pollution sources and associated risks. This study used a combined molecular approach, along with measurements of water quality, to gain information on pollution sources, and risk levels, in a newly designated recreational bathing site in the River Wharfe (UK). Physico-chemical parameters were monitored in situ, with water quality multiparameter monitoring sondes installed during the 2021 bathing season. The molecular approach was based on quantitative PCR (qPCR)-aided Microbial Source Tracking (MST) and 16S rRNA gene metabarcoding to obtain a fingerprint of bacterial communities and identify potential bioindicators. The analysis from the water quality sondes showed that ammonium was the main parameter determining the distribution of FIB values. Lower faecal pollution levels were detected in the main river when compared to tributaries, except for samples in the river located downstream of a wastewater treatment plant. The faecal pollution type (anthropogenic vs. zoogenic) changed the diversity and the structure of bacterial communities, giving a distinctive fingerprint that can be used to inform source. DNA-based methods showed that the presence of human-derived bacteria was associated with Escherichia coli spikes, coinciding with higher bacterial diversity and the presence of potential pathogenic bacteria mainly of the genus Mycobacterium, Aeromonas and Clostridium. Samples collected after a heavy rainfall event were associated with an increase in Bacteroidales, which are markers of faecal pollution, including Bacteroides graminisolvens, a ruminant marker associated with surface run-off from agricultural sources. The combined use of qPCR and 16S rRNA sequencing was able to identify pollution sources, and novel bacterial indicators, thereby aiding decision-making and management strategies in recreational bathing rivers.
Collapse
Affiliation(s)
- Esther Karunakaran
- Department of Chemical and Biological Engineering, University of Sheffield, Sheffield S1 3JD, UK
| | - Rick Battarbee
- Environmental Change Research Centre, University College London, London WC1E 6BT, UK; Addingham Environment Group, Addingham, West Yorkshire LS29 0PD, UK
| | - Simon Tait
- Department of Civil and Structural Engineering, University of Sheffield, Sheffield S1 3JD, UK
| | - Bruno Melo Brentan
- Hydraulic Engineering and Water Resource Department, Federal University of Minas Gerais, Belo Horizonte 31270, Brazil
| | - Cathal Berney
- Addingham Environment Group, Addingham, West Yorkshire LS29 0PD, UK
| | - James Grinham
- Department of Chemical and Biological Engineering, University of Sheffield, Sheffield S1 3JD, UK
| | - Maria Angeles Herrero
- Department of Civil and Structural Engineering, University of Sheffield, Sheffield S1 3JD, UK
| | - Ronex Omolo
- Department of Civil and Structural Engineering, University of Sheffield, Sheffield S1 3JD, UK
| | - Isabel Douterelo
- Department of Civil and Structural Engineering, University of Sheffield, Sheffield S1 3JD, UK.
| |
Collapse
|
3
|
Xu J, Shi Z, Xu L, Zheng X, Zong Y, Luo G, Zhang C, Liu M, Xie L. Recovery capability of anaerobic digestion from ammonia stress: Metabolic activity, energy generation, and genome-centric metagenomics. BIORESOURCE TECHNOLOGY 2024; 394:130203. [PMID: 38109977 DOI: 10.1016/j.biortech.2023.130203] [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: 10/27/2023] [Revised: 12/06/2023] [Accepted: 12/11/2023] [Indexed: 12/20/2023]
Abstract
Excessive ammonia stresses anaerobic digestion (AD) significantly. Although there has been progress in understanding AD under ammonia exposure, investigations on AD liberated from ammonia exposure are limited. Here, the recovery capability of AD from ammonia stress was evaluated, by examining specific methanogenic activity, energy-conserving capability, microbial community succession, and metabolic pathway reconstruction. The findings demonstrated that ammonia stress relief resulted in < 50% methane recovery, with propionate conversion identified as the critical impediment to AD reactivation. Energy generation could not recovered either. Efforts to mitigate ammonia stress failed to restore acetoclastic methanogens, e.g., Methanothrix soehngenii, and proved futile in awakening propionate oxidizers, e.g., Desulfobulbus. Interestingly, a symbiotic metabolism emerged, prevailing in stress-relieved AD due to its energy-conserving advantage. This study underscores the importance of targeted interventions, including stimulating acetoclastic methanogenesis, propionate oxidation, and energy generation, as priorities for AD recovery following ammonia stress, rather than focusing solely on ammonia level management.
Collapse
Affiliation(s)
- Jun Xu
- Key Laboratory of Yangtze River Water Environment, Ministry of Education, College of Environmental Science and Engineering, Tongji University, Shanghai 200092, PR China
| | - Zhijian Shi
- Shanghai Key Laboratory of Atmospheric Particle Pollution and Prevention (LAP3), Department of Environmental Science and Engineering, Fudan University, Shanghai 200433, PR China; Shanghai Technical Service Platform for Pollution Control and Resource Utilization of Organic Wastes, Shanghai 200438, PR China
| | - Ling Xu
- Key Laboratory of Yangtze River Water Environment, Ministry of Education, College of Environmental Science and Engineering, Tongji University, Shanghai 200092, PR China
| | - Xiaomei Zheng
- Key Laboratory of Yangtze River Water Environment, Ministry of Education, College of Environmental Science and Engineering, Tongji University, Shanghai 200092, PR China
| | - Yang Zong
- Key Laboratory of Yangtze River Water Environment, Ministry of Education, College of Environmental Science and Engineering, Tongji University, Shanghai 200092, PR China
| | - Gang Luo
- Shanghai Key Laboratory of Atmospheric Particle Pollution and Prevention (LAP3), Department of Environmental Science and Engineering, Fudan University, Shanghai 200433, PR China; Shanghai Technical Service Platform for Pollution Control and Resource Utilization of Organic Wastes, Shanghai 200438, PR China; Shanghai Institute of Pollution Control and Ecological Security, Shanghai 200092, PR China
| | - Chen Zhang
- Shanghai Municipal Engineering Design Institute (Group) Co., LTD., Shanghai 200092, PR China
| | - Mingxian Liu
- Shanghai Key Lab of Chemical Assessment and Sustainability, School of Chemical Science and Engineering, Tongji University, Shanghai 200092, PR China
| | - Li Xie
- Key Laboratory of Yangtze River Water Environment, Ministry of Education, College of Environmental Science and Engineering, Tongji University, Shanghai 200092, PR China; Shanghai Institute of Pollution Control and Ecological Security, Shanghai 200092, PR China.
| |
Collapse
|
4
|
Singh Y, Rani J, Kushwaha J, Priyadarsini M, Pandey KP, Sheth PN, Yadav SK, Mahesh MS, Dhoble AS. Scientific characterization methods for better utilization of cattle dung and urine: a concise review. Trop Anim Health Prod 2023; 55:274. [PMID: 37470864 DOI: 10.1007/s11250-023-03691-4] [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: 12/28/2022] [Accepted: 07/06/2023] [Indexed: 07/21/2023]
Abstract
Cattle are usually raised for food, manure, leather, therapeutic, and draught purposes. Biowastes from cattle, such as dung and urine, harbor a diverse group of crucial compounds, metabolites/chemicals, and microorganisms that may benefit humans for agriculture, nutrition, therapeutics, industrial, and other utility products. Several bioactive compounds have been identified in cattle dung and urine, which possess unique properties and may vary based on agro-climatic zones and feeding practices. Therefore, cattle dung and urine have great significance, and a balanced nutritional diet may be a key to improved quality of these products/by-products. This review primarily focuses on the scientific aspects of biochemical and microbial characterization of cattle biowastes. Various methods including genomics for analyzing cattle dung and gas chromatography-mass spectroscopy for cattle urine have been reviewed. The presented information might open doors for the further characterization of cattle resources for heterogeneous applications in the production of utility items and addressing research gaps. Methods for cattle's dung and urine characterization.
Collapse
Affiliation(s)
- Yashpal Singh
- School of Biochemical Engineering, Indian Institute of Technology (BHU) Varanasi, Uttar Pradesh, 221005, Varanasi, India
| | - Jyoti Rani
- School of Biochemical Engineering, Indian Institute of Technology (BHU) Varanasi, Uttar Pradesh, 221005, Varanasi, India
| | - Jeetesh Kushwaha
- School of Biochemical Engineering, Indian Institute of Technology (BHU) Varanasi, Uttar Pradesh, 221005, Varanasi, India
| | - Madhumita Priyadarsini
- School of Biochemical Engineering, Indian Institute of Technology (BHU) Varanasi, Uttar Pradesh, 221005, Varanasi, India
| | - Kailash Pati Pandey
- School of Biochemical Engineering, Indian Institute of Technology (BHU) Varanasi, Uttar Pradesh, 221005, Varanasi, India
| | - Pratik N Sheth
- Department of Chemical Engineering, Birla Institute of Technology and Science (BITS), Pilani, 333031, Rajasthan, India
| | - Sushil Kumar Yadav
- Department of Pharmacy, Birla Institute of Technology and Science (BITS), Pilani, 333031, Rajasthan, India
| | - M S Mahesh
- Livestock Farm Complex, Faculty of Veterinary and Animal Sciences, Banaras Hindu University, Rajiv Gandhi South Campus, Mirzapur, 231001, Uttar Pradesh, India
| | - Abhishek S Dhoble
- School of Biochemical Engineering, Indian Institute of Technology (BHU) Varanasi, Uttar Pradesh, 221005, Varanasi, India.
| |
Collapse
|
5
|
Li X, Sun P, Gong L, Shi W, Xiang Z, Li M, Su L, Qin C. Bacteroides rhinocerotis sp. nov., isolated from the fresh feces of rhinoceros in Beijing Zoo. Arch Microbiol 2023; 205:169. [PMID: 37017778 DOI: 10.1007/s00203-023-03513-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Revised: 03/10/2023] [Accepted: 03/23/2023] [Indexed: 04/06/2023]
Abstract
A Gram-negative strain, anaerobic, non-motile, non-spore-forming, rod-shaped bacterial strain named as NGMCC 1.200684 T was isolated from the fresh feces of rhinoceros in Beijing Zoo. Based on 16S rRNA gene sequences, phylogenetic analysis indicated that strain NGMCC 1.200684 T belonged to the genus Bacteroides and was most strongly related to the type strain of Bacteroides uniformis ATCC 8492 T (96.88%). The G + C content of the genomic DNA was determined to be 46.62%. Between strains NGMCC 1.200684 T and B. uniformis ATCC 8492 T, the average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) were 93.89 and 67.60%, respectively. Strain NGMCC 1.200684 T can produce acid from fermentation of several substrates, including glucose, mannitol, lactose, saccharose, maltose, salicin, xylose, cellobiose, mannose, raffinose, sorbitol, trehalose, D-galactose, and maltotriose. The major cellular fatty acids (> 10%) were identified as anteiso-C15:0, iso-C15:0, iso-C14:0, and iso-C17:0 3-OH. The polar lipid profiles of strain NGMCC 1.200684 T were determined to contain diphosphatidyl glycerol, phosphatidylglycerol, phosphatidylethanolamine, three unknown phospholipids, and two unknown amino-phospholipids. Based on phenotypic, phylogenetic, and chemotaxonomic characteristics, a novel species of the genus Bacteroides, Bacteroides rhinocerotis sp. nov. is proposed. The type strain is NGMCC 1.200684 T (= CGMCC 1.18013 T = JCM 35702 T).
Collapse
Affiliation(s)
- Xue Li
- NHC Key Laboratory of Human Disease Comparative Medicine, Beijing Engineering Research Center for Experimental Animal Models of Human Critical Diseases, International Center for Technology and Innovation of Animal Model, Comparative Medicine Center, Institute of Laboratory Animal Sciences, Chinese Academy of Medical Sciences (CAMS) & Peking Union Medical College (PUMC), Beijing, 100021, China
- Changping National Laboratory (CPNL), Beijing, 102299, China
| | - Peilin Sun
- NHC Key Laboratory of Human Disease Comparative Medicine, Beijing Engineering Research Center for Experimental Animal Models of Human Critical Diseases, International Center for Technology and Innovation of Animal Model, Comparative Medicine Center, Institute of Laboratory Animal Sciences, Chinese Academy of Medical Sciences (CAMS) & Peking Union Medical College (PUMC), Beijing, 100021, China
- Changping National Laboratory (CPNL), Beijing, 102299, China
| | - Liang Gong
- NHC Key Laboratory of Human Disease Comparative Medicine, Beijing Engineering Research Center for Experimental Animal Models of Human Critical Diseases, International Center for Technology and Innovation of Animal Model, Comparative Medicine Center, Institute of Laboratory Animal Sciences, Chinese Academy of Medical Sciences (CAMS) & Peking Union Medical College (PUMC), Beijing, 100021, China
- Changping National Laboratory (CPNL), Beijing, 102299, China
| | - Weixiong Shi
- NHC Key Laboratory of Human Disease Comparative Medicine, Beijing Engineering Research Center for Experimental Animal Models of Human Critical Diseases, International Center for Technology and Innovation of Animal Model, Comparative Medicine Center, Institute of Laboratory Animal Sciences, Chinese Academy of Medical Sciences (CAMS) & Peking Union Medical College (PUMC), Beijing, 100021, China
- Changping National Laboratory (CPNL), Beijing, 102299, China
| | - Zhiguang Xiang
- NHC Key Laboratory of Human Disease Comparative Medicine, Beijing Engineering Research Center for Experimental Animal Models of Human Critical Diseases, International Center for Technology and Innovation of Animal Model, Comparative Medicine Center, Institute of Laboratory Animal Sciences, Chinese Academy of Medical Sciences (CAMS) & Peking Union Medical College (PUMC), Beijing, 100021, China
- Changping National Laboratory (CPNL), Beijing, 102299, China
| | - Ming Li
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Technology Support Platform, Beijing, 100193, China
| | - Lei Su
- NHC Key Laboratory of Human Disease Comparative Medicine, Beijing Engineering Research Center for Experimental Animal Models of Human Critical Diseases, International Center for Technology and Innovation of Animal Model, Comparative Medicine Center, Institute of Laboratory Animal Sciences, Chinese Academy of Medical Sciences (CAMS) & Peking Union Medical College (PUMC), Beijing, 100021, China.
- Changping National Laboratory (CPNL), Beijing, 102299, China.
| | - Chuan Qin
- NHC Key Laboratory of Human Disease Comparative Medicine, Beijing Engineering Research Center for Experimental Animal Models of Human Critical Diseases, International Center for Technology and Innovation of Animal Model, Comparative Medicine Center, Institute of Laboratory Animal Sciences, Chinese Academy of Medical Sciences (CAMS) & Peking Union Medical College (PUMC), Beijing, 100021, China
- Changping National Laboratory (CPNL), Beijing, 102299, China
| |
Collapse
|
6
|
Huo W, Fu X, Bao M, Ye R, Shao Y, Liu Y, Bi J, Shi X, Lu W. Strategy of electron acceptors for ethanol-driven chain elongation from kitchen waste. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 846:157492. [PMID: 35870578 DOI: 10.1016/j.scitotenv.2022.157492] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/18/2022] [Revised: 07/08/2022] [Accepted: 07/15/2022] [Indexed: 06/15/2023]
Abstract
A two-phase kitchen waste (KW) fermentation was proposed in the current study to enhance medium-chain fatty acids (MCFAs) production from kitchen waste. In particular, effect of acetate to butyrate ratio (ABR) on MCFAs production was investigated which can be regulated by different pH and organic loading during the acidification phase. Medium ABR (1.00) was obtained when pH is 5.5 and organic loading is 20 g VS/L in FW acidification fermentation. Subsequent chain elongation fermentation demonstrated that the highest yield of caproate 9.67 g/L with selectivity of 79 %, and highest ethanol conversion efficiency of 1.11 was achieved in medium ABR system. Microbial community study showed that medium ABR significantly enrich the functional bacteria especially Clostridium kluyveri. The study provides a new method for chain elongation enhancement without addition of other additives in kitchen waste fermentation system and gives a guide for the regulation of the short-chain fatty acids distribution in its acidification phase.
Collapse
Affiliation(s)
- Weizhong Huo
- School of Environment, Tsinghua University, Beijing 100084, China
| | - Xindi Fu
- School of Environment, Tsinghua University, Beijing 100084, China; Everbright Environtech (China) Ltd., Nanjing 211102, China
| | - Menggang Bao
- School of Environment, Tsinghua University, Beijing 100084, China
| | - Rong Ye
- School of Environment, Tsinghua University, Beijing 100084, China
| | - Yuchao Shao
- School of Environment, Tsinghua University, Beijing 100084, China
| | - Yanqing Liu
- School of Environment, Tsinghua University, Beijing 100084, China
| | - Jiangtao Bi
- School of Ecology and Environment, Ningxia University, Ningxia 750021, China
| | - Xiong Shi
- Yangtze Eco-Environment Engineering Research Center, China Three Gorges Corporation, Beijing 100038, China; National Engineering Research Center of Eco-Environment Protection for Yangtze River Economic Belt, China
| | - Wenjing Lu
- School of Environment, Tsinghua University, Beijing 100084, China.
| |
Collapse
|
7
|
New insights into microbial interactions and putative competitive mechanisms during the hydrogen production from tequila vinasses. Appl Microbiol Biotechnol 2022; 106:6861-6876. [PMID: 36071291 DOI: 10.1007/s00253-022-12143-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2021] [Revised: 06/02/2022] [Accepted: 08/24/2022] [Indexed: 11/02/2022]
Abstract
This study aimed to characterize the prokaryotic community and putative microbial interactions involved in hydrogen (H2) production during the dark fermentation (DF) process, applying principal components analysis (PCA) to correlate changes in operational, physicochemical, and biological variables. For this purpose, a continuous stirred-tank reactor-type digester fed with tequila vinasses was operated at 24, 18, and 12 h of hydraulic retention times (HRTs) to apply organic loading rates of 20, 36, and 54 g-COD L-1 d-1, corresponding to stages I, II, and III, respectively. Results indicated high population dynamics for Archaea during the DF process toward a decrease in total sequences from 6299 to 99. Concerning the Bacteria community, lactic acid bacteria (LAB) were dominant reaching a relative abundance of 57.67%, while dominant H2-producing bacteria (HPB) decreased from 25.76% to 21.06% during stage III. Putative competitive exclusion mechanisms such as competition for substrates, bacteriocins production, and micronutrient depletion carried out by Archaea and non-H2-producing bacteria (non-HPB), especially LAB, could negatively impact the dominance of HPB such as Ethanoligenens harbinense and Clostridium tyrobutyricum. As a consequence, low maximal volumetric H2 production rate (672 mL-H2 L-1 d-1) and yield (3.88 mol-H2 assimilated sugars-1) were obtained. The global scenario obtained by PCA correlations suggested that C. tyrobutyricum positively impacted H2 molar yield through butyrate fermentation using the butyryl-CoA:acetate CoA transferase pathway, while the most abundant HPB E. harbinense decreased its relative abundance at the shortest HRT toward the dominance of non-HPB. This study provides new insights into the microbial interactions and helps to better understand the DF performance for H2 production using tequila vinasses as substrate. KEY POINTS: • E. harbinense and C. tyrobutyricum were responsible for H2 production. • Clostridiales used acetate and butyrate fermentations for H2 production. • LAB won the competition for sugars against Clostridiales during DF. • Putative bacteriocins production and micronutrients depletion could favor LAB.
Collapse
|
8
|
Wei Y, Li Y, Wang Y, Luo X, Du F, Liu W, Xie L, Chen J, Ren Z, Hou S, Wang S, Fu S, Dang Y, Li P, Liu X. The microbial diversity in industrial effluents makes high-throughput sequencing-based source tracking of the effluents possible. ENVIRONMENTAL RESEARCH 2022; 212:113640. [PMID: 35688222 DOI: 10.1016/j.envres.2022.113640] [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: 04/25/2022] [Revised: 06/02/2022] [Accepted: 06/05/2022] [Indexed: 06/15/2023]
Abstract
In order to explore the microbial diversity in industrial effluents, and on this basis, to verify the feasibility of tracking industrial effluents in sewer networks based on sequencing data, we collected 28 sewage samples from the industrial effluents relative to four factories in Shenzhen, China, and sequenced the 16S rRNA genes to profile the microbial compositions. We identified 5413 operational taxonomic units (OTUs) in total, and found that microbial compositions were highly diverse among samples from different locations in the sewer system, with only 107 OTUs shared by 90% of the samples. These shared OTUs were enriched in the phylum of Proteobacteria, the families of Comamonadaceae and Pseudomonadaceae, as well as the genus of Pseudomonas, with both degradation related and pathogenic bacteria. More importantly, we found differences in microbial composition among samples relevant to different factories, and identified microbial markers differentiating effluents from these factories, which can be used to track the sources of the effluents. This study improved our understanding of microbial diversity in industrial effluents, proved the feasibility of industrial effluent source tracking based on sequencing data, and provided an alternative technique solution for environmental surveillance and management.
Collapse
Affiliation(s)
- Yan Wei
- Beijing Key Lab for Source Control Technology of Water Pollution, College of Environmental Science and Engineering, Beijing Forestry University, Beijing 100083, China; Engineering Research Center for Water Pollution Source Control & Eco-remediation, College of Environmental Science and Engineering, Beijing Forestry University, Beijing 100083, China; Ping An Digital Information Technology (Shenzhen) Co., Ltd., Shenzhen 518000, China
| | - Yumeng Li
- Beijing Key Lab for Source Control Technology of Water Pollution, College of Environmental Science and Engineering, Beijing Forestry University, Beijing 100083, China; Engineering Research Center for Water Pollution Source Control & Eco-remediation, College of Environmental Science and Engineering, Beijing Forestry University, Beijing 100083, China
| | - Yayu Wang
- BGI-Shenzhen, Shenzhen, Guangdong 518083, China
| | - Xinyue Luo
- BGI-Shenzhen, Shenzhen, Guangdong 518083, China
| | - Feirong Du
- Ping An Digital Information Technology (Shenzhen) Co., Ltd., Shenzhen 518000, China
| | - Weifang Liu
- Shenzhen Howay Technology Co., Ltd., Shenzhen 518000, China
| | - Li Xie
- Shenzhen Howay Technology Co., Ltd., Shenzhen 518000, China
| | | | - Ziwei Ren
- Beijing Key Lab for Source Control Technology of Water Pollution, College of Environmental Science and Engineering, Beijing Forestry University, Beijing 100083, China; Engineering Research Center for Water Pollution Source Control & Eco-remediation, College of Environmental Science and Engineering, Beijing Forestry University, Beijing 100083, China
| | - Shiqi Hou
- Beijing Key Lab for Source Control Technology of Water Pollution, College of Environmental Science and Engineering, Beijing Forestry University, Beijing 100083, China; Engineering Research Center for Water Pollution Source Control & Eco-remediation, College of Environmental Science and Engineering, Beijing Forestry University, Beijing 100083, China
| | - Sunhaoyu Wang
- Beijing Key Lab for Source Control Technology of Water Pollution, College of Environmental Science and Engineering, Beijing Forestry University, Beijing 100083, China; Engineering Research Center for Water Pollution Source Control & Eco-remediation, College of Environmental Science and Engineering, Beijing Forestry University, Beijing 100083, China
| | - Shaojie Fu
- Beijing Key Lab for Source Control Technology of Water Pollution, College of Environmental Science and Engineering, Beijing Forestry University, Beijing 100083, China; Engineering Research Center for Water Pollution Source Control & Eco-remediation, College of Environmental Science and Engineering, Beijing Forestry University, Beijing 100083, China
| | - Yan Dang
- Beijing Key Lab for Source Control Technology of Water Pollution, College of Environmental Science and Engineering, Beijing Forestry University, Beijing 100083, China; Engineering Research Center for Water Pollution Source Control & Eco-remediation, College of Environmental Science and Engineering, Beijing Forestry University, Beijing 100083, China
| | - Pengsong Li
- Beijing Key Lab for Source Control Technology of Water Pollution, College of Environmental Science and Engineering, Beijing Forestry University, Beijing 100083, China; Engineering Research Center for Water Pollution Source Control & Eco-remediation, College of Environmental Science and Engineering, Beijing Forestry University, Beijing 100083, China.
| | - Xin Liu
- BGI-Shenzhen, Shenzhen, Guangdong 518083, China; BGI-Beijing, Beijing 100101, China.
| |
Collapse
|
9
|
Roguet A, Newton RJ, Eren AM, McLellan SL. Guts of the Urban Ecosystem: Microbial Ecology of Sewer Infrastructure. mSystems 2022; 7:e0011822. [PMID: 35762794 PMCID: PMC9426572 DOI: 10.1128/msystems.00118-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Accepted: 05/25/2022] [Indexed: 11/20/2022] Open
Abstract
Microbes have inhabited the oceans and soils for millions of years and are uniquely adapted to their habitat. In contrast, sewer infrastructure in modern cities dates back only ~150 years. Sewer pipes transport human waste and provide a view into public health, but the resident organisms that likely modulate these features are relatively unexplored. Here, we show that the bacterial assemblages sequenced from untreated wastewater in 71 U.S. cities were highly coherent at a fine sequence level, suggesting that urban infrastructure separated by great spatial distances can give rise to strikingly similar communities. Within the overall microbial community structure, temperature had a discernible impact on the distribution patterns of closely related amplicon sequence variants, resulting in warm and cold ecotypes. Two bacterial genera were dominant in most cities regardless of their size or geographic location; on average, Arcobacter accounted for 11% and Acinetobacter 10% of the entire community. Metagenomic analysis of six cities revealed these highly abundant resident organisms carry clinically important antibiotic resistant genes blaCTX-M, blaOXA, and blaTEM. In contrast, human fecal bacteria account for only ~13% of the community; therefore, antibiotic resistance gene inputs from human sources to the sewer system could be comparatively small, which will impact measurement capabilities when monitoring human populations using wastewater. With growing awareness of the metabolic potential of microbes within these vast networks of pipes and the ability to examine the health of human populations, it is timely to increase our understanding of the ecology of these systems. IMPORTANCE Sewer infrastructure is a relatively new habitat comprised of thousands of kilometers of pipes beneath cities. These wastewater conveyance systems contain large reservoirs of microbial biomass with a wide range of metabolic potential and are significant reservoirs of antibiotic resistant organisms; however, we lack an adequate understanding of the ecology or activity of these communities beyond wastewater treatment plants. The striking coherence of the sewer microbiome across the United States demonstrates that the sewer environment is highly selective for a particular microbial community composition. Therefore, results from more in-depth studies or proven engineering controls in one system could be extrapolated more broadly. Understanding the complex ecology of sewer infrastructure is critical for not only improving our ability to treat human waste and increasing the sustainability of our cities but also to create scalable and effective sewage microbial observatories, which are inevitable investments of the future to monitor health in human populations.
Collapse
Affiliation(s)
- Adélaïde Roguet
- School of Freshwater Sciences, University of Wisconsin-Milwaukee, Milwaukee, Wisconsin, USA
| | - Ryan J. Newton
- School of Freshwater Sciences, University of Wisconsin-Milwaukee, Milwaukee, Wisconsin, USA
| | - A. Murat Eren
- Helmholtz Institute for Functional Marine Biodiversity, Oldenburg, Germany
- Josephine Bay Paul Center, Marine Biological Laboratory, Woods Hole, Massachusetts, USA
| | - Sandra L. McLellan
- School of Freshwater Sciences, University of Wisconsin-Milwaukee, Milwaukee, Wisconsin, USA
| |
Collapse
|
10
|
Tello Martín ML, Lavega R, Carrasco JC, Pérez M, Pérez-Pulido AJ, Thon M, Pérez Benito E. Influence of Agaricus bisporus establishment and fungicidal treatments on casing soil metataxonomy during mushroom cultivation. BMC Genomics 2022; 23:442. [PMID: 35701764 PMCID: PMC9199190 DOI: 10.1186/s12864-022-08638-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2021] [Accepted: 05/16/2022] [Indexed: 11/15/2022] Open
Abstract
The cultivation of edible mushroom is an emerging sector with a potential yet to be discovered. Unlike plants, it is a less developed agriculture where many studies are lacking to optimize the cultivation. In this work we have employed high-throughput techniques by next generation sequencing to screen the microbial structure of casing soil employed in mushroom cultivation (Agaricus bisporus) while sequencing V3-V4 of the 16S rRNA gene for bacteria and the ITS2 region of rRNA for. In addition, the microbiota dynamics and evolution (bacterial and fungal communities) in peat-based casing along the process of incubation of A. bisporus have been studied, while comparing the effect of fungicide treatment (chlorothalonil and metrafenone). Statistically significant changes in populations of bacteria and fungi were observed. Microbial composition differed significantly based on incubation day, changing radically from the original communities in the raw material to a specific microbial composition driven by the A. bisporus mycelium growth. Chlorothalonil treatment seems to delay casing colonization by A. bisporus. Proteobacteria and Bacteroidota appeared as the most dominant bacterial phyla. We observed a great change in the structure of the bacteria populations between day 0 and the following days. Fungi populations changed more gradually, with A. bisporus displacing the rest of the species as the cultivation cycle progresses. A better understanding of the microbial communities in the casing will hopefully allow us to increase the biological efficiency of the crop.
Collapse
Affiliation(s)
- Maria Luisa Tello Martín
- Mushroom Technological Research Center of La Rioja (CTICH), Ctra. Calahorra km 4, 26560, Autol, La Rioja, Spain.
| | - Rebeca Lavega
- Mushroom Technological Research Center of La Rioja (CTICH), Ctra. Calahorra km 4, 26560, Autol, La Rioja, Spain
| | - Jaime Carrasco Carrasco
- Mushroom Technological Research Center of La Rioja (CTICH), Ctra. Calahorra km 4, 26560, Autol, La Rioja, Spain.,Department of Plant Sciences, University of Oxford, SParks Rd, Oxford, OX1 3RB, UK
| | - Margarita Pérez
- Mushroom Technological Research Center of La Rioja (CTICH), Ctra. Calahorra km 4, 26560, Autol, La Rioja, Spain
| | - Antonio J Pérez-Pulido
- Andalusian Centre for Developmental Biology (CABD, UPO-CSIC-JA). Faculty of Experimental Sciences (Genetics Dept.), University Pablo de Olavide (Sevilla), 41013, Sevilla, Spain
| | - Michael Thon
- Universidad de Salamanca, Instituto de Investigación en Agrobiotecnología (CIALE), Calle Río Duero 12, 37185, Villamayor, Salamanca, Spain
| | - Ernesto Pérez Benito
- Universidad de Salamanca, Instituto de Investigación en Agrobiotecnología (CIALE), Calle Río Duero 12, 37185, Villamayor, Salamanca, Spain
| |
Collapse
|
11
|
Sun XW, Abdugheni R, Huang HJ, Wang YJ, Jiang MZ, Liu C, Zhou N, Jiang H, Liu SJ. Bacteroides propionicigenes sp. nov., isolated from human faeces. Int J Syst Evol Microbiol 2022; 72. [DOI: 10.1099/ijsem.0.005397] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
An anaerobic bacterial strain, designated as NSJ-90T, was isolated from the faeces of a healthy adult in China. Cells of strain NSJ-90T were Gram-stain-negative, non-motile, non-spore-forming and rod-shaped. Based on 16S rRNA gene sequence analysis, strain NSJ-90T belonged to the genus
Bacteroides
and was phylogenetically closely related to
Bacteroides clarus
YIT 12056T (16S rRNA gene identity was 97.04 %). The DNA G+C content of strain NSJ-90T was 44.85 mol% (calculated from the genome). The average nucleotide identity between strain NSJ-90T and
B. clarus
YIT 12056T was 87.60 %. The major cellular fatty acids (>10 %) of strain NSJ-90T were iso-C15 : 0, anteiso-C15 : 0 and iso-C17 : 0 3-OH. Menaquinone-10 was detected as the respiratory quinone. The major products of glucose fermentation were acetic, propionic and isovaleric acids. Based on its phylogenetic, phenotypic and chemotaxonomic characteristics, we propose that strain NSJ-90T represents a novel species of the genus
Bacteroides
, for which the name Bacteroides propionicigenes sp. nov. is proposed. The type strain is NSJ-90T (=CGMCC 1.17886T=KCTC 25305T).
Collapse
Affiliation(s)
- Xin-Wei Sun
- State Key Laboratory of Microbial Biotechnology, Shandong University, Qingdao 266000, PR China
| | - Rashidin Abdugheni
- University of Chinese Academy of Sciences, Beijing 100049, PR China
- State Key Laboratory of Microbial Resources, and Environmental Microbiology Research Center (EMRC), Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China
| | - Hao-Jie Huang
- State Key Laboratory of Microbial Resources, and Environmental Microbiology Research Center (EMRC), Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China
- State Key Laboratory of Microbial Biotechnology, Shandong University, Qingdao 266000, PR China
| | - Yu-Jing Wang
- University of Chinese Academy of Sciences, Beijing 100049, PR China
- State Key Laboratory of Microbial Resources, and Environmental Microbiology Research Center (EMRC), Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China
| | - Min-Zhi Jiang
- State Key Laboratory of Microbial Biotechnology, Shandong University, Qingdao 266000, PR China
| | - Chang Liu
- State Key Laboratory of Microbial Resources, and Environmental Microbiology Research Center (EMRC), Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China
| | - Nan Zhou
- State Key Laboratory of Microbial Resources, and Environmental Microbiology Research Center (EMRC), Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China
| | - He Jiang
- State Key Laboratory of Microbial Biotechnology, Shandong University, Qingdao 266000, PR China
| | - Shuang-Jiang Liu
- University of Chinese Academy of Sciences, Beijing 100049, PR China
- State Key Laboratory of Microbial Resources, and Environmental Microbiology Research Center (EMRC), Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China
- State Key Laboratory of Microbial Biotechnology, Shandong University, Qingdao 266000, PR China
| |
Collapse
|
12
|
Kabaivanova L, Hubenov V, Dimitrova L, Simeonov I, Wang H, Petrova P. Archaeal and Bacterial Content in a Two-Stage Anaerobic System for Efficient Energy Production from Agricultural Wastes. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27051512. [PMID: 35268611 PMCID: PMC8911581 DOI: 10.3390/molecules27051512] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Revised: 02/17/2022] [Accepted: 02/21/2022] [Indexed: 12/22/2022]
Abstract
Anaerobic digestion (AD) is a microbially-driven process enabling energy production. Microorganisms are the core of anaerobic digesters and play an important role in the succession of hydrolysis, acidogenesis, acetogenesis, and methanogenesis processes. The diversity of participating microbial communities can provide new information on digester performance for biomass valorization and biofuel production. In this study anaerobic systems were used, operating under mesophilic conditions that realized biodegradation processes of waste wheat straw pretreated with NaOH-a renewable source for hydrogen and methane production. These processes could be managed and optimized for hydrogen and methane separately but combining them in a two-stage system can lead to higher yields and a positive energy balance. The aim of the study was to depict a process of biohydrogen production from lignocellulosic waste followed by a second one leading to the production of biomethane. Archaeal and bacterial consortia in a two-stage system operating with wheat straw were identified for the first time and the role of the most important representatives was elucidated. The mixed cultures were identified by the molecular-biological methods of metagenomics. The results showed that biohydrogen generation is most probably due to the presence of Proteiniphilum saccharofermentans, which was 28.2% to 45.4% of the microbial community in the first and the second bioreactor, respectively. Archaeal representatives belonging to Methanobacterium formicicum (0.71% of the community), Methanosarcina spelaei (0.03%), Methanothrix soehngenii (0.012%), and Methanobacterium beijingense (0.01%) were proven in the methane-generating reactor. The correlation between substrate degradation and biogas accumulation was calculated, together with the profile of fatty acids as intermediates produced during the processes. The hydrogen concentration in the biogas reached 14.43%, and the Methane concentration was 69%. Calculations of the energy yield during the two-stage process showed 1195.89 kWh·t-1 compared to a 361.62 kWh·t-1 cumulative yield of energy carrier for a one-stage process.
Collapse
Affiliation(s)
- Lyudmila Kabaivanova
- Institute of Microbiology, Bulgarian Academy of Sciences, 1113 Sofia, Bulgaria; (V.H.); (L.D.); (I.S.)
- Correspondence: (L.K.); (P.P.); Tel.: +359-2-9793167/79 (L.K. & P.P.)
| | - Venelin Hubenov
- Institute of Microbiology, Bulgarian Academy of Sciences, 1113 Sofia, Bulgaria; (V.H.); (L.D.); (I.S.)
| | - Lyudmila Dimitrova
- Institute of Microbiology, Bulgarian Academy of Sciences, 1113 Sofia, Bulgaria; (V.H.); (L.D.); (I.S.)
| | - Ivan Simeonov
- Institute of Microbiology, Bulgarian Academy of Sciences, 1113 Sofia, Bulgaria; (V.H.); (L.D.); (I.S.)
| | - Haoping Wang
- French-Chinese Laboratory LaFCAS, School of Automation, Nanjing University of Science and Technology, Nanjing 210094, China;
| | - Penka Petrova
- Institute of Microbiology, Bulgarian Academy of Sciences, 1113 Sofia, Bulgaria; (V.H.); (L.D.); (I.S.)
- Correspondence: (L.K.); (P.P.); Tel.: +359-2-9793167/79 (L.K. & P.P.)
| |
Collapse
|
13
|
Characteristics and Rates of Microbial Processes in Clays of Different Mineral and Elemental Composition in Relation to Safety Prediction for ESB Clay Materials. APPLIED SCIENCES-BASEL 2022. [DOI: 10.3390/app12041843] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Microbial activity in clay barrier materials during radioactive waste disposal can lead to a violation of important physicochemical properties of the barrier system as a whole, thereby reducing the safety of the storage facility. This work evaluates the activity of the microbial complex of five bentonite and two kaolin clays. All clay materials were found to contain microorganisms, mostly with organotrophic aerobic and anaerobic metabolism capable of forming hydrogen sulfide and transforming basic and impurity clay minerals. The activity of microorganisms can increase with the ingress of degradation products of aluminophosphate matrices and cement barriers, as well as radiolysis products. For all clay the rates of microbial processes were shown to exhibit a direct correlation with the content of organic matter, kaolinite, and potassium feldspar, and an inverse correlation with montmorillonite content. A systematic methodological approach is proposed for clay materials and their susceptibility to microbial processes. The approach makes it possible, based on the content of organic matter, biophilic elements in the samples, parameters of the respiratory activity of the microbial complex, the formation of hydrogen sulfide, and other parameters, to assess in advance the possibility of using them in barriers.
Collapse
|
14
|
Ueki A, Tonouchi A, Kaku N, Ueki K. Prevotella herbatica sp. nov., a plant polysaccharide-decomposing anaerobic bacterium isolated from a methanogenic reactor. Int J Syst Evol Microbiol 2022; 72. [DOI: 10.1099/ijsem.0.005221] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
An obligately anaerobic bacterial strain (WR041T) was isolated from a plant residue sample in a methanogenic reactor. Cells of the strain were Gram-stain-negative, non-motile, non-spore-forming rods.
Prevotella paludivivens
JCM 13650T was the closest species of the strain based on 16S rRNA gene sequencing (98.9 % similarity). Genome analysis of strain WR041T indicated that the genome size of the strain was 3.52 Mb and the genomic DNA G+C content was 37.5 mol%. Although the 16S rRNA gene sequence similarity of strain WR041T with the closest species was higher than the threshold value of the recommended species delineation (98.7 %), the average nucleotide identity and the digital DNA–DNA hybridization value between them were 91–92 and 45.5 %, respectively, suggesting that strain WR041T represents a novel species in the genus. Strain WR041T essentially required haemin and CO2/Na2CO3 for growth. The strain was saccharolytic and decomposed various polysaccharides (glucomannan, inulin, laminarin, pectin, starch and xylan) and produced acetate and succinate. The optimum growth conditions were 35 °C and pH 6.8. The major cellular fatty acids were branched-chain fatty acids such as anteiso-C15 : 0 and iso-C15 : 0. Menaquinones MK-11 and MK-12 were the major respiratory quinones. Many protein-coding genes which were not found in the genome of
P. paludivivens
as orthologous genes were detected in the genome of strain WR041T. Based on the differences in the phylogenetic, genomic and physiological characteristics between strain WR041T and related species, the name Prevotella herbatica sp. nov. is proposed to accommodate strain WR041T (=NBRC 115134T = DSM 112534T).
Collapse
Affiliation(s)
- Atsuko Ueki
- Faculty of Agriculture, Yamagata University, Wakaba-machi 1-23, Tsuruoka, Yamagata 997-8555, Japan
| | - Akio Tonouchi
- Faculty of Agriculture and Life Science, Hirosaki University, Bunkyo-cho 3, Hirosaki, Aomori 036-8561, Japan
| | - Nobuo Kaku
- Faculty of Agriculture, Yamagata University, Wakaba-machi 1-23, Tsuruoka, Yamagata 997-8555, Japan
| | - Katsuji Ueki
- Faculty of Agriculture, Yamagata University, Wakaba-machi 1-23, Tsuruoka, Yamagata 997-8555, Japan
| |
Collapse
|
15
|
Granatto CF, Grosseli GM, Sakamoto IK, Fadini PS, Varesche MBA. Influence of cosubstrate and hydraulic retention time on the removal of drugs and hygiene products in sanitary sewage in an anaerobic Expanded Granular Sludge Bed reactor. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2021; 299:113532. [PMID: 34614559 DOI: 10.1016/j.jenvman.2021.113532] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/03/2021] [Revised: 07/24/2021] [Accepted: 08/09/2021] [Indexed: 06/13/2023]
Abstract
Diclofenac (DCF), ibuprofen (IBU), propranolol (PRO), triclosan (TCS) and linear alkylbenzene sulfonate (LAS) can be recalcitrant in Wastewater Treatment Plants (WWTP). The removal of these compounds was investigated in scale-up (69 L) Expanded Granular Sludge Bed (EGSB) reactor, fed with sanitary sewage from the São Carlos-SP (Brazil) WWTP and 200 mg L-1 of ethanol. The EGSB was operated in three phases: (I) hydraulic retention time (HRT) of 36±4 h; (II) HRT of 20±2 h and (III) HRT of 20±2 h with ethanol. Phases I and II showed no significant difference in the removal of LAS (63 ± 11-65 ± 12 %), DCF (37 ± 18-35 ± 11 %), IBU (43 ± 18-44 ± 16 %) and PRO (46 ± 25-51 ± 23 %) for 13±2-15 ± 2 mg L-1, 106 ± 32-462 ± 294 μg L-1, 166 ± 55-462 ± 213 μg L-1 and 201 ± 113-250 ± 141 μg L-1 influent, respectively. Higher TCS removal was obtained in phase I (72 ± 17 % for 127 ± 120 μg L-1 influent) when compared to phase II (51 ± 13 % for 135 ± 119 μg L-1 influent). This was due to its greater adsorption (40 %) in the initial phase. Phase III had higher removal of DCF (42 ± 10 % for 107 ± 26 μg L-1 influent), IBU (50 ± 15 % for 164 ± 47 μg L-1 influent) and TCS (85 ± 15 % for 185 ± 148 μg L-1 influent) and lower removal of LAS (35 ± 14 % for 12 ± 3 mg L-1 influent) and PRO (-142 ± 177 % for 188 ± 88 μg L-1 influent). Bacteria similar to Syntrophobacter, Smithella, Macellibacteroides, Syntrophus, Blvii28_wastewater-sludge_group and Bacteroides were identified in phase I with relative abundance of 3.1 %-4.7 %. Syntrophobacter was more abundant (15.4 %) in phase II, while in phase III, it was Smithella (12.7 %) and Caldisericum (15.1 %). Regarding the Archaea Domain, Methanosaeta was more abundant in phases I (84 %) and II (67 %), while in phase III it was Methanobacterium (86 %).
Collapse
Affiliation(s)
- Caroline F Granatto
- Department of Hydraulics and Sanitation, São Carlos School of Engineering, University of São Paulo, Ave Trabalhador São-Carlense, No. 400, Zipcode 13566-590, São Carlos, SP, Brazil.
| | - Guilherme M Grosseli
- Federal University of São Carlos, Washington LuizHighway, Km 235, Zipcode 13565-905, São Carlos, SP, Brazil.
| | - Isabel K Sakamoto
- Department of Hydraulics and Sanitation, São Carlos School of Engineering, University of São Paulo, Ave Trabalhador São-Carlense, No. 400, Zipcode 13566-590, São Carlos, SP, Brazil.
| | - Pedro S Fadini
- Federal University of São Carlos, Washington LuizHighway, Km 235, Zipcode 13565-905, São Carlos, SP, Brazil.
| | - Maria Bernadete A Varesche
- Department of Hydraulics and Sanitation, São Carlos School of Engineering, University of São Paulo, Ave Trabalhador São-Carlense, No. 400, Zipcode 13566-590, São Carlos, SP, Brazil.
| |
Collapse
|
16
|
Ge Y, Zhang G, Yang J, Lai XH, Jin D, Lu S, Pu J, Huang Y, Luo X, Zheng H, Zhang X, Xu J. Bacteroides luhongzhouii sp. nov. and Bacteroides zhangwenhongii sp. nov., isolated from human faeces. Int J Syst Evol Microbiol 2021; 71. [PMID: 33881983 DOI: 10.1099/ijsem.0.004772] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
Four unknown strains, characterized as Gram-stain-negative, strictly anaerobic, non-motile and rod-shaped, were isolated from fresh faeces of healthy humans in PR China. Pairwise sequence comparisons of the 16S rRNA genes showed that these isolates were separated into two clusters. Cluster I (strains HF-5141T and HF-106) was most closely related to Bacteroides xylanisolvens XB1AT (98.0-98.3 % similarity) and Bacteroides ovatus ATCC 8483T (97.3-97.5 %), whereas cluster II (strains HF-5287T and HF-5300) exhibited a similarity range of 96.8-97.0 % to Bacteroides finegoldii JCM 13345T, 96.7-96.9 % to Bacteroides faecis MAJ27T and 96.4-96.5 % to Bacteroides xylanisolvens XB1AT. The DNA G+C contents of type strains HF-5141T and HF-5287T were 41.5 and 42.6 mol%, respectively. These strains had anteiso-C15 : 0 as the major cellular fatty acid, MK-9 and MK-11 as the predominant respiratory quinones, and phosphatidylethanolamine, aminophospholipids and phospholipids as major polar lipids, which is typical for members of the genus Bacteroides. However, the average nucleotide identity and digital DNA-DNA hybridization values, accompanied by different phenotypic and biochemical characteristics, distinguished them from their corresponding closest relatives as well as from other recognized members of the genus Bacteroides. Therefore, strains HF-5141T and HF-5287T represent two novel species in the genus Bacteroides, for which the names Bacteroides luhongzhouii sp. nov. and Bacteroides zhangwenhongii sp. nov. are proposed, with HF-5141T (=CGMCC 1.16787T=GDMCC 1.1591T=JCM 33480T) and HF-5287T (=CGMCC 1.16724T=GDMCC 1.1590T=JCM 33481T) as type strains.
Collapse
Affiliation(s)
- Yajun Ge
- Shanghai Public Health Clinical Center, Fudan University, Shanghai 201508, PR China
| | - Gui Zhang
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Changping, Beijing 102206, PR China
| | - Jing Yang
- Research Units of Discovery of Unknown Bacteria and Function, Chinese Academy of Medical Sciences, Beijing, PR China.,State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Changping, Beijing 102206, PR China.,Shanghai Public Health Clinical Center, Fudan University, Shanghai 201508, PR China
| | - Xin-He Lai
- Henan Key Laboratory of Biomolecular Recognition and Sensing, College of Chemistry and Chemical Engineering, Henan Joint International Research Laboratory of Chemo/Biosensing and Early Diagnosis of Major Diseases, Shangqiu Normal University, Shangqiu 476000, PR China
| | - Dong Jin
- Research Units of Discovery of Unknown Bacteria and Function, Chinese Academy of Medical Sciences, Beijing, PR China.,State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Changping, Beijing 102206, PR China.,Shanghai Public Health Clinical Center, Fudan University, Shanghai 201508, PR China
| | - Shan Lu
- Research Units of Discovery of Unknown Bacteria and Function, Chinese Academy of Medical Sciences, Beijing, PR China.,State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Changping, Beijing 102206, PR China.,Shanghai Public Health Clinical Center, Fudan University, Shanghai 201508, PR China
| | - Ji Pu
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Changping, Beijing 102206, PR China
| | - Ying Huang
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Changping, Beijing 102206, PR China
| | - Xuelian Luo
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Changping, Beijing 102206, PR China
| | - Han Zheng
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Changping, Beijing 102206, PR China.,Shanghai Public Health Clinical Center, Fudan University, Shanghai 201508, PR China
| | - Xiaoyan Zhang
- Shanghai Public Health Clinical Center, Fudan University, Shanghai 201508, PR China
| | - Jianguo Xu
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Changping, Beijing 102206, PR China.,Shanghai Public Health Clinical Center, Fudan University, Shanghai 201508, PR China.,Research Units of Discovery of Unknown Bacteria and Function, Chinese Academy of Medical Sciences, Beijing, PR China
| |
Collapse
|
17
|
Dal Ferro N, De Mattia C, Gandini MA, Maucieri C, Stevanato P, Squartini A, Borin M. Green walls to treat kitchen greywater in urban areas: Performance from a pilot-scale experiment. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 757:144189. [PMID: 33316535 DOI: 10.1016/j.scitotenv.2020.144189] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2020] [Revised: 11/28/2020] [Accepted: 11/30/2020] [Indexed: 06/12/2023]
Abstract
An increase in water use in urban areas is forcing scientists and policy makers to find alternative solutions for freshwater management, aimed at attaining integrated water resources management. Here, we tested in a 2-year experiment (June 2017-April 2019) the treatment performance of an innovative wall cascade constructed wetland (WCCW) system. The aim was to combine the multifunctional benefits of green walls (e.g. aesthetic, surface area requirements) with those of constructed wetland systems (e.g. high pollutants removal efficiencies, water recycling) to treat kitchen greywaters. The WCCW was a terraced system of six phytoremediation lines, each of which was composed of three plastic tanks (3 × 0.04 m3), filled with lightweight porous media, and vegetated with different ornamental species, namely Mentha aquatica L., Oenanthe javanica (Blume) DC., and Lysimachia nummularia L. Physicochemical (temperature, pH, electrical conductivity, dissolved oxygen, turbidity) and chemical parameters (chemical oxygen demand, biochemical oxygen demand, anionic surfactants, Kjeldahl, ammonium and nitric nitrogen, total orthophosphate) were monitored at a frequency of at least 15 days, depending on the season and WCCW management. Results showed that the WCCW significantly reduced the main water pollutants (e.g. organic compounds, nutrients), suggesting its potential application in urban environments for water recycling in the context of green infrastructures and ecological sanitation. A culture-independent taxonomic assessment of suspended bacterial communities before and after the treatment showed clear treatment-related shifts, being the functional ecology attributes changed according to changes in greywater chemical parameters. Future research should attempt to optimize the WCCW system management by regulating the nutrients balance to avoid macronutrients deficiency, and setting the most suitable water flow dynamics (hydraulic retention time, saturation-desaturation cycles) to improve the greywater treatment.
Collapse
Affiliation(s)
- Nicola Dal Ferro
- Department of Agronomy, Food, Natural resources, Animals and Environment, University of Padova, Viale dell'Universita' 16, 35020 Legnaro, Padova, Italy.
| | - Chiara De Mattia
- Department of Agronomy, Food, Natural resources, Animals and Environment, University of Padova, Viale dell'Universita' 16, 35020 Legnaro, Padova, Italy
| | - Mario Andres Gandini
- Department of Energy and Mechanics, Universidad Autónoma de Occidente, Calle 25 No. 115-85, Cali, Colombia
| | - Carmelo Maucieri
- Department of Agronomy, Food, Natural resources, Animals and Environment, University of Padova, Viale dell'Universita' 16, 35020 Legnaro, Padova, Italy
| | - Piergiorgio Stevanato
- Department of Agronomy, Food, Natural resources, Animals and Environment, University of Padova, Viale dell'Universita' 16, 35020 Legnaro, Padova, Italy
| | - Andrea Squartini
- Department of Agronomy, Food, Natural resources, Animals and Environment, University of Padova, Viale dell'Universita' 16, 35020 Legnaro, Padova, Italy
| | - Maurizio Borin
- Department of Agronomy, Food, Natural resources, Animals and Environment, University of Padova, Viale dell'Universita' 16, 35020 Legnaro, Padova, Italy
| |
Collapse
|
18
|
Inaba T, Aoyagi T, Hori T, Charfi A, Suh C, Lee JH, Sato Y, Ogata A, Aizawa H, Habe H. Clarifying prokaryotic and eukaryotic biofilm microbiomes in anaerobic membrane bioreactor by non-destructive microscopy and high-throughput sequencing. CHEMOSPHERE 2020; 254:126810. [PMID: 32334259 DOI: 10.1016/j.chemosphere.2020.126810] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2019] [Revised: 04/05/2020] [Accepted: 04/14/2020] [Indexed: 06/11/2023]
Abstract
Anaerobic membrane bioreactor (AnMBR) is used for the treatment of organic solid waste. Clogging of filtration membrane pores, called membrane fouling, is one of the most serious issues for the sustainable operation of AnMBR. Although the physical and chemical mechanisms of the membrane fouling have been widely studied, the biological mechanisms are still unclear. The biofilm formation and development on the membrane might cause the membrane fouling. In this study, the prokaryotic and eukaryotic microbiomes of the membrane-attached biofilms in an AnMBR treating a model slurry of organic solid waste were investigated by non-destructive microscopy and high-throughput sequencing of 16S and 18S rRNA genes. The non-destructive visualization indicated that the biofilm was layered with different structures. The lowermost residual fouling layer was mesh-like and composed of filamentous microorganisms, while the upper cake layer was mainly the non-dense and non-cell region. The principal coordinate and phylogenetic analyses of the sequence data showed that the biofilm microbiomes were different from the sludge. The lowermost layer consisted of operational taxonomic units that were related to Leptolinea tardivitalis and Methanosaeta concilii (9.53-10.07% and 1.14-1.64% of the total prokaryotes, respectively) and Geotrichum candidum (30.22-82.31% of the total eukaryotes), all of which exhibited the filamentous morphology. Moreover, the upper layer was inhabited by the presumably cake-degrading bacteria and predatory eukaryotes. The biofilm microbiome features were consistent with the microscope-visualized structure. These results demonstrated that the biofilm structure and microbiome were the layer specific, which provides better understanding of biological mechanisms of membrane fouling in the AnMBR.
Collapse
Affiliation(s)
- Tomohiro Inaba
- Environmental Management Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 16-1 Onogawa, Tsukuba, Ibaraki, 305-8569, Japan
| | - Tomo Aoyagi
- Environmental Management Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 16-1 Onogawa, Tsukuba, Ibaraki, 305-8569, Japan
| | - Tomoyuki Hori
- Environmental Management Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 16-1 Onogawa, Tsukuba, Ibaraki, 305-8569, Japan.
| | - Amine Charfi
- LG-Hitachi Water Solutions, Gasan R&D Campus, 51, Gasan Digital 1-ro, Geumcheon-gu, Seoul, 08592, South Korea
| | - Changwon Suh
- LG-Hitachi Water Solutions, Gasan R&D Campus, 51, Gasan Digital 1-ro, Geumcheon-gu, Seoul, 08592, South Korea
| | - Jong Hoon Lee
- LG-Hitachi Water Solutions, Gasan R&D Campus, 51, Gasan Digital 1-ro, Geumcheon-gu, Seoul, 08592, South Korea
| | - Yuya Sato
- Environmental Management Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 16-1 Onogawa, Tsukuba, Ibaraki, 305-8569, Japan
| | - Atsushi Ogata
- Environmental Management Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 16-1 Onogawa, Tsukuba, Ibaraki, 305-8569, Japan
| | - Hidenobu Aizawa
- Environmental Management Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 16-1 Onogawa, Tsukuba, Ibaraki, 305-8569, Japan
| | - Hiroshi Habe
- Environmental Management Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 16-1 Onogawa, Tsukuba, Ibaraki, 305-8569, Japan
| |
Collapse
|
19
|
Wang C, Zhao J, Zhang H, Lee YK, Zhai Q, Chen W. Roles of intestinal bacteroides in human health and diseases. Crit Rev Food Sci Nutr 2020; 61:3518-3536. [PMID: 32757948 DOI: 10.1080/10408398.2020.1802695] [Citation(s) in RCA: 53] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Bacteroides, an abundant genus in the intestines of mammals, has been recently considered as the next generation probiotics (NGP) candidate due to its potential role in promoting host health. However, the role of Bacteroides in the development of intestinal dysfunctions such as diarrhea, inflammatory bowel disease, and colorectal cancer should not be overlooked. In the present study, we focused on nine most widely occurred and abundant Bacteroides species and discussed their roles in host immunity, glucose and lipid metabolism and the prevention or induction of diseases. Besides, we also discussed the current methods used in the safety evaluation of Bacteroides species and key opinions about the concerns of these strains for the future use.
Collapse
Affiliation(s)
- Chen Wang
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, P.R. China.,School of Food Science and Technology, Jiangnan University, Wuxi, China
| | - Jianxin Zhao
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, P.R. China.,School of Food Science and Technology, Jiangnan University, Wuxi, China
| | - Hao Zhang
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, P.R. China.,School of Food Science and Technology, Jiangnan University, Wuxi, China.,National Engineering Research Center for Functional Food, Jiangnan University, Wuxi, China.,Research Institute, Wuxi Translational Medicine Research Center and Jiangsu Translational Medicine, Wuxi, China.,(Yangzhou) Institute of Food Biotechnology, Jiangnan University, Yangzhou, China
| | - Yuan-Kun Lee
- Department of Microbiology & Immunology, National University of Singapore, Singapore, Singapore
| | - Qixiao Zhai
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, P.R. China.,School of Food Science and Technology, Jiangnan University, Wuxi, China.,International Joint Research Laboratory for Probiotics, Jiangnan University, Wuxi, China
| | - Wei Chen
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, P.R. China.,School of Food Science and Technology, Jiangnan University, Wuxi, China.,National Engineering Research Center for Functional Food, Jiangnan University, Wuxi, China.,Beijing Innovation Centre of Food Nutrition and Human Health, Beijing Technology and Business University (BTBU), Beijing, P.R. China
| |
Collapse
|
20
|
Ecological and Technical Mechanisms for Cross-Reaction of Human Fecal Indicators with Animal Hosts. Appl Environ Microbiol 2020; 86:AEM.02319-19. [PMID: 31862726 DOI: 10.1128/aem.02319-19] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2019] [Accepted: 12/15/2019] [Indexed: 12/13/2022] Open
Abstract
Quantitative PCR (qPCR) assays for human/sewage marker genes have demonstrated sporadic positive results in animal feces despite their high specificities to sewage and human feces. It is unclear whether these positive reactions are caused by true occurrences of microorganisms containing the marker gene (i.e., indicator organisms) or nonspecific amplification (false positive). The distribution patterns of human/sewage indicator organisms in animals have not been explored in depth, which is crucial for evaluating a marker gene's true- or false-positive reactions. Here, we analyzed V6 region 16S rRNA gene sequences from 257 animal fecal samples and tested a subset of 184 using qPCR for human/sewage marker genes. Overall, specificities of human/sewage marker genes within sequencing data were 99.6% (BacV6-21), 96.9% (Lachno3), and 96.1% (HF183, indexed by its inferred V6 sequence). Occurrence of some true cross-reactions was associated with atypical compositions of organisms within the genera Blautia or Bacteroides For human/sewage marker qPCR assays, specificities were 96.7% (HF183/Bac287R), 96.2% (BacV6-21), 95.6% (human Bacteroides [HB]), and 94.0% (Lachno3). Select assays duplexed with either Escherichia coli or Enterococcus spp. were also validated. Most of the positive qPCR results in animals were low level and, on average, 2 orders of magnitude lower than the copy numbers of E. coli and Enterococcus spp. The lower specificity in qPCR assays compared to sequencing data was mainly caused by amplification of sequences highly similar to the marker gene and not the occurrence of the exact marker sequence in animal fecal samples.IMPORTANCE Identifying human sources of fecal pollution is critical to remediate sanitation concerns. Large financial investments are required to address these concerns; therefore, a high level of confidence in testing results is needed. Human fecal marker genes validated in this study showed high specificity in both sequencing data and qPCR results. Human marker sequences were rarely found in individual animals, and in most cases, the animals had atypical microbial communities. Sequencing also revealed the presence of closely related organisms that could account for nonspecific amplification in certain assays. Both the true cross-reactions and the nonspecific amplification had low signals well below E. coli or Enterococcus levels and likely would not impact the assay's ability to reliably detect human fecal pollution. No animal source had multiple human/sewage marker genes present; therefore, using a combination of marker genes would increase the confidence of human fecal pollution detection.
Collapse
|
21
|
Baba Y, Matsuki Y, Takizawa S, Suyama Y, Tada C, Fukuda Y, Saito M, Nakai Y. Pretreatment of Lignocellulosic Biomass with Cattle Rumen Fluid for Methane Production: Fate of Added Rumen Microbes and Indigenous Microbes of Methane Seed Sludge. Microbes Environ 2019; 34:421-428. [PMID: 31748428 PMCID: PMC6934390 DOI: 10.1264/jsme2.me19113] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2019] [Accepted: 09/17/2019] [Indexed: 11/29/2022] Open
Abstract
The pretreatment of lignocellulosic substrates with cattle rumen fluid was successfully developed to increase methane production. In the present study, a 16S rRNA gene-targeted amplicon sequencing approach using the MiSeq platform was applied to elucidate the effects of the rumen fluid treatment on the microbial community structure in laboratory-scale batch methane fermenters. Methane production in fermenters fed rumen fluid-treated rapeseed (2,077.3 mL CH4 reactor-1 for a 6-h treatment) was markedly higher than that in fermenters fed untreated rapeseed (1,325.8 mL CH4 reactor-1). Microbial community profiling showed that the relative abundance of known lignocellulose-degrading bacteria corresponded to lignocellulose-degrading enzymatic activities. Some dominant indigenous cellulolytic and hemicellulolytic bacteria in seed sludge (e.g., Cellulosilyticum lentocellum and Ruminococcus flavefaciens) and rumen fluid (e.g., Butyrivibrio fibrisolvens and Prevotella ruminicola) became undetectable or markedly decreased in abundance in the fermenters fed rumen fluid-treated rapeseed, whereas some bacteria derived from seed sludge (e.g., Ruminofilibacter xylanolyticum) and rumen fluid (e.g., R. albus) remained detectable until the completion of methane production. Thus, several lignocellulose-degrading bacteria associated with rumen fluid proliferated in the fermenters, and may play an important role in the degradation of lignocellulosic compounds in the fermenter.
Collapse
Affiliation(s)
- Yasunori Baba
- Laboratory of Sustainable Animal Environmental Science, Graduate School of Agricultural Science, Tohoku UniversityYomogida 232–3, Naruko-onsen, Osaki, Miyagi 989–6711Japan
- Research Fellow of the Japanese Society for the Promotion of Science (JSPS)Japan
- Research Institute for Bioresources and Biotechnology, Ishikawa Prefectural UniversitySuematsu1–308, Nonoichi, Ishikawa 921–8836Japan
| | - Yu Matsuki
- Laboratory of Forest Ecology, Graduate School of Agricultural Science, Tohoku UniversityYomogida 232–3, Naruko-onsen, Osaki, Miyagi 989–6711Japan
| | - Shuhei Takizawa
- Laboratory of Sustainable Animal Environmental Science, Graduate School of Agricultural Science, Tohoku UniversityYomogida 232–3, Naruko-onsen, Osaki, Miyagi 989–6711Japan
| | - Yoshihisa Suyama
- Laboratory of Forest Ecology, Graduate School of Agricultural Science, Tohoku UniversityYomogida 232–3, Naruko-onsen, Osaki, Miyagi 989–6711Japan
| | - Chika Tada
- Laboratory of Sustainable Animal Environmental Science, Graduate School of Agricultural Science, Tohoku UniversityYomogida 232–3, Naruko-onsen, Osaki, Miyagi 989–6711Japan
| | - Yasuhiro Fukuda
- Laboratory of Sustainable Animal Environmental Science, Graduate School of Agricultural Science, Tohoku UniversityYomogida 232–3, Naruko-onsen, Osaki, Miyagi 989–6711Japan
| | - Masanori Saito
- Laboratory of Environmental Crop Science, Graduate School of Agricultural Science, Tohoku UniversityYomogida 232–3, Naruko-onsen, Osaki, Miyagi 989–6711Japan
| | - Yutaka Nakai
- Laboratory of Sustainable Animal Environmental Science, Graduate School of Agricultural Science, Tohoku UniversityYomogida 232–3, Naruko-onsen, Osaki, Miyagi 989–6711Japan
- Department of Agro-Food Science, Faculty of Agro-Food Science, Niigata Agro-Food University2416 Hiranedai, Tainai, Niigata, 959–2702Japan
| |
Collapse
|
22
|
Yu SY, Kim JS, Oh BS, Park SH, Kang SW, Park JE, Choi SH, Han KI, Lee KC, Eom MK, Suh MK, Lee DH, Yoon H, Kim BY, Yang SJ, Lee JS, Lee JH. Bacteroides faecalis sp. nov., isolated from human faeces. Int J Syst Evol Microbiol 2019; 69:3824-3829. [PMID: 31511127 DOI: 10.1099/ijsem.0.003690] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A novel Gram-stain-negative and strictly anaerobic bacterial strain, designated KGMB02408T, was isolated from faeces of a healthy human in the Republic of Korea. The isolate was characterized as non-motile, non-spore-forming and rod-shaped (variable in length). The results of phylogenetic analysis based on 16S rRNA gene sequences revealed that strain KGMB02408T belonged to the genus Bacteroides and was most closely related to Bacteroides faecichinchillae JCM 17102T (=KCTC 15666T; 96.5 %). Based on its whole-genome sequence, the DNA G+C content of the isolate was 39.5 mol%. The average nucleotide identity value between strain KGMB02408T and related species, B. faecichinchillae JCM 17102T, was 93.8 %. The major cellular fatty acids (>10 %) of the isolate were anteiso-C15 : 0, iso-C17 : 0-OH, summed feature 11 (iso-C17 : 0-OH and/or C18 : 2 DMA) and C16 : 0. Menaquinone-8 (28.6 %) and menaquinone-10 (47.1 %) were detected as the major respiratory quinones in the isolate. The major end products of glucose fermentation produced by strain KGMB02408T were lactic acid, acetic acid and formic acid. Based on its phylogenetic, phenotypic and chemotaxonomic characteristics, strain KGMB02408T represents a novel species of the genus Bacteroides in the family Bacteroidaceae. The type strain is KGMB02408T (=KCTC 15687T=DSM 107828T).
Collapse
Affiliation(s)
- Seung Yeob Yu
- Korean Collection for Type Cultures, Korea Research Institute of Bioscience and Biotechnology, Jeongeup-si, Republic of Korea
| | - Ji-Sun Kim
- Korean Collection for Type Cultures, Korea Research Institute of Bioscience and Biotechnology, Jeongeup-si, Republic of Korea
| | - Byeong Seob Oh
- Korean Collection for Type Cultures, Korea Research Institute of Bioscience and Biotechnology, Jeongeup-si, Republic of Korea
| | - Seung-Hwan Park
- Korean Collection for Type Cultures, Korea Research Institute of Bioscience and Biotechnology, Jeongeup-si, Republic of Korea
| | - Se Won Kang
- Korean Collection for Type Cultures, Korea Research Institute of Bioscience and Biotechnology, Jeongeup-si, Republic of Korea
| | - Jam-Eon Park
- Korean Collection for Type Cultures, Korea Research Institute of Bioscience and Biotechnology, Jeongeup-si, Republic of Korea
| | - Seung-Hyeon Choi
- Korean Collection for Type Cultures, Korea Research Institute of Bioscience and Biotechnology, Jeongeup-si, Republic of Korea
| | - Kook-Il Han
- Korean Collection for Type Cultures, Korea Research Institute of Bioscience and Biotechnology, Jeongeup-si, Republic of Korea
| | - Keun Chul Lee
- Korean Collection for Type Cultures, Korea Research Institute of Bioscience and Biotechnology, Jeongeup-si, Republic of Korea
| | - Mi Kyung Eom
- Korean Collection for Type Cultures, Korea Research Institute of Bioscience and Biotechnology, Jeongeup-si, Republic of Korea
| | - Min Kuk Suh
- Korean Collection for Type Cultures, Korea Research Institute of Bioscience and Biotechnology, Jeongeup-si, Republic of Korea
| | - Dong Ho Lee
- Seoul National University Bundang Hospital, 82 Gumi-ro, 173 Beon-gil, Bundang-Gu, Seongnam-si, Gyeonggi-do, Republic of Korea
| | - Hyuk Yoon
- Seoul National University Bundang Hospital, 82 Gumi-ro, 173 Beon-gil, Bundang-Gu, Seongnam-si, Gyeonggi-do, Republic of Korea
| | - Byung-Yong Kim
- ChunLab, Inc., 2477 Nambusunhwan-ro, Seocho-gu, Republic of Korea
| | - Seung-Jo Yang
- ChunLab, Inc., 2477 Nambusunhwan-ro, Seocho-gu, Republic of Korea
| | - Jung-Sook Lee
- University of Science and Technology, 217 Gajeong-ro, Yuseong-gu, Daejeon, Republic of Korea.,Korean Collection for Type Cultures, Korea Research Institute of Bioscience and Biotechnology, Jeongeup-si, Republic of Korea
| | - Ju Huck Lee
- Korean Collection for Type Cultures, Korea Research Institute of Bioscience and Biotechnology, Jeongeup-si, Republic of Korea
| |
Collapse
|
23
|
Vadde KK, Feng Q, Wang J, McCarthy AJ, Sekar R. Next-generation sequencing reveals fecal contamination and potentially pathogenic bacteria in a major inflow river of Taihu Lake. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2019; 254:113108. [PMID: 31491696 DOI: 10.1016/j.envpol.2019.113108] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2019] [Revised: 08/14/2019] [Accepted: 08/23/2019] [Indexed: 06/10/2023]
Abstract
Taihu Lake is one of the largest freshwater lakes in China and serves as an important source for drinking water. This lake is suffering from eutrophication, cyanobacterial blooms and fecal pollution, and the inflow Tiaoxi River is one of the main contributors. The goal here was to characterize the bacterial community structure of Tiaoxi River water by next-generation sequencing (NGS), paying attention to bacteria that are either fecal-associated or pathogenic, and to examine the relationship between environmental parameters and bacterial community structure. Water samples collected from 15 locations in three seasons, and fecal samples collected from different hosts and wastewater samples were used for bacterial community analysis. The phyla Proteobacteria, Actinobacteria, Bacteroidetes, and Cyanobacteria were predominant in most of the water samples tested. In fecal samples, Bacteroidetes, Firmicutes, and Proteobacteria were abundant, while wastewater samples were dominated by Proteobacteria, Bacteroidetes, Acidobacteria, and Chloroflexi. The cluster analysis and principal coordinate analysis indicated that bacterial community structure was significantly different between water, fecal and sewage samples. Shared OTUs between water samples and chicken, pig, and human fecal samples ranged from 4.5 to 9.8% indicating the presence of avian, pig and human fecal contamination in Tiaoxi River. At genus level, five bacterial genera of fecal origin and sequences of seven potential pathogens were detected in many locations and their presence was correlated well with the land use pattern. The sequencing data revealed that Faecalibacterium could be a potential target for human-associated microbial source-tracking qPCR assays. Our results suggest that pH, conductivity, and temperature were the main environmental factors in shaping the bacterial community based on redundancy analysis. Overall, NGS is a valuable tool for preliminary investigation of environmental samples to identify the potential human health risk, providing specific information about fecal and potentially pathogenic bacteria that can be followed up by specific methods.
Collapse
Affiliation(s)
- Kiran Kumar Vadde
- Department of Biological Sciences, Xi'an Jiaotong-Liverpool University, Suzhou, China
| | - Qiaoli Feng
- Department of Biological Sciences, Xi'an Jiaotong-Liverpool University, Suzhou, China
| | - Jianjun Wang
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, China; University of Chinese Academy of Sciences, Beijing, China
| | - Alan J McCarthy
- Microbiology Research Group, Institute of Integrative Biology, University of Liverpool, UK
| | - Raju Sekar
- Department of Biological Sciences, Xi'an Jiaotong-Liverpool University, Suzhou, China.
| |
Collapse
|
24
|
Planý M, Czolderová M, Kraková L, Puškárová A, Bučková M, Šoltys K, Budiš J, Szemes T, Mackulak T, Wu JH, Pangallo D. Biogas production: evaluation of the influence of K2FeO4 pretreatment of maple leaves (Acer platanoides) on microbial consortia composition. Bioprocess Biosyst Eng 2019; 42:1151-1163. [DOI: 10.1007/s00449-019-02112-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2018] [Accepted: 03/20/2019] [Indexed: 10/27/2022]
|
25
|
Torregrosa M, Schwarz A, Nancucheo I, Balladares E. Evaluation of the bio-protection mechanism in diffusive exchange permeable reactive barriers for the treatment of acid mine drainage. THE SCIENCE OF THE TOTAL ENVIRONMENT 2019; 655:374-383. [PMID: 30471606 DOI: 10.1016/j.scitotenv.2018.11.083] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/10/2018] [Revised: 11/06/2018] [Accepted: 11/06/2018] [Indexed: 06/09/2023]
Abstract
This research studied the bio-protection mechanism based on chemical gradients in diffusive exchange permeable reactive barriers, evaluating the thickness of the reactive layers in the treatment of concentrated acid mine drainage (AMD). Six bench-scale reactors were constructed with reactive layer thicknesses of 2.5, 5, and 7.5 cm in duplicate. The reactors were first fed a sulfated solution for 55 days, followed by concentrated AMD for 166 days. The change of feed to AMD mainly affected the reactors with thinner 2.5 cm layers in comparison to the reactors with 5 and 7.5 cm layers. Cu and Zn removal efficiency was practically 100% in all the reactors; however, in the thinner layer reactors, metal breakthrough occurred towards the end of the experiment concurrently with inhibitory metal concentrations in the reactive layers. On the contrary, the reactors with layer thicknesses of 5 and 7.5 cm evaluated did not present toxic concentrations of these metals at any of the monitoring points. The bio-protection criterion qD correctly predicted that the thin-layer reactor would be the most affected by the toxicity of AMD. The criterion also indicated that all the reactors should fail. Nevertheless, the fault in the thinner layer reactor registered in the effluent after >150 days; therefore, the possibility of failure in the 5 and 7.5 cm thickness reactors is not rejected, as it could have occurred if the experiment had continued.
Collapse
Affiliation(s)
- Martin Torregrosa
- Departamento de Ingeniería Civil y Centro de Recursos Hídricos para el Agua y la Minería (CRHIAM), Universidad de Concepción, Barrio Universitario, Concepción, Chile.
| | - Alex Schwarz
- Departamento de Ingeniería Civil y Centro de Recursos Hídricos para el Agua y la Minería (CRHIAM), Universidad de Concepción, Barrio Universitario, Concepción, Chile.
| | - Ivan Nancucheo
- Facultad de Ingeniería y Tecnología, Universidad San Sebastián, Lientur 1457, Concepción, Chile.
| | - Eduardo Balladares
- Departamento de Ingeniería Metalúrgica, Universidad de Concepción, Barrio Universitario, Concepción, Chile.
| |
Collapse
|
26
|
Highly Specific Sewage-Derived Bacteroides Quantitative PCR Assays Target Sewage-Polluted Waters. Appl Environ Microbiol 2019; 85:AEM.02696-18. [PMID: 30635376 DOI: 10.1128/aem.02696-18] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2018] [Accepted: 01/02/2019] [Indexed: 12/17/2022] Open
Abstract
The identification of sewage contamination in water has primarily relied on the detection of human-associated Bacteroides using markers within the V2 region of the 16S rRNA gene. Despite the establishment of multiple assays that target the HF183 cluster (i.e., Bacteroides dorei) and other Bacteroides organisms (e.g., Bacteroides thetaiota omicron), the potential for more human-associated markers in this genus has not been explored in depth. We examined the Bacteroides population structure in sewage and animal hosts across the V4V5 and V6 hypervariable regions. Using near-full-length cloned sequences, we identified the sequences in the V4V5 and V6 hypervariable regions that are linked to the HF183 marker in the V2 region and found these sequences were present in multiple animals. In addition, the V4V5 and V6 regions contained human fecal marker sequences for organisms that were independent of the HF183 cluster. The most abundant Bacteroides in untreated sewage was not human associated but pipe derived. Two TaqMan quantitative PCR (qPCR) assays targeting the V4V5 and V6 regions of this organism were developed. Validation studies using fecal samples from seven animal hosts (n = 76) and uncontaminated water samples (n = 30) demonstrated the high specificity of the assays for sewage. Freshwater Bacteroides were also identified in uncontaminated water samples, demonstrating that measures of total Bacteroides do not reflect fecal pollution. A comparison of two previously described human Bacteroides assays (HB and HF183/BacR287) in municipal wastewater influent and sewage-contaminated urban water samples revealed identical results, illustrating the assays target the same organism. The detection of sewage-derived Bacteroides provided an independent measure of sewage-impacted waters.IMPORTANCE Bacteroides are major members of the gut microbiota, and host-specific organisms within this genus have been used extensively to gain information on pollution sources. This study provides a broad view of the population structure of Bacteroides within sewage to contextualize the well-studied HF183 marker for a human-associated Bacteroides The study also delineates host-specific sequence patterns across multiple hypervariable regions of the 16S rRNA gene to improve our ability to use sequence data to assess water quality. Here, we demonstrate that regions downstream of the HF183 marker are nonspecific but other potential human-associated markers are present. Furthermore, we show the most abundant Bacteroides in sewage is free living, rather than host associated, and specifically found in sewage. Quantitative PCR assays that target organisms specific to sewer pipes offer measures that are independent of the human microbiome for identifying sewage pollution in water.
Collapse
|
27
|
Lazuka A, Auer L, O’Donohue M, Hernandez-Raquet G. Anaerobic lignocellulolytic microbial consortium derived from termite gut: enrichment, lignocellulose degradation and community dynamics. BIOTECHNOLOGY FOR BIOFUELS 2018; 11:284. [PMID: 30356893 PMCID: PMC6191919 DOI: 10.1186/s13068-018-1282-x] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/12/2018] [Accepted: 10/06/2018] [Indexed: 05/25/2023]
Abstract
BACKGROUND Lignocellulose is the most abundant renewable carbon resource that can be used for biofuels and commodity chemicals production. The ability of complex microbial communities present in natural environments that are specialized in biomass deconstruction can be exploited to develop lignocellulose bioconversion processes. Termites are among the most abundant insects on earth and play an important role in lignocellulose decomposition. Although their digestive microbiome is recognized as a potential reservoir of microorganisms producing lignocellulolytic enzymes, the potential to enrich and maintain the lignocellulolytic activity of microbial consortia derived from termite gut useful for lignocellulose biorefinery has not been assessed. Here, we assessed the possibility of enriching a microbial consortium from termite gut and maintaining its lignocellulose degradation ability in controlled anaerobic bioreactors. RESULTS We enriched a termite gut-derived consortium able to transform lignocellulose into carboxylates under anaerobic conditions. To assess the impact of substrate natural microbiome on the enrichment and the maintenance of termite gut microbiome, the enrichment process was performed using both sterilized and non-sterilized straw. The enrichment process was carried out in bioreactors operating under industrially relevant aseptic conditions. Two termite gut-derived microbial consortia were obtained from Nasutitermes ephratae by sequential batch culture on raw wheat straw as the sole carbon source. Analysis of substrate loss, carboxylate production and microbial diversity showed that regardless of the substrate sterility, the diversity of communities selected by the enrichment process strongly changed compared to that observed in the termite gut. Nevertheless, the community obtained on sterile straw displayed higher lignocellulose degradation capacity; it showed a high xylanase activity and an initial preference for hemicellulose. CONCLUSIONS This study demonstrates that it is possible to enrich and maintain a microbial consortium derived from termite gut microbiome in controlled anaerobic bioreactors, producing useful carboxylates from raw biomass. Our results suggest that the microbial community is shaped both by the substrate and the conditions that prevail during enrichment. However, when aseptic conditions are applied, it is also affected by the biotic pressure exerted by microorganisms naturally present in the substrate and in the surrounding environment. Besides the efficient lignocellulolytic consortium enriched in this study, our results revealed high levels of xylanase activity that can now be further explored for enzyme identification and overexpression for biorefinery purposes.
Collapse
Affiliation(s)
- Adèle Lazuka
- Laboratoire d’Ingénierie des Systèmes Biologiques et des Procédés - LISBP, UMR5504, UMR792, CNRS, INRA, INSA, Université de Toulouse, 135 Avenue de Rangueil, 31077 Toulouse Cedex 04, France
| | - Lucas Auer
- Laboratoire d’Ingénierie des Systèmes Biologiques et des Procédés - LISBP, UMR5504, UMR792, CNRS, INRA, INSA, Université de Toulouse, 135 Avenue de Rangueil, 31077 Toulouse Cedex 04, France
| | - Michael O’Donohue
- Laboratoire d’Ingénierie des Systèmes Biologiques et des Procédés - LISBP, UMR5504, UMR792, CNRS, INRA, INSA, Université de Toulouse, 135 Avenue de Rangueil, 31077 Toulouse Cedex 04, France
| | - Guillermina Hernandez-Raquet
- Laboratoire d’Ingénierie des Systèmes Biologiques et des Procédés - LISBP, UMR5504, UMR792, CNRS, INRA, INSA, Université de Toulouse, 135 Avenue de Rangueil, 31077 Toulouse Cedex 04, France
| |
Collapse
|
28
|
Andrieu C, Mailhe M, Ricaboni D, Fonkou MDM, Bilen M, Cadoret F, Tomei E, Armstrong N, Vitton V, Benezech A, Davoust B, Levasseur A, Lagier JC, Fournier PE, Raoult D. Noncontiguous finished genome sequences and description of Bacteroides mediterraneensis sp. nov., Bacteroides ihuae sp. nov., Bacteroides togonis sp. nov., Bacteroides ndongoniae sp. nov., Bacteroides ilei sp. nov. and Bacteroides congonensis sp. nov. identified by culturomics. New Microbes New Infect 2018; 26:73-88. [PMID: 30258636 PMCID: PMC6154776 DOI: 10.1016/j.nmni.2018.06.006] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2018] [Revised: 06/08/2018] [Accepted: 06/13/2018] [Indexed: 12/22/2022] Open
Abstract
Culturomics is a concept developing different culture conditions in order to enlarge our knowledge of the human microbiota through the discovery of previously uncultured bacteria. This enabled us to isolate six new species of the Bacteroides genus: Bacteroides mediterraneensis strain Marseille-P2644, Bacteroides ihuae strain Marseille-P2824, Bacteroides togonis strain Marseille-P3166, Bacteroides ndongoniae strain Marseille-P3108, Bacteroides ilei strain Marseille-P3208 and Bacteroides congonensis strain Marseille-P3132. Those bacteria are Gram-negative anaerobic bacilli. We describe here their phenotypic features, together with phylogenetic analysis, matrix-assisted laser desorption/ionization time-of-flight mass spectrometry spectrum, fatty acid composition, and genome sequencing and annotation.
Collapse
Affiliation(s)
- C Andrieu
- Aix-Marseille Université, IRD, APHM, MEPHI, IHU-Méditerranée Infection, Marseille, France
| | - M Mailhe
- Aix-Marseille Université, IRD, APHM, MEPHI, IHU-Méditerranée Infection, Marseille, France
| | - D Ricaboni
- Aix-Marseille Université, IRD, APHM, MEPHI, IHU-Méditerranée Infection, Marseille, France.,Département des Sciences Cliniques et Biomédicales, Luigi Sacco, Division des Maladies Infectieuses III, Université de Milan, Milan, Italy
| | - M D M Fonkou
- Aix-Marseille Université, IRD, APHM, MEPHI, IHU-Méditerranée Infection, Marseille, France
| | - M Bilen
- Aix-Marseille Université, IRD, APHM, MEPHI, IHU-Méditerranée Infection, Marseille, France
| | - F Cadoret
- Aix-Marseille Université, IRD, APHM, MEPHI, IHU-Méditerranée Infection, Marseille, France
| | - E Tomei
- Aix-Marseille Université, IRD, AP-HM, SSA, VITROME, IHU-Méditerranée Infection, Marseille, France
| | - N Armstrong
- Aix-Marseille Université, IRD, APHM, MEPHI, IHU-Méditerranée Infection, Marseille, France
| | - V Vitton
- Service de Gastroentérologie, Hopital Nord, Assistance Publique-Hopitaux de Marseille, Marseille, France
| | - A Benezech
- Service de Gastroentérologie, Hopital Nord, Assistance Publique-Hopitaux de Marseille, Marseille, France
| | - B Davoust
- Aix-Marseille Université, IRD, APHM, MEPHI, IHU-Méditerranée Infection, Marseille, France
| | - A Levasseur
- Aix-Marseille Université, IRD, APHM, MEPHI, IHU-Méditerranée Infection, Marseille, France
| | - J-C Lagier
- Aix-Marseille Université, IRD, APHM, MEPHI, IHU-Méditerranée Infection, Marseille, France
| | - P-E Fournier
- Aix-Marseille Université, IRD, AP-HM, SSA, VITROME, IHU-Méditerranée Infection, Marseille, France
| | - D Raoult
- Aix-Marseille Université, IRD, APHM, MEPHI, IHU-Méditerranée Infection, Marseille, France.,Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia
| |
Collapse
|
29
|
Ismaeil M, Yoshida N, Katayama A. Bacteroides sedimenti sp. nov., isolated from a chloroethenes-dechlorinating consortium enriched from river sediment. J Microbiol 2018; 56:619-627. [DOI: 10.1007/s12275-018-8187-z] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2018] [Revised: 06/11/2018] [Accepted: 06/21/2018] [Indexed: 11/30/2022]
|
30
|
Ueki A, Kaku N, Ueki K. Role of anaerobic bacteria in biological soil disinfestation for elimination of soil-borne plant pathogens in agriculture. Appl Microbiol Biotechnol 2018; 102:6309-6318. [DOI: 10.1007/s00253-018-9119-x] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2018] [Revised: 05/20/2018] [Accepted: 05/21/2018] [Indexed: 01/15/2023]
|
31
|
Kokabian B, Smith R, Brooks JP, Gude VG. Bioelectricity production in photosynthetic microbial desalination cells under different flow configurations. J IND ENG CHEM 2018. [DOI: 10.1016/j.jiec.2017.09.017] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
|
32
|
Auer L, Lazuka A, Sillam-Dussès D, Miambi E, O'Donohue M, Hernandez-Raquet G. Uncovering the Potential of Termite Gut Microbiome for Lignocellulose Bioconversion in Anaerobic Batch Bioreactors. Front Microbiol 2017; 8:2623. [PMID: 29312279 PMCID: PMC5744482 DOI: 10.3389/fmicb.2017.02623] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2017] [Accepted: 12/15/2017] [Indexed: 11/16/2022] Open
Abstract
Termites are xylophages, being able to digest a wide variety of lignocellulosic biomass including wood with high lignin content. This ability to feed on recalcitrant plant material is the result of complex symbiotic relationships, which involve termite-specific gut microbiomes. Therefore, these represent a potential source of microorganisms for the bioconversion of lignocellulose in bioprocesses targeting the production of carboxylates. In this study, gut microbiomes of four termite species were studied for their capacity to degrade wheat straw and produce carboxylates in controlled bioreactors. All of the gut microbiomes successfully degraded lignocellulose and up to 45% w/w of wheat straw degradation was observed, with the Nasutitermes ephratae gut-microbiome displaying the highest levels of wheat straw degradation, carboxylate production and enzymatic activity. Comparing the 16S rRNA gene diversity of the initial gut inocula to the bacterial communities in lignocellulose degradation bioreactors revealed important changes in community diversity. In particular, taxa such as Spirochaetes and Fibrobacteres that were highly abundant in the initial gut inocula were replaced by Firmicutes and Proteobacteria at the end of incubation in wheat straw bioreactors. Overall, this study demonstrates that termite-gut microbiomes constitute a reservoir of lignocellulose-degrading bacteria that can be harnessed in artificial conditions for biomass conversion processes that lead to the production of useful molecules.
Collapse
Affiliation(s)
- Lucas Auer
- Laboratoire d'Ingénierie des Systèmes Biologiques et des Procédés, Université de Toulouse, Centre National de la Recherche Scientifique, Institut National de la Recherche Agronomique, INSA, Toulouse, France
| | - Adèle Lazuka
- Laboratoire d'Ingénierie des Systèmes Biologiques et des Procédés, Université de Toulouse, Centre National de la Recherche Scientifique, Institut National de la Recherche Agronomique, INSA, Toulouse, France
| | - David Sillam-Dussès
- Laboratoire d'Éthologie Expérimentale et Comparée, Université Paris 13 - Sorbonne Paris Cité, Villetaneuse, France
- Institut d'Ecologie et des Sciences de l'Environnement de Paris, Institut de Recherche Pour le Développement – Sorbonne Universités, Bondy, France
| | - Edouard Miambi
- Institut d'Ecologie et des Sciences de l'Environnement de Paris, Université Paris-Est Créteil, Créteil, France
| | - Michael O'Donohue
- Laboratoire d'Ingénierie des Systèmes Biologiques et des Procédés, Université de Toulouse, Centre National de la Recherche Scientifique, Institut National de la Recherche Agronomique, INSA, Toulouse, France
| | - Guillermina Hernandez-Raquet
- Laboratoire d'Ingénierie des Systèmes Biologiques et des Procédés, Université de Toulouse, Centre National de la Recherche Scientifique, Institut National de la Recherche Agronomique, INSA, Toulouse, France
| |
Collapse
|
33
|
Dai YM, Zhang LL, Li Y, Li YQ, Deng XH, Wang TT, Yang F, Tian YQ, Li N, Zhou XM, Liu XF, Li WJ. Characterization of Trichococcus paludicola sp. nov. and Trichococcus alkaliphilus sp. nov., isolated from a high-elevation wetland, by phenotypic and genomic analyses. Int J Syst Evol Microbiol 2017; 68:99-105. [PMID: 29116035 DOI: 10.1099/ijsem.0.002464] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Two psychrotolerant facultative anaerobes, strains B7-2T and B5T, were isolated from the Zoige Wetland on the Qinghai-Tibetan Plateau. The 16S rRNA gene sequences of strains B7-2T and B5T shared high similarity (>99 %) with those of the type strains of the genus Trichococcus, while their digital DNA-DNA hybridization values with each other (49 %) and with the reference type strains (48-23 %) were lower than 70 %, which suggest that they represent two novel species of the genus Trichococcus. Cells of strains B7-2T and B5T were immotile cocci, grew in the temperature range of 4-37 °C (optimum 25 °C) and were alkaliphilic with optimum growth at pH 9.0. The major components of the cellular fatty acids were C16 : 0, anteiso-C17 : 0 and C18 : 0 for strain B7-2T, and C16 : 0, anteiso-C17 : 0, C18 : 1ω9c and C18 : 0 for strain B5T. The genomic DNA G+C contents were 46.0 and 46.7 mol% for strains B7-2T and B5T, respectively. Based on physiological and genomic characteristics, it is suggested that strains B7-2T and B5T represent two novel species within the genus Trichococcus, for which the names Trichococcus paludicola sp. nov. and Trichococcus alkaliphilus sp. nov. are proposed. The type strains are B7-2T (=DSM 104691T=KCTC 33886T) and B5T (=DSM 104692T=KCTC 33885T), respectively.
Collapse
Affiliation(s)
- Yu-Mei Dai
- Key Laboratory of Environmental and Applied Microbiology, Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Sichuan 610041, PR China
| | - Ling-Li Zhang
- Key Laboratory of Environmental and Applied Microbiology, Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Sichuan 610041, PR China.,University of Chinese Academy of Sciences, Beijing 100049, PR China
| | - Yan Li
- Key Laboratory of Environmental and Applied Microbiology, Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Sichuan 610041, PR China.,University of Chinese Academy of Sciences, Beijing 100049, PR China
| | - Yu-Qian Li
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, College of Ecology and Evolution, Sun Yat-Sen University, Guangzhou 510275, PR China.,Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, School of Life Sciences, Xiamen University, Xiamen 361005, PR China
| | - Xiao-Hui Deng
- Key Laboratory of Environmental and Applied Microbiology, Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Sichuan 610041, PR China
| | - Ting-Ting Wang
- Key Laboratory of Environmental and Applied Microbiology, Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Sichuan 610041, PR China
| | - Feng Yang
- Key Laboratory of Environmental and Applied Microbiology, Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Sichuan 610041, PR China.,University of Chinese Academy of Sciences, Beijing 100049, PR China
| | - Yong-Qiang Tian
- Key laboratory of Leather Chemistry and Engineering, College of Light Industry, Textile and Food Engineering, Sichuan University, Chengdu, Sichuan 610051, PR China
| | - Na Li
- Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization; Ecological Restoration, Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Sichuan 610041, PR China
| | - Xing-Mei Zhou
- Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization; Ecological Restoration, Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Sichuan 610041, PR China
| | - Xiao-Feng Liu
- Key Laboratory of Environmental and Applied Microbiology, Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Sichuan 610041, PR China
| | - Wen-Jun Li
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, College of Ecology and Evolution, Sun Yat-Sen University, Guangzhou 510275, PR China
| |
Collapse
|
34
|
Kim J, Kim H, Lee C. Ulva biomass as a co-substrate for stable anaerobic digestion of spent coffee grounds in continuous mode. BIORESOURCE TECHNOLOGY 2017; 241:1182-1190. [PMID: 28625349 DOI: 10.1016/j.biortech.2017.06.012] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/03/2017] [Revised: 05/31/2017] [Accepted: 06/03/2017] [Indexed: 05/22/2023]
Abstract
Ulva biomass was evaluated as a co-substrate for anaerobic digestion of spent coffee grounds at varying organic loads (0.7-1.6g chemical oxygen demand (COD)/Ld) and substrate compositions. Co-digestion with Ulva (25%, COD basis) proved beneficial for SCG biomethanation in both terms of process performance and stability. The beneficial effect is much more pronounced at higher organic and hydraulic loads, with the highest COD removal and methane yield being 51.8% and 0.19L/g COD fed, respectively. The reactor microbial community structure changed dynamically during the experiment, and a dominance shift from hydrogenotrophic to aceticlastic methanogens occurred with increase in organic loading rate. Network analysis provides a comprehensive view of the microbial interactions involved in the system and confirms a direct positive correlation between Ulva input and methane productivity. A group of populations, including Methanobacterium- and Methanoculleus-related methanogens, was identified as a possible indicator for monitoring the biomethanation performance.
Collapse
Affiliation(s)
- Jaai Kim
- School of Urban and Environmental Engineering, Ulsan National Institute of Science and Technology (UNIST), 50 UNIST-gil, Eonyang-eup, Ulju-gun, Ulsan 44919, Republic of Korea
| | - Hakchan Kim
- School of Urban and Environmental Engineering, Ulsan National Institute of Science and Technology (UNIST), 50 UNIST-gil, Eonyang-eup, Ulju-gun, Ulsan 44919, Republic of Korea
| | - Changsoo Lee
- School of Urban and Environmental Engineering, Ulsan National Institute of Science and Technology (UNIST), 50 UNIST-gil, Eonyang-eup, Ulju-gun, Ulsan 44919, Republic of Korea.
| |
Collapse
|
35
|
Bu F, Du S, Xie L, Cao R, Zhou Q. Swine manure treatment by anaerobic membrane bioreactor with carbon, nitrogen and phosphorus recovery. WATER SCIENCE AND TECHNOLOGY : A JOURNAL OF THE INTERNATIONAL ASSOCIATION ON WATER POLLUTION RESEARCH 2017; 76:1939-1949. [PMID: 29068326 DOI: 10.2166/wst.2017.278] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Swine manure wastewater was treated in an anaerobic membrane bioreactor (AnMBR) that combined a continuous stirred tank reactor (CSTR) and a hollow-fiber ultrafiltration membrane, and the feasibility of ammonia and phosphorus recovery in the permeate was investigated. The AnMBR system was operated steadily with a high mixed liquor suspended solids (MLSS) concentration of 32.32 ± 6.24 g/L for 120 days, achieving an average methane yield of 280 mL/gVSadded and total chemical oxygen demand removal efficiency of 96%. The methane yield of the AnMBR is 83% higher than that of the single CSTR. The membrane fouling mechanism was examined, and MLSS and the polysaccharide contents of the extracellular polymeric substances were found to be the direct causes of membrane fouling. The effects of the permeation/relaxation rate and physical, chemical cleaning on membrane fouling were assessed for membrane fouling control, and results showed that a decrease in the permeation/relaxation rate together with chemical cleaning effectively reduced membrane fouling. In addition, a crystallization process was used for ammonia and phosphorus recovery from the permeate, and pH 9 was the optimal condition for struvite formation. The study has an instructive significance to the industrial applications of AnMBRs in treating high strength wastewater with nutrient recovery.
Collapse
Affiliation(s)
- Fan Bu
- Key Laboratory of Yangtze River Water Environment, Tongji University, 1239 Siping Road, Shanghai 200092, China E-mail:
| | - Shiyun Du
- Key Laboratory of Yangtze River Water Environment, Tongji University, 1239 Siping Road, Shanghai 200092, China E-mail:
| | - Li Xie
- Key Laboratory of Yangtze River Water Environment, Tongji University, 1239 Siping Road, Shanghai 200092, China E-mail:
| | - Rong Cao
- Key Laboratory of Yangtze River Water Environment, Tongji University, 1239 Siping Road, Shanghai 200092, China E-mail:
| | - Qi Zhou
- Key Laboratory of Yangtze River Water Environment, Tongji University, 1239 Siping Road, Shanghai 200092, China E-mail:
| |
Collapse
|
36
|
Fonkou M, Morand A, Fournier PE, Raoult D, Dubourg G. 'Bacteroides ihuae' sp. nov., a new bacterial species isolated from the human respiratory microbiome. New Microbes New Infect 2017; 17:52-53. [PMID: 28289545 PMCID: PMC5338718 DOI: 10.1016/j.nmni.2017.01.011] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2016] [Revised: 01/19/2017] [Accepted: 01/25/2017] [Indexed: 11/26/2022] Open
Abstract
We present the main features of 'Bacteroides ihuae' sp. nov., strain Marseille-P2824T (CSUR P2824), isolated from the sputum of healthy Frenchwoman living in Marseille.
Collapse
Affiliation(s)
- M.D.M. Fonkou
- Aix-Marseille Université, URMITE, UM 63, CNRS 7278, IRD 198, INSERM U1095, Faculté de Médecine, Marseille, France
| | - A. Morand
- Aix-Marseille Université, URMITE, UM 63, CNRS 7278, IRD 198, INSERM U1095, Faculté de Médecine, Marseille, France
| | - P.-E. Fournier
- Aix-Marseille Université, URMITE, UM 63, CNRS 7278, IRD 198, INSERM U1095, Faculté de Médecine, Marseille, France
| | - D. Raoult
- Aix-Marseille Université, URMITE, UM 63, CNRS 7278, IRD 198, INSERM U1095, Faculté de Médecine, Marseille, France
- Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia
| | - G. Dubourg
- Aix-Marseille Université, URMITE, UM 63, CNRS 7278, IRD 198, INSERM U1095, Faculté de Médecine, Marseille, France
| |
Collapse
|
37
|
Baba Y, Matsuki Y, Mori Y, Suyama Y, Tada C, Fukuda Y, Saito M, Nakai Y. Pretreatment of lignocellulosic biomass by cattle rumen fluid for methane production: Bacterial flora and enzyme activity analysis. J Biosci Bioeng 2017; 123:489-496. [DOI: 10.1016/j.jbiosc.2016.11.008] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2016] [Revised: 10/18/2016] [Accepted: 11/19/2016] [Indexed: 01/19/2023]
|
38
|
Hahnke RL, Meier-Kolthoff JP, García-López M, Mukherjee S, Huntemann M, Ivanova NN, Woyke T, Kyrpides NC, Klenk HP, Göker M. Genome-Based Taxonomic Classification of Bacteroidetes. Front Microbiol 2016; 7:2003. [PMID: 28066339 PMCID: PMC5167729 DOI: 10.3389/fmicb.2016.02003] [Citation(s) in RCA: 145] [Impact Index Per Article: 18.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2016] [Accepted: 11/30/2016] [Indexed: 01/15/2023] Open
Abstract
The bacterial phylum Bacteroidetes, characterized by a distinct gliding motility, occurs in a broad variety of ecosystems, habitats, life styles, and physiologies. Accordingly, taxonomic classification of the phylum, based on a limited number of features, proved difficult and controversial in the past, for example, when decisions were based on unresolved phylogenetic trees of the 16S rRNA gene sequence. Here we use a large collection of type-strain genomes from Bacteroidetes and closely related phyla for assessing their taxonomy based on the principles of phylogenetic classification and trees inferred from genome-scale data. No significant conflict between 16S rRNA gene and whole-genome phylogenetic analysis is found, whereas many but not all of the involved taxa are supported as monophyletic groups, particularly in the genome-scale trees. Phenotypic and phylogenomic features support the separation of Balneolaceae as new phylum Balneolaeota from Rhodothermaeota and of Saprospiraceae as new class Saprospiria from Chitinophagia. Epilithonimonas is nested within the older genus Chryseobacterium and without significant phenotypic differences; thus merging the two genera is proposed. Similarly, Vitellibacter is proposed to be included in Aequorivita. Flexibacter is confirmed as being heterogeneous and dissected, yielding six distinct genera. Hallella seregens is a later heterotypic synonym of Prevotella dentalis. Compared to values directly calculated from genome sequences, the G+C content mentioned in many species descriptions is too imprecise; moreover, corrected G+C content values have a significantly better fit to the phylogeny. Corresponding emendations of species descriptions are provided where necessary. Whereas most observed conflict with the current classification of Bacteroidetes is already visible in 16S rRNA gene trees, as expected whole-genome phylogenies are much better resolved.
Collapse
Affiliation(s)
- Richard L. Hahnke
- Department of Microorganisms, Leibniz Institute DSMZ–German Collection of Microorganisms and Cell CulturesBraunschweig, Germany
| | - Jan P. Meier-Kolthoff
- Department of Microorganisms, Leibniz Institute DSMZ–German Collection of Microorganisms and Cell CulturesBraunschweig, Germany
| | - Marina García-López
- Department of Microorganisms, Leibniz Institute DSMZ–German Collection of Microorganisms and Cell CulturesBraunschweig, Germany
| | - Supratim Mukherjee
- Department of Energy Joint Genome Institute (DOE JGI)Walnut Creek, CA, USA
| | - Marcel Huntemann
- Department of Energy Joint Genome Institute (DOE JGI)Walnut Creek, CA, USA
| | - Natalia N. Ivanova
- Department of Energy Joint Genome Institute (DOE JGI)Walnut Creek, CA, USA
| | - Tanja Woyke
- Department of Energy Joint Genome Institute (DOE JGI)Walnut Creek, CA, USA
| | - Nikos C. Kyrpides
- Department of Energy Joint Genome Institute (DOE JGI)Walnut Creek, CA, USA
- Department of Biological Sciences, Faculty of Science, King Abdulaziz UniversityJeddah, Saudi Arabia
| | | | - Markus Göker
- Department of Microorganisms, Leibniz Institute DSMZ–German Collection of Microorganisms and Cell CulturesBraunschweig, Germany
| |
Collapse
|
39
|
Zhang D, Wang Y, Zheng D, Guo P, Cheng W, Cui Z. New combination of xylanolytic bacteria isolated from the lignocellulose degradation microbial consortium XDC-2 with enhanced xylanase activity. BIORESOURCE TECHNOLOGY 2016; 221:686-690. [PMID: 27671341 DOI: 10.1016/j.biortech.2016.09.087] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/12/2016] [Revised: 09/18/2016] [Accepted: 09/19/2016] [Indexed: 06/06/2023]
Abstract
Three bacterial strains with extracellular xylanase activity were isolated from the microbial consortium XDC-2. The aerobic strain A7, belonging to Bacillus sp., was combined with the anaerobe Clostridium sp. strain AA3 and/or Bacteroides sp. strain AA4 to obtain an efficient natural xylanolytic complex enzyme. The synthetic microbial community M1 consisting of strains Bacillus and Clostridium showed enhanced extracellular xylanase activity and production, and higher lignocelluloses degradation capability than any of the pure cultures and other synthetic microbial communities. Neither corn straw degradation nor extracellular xylanase activity was enhanced in the other synthetic microbial communities, Bacillus, Bacteroides with or without Clostridium. Quantitative polymerase chain reaction showed that the aerobic strain Bacillus enabled the growth of the anaerobic strain Clostridium, but not that of the anaerobic strain Bacteroides. These findings suggest that strains Bacillus and Clostridium can coexist well and have a positive synergistic interaction for extracellular xylanase secretion and lignocellulose degradation.
Collapse
Affiliation(s)
- Dongdong Zhang
- Institute of Marine Biology, Ocean College, Zhejiang University, Zhoushan 316021, China
| | - Yi Wang
- Institute of Agricultural Products Processing and Nuclear Agriculture Technology Research, Hubei Academy of Agricultural Sciences, Wuhan 430064, China
| | - Dan Zheng
- Institute of Agricultural Products Processing and Nuclear Agriculture Technology Research, Hubei Academy of Agricultural Sciences, Wuhan 430064, China
| | - Peng Guo
- Institute of Agricultural Products Processing and Nuclear Agriculture Technology Research, Hubei Academy of Agricultural Sciences, Wuhan 430064, China.
| | - Wei Cheng
- Institute of Agricultural Products Processing and Nuclear Agriculture Technology Research, Hubei Academy of Agricultural Sciences, Wuhan 430064, China
| | - Zongjun Cui
- College of Agronomy and Biotechnology, China Agricultural University, Beijing 100193, China
| |
Collapse
|
40
|
Hodgson DM, Smith A, Dahale S, Stratford JP, Li JV, Grüning A, Bushell ME, Marchesi JR, Avignone Rossa C. Segregation of the Anodic Microbial Communities in a Microbial Fuel Cell Cascade. Front Microbiol 2016; 7:699. [PMID: 27242723 PMCID: PMC4863660 DOI: 10.3389/fmicb.2016.00699] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2016] [Accepted: 04/26/2016] [Indexed: 11/13/2022] Open
Abstract
Metabolic interactions within microbial communities are essential for the efficient degradation of complex organic compounds, and underpin natural phenomena driven by microorganisms, such as the recycling of carbon-, nitrogen-, and sulfur-containing molecules. These metabolic interactions ultimately determine the function, activity and stability of the community, and therefore their understanding would be essential to steer processes where microbial communities are involved. This is exploited in the design of microbial fuel cells (MFCs), bioelectrochemical devices that convert the chemical energy present in substrates into electrical energy through the metabolic activity of microorganisms, either single species or communities. In this work, we analyzed the evolution of the microbial community structure in a cascade of MFCs inoculated with an anaerobic microbial community and continuously fed with a complex medium. The analysis of the composition of the anodic communities revealed the establishment of different communities in the anodes of the hydraulically connected MFCs, with a decrease in the abundance of fermentative taxa and a concurrent increase in respiratory taxa along the cascade. The analysis of the metabolites in the anodic suspension showed a metabolic shift between the first and last MFC, confirming the segregation of the anodic communities. Those results suggest a metabolic interaction mechanism between the predominant fermentative bacteria at the first stages of the cascade and the anaerobic respiratory electrogenic population in the latter stages, which is reflected in the observed increase in power output. We show that our experimental system represents an ideal platform for optimization of processes where the degradation of complex substrates is involved, as well as a potential tool for the study of metabolic interactions in complex microbial communities.
Collapse
Affiliation(s)
- Douglas M Hodgson
- Department of Microbial and Cellular Sciences, University of Surrey Guildford, UK
| | - Ann Smith
- Cardiff School of Biosciences, Cardiff University Cardiff, UK
| | - Sonal Dahale
- Department of Microbial and Cellular Sciences, University of Surrey Guildford, UK
| | - James P Stratford
- Warwick Integrative Synthetic Biology Centre, University of Warwick Coventry, UK
| | - Jia V Li
- Centre for Digestive and Gut Health, Department of Surgery and Cancer, Imperial College LondonLondon, UK; Division of Computational and Systems Medicine, Department of Surgery and Cancer, Imperial College LondonLondon, UK
| | - André Grüning
- Department of Computer Science, University of Surrey Guildford, UK
| | - Michael E Bushell
- Department of Microbial and Cellular Sciences, University of Surrey Guildford, UK
| | - Julian R Marchesi
- Cardiff School of Biosciences, Cardiff UniversityCardiff, UK; Centre for Digestive and Gut Health, Department of Surgery and Cancer, Imperial College LondonLondon, UK
| | - C Avignone Rossa
- Department of Microbial and Cellular Sciences, University of Surrey Guildford, UK
| |
Collapse
|
41
|
Sun G, Rodrigues DDS, Thygesen A, Daniel G, Fernando D, Meyer AS. Inocula selection in microbial fuel cells based on anodic biofilm abundance of Geobacter sulfurreducens. Chin J Chem Eng 2016. [DOI: 10.1016/j.cjche.2015.11.002] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
|
42
|
Microwave and ultrasound pre-treatments influence microbial community structure and digester performance in anaerobic digestion of waste activated sludge. Appl Microbiol Biotechnol 2016; 100:5339-52. [DOI: 10.1007/s00253-016-7321-2] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2015] [Revised: 01/10/2016] [Accepted: 01/12/2016] [Indexed: 01/29/2023]
|
43
|
Lazuka A, Auer L, Bozonnet S, Morgavi DP, O'Donohue M, Hernandez-Raquet G. Efficient anaerobic transformation of raw wheat straw by a robust cow rumen-derived microbial consortium. BIORESOURCE TECHNOLOGY 2015; 196:241-9. [PMID: 26247975 DOI: 10.1016/j.biortech.2015.07.084] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/26/2015] [Revised: 07/23/2015] [Accepted: 07/24/2015] [Indexed: 05/15/2023]
Abstract
A rumen-derived microbial consortium was enriched on raw wheat straw as sole carbon source in a sequential batch-reactor (SBR) process under strict mesophilic anaerobic conditions. After five cycles of enrichment the procedure enabled to select a stable and efficient lignocellulolytic microbial consortium, mainly constituted by members of Firmicutes and Bacteroidetes phyla. The enriched community, designed rumen-wheat straw-derived consortium (RWS) efficiently hydrolyzed lignocellulosic biomass, degrading 55.5% w/w of raw wheat straw over 15days at 35°C and accumulating carboxylates as main products. Cellulolytic and hemicellulolytic activities, mainly detected on the cell bound fraction, were produced in the earlier steps of degradation, their production being correlated with the maximal lignocellulose degradation rates. Overall, these results demonstrate the potential of RWS to convert unpretreated lignocellulosic substrates into useful chemicals.
Collapse
Affiliation(s)
- Adèle Lazuka
- Université de Toulouse, INSA, UPS, LISBP, 135 Avenue de Rangueil, F-31077 Toulouse Cedex 4, France; INRA, UMR792, Ingénierie des Systèmes Biologiques et des Procédés, F-31400 Toulouse, France; CNRS, UMR5504, F-31400 Toulouse, France
| | - Lucas Auer
- Université de Toulouse, INSA, UPS, LISBP, 135 Avenue de Rangueil, F-31077 Toulouse Cedex 4, France; INRA, UMR792, Ingénierie des Systèmes Biologiques et des Procédés, F-31400 Toulouse, France; CNRS, UMR5504, F-31400 Toulouse, France
| | - Sophie Bozonnet
- Université de Toulouse, INSA, UPS, LISBP, 135 Avenue de Rangueil, F-31077 Toulouse Cedex 4, France; INRA, UMR792, Ingénierie des Systèmes Biologiques et des Procédés, F-31400 Toulouse, France; CNRS, UMR5504, F-31400 Toulouse, France
| | - Diego P Morgavi
- INRA, UR1213 Herbivores, Centre de Theix, F-63122 St-Genès-Champanelle, France
| | - Michael O'Donohue
- Université de Toulouse, INSA, UPS, LISBP, 135 Avenue de Rangueil, F-31077 Toulouse Cedex 4, France; INRA, UMR792, Ingénierie des Systèmes Biologiques et des Procédés, F-31400 Toulouse, France; CNRS, UMR5504, F-31400 Toulouse, France
| | - Guillermina Hernandez-Raquet
- Université de Toulouse, INSA, UPS, LISBP, 135 Avenue de Rangueil, F-31077 Toulouse Cedex 4, France; INRA, UMR792, Ingénierie des Systèmes Biologiques et des Procédés, F-31400 Toulouse, France; CNRS, UMR5504, F-31400 Toulouse, France.
| |
Collapse
|
44
|
Wang H, Tao Y, Temudo M, Bijl H, Kloek J, Ren N, van Lier JB, de Kreuk M. Biomethanation from enzymatically hydrolyzed brewer's spent grain: Impact of rapid increase in loadings. BIORESOURCE TECHNOLOGY 2015; 190:167-74. [PMID: 25941758 DOI: 10.1016/j.biortech.2015.04.073] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/04/2015] [Revised: 04/17/2015] [Accepted: 04/21/2015] [Indexed: 05/28/2023]
Abstract
Enzymatically hydrolyzed brewer's spent grain (BSG) was digested in two expanded granular sludge beds (EGSBs, named BSG1 and BSG2, respectively). Both reactors were operated with the same organic loading rate (OLR) from 1 to 10kgCODm(-3)d(-1) during the first 45days. Hereafter a rapid OLR increase was applied to BSG2 from 10 to 16kgCODm(-3)d(-1) within three weeks, while the OLR of BSG1 was increased by less than 2kgCODm(-3)d(-1) in the same period. Results showed that a 30% decrease in COD removal and 70% decrease in methane yield appeared in BSG2 after the rapid OLR increase, and volatile fatty acid (VFA) accumulated more than thirty times compared to BSG1. The biomass structure deteriorated and 15% of the biomass was lost from the BSG2 reactor. 454-PyroTag and qPCR analysis revealed a rapid growth of acidifiers (i.e., Bacteroides) and a unique microbial community in BSG2 following the rapid increase in OLR.
Collapse
Affiliation(s)
- Haoyu Wang
- State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, 150090 Harbin, China; Section of Sanitary Engineering, Department of Water Management, Delft University of Technology, No. 1 Stevinweg, 2600 CD Delft, The Netherlands
| | - Yu Tao
- State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, 150090 Harbin, China; Section of Sanitary Engineering, Department of Water Management, Delft University of Technology, No. 1 Stevinweg, 2600 CD Delft, The Netherlands
| | - Margarida Temudo
- DSM Biotechnology Center, P.O. Box 1, 2600 MA Delft, The Netherlands
| | - Henk Bijl
- DSM Biotechnology Center, P.O. Box 1, 2600 MA Delft, The Netherlands
| | - Joris Kloek
- DSM Biotechnology Center, P.O. Box 1, 2600 MA Delft, The Netherlands
| | - Nanqi Ren
- State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, 150090 Harbin, China.
| | - Jules B van Lier
- Section of Sanitary Engineering, Department of Water Management, Delft University of Technology, No. 1 Stevinweg, 2600 CD Delft, The Netherlands
| | - Merle de Kreuk
- Section of Sanitary Engineering, Department of Water Management, Delft University of Technology, No. 1 Stevinweg, 2600 CD Delft, The Netherlands
| |
Collapse
|
45
|
Grüning A, Beecroft NJ, Avignone-Rossa C. Low-potential respirators support electricity production in microbial fuel cells. MICROBIAL ECOLOGY 2015; 70:266-273. [PMID: 25388758 DOI: 10.1007/s00248-014-0518-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/16/2014] [Accepted: 10/09/2014] [Indexed: 06/04/2023]
Abstract
In this paper, we analyse how electric power production in microbial fuel cells (MFCs) depends on the composition of the anodic biofilm in terms of metabolic capabilities of identified sets of species. MFCs are a promising technology for organic waste treatment and sustainable bioelectricity production. Inoculated with natural communities, they present a complex microbial ecosystem with syntrophic interactions between microbes with different metabolic capabilities. Our results demonstrate that low-potential anaerobic respirators--that is those that are able to use terminal electron acceptors with a low redox potential--are important for good power production. Our results also confirm that community metabolism in MFCs with natural inoculum and fermentable feedstock is a two-stage system with fermentation followed by anode respiration.
Collapse
Affiliation(s)
- André Grüning
- Faculty of Engineering and Physical Sciences, Department of Computing Science, University of Surrey, Guildford, GU72XH, UK,
| | | | | |
Collapse
|
46
|
Yu L, Yu Y, Jiang W, Wei H, Sun C. Integrated treatment of municipal sewage sludge by deep dewatering and anaerobic fermentation for biohydrogen production. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2015; 22:2599-2609. [PMID: 25192669 DOI: 10.1007/s11356-014-3514-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/07/2014] [Accepted: 08/24/2014] [Indexed: 06/03/2023]
Abstract
The increasing sludge generated in wastewater treatment plants poses a threat to the environment. Based on the traditional processes, sludge dewatered by usual methods was further dewatered by hydraulic compression and the filtrate released was treated by anaerobic fermentation. The difficulties in sludge dewatering were associated with the existence of sludge flocs or colloidal materials. A suitable CaO dosage of 125 mg/g dry sludge (DS) could further decrease the moisture content of sludge from 82.4 to 50.9 %. The filtrate from the dewatering procedure was a potential substrate for biohydrogen production. Adding zero-valent iron (ZVI) into the anaerobic system improved the biohydrogen yield by 20 %, and the COD removal rate was lifted by 10 % as well. Meanwhile, the sludge morphology and microbial community were altered. The novel method could greatly reduce the sludge volume and successfully treated filtrate along with the conversion of organics into biohydrogen.
Collapse
Affiliation(s)
- Li Yu
- Dalian National Laboratory for Clean Energy, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, Liaoning, 116023, People's Republic of China
| | | | | | | | | |
Collapse
|
47
|
Inoue JI, Oshima K, Suda W, Sakamoto M, Iino T, Noda S, Hongoh Y, Hattori M, Ohkuma M. Distribution and evolution of nitrogen fixation genes in the phylum Bacteroidetes. Microbes Environ 2015; 30:44-50. [PMID: 25736980 PMCID: PMC4356463 DOI: 10.1264/jsme2.me14142] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Diazotrophs had not previously been identified among bacterial species in the phylum Bacteroidetes until the rapid expansion of bacterial genome sequences, which revealed the presence of nitrogen fixation (nif) genes in this phylum. We herein determined the draft genome sequences of Bacteroides graminisolvens JCM 15093(T) and Geofilum rubicundum JCM 15548(T). In addition to these and previously reported 'Candidatus Azobacteroides pseudotrichonymphae' and Paludibacter propionicigenes, an extensive survey of the genome sequences of diverse Bacteroidetes members revealed the presence of a set of nif genes (nifHDKENB) in strains of Dysgonomonas gadei, Dysgonomonas capnocytophagoides, Saccharicrinis fermentans, and Alkaliflexus imshenetskii. These eight species belonged to and were distributed sporadically within the order Bacteroidales. Acetylene reduction activity was detected in the five species examined, strongly suggesting their diazotrophic nature. Phylogenetic analyses showed monophyletic clustering of the six Nif protein sequences in the eight Bacteroidales species, implying that nitrogen fixation is ancestral to Bacteroidales and has been retained in these species, but lost in many other lineages. The identification of nif genes in Bacteroidales facilitates the prediction of the organismal origins of related sequences directly obtained from various environments.
Collapse
Affiliation(s)
- Jun-ichi Inoue
- Japan Collection of Microorganisms/Microbe Division, RIKEN BioResource Center, Koyadai 3–1–1, Tsukuba, Ibaraki 305–0074, Japan; Synaptech Co. Ltd., Ohte 1–2–37–C–105, Kofu, Yamanashi 400–0015, Japan
| | | | | | | | | | | | | | | | | |
Collapse
|
48
|
Wang C, Zuo J, Chen X, Xing W, Xing L, Li P, Lu X, Li C. Microbial community structures in an integrated two-phase anaerobic bioreactor fed by fruit vegetable wastes and wheat straw. J Environ Sci (China) 2014; 26:2484-2492. [PMID: 25499496 DOI: 10.1016/j.jes.2014.06.035] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2014] [Revised: 04/06/2014] [Accepted: 06/06/2014] [Indexed: 06/04/2023]
Abstract
The microbial community structures in an integrated two-phase anaerobic reactor (ITPAR) were investigated by 16S rDNA clone library technology. The 75L reactor was designed with a 25L rotating acidogenic unit at the top and a 50L conventional upflow methanogenic unit at the bottom, with a recirculation connected to the two units. The reactor had been operated for 21 stages to co-digest fruit/vegetable wastes and wheat straw, which showed a very good biogas production and decomposition of cellulosic materials. The results showed that many kinds of cellulose and glycan decomposition bacteria related with Bacteroidales, Clostridiales and Syntrophobacterales were dominated in the reactor, with more bacteria community diversities in the acidogenic unit. The methanogens were mostly related with Methanosaeta, Methanosarcina, Methanoculleus, Methanospirillum and Methanobacterium; the predominating genus Methanosaeta, accounting for 40.5%, 54.2%, 73.6% and 78.7% in four samples from top to bottom, indicated a major methanogenesis pathway by acetoclastic methanogenesis in the methanogenic unit. The beta diversity indexes illustrated a more similar distribution of bacterial communities than that of methanogens between acidogenic unit and methanogenic unit. The differentiation of methanogenic community composition in two phases, as well as pH values and volatile fatty acid (VFA) concentrations confirmed the phase separation of the ITPAR. Overall, the results of this study demonstrated that the special designing of ITPAR maintained a sufficient number of methanogens, more diverse communities and stronger syntrophic associations among microorganisms, which made two phase anaerobic digestion of cellulosic materials more efficient.
Collapse
Affiliation(s)
- Chong Wang
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha 410128, China; State Key Joint Laboratory of Environment Simulation and Pollution Control (SKLESPC), School of Environment, Tsinghua University, Beijing 100084, China.
| | - Jiane Zuo
- State Key Joint Laboratory of Environment Simulation and Pollution Control (SKLESPC), School of Environment, Tsinghua University, Beijing 100084, China.
| | - Xiaojie Chen
- State Key Joint Laboratory of Environment Simulation and Pollution Control (SKLESPC), School of Environment, Tsinghua University, Beijing 100084, China
| | - Wei Xing
- State Key Joint Laboratory of Environment Simulation and Pollution Control (SKLESPC), School of Environment, Tsinghua University, Beijing 100084, China
| | - Linan Xing
- State Key Joint Laboratory of Environment Simulation and Pollution Control (SKLESPC), School of Environment, Tsinghua University, Beijing 100084, China
| | - Peng Li
- State Key Joint Laboratory of Environment Simulation and Pollution Control (SKLESPC), School of Environment, Tsinghua University, Beijing 100084, China
| | - Xiangyang Lu
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha 410128, China.
| | - Chao Li
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha 410128, China; Bioprocess control (Sweden) Co., Ltd., Beijing Representative Office, Beijing 100027, China
| |
Collapse
|
49
|
Kim J, Jung H, Lee C. Shifts in bacterial and archaeal community structures during the batch biomethanation of Ulva biomass under mesophilic conditions. BIORESOURCE TECHNOLOGY 2014; 169:502-509. [PMID: 25086435 DOI: 10.1016/j.biortech.2014.07.041] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/05/2014] [Revised: 07/08/2014] [Accepted: 07/09/2014] [Indexed: 06/03/2023]
Abstract
Mesophilic biomethanation of Ulva biomass was performed in a batch bioreactor, and a high organic removal of 77% was obtained on the basis of chemical oxygen demand (COD) after a month of operation. The estimated methane yield was 0.43 ± 0.02 L CH4/g COD(removed) which is close to the theoretical methane potential. Transitions of bacterial and archaeal community structures, associated with process performance data, were investigated using a combination of molecular fingerprinting and biostatistical tools. During the operation, archaeal community structure had no significant changes while bacterial community structure shifted continuously and dynamically. The reactor completely stabilized volatile fatty acids (primarily acetate and propionate) accumulated from the acidogenesis phase, with Methanosaeta- and Methanolinea-related microbes respectively being the main aceticlastic and hydrogenotrophic methanogens. Methanolinea- and Syntrophobacter-related populations were likely the key members to form a syntrophic propionate-degrading consortium. A Methanolinea-related population was likely the dominant methane producer in the experimental reactor.
Collapse
Affiliation(s)
- Jaai Kim
- School of Urban and Environmental Engineering, Ulsan National Institute of Science and Technology (UNIST), 50 UNIST-gil, Eonyang-eup, Ulju-gun, Ulsan 689-798, Republic of Korea
| | - Heejung Jung
- School of Urban and Environmental Engineering, Ulsan National Institute of Science and Technology (UNIST), 50 UNIST-gil, Eonyang-eup, Ulju-gun, Ulsan 689-798, Republic of Korea
| | - Changsoo Lee
- School of Urban and Environmental Engineering, Ulsan National Institute of Science and Technology (UNIST), 50 UNIST-gil, Eonyang-eup, Ulju-gun, Ulsan 689-798, Republic of Korea.
| |
Collapse
|
50
|
Xing W, Chen X, Zuo J, Wang C, Lin J, Wang K. A half-submerged integrated two-phase anaerobic reactor for agricultural solid waste codigestion. Biochem Eng J 2014. [DOI: 10.1016/j.bej.2014.03.016] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
|