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Qiu T, Shen L, Guo Y, Gao M, Gao H, Li Y, Zhao G, Wang X. Impact of aeration rate on the transfer range of antibiotic-resistant plasmids during manure composting. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2024; 361:124851. [PMID: 39216666 DOI: 10.1016/j.envpol.2024.124851] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2024] [Revised: 08/14/2024] [Accepted: 08/27/2024] [Indexed: 09/04/2024]
Abstract
Conjugative plasmids are important vectors of mobile antibiotic resvistance genes (ARGs), facilitating their horizontal transfer within the environment. While composting is recognized as an effective method to reduce antibiotics and ARGs in animal manure, its impact on the bacterial host communities containing antibiotic-resistant plasmids remains unclear. In this study, we investigated the permissiveness of bacterial community during composting when challenged with multidrug-resistant conjugative RP4 plasmids, employing Pseudomonas putida as the donor strain. Ultimately, this represents the first exploration of the effects of aeration rates on the range of RP4 plasmid transfer hosts. Transconjugants were analyzed through fluorescent reporter gene-based fluorescence-activated cell sorting and Illumina sequencing. Overall, aeration rates were found to influence various physicochemical parameters of compost, including temperature, pH, total organic matter, total nitrogen, and potassium. Regarding RP4 plasmid host bacteria, the dominant phylum was determined to shift from Bacteroidetes in the raw material to Proteobacteria in the compost. Notably, a moderate-intensity aeration rate (0.05 L/min/L) was found to be more effective in reducing the diversity and richness of the RP4 plasmid host bacterial community. Following composting, the total percentage of dominant transconjugant-related genera decreased by 66.15-76.62%. Ultimately, this study determined that the aeration rate negatively impacts RP4 plasmid host abundance primarily through alterations to the environmental factors during composting. In summary, these findings enhance our understanding of plasmid host bacterial communities under varying composting aeration rates and offer novel insights into preventing the dissemination of ARGs from animal manure to farmland.
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Affiliation(s)
- Tianlei Qiu
- Beijing Key Laboratory of Agricultural Genetic Resources and Biotechnology, Institute of Biotechnology, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Lei Shen
- College of Life Sciences, Langfang Normal University, Langfang, China
| | - Yajie Guo
- Beijing Key Laboratory of Agricultural Genetic Resources and Biotechnology, Institute of Biotechnology, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Min Gao
- Beijing Key Laboratory of Agricultural Genetic Resources and Biotechnology, Institute of Biotechnology, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Haoze Gao
- National Engineering Research Center of Tree Breeding and Ecological Restoration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
| | - Ying Li
- National Engineering Research Center of Tree Breeding and Ecological Restoration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
| | - Guozhu Zhao
- National Engineering Research Center of Tree Breeding and Ecological Restoration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
| | - Xuming Wang
- Beijing Key Laboratory of Agricultural Genetic Resources and Biotechnology, Institute of Biotechnology, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China.
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Chen J, Mou L, Wang L, Wu G, Dai X, Chen Q, Zhang J, Luo X, Xu F, Zhang M, Duan Y, Pang H, Wang Y, Cai Y, Tan Z. Mixed Bacillus subtilis and Lactiplantibacillus plantarum-fermented feed improves gut microbiota and immunity of Bamei piglet. Front Microbiol 2024; 15:1442373. [PMID: 39268530 PMCID: PMC11390403 DOI: 10.3389/fmicb.2024.1442373] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2024] [Accepted: 08/02/2024] [Indexed: 09/15/2024] Open
Abstract
Antibiotics are widely used in the breeding production of Bamei pigs, affecting the quality and safety of pork and causing enormous harm to human health, the environment, and public health. The use of probiotic fermented feed to replace antibiotic feed is one of the solutions, which has the potential to improve the intestinal microbiota, promote animal growth, and enhance immunity. The purpose of this study was to evaluate the effect of fermented feed with Lactiplantibacillus (L.) plantarum QP28-1a or Bacillus (B.) subtilis QB8a on feed, growth performance, gut microbiota, and immunity of weaned piglets. A total of 60 freshly weaned piglets from the Tibetan Plateau were randomly divided into five groups and fed basal feed, L. plantarum fermented feed, B. subtilis fermented feed, mixed fermented feed, and antibiotic fermented feed for 60 days, respectively. The results showed fermented feed supplemented with L. plantarum QP28-1a or B. subtilis QB8a significantly lowered the pH of the feed (P < 0.05), produced lactic acid and acetic acid, inhibited the growth of harmful bacteria in the feed, and reduced the feed conversion rate in the group fed mixed fermented feed (P < 0.05). The fermented feed increased the α-diversity and prominently altered the β-diversity of the intestinal microbiota, increasing the relative abundance of beneficial bacteria such as Lactobacillus and Turicibacter and decreasing the relative abundance of conditional pathogens such as Streptococcus and Clostridium, improving the intestinal microbiota of the Bamei piglets. Notably, the mixed fermented feed improved the immunity of Bamei piglets by modulating the production of pro-inflammatory cytokines, anti-inflammatory cytokines, and inflammatory-related signaling pathways. Spearman's correlation analysis revealed that the increased expression of immune-related cytokines may be associated with a significant enrichment of Lactobacillus, Prevotellaceae, Erysipelotrichaceae, and Ruminococcaceae in the gut. In conclusion, the probiotic fermented feed maintained an acidic environment conducive to suppressing pathogens, reduced the feed conversion ratio, optimized the intestinal microbiota, improved immunity, and alleviated intestinal inflammation that may be caused by weaning, demonstrating the excellent application prospects of L. plantarum QP28-1a and B. subtilis QB8a fermented feed in the feeding of Bamei piglets.
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Affiliation(s)
- Jun Chen
- Henan Key Laboratory of Ion-Beam Green Agriculture Bioengineering, School of Agricultural Sciences, Zhengzhou University, Zhengzhou, China
| | - Liyu Mou
- Henan Key Laboratory of Ion-Beam Green Agriculture Bioengineering, School of Agricultural Sciences, Zhengzhou University, Zhengzhou, China
| | - Lei Wang
- Plateau Livestock Genetic Resources Protection and Innovative Utilization Key Laboratory of Qinghai Province, Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Qinghai Academy of Animal Science and Veterinary Medicine, Qinghai University, Xining, China
| | - Guofang Wu
- Plateau Livestock Genetic Resources Protection and Innovative Utilization Key Laboratory of Qinghai Province, Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Qinghai Academy of Animal Science and Veterinary Medicine, Qinghai University, Xining, China
| | - Ximei Dai
- Laboratory of Zhongyuan Light, School of Physics, Zhengzhou University, Zhengzhou, China
| | - Qiufang Chen
- Laboratory of Zhongyuan Light, School of Physics, Zhengzhou University, Zhengzhou, China
| | - Jianbo Zhang
- Plateau Livestock Genetic Resources Protection and Innovative Utilization Key Laboratory of Qinghai Province, Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Qinghai Academy of Animal Science and Veterinary Medicine, Qinghai University, Xining, China
| | - Xuan Luo
- Plateau Livestock Genetic Resources Protection and Innovative Utilization Key Laboratory of Qinghai Province, Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Qinghai Academy of Animal Science and Veterinary Medicine, Qinghai University, Xining, China
| | - Fafang Xu
- Bamei Pig Original Breeding Base of Huzhu County, Huzhou, China
| | - Miao Zhang
- Henan Key Laboratory of Ion-Beam Green Agriculture Bioengineering, School of Agricultural Sciences, Zhengzhou University, Zhengzhou, China
| | - Yaoke Duan
- Henan Key Laboratory of Ion-Beam Green Agriculture Bioengineering, School of Agricultural Sciences, Zhengzhou University, Zhengzhou, China
| | - Huili Pang
- Henan Key Laboratory of Ion-Beam Green Agriculture Bioengineering, School of Agricultural Sciences, Zhengzhou University, Zhengzhou, China
| | - Yanping Wang
- Henan Key Laboratory of Ion-Beam Green Agriculture Bioengineering, School of Agricultural Sciences, Zhengzhou University, Zhengzhou, China
| | - Yimin Cai
- Henan Key Laboratory of Ion-Beam Green Agriculture Bioengineering, School of Agricultural Sciences, Zhengzhou University, Zhengzhou, China
| | - Zhongfang Tan
- Henan Key Laboratory of Ion-Beam Green Agriculture Bioengineering, School of Agricultural Sciences, Zhengzhou University, Zhengzhou, China
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Hu X, Yang Z, Zhao Y, Dong Y, Wang C, Zhang L, Yu Y, Wu K, Ren L. Medium optimization and dust suppression performance analysis of microbial-based dust suppressant compound by response surface curve method. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2024; 31:24525-24535. [PMID: 38443533 DOI: 10.1007/s11356-024-32748-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Accepted: 02/28/2024] [Indexed: 03/07/2024]
Abstract
At present, microbial dust suppressants based on microbial communities lack necessary systematic analysis of factors affecting dust suppression performance. Therefore, in this study, the response surface curve method was used to optimize the culture conditions for enrichment of urease-producing microorganisms from activated sludge. The results indicated that when urea = 9.67 g L-1, NH4Cl = 5.21 g L-1, and pH = 9.57, the maximum urease activity of urease-producing microbial community (UPMC) was 8.22 mM min-1. The UPMC under optimized culture conditions reached a mineralization rate of 98.8% on the 1st day of mineralization. Ureolysis is one of the biological mechanisms that trigger microbial mineralization with the consequent effect of dust suppression. The analysis of microbial community structure indicated that the urease-producing bacteria Sporosarcina sp. had the highest abundance at the genus level in the microbial-based dust suppressant compound. Jeotgalicoccus sp. plays an important role in improving and maintaining the stability of urease. In addition, the optimal UPMC had low pathogenicity, which is extremely attractive for the safe application of microbial dust suppressants.
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Affiliation(s)
- Xiangming Hu
- College of Safety and Environmental Engineering, Shandong University of Science and Technology, 579 Qianwangang Road, Qingdao, 266590, Shandong Province, China
- State Key Laboratory of Mine Lab Disaster Prevention and Control Co-Found By Shandong Province and the Ministry of Science and Technology, Shandong University of Science and Technology, Qingdao, 266590, Shandong, China
| | - Zhiyuan Yang
- College of Safety and Environmental Engineering, Shandong University of Science and Technology, 579 Qianwangang Road, Qingdao, 266590, Shandong Province, China
| | - Yanyun Zhao
- College of Safety and Environmental Engineering, Shandong University of Science and Technology, 579 Qianwangang Road, Qingdao, 266590, Shandong Province, China
| | - Yue Dong
- College of Safety and Environmental Engineering, Shandong University of Science and Technology, 579 Qianwangang Road, Qingdao, 266590, Shandong Province, China.
| | - Chengcheng Wang
- College of Safety and Environmental Engineering, Shandong University of Science and Technology, 579 Qianwangang Road, Qingdao, 266590, Shandong Province, China
| | - Linlin Zhang
- College of Safety and Environmental Engineering, Shandong University of Science and Technology, 579 Qianwangang Road, Qingdao, 266590, Shandong Province, China
| | - Yiyun Yu
- College of Safety and Environmental Engineering, Shandong University of Science and Technology, 579 Qianwangang Road, Qingdao, 266590, Shandong Province, China
| | - Kai Wu
- College of Safety and Environmental Engineering, Shandong University of Science and Technology, 579 Qianwangang Road, Qingdao, 266590, Shandong Province, China
| | - Liyan Ren
- College of Safety and Environmental Engineering, Shandong University of Science and Technology, 579 Qianwangang Road, Qingdao, 266590, Shandong Province, China
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Bloemendaal M, Veniaminova E, Anthony DC, Gorlova A, Vlaming P, Khairetdinova A, Cespuglio R, Lesch KP, Arias Vasquez A, Strekalova T. Serotonin Transporter (SERT) Expression Modulates the Composition of the Western-Diet-Induced Microbiota in Aged Female Mice. Nutrients 2023; 15:3048. [PMID: 37447374 PMCID: PMC10346692 DOI: 10.3390/nu15133048] [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: 06/09/2023] [Revised: 06/27/2023] [Accepted: 06/29/2023] [Indexed: 07/15/2023] Open
Abstract
Background. The serotonin transporter (SERT), highly expressed in the gut and brain, is implicated in metabolic processes. A genetic variant of the upstream regulatory region of the SLC6A4 gene encoding SERT, the so-called short (s) allele, in comparison with the long (l) allele, results in the decreased function of this transporter, altered serotonergic regulation, an increased risk of psychiatric pathology and type-2 diabetes and obesity, especially in older women. Aged female mice with the complete (Sert-/-: KO) or partial (Sert+/-: HET) loss of SERT exhibit more pronounced negative effects following their exposure to a Western diet in comparison to wild-type (Sert+/+: WT) animals. Aims. We hypothesized that these effects might be mediated by an altered gut microbiota, which has been shown to influence serotonin metabolism. We performed V4 16S rRNA sequencing of the gut microbiota in 12-month-old WT, KO and HET female mice that were housed on a control or Western diet for three weeks. Results. The relative abundance of 11 genera was increased, and the abundance of 6 genera was decreased in the Western-diet-housed mice compared to the controls. There were correlations between the abundance of Streptococcus and Ruminococcaceae_UCG-014 and the expression of the pro-inflammatory marker Toll-like-Receptor 4 (Tlr4) in the dorsal raphe, as well as the expression of the mitochondrial activity marker perixome-proliferator-activated-receptor-cofactor-1b (Ppargc1b) in the prefrontal cortex. Although there was no significant impact of genotype on the microbiota in animals fed with the Control diet, there were significant interactions between diet and genotype. Following FDR correction, the Western diet increased the relative abundance of Intestinimonas and Atopostipes in the KO animals, which was not observed in the other groups. Erysipelatoclostridium abundance was increased by the Western diet in the WT group but not in HET or KO animals. Conclusions. The enhanced effects of a challenge with a Western diet in SERT-deficient mice include the altered representation of several gut genera, such as Intestinimonas, Atopostipes and Erysipelatoclostridium, which are also implicated in serotonergic and lipid metabolism. The manipulation of these genera may prove useful in individuals with the short SERT allele.
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Affiliation(s)
- Mirjam Bloemendaal
- Departments of Psychiatry & Human Genetics, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands; (P.V.); (A.A.V.)
| | - Ekaterina Veniaminova
- Laboratory of Psychiatric Neurobiology, Institute of Molecular Medicine and Department of Normal Physiology, Sechenov First Moscow State Medical University, 119991 Moscow, Russia; (E.V.); (A.G.); (A.K.); (R.C.)
| | | | - Anna Gorlova
- Laboratory of Psychiatric Neurobiology, Institute of Molecular Medicine and Department of Normal Physiology, Sechenov First Moscow State Medical University, 119991 Moscow, Russia; (E.V.); (A.G.); (A.K.); (R.C.)
| | - Priscilla Vlaming
- Departments of Psychiatry & Human Genetics, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands; (P.V.); (A.A.V.)
| | - Adel Khairetdinova
- Laboratory of Psychiatric Neurobiology, Institute of Molecular Medicine and Department of Normal Physiology, Sechenov First Moscow State Medical University, 119991 Moscow, Russia; (E.V.); (A.G.); (A.K.); (R.C.)
| | - Raymond Cespuglio
- Laboratory of Psychiatric Neurobiology, Institute of Molecular Medicine and Department of Normal Physiology, Sechenov First Moscow State Medical University, 119991 Moscow, Russia; (E.V.); (A.G.); (A.K.); (R.C.)
- Neuroscience Research Center of Lyon, Claude-Bernard Lyon-1 University, 69500 Bron, France
| | - Klaus Peter Lesch
- Division of Molecular Psychiatry, Center of Mental Health, University of Würzburg, 97080 Würzburg, Germany; (K.P.L.); (T.S.)
- Department of Psychiatry and Neuropsychology, School for Mental Health and Neuroscience, Maastricht University, 6229 HX Maastricht, The Netherlands
| | - Alejandro Arias Vasquez
- Departments of Psychiatry & Human Genetics, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands; (P.V.); (A.A.V.)
| | - Tatyana Strekalova
- Division of Molecular Psychiatry, Center of Mental Health, University of Würzburg, 97080 Würzburg, Germany; (K.P.L.); (T.S.)
- Department of Psychiatry and Neuropsychology, School for Mental Health and Neuroscience, Maastricht University, 6229 HX Maastricht, The Netherlands
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Yongsawas R, In-on A, Inta A, Kampuansai J, Pandith H, Suwannarach N, Lumyong S, Chitov T, Disayathanoowat T. Bacterial Communities in Lanna Fermented Soybeans from Three Different Ethnolinguistic Groups in Northern Thailand. Microorganisms 2023; 11:649. [PMID: 36985222 PMCID: PMC10056180 DOI: 10.3390/microorganisms11030649] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Revised: 02/25/2023] [Accepted: 02/28/2023] [Indexed: 03/06/2023] Open
Abstract
Northern Thailand, the main part of the Lanna region, is home to a diverse range of ethnic groups, each with their own food and cultural heritage. The bacterial compositions in fermented soybean (FSB) products indigenous to three Lanna ethnolinguistic groups, including Karen, Lawa, and Shan, were investigated in this study. Bacterial DNA was extracted from the FSB samples and subjected to 16S rRNA gene sequencing using the Illumina sequencing platform. Metagenomic data showed that the predominant bacteria in all FSBs were members of the genus Bacillus (49.5-86.8%), and the Lawa FSB had the greatest bacterial diversity. The presence of genera Ignatzschineria, Yaniella, Atopostipes in the Karen and Lawa FSBs and Proteus in the Shan FSB might be indicators of food hygiene problems during processing. The network analysis predicted antagonistic effects of Bacillus against some indicator and pathogenic bacteria. The functional prediction revealed some potential functional properties of these FSBs. The presence of Bacillus in all FSBs and Vagococcus in the Shan FSB suggests that these FSBs could potentially be good sources of beneficial bacteria, and they should be conserved and promoted for health and food security reasons. However, food processing hygiene measures should be introduced and monitored to warrant their properties as health foods.
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Affiliation(s)
- Rujipas Yongsawas
- Department of Biology, Faculty of Science, Chiang Mai University, Chiang Mai 50200, Thailand
- Doctor of Philosophy Program in Applied Microbiology (International Program) in Faculty of Science, Chiang Mai University, Chiang Mai 50200, Thailand
| | - Ammarin In-on
- Department of Biology, Faculty of Science, Chiang Mai University, Chiang Mai 50200, Thailand
| | - Angkana Inta
- Department of Biology, Faculty of Science, Chiang Mai University, Chiang Mai 50200, Thailand
| | - Jatupol Kampuansai
- Department of Biology, Faculty of Science, Chiang Mai University, Chiang Mai 50200, Thailand
| | - Hataichanok Pandith
- Department of Biology, Faculty of Science, Chiang Mai University, Chiang Mai 50200, Thailand
| | - Nakarin Suwannarach
- Department of Biology, Faculty of Science, Chiang Mai University, Chiang Mai 50200, Thailand
- Research Center of Microbial Diversity and Sustainable Utilization, Faculty of Science, Chiang Mai University, Chiang Mai 50200, Thailand
| | - Saisamorn Lumyong
- Department of Biology, Faculty of Science, Chiang Mai University, Chiang Mai 50200, Thailand
- Research Center of Microbial Diversity and Sustainable Utilization, Faculty of Science, Chiang Mai University, Chiang Mai 50200, Thailand
- Academy of Science, The Royal Society of Thailand, Bangkok 10300, Thailand
| | - Thararat Chitov
- Department of Biology, Faculty of Science, Chiang Mai University, Chiang Mai 50200, Thailand
| | - Terd Disayathanoowat
- Department of Biology, Faculty of Science, Chiang Mai University, Chiang Mai 50200, Thailand
- Research Center of Microbial Diversity and Sustainable Utilization, Faculty of Science, Chiang Mai University, Chiang Mai 50200, Thailand
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Hu XM, Liu JD, Feng Y, Zhao YY, Wang XW, Liu WH, Zhang M, Liu Y. Application of urease-producing microbial community in seawater to dust suppression in desert. ENVIRONMENTAL RESEARCH 2023; 219:115121. [PMID: 36549485 DOI: 10.1016/j.envres.2022.115121] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Revised: 12/08/2022] [Accepted: 12/18/2022] [Indexed: 06/17/2023]
Abstract
In order to solve the dust problem caused by sandstorms, this paper aims to propose a new method of enriching urease-producing microbial communities in seawater in a non-sterile environment. Besides, the difference of dust suppression performance of enriched microorganisms under different pH conditions was also explored to adapt the dust. The Fourier-transform infrared spectrometry (FTIR) and Scanning electron microscopy (SEM) confirmed the formation of CaCO3. The X-ray diffraction (XRD) further showed that the crystal forms of CaCO3 were calcite and vaterite. When urease activity was equivalent, the alkaline environment was conducive to the transformation of CaCO3 to more stable calcite. The mineralization rate at pH = 10 reached the maximum value on the 7th day, which was 97.49 ± 1.73%. Moreover, microbial community analysis results showed that the relative abundance of microbial community structure was different under different pH enrichment. Besides, the relative abundance of Sporosarcina, a representative genus of urease-producing microbial community, increased with the increase of pH under culture conditions, which consistent with the mineralization performance results. In addition, the genus level species network diagram also showed that in the microbial community, Sporosarcina was negatively correlated with another urease-producing genus Bacillus, and had a reciprocal relationship with Atopostipes, which means that the urease-producing microbial community was structurally stable. The enrichment of urease-producing microbial communities in seawater will provide empirical support for the large-scale engineering application of MICP technology in preventing and controlling sandstorms in deserts.
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Affiliation(s)
- Xiang-Ming Hu
- College of Safety and Environmental Engineering, Shandong University of Science and Technology, Qingdao, Shandong 266590, China; State Key Laboratory of Mine Lab Disaster Prevention and Control Co-found by Shandong Province and the Ministry of Science and Technology, Shandong University of Science and Technology, Qingdao 266590, Shandong, China
| | - Jin-Di Liu
- College of Safety and Environmental Engineering, Shandong University of Science and Technology, Qingdao, Shandong 266590, China; State Key Laboratory of Mine Lab Disaster Prevention and Control Co-found by Shandong Province and the Ministry of Science and Technology, Shandong University of Science and Technology, Qingdao 266590, Shandong, China
| | - Yue Feng
- College of Safety and Environmental Engineering, Shandong University of Science and Technology, Qingdao, Shandong 266590, China; State Key Laboratory of Mine Lab Disaster Prevention and Control Co-found by Shandong Province and the Ministry of Science and Technology, Shandong University of Science and Technology, Qingdao 266590, Shandong, China
| | - Yan-Yun Zhao
- College of Safety and Environmental Engineering, Shandong University of Science and Technology, Qingdao, Shandong 266590, China; State Key Laboratory of Mine Lab Disaster Prevention and Control Co-found by Shandong Province and the Ministry of Science and Technology, Shandong University of Science and Technology, Qingdao 266590, Shandong, China
| | - Xu-Wei Wang
- College of Safety and Environmental Engineering, Shandong University of Science and Technology, Qingdao, Shandong 266590, China; State Key Laboratory of Mine Lab Disaster Prevention and Control Co-found by Shandong Province and the Ministry of Science and Technology, Shandong University of Science and Technology, Qingdao 266590, Shandong, China
| | - Wen-Hao Liu
- College of Safety and Environmental Engineering, Shandong University of Science and Technology, Qingdao, Shandong 266590, China; State Key Laboratory of Mine Lab Disaster Prevention and Control Co-found by Shandong Province and the Ministry of Science and Technology, Shandong University of Science and Technology, Qingdao 266590, Shandong, China
| | - Ming Zhang
- College of Safety and Environmental Engineering, Shandong University of Science and Technology, Qingdao, Shandong 266590, China; State Key Laboratory of Mine Lab Disaster Prevention and Control Co-found by Shandong Province and the Ministry of Science and Technology, Shandong University of Science and Technology, Qingdao 266590, Shandong, China
| | - Yu Liu
- College of Safety and Environmental Engineering, Shandong University of Science and Technology, Qingdao, Shandong 266590, China; State Key Laboratory of Mine Lab Disaster Prevention and Control Co-found by Shandong Province and the Ministry of Science and Technology, Shandong University of Science and Technology, Qingdao 266590, Shandong, China.
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Khadka S, Omura S, Sato F, Tsunoda I. Adjuvant Injections Altered the Ileal and Fecal Microbiota Differently with Changes in Immunoglobulin Isotypes and Antimycobacterial Antibody Responses. Int J Mol Sci 2023; 24:ijms24032818. [PMID: 36769136 PMCID: PMC9917480 DOI: 10.3390/ijms24032818] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2022] [Revised: 01/28/2023] [Accepted: 01/30/2023] [Indexed: 02/05/2023] Open
Abstract
Alterations in the gut microbiota, "dysbiosis," have been reported in autoimmune diseases, including multiple sclerosis (MS), and their animal models. Although the animal models were induced by injections of autoantigens with adjuvants, including complete Freund's adjuvant (CFA) and pertussis toxin (PT), the effects of adjuvant injections on the microbiota are largely unknown. We aimed to clarify whether adjuvant injections could affect the microbiota in the ileum and feces. Using 16S rRNA sequencing, we found decreased alpha diversities of the gut microbiota in mice injected with CFA and PT, compared with naïve mice. Overall, microbial profiles visualized by principal component analysis demonstrated dysbiosis in feces, but not in the ileum, of adjuvant-injected mice, where the genera Lachnospiraceae NK4A136 group and Alistipes contributed to dysbiosis. When we compared the relative abundances of individual bacteria, we found changes in 16 bacterial genera in feces and seven genera in the ileum of adjuvant-injected mice, in which increased serum levels of antibody against mycobacteria (a component of CFA) and total IgG2c were correlated with the genus Facklamia. On the other hand, increased IgG1 and IgA concentrations were correlated with the genus Atopostipes. Therefore, adjuvant injections alone could alter the overall microbial profiles (i.e., microbiota) and individual bacterial abundances with altered antibody responses; dysbiosis in animal models could be partly due to adjuvant injections.
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Zhang Y, Li X, Lu L, Huang F, Liu H, Zhang Y, Yang L, Usman M, Li S. Urbanization Reduces Phyllosphere Microbial Network Complexity and Species Richness of Camphor Trees. Microorganisms 2023; 11:microorganisms11020233. [PMID: 36838198 PMCID: PMC9966171 DOI: 10.3390/microorganisms11020233] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Revised: 12/31/2022] [Accepted: 01/04/2023] [Indexed: 01/18/2023] Open
Abstract
Studies on microbial communities associated with foliage in natural ecosystems have grown in number in recent years yet have rarely focused on urban ecosystems. With urbanization, phyllosphere microorganisms in the urban environment have come under pressures from increasing human activities. To explore the effects of urbanization on the phyllosphere microbial communities of urban ecosystems, we investigated the phyllosphere microbial structure and the diversity of camphor trees in eight parks along a suburban-to-urban gradient. The results showed that the number of ASVs (amplicon sequence variants), unique on the phyllosphere microbial communities of three different urbanization gradients, was 4.54 to 17.99 times higher than that of the shared ASVs. Specific microbial biomarkers were also found for leaf samples from each urbanization gradient. Moreover, significant differences (R2 = 0.133, p = 0.005) were observed in the phyllosphere microbial structure among the three urbanization gradients. Alpha diversity and co-occurrence patterns of bacterial communities showed that urbanization can strongly reduce the complexity and species richness of the phyllosphere microbial network of camphor trees. Correlation analysis with environmental factors showed that leaf total carbon (C), nitrogen (N), and sulfur (S), as well as leaf C/N, soil pH, and artificial light intensity at night (ALIAN) were the important drivers in determining the divergence of phyllosphere microbial communities across the urbanization gradient. Together, we found that urbanization can affect the composition of the phyllosphere bacterial community of camphor trees, and that the interplay between human activities and plant microbial communities may contribute to shaping the urban microbiome.
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Affiliation(s)
- Yifang Zhang
- College of Environmental Science and Engineering, China West Normal University, Nanchong 637009, China
- Key Laboratory of Urban Environment and Health, Ningbo Observation and Research Station, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
| | - Xiaomin Li
- Key Laboratory of Urban Environment and Health, Ningbo Observation and Research Station, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
| | - Lu Lu
- College of Environmental Science and Engineering, China West Normal University, Nanchong 637009, China
- Correspondence: (L.L.); (S.L.)
| | - Fuyi Huang
- Key Laboratory of Urban Environment and Health, Ningbo Observation and Research Station, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
| | - Hao Liu
- Department of Health and Environmental Sciences, Xi’an Jiaotong-Liverpool University, 111 Ren’ai Road, Suzhou 215123, China
| | - Yu Zhang
- State Key Lab of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Luhua Yang
- Key Laboratory of Urban Environment and Health, Ningbo Observation and Research Station, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
| | - Muhammad Usman
- PEIE Research Chair for the Development of Industrial Estates and Free Zones, Center for Environmental Studies and Research, Sultan Qaboos University, Al-Khoud, Muscat 123, Oman
| | - Shun Li
- Key Laboratory of Urban Environment and Health, Ningbo Observation and Research Station, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
- Correspondence: (L.L.); (S.L.)
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9
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Potential for Natural Attenuation of Domestic and Agricultural Pollution in Karst Groundwater Environments. WATER 2022. [DOI: 10.3390/w14101597] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
In karst areas, anthropogenic contaminants reach the subsurface with detrimental effects on the groundwater ecosystem and downstream springs, which often serve as drinking water sources for the local human communities. We analyzed the water chemistry and microbial community composition in upstream and downstream locations of five hydrokarst systems (HKS) during four seasons. Conductivity and nitrates were higher in the downstream springs than in the pre-karst waters, whereas the concentration of organic matter, considered here as a pollution indicator, was lower. The microbial community composition varied largely between upstream and downstream locations, with multiple species of potentially pathogenic bacteria decreasing in the HKS. Bacteria indicative of pollution decreased as well when passing through the HKS, but potential biodegraders increased. This suggests that the HKS can filter out part of the polluting organic matter and, with it, part of the associated microorganisms. Nevertheless, the water quality, including the presence of pathogens in downstream springs, must be further monitored to control whether the water is appropriate for consumption. In parallel, the human populations located upstream must be advised of the risks resulting from their daily activities, improper stocking of their various wastes and dumping of their refuse in surface streams.
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10
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Liu W, Zhao Y, Hu X, Li X, Geng Z, Wang Q, Liu J, Wang H, You G. High performance of coal dust suppression with waste activated sludge using microbially induced calcite precipitation technology. POWDER TECHNOL 2022. [DOI: 10.1016/j.powtec.2022.117464] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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11
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Helmi H, Astuti DI, Putri SP, Sato A, Laviña WA, Fukusaki E, Aditiawati P. Dynamic Changes in the Bacterial Community and Metabolic Profile during Fermentation of Low-Salt Shrimp Paste (Terasi). Metabolites 2022; 12:metabo12020118. [PMID: 35208193 PMCID: PMC8874951 DOI: 10.3390/metabo12020118] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2021] [Revised: 01/19/2022] [Accepted: 01/19/2022] [Indexed: 11/24/2022] Open
Abstract
Low-salt shrimp paste, or terasi, is an Indonesian fermented food made from planktonic shrimp mixed with a low concentration of salt. Since high daily intake of sodium is deemed unhealthy, reduction of salt content in shrimp paste production is desired. Until now, there is no reported investigation on the bacterial population and metabolite composition of terasi during fermentation. In this study, the bacterial community of terasi was assessed using high-throughput sequencing of the 16S rRNA V3–V4 region. From this analysis, Tetragenococcus, Aloicoccus, Alkalibacillus, Atopostipes, and Alkalibacterium were found to be the dominant bacterial genus in low-salt shrimp paste. GC/MS-based metabolite profiling was also conducted to monitor the metabolite changes during shrimp paste fermentation. Results showed that acetylated amino acids increased, while glutamine levels decreased, during the fermentation of low-salt shrimp paste. At the start of shrimp paste fermentation, Tetragenococcus predominated with histamine and cadaverine accumulation. At the end of fermentation, there was an increase in 4-hydroxyphenyl acetic acid and indole-3-acetic acid levels, as well as the predominance of Atopostipes. Moreover, we found that aspartic acid increased during fermentation. Based on our findings, we recommend that fermentation of low-salt shrimp paste be done for 7 to 21 days, in order to produce shrimp paste that has high nutritional content and reduced health risk.
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Affiliation(s)
- Henny Helmi
- School of Life Sciences and Technology, Institut Teknologi Bandung, Jalan Ganesha No.10, Bandung 40132, Indonesia; (H.H.); (D.I.A.); (S.P.P.)
- Department of Biology, Bangka Belitung University, Kampus Terpadu Balunijuk, Jalan Raya Balunijuk, Merawang, Bangka 33172, Indonesia
| | - Dea Indriani Astuti
- School of Life Sciences and Technology, Institut Teknologi Bandung, Jalan Ganesha No.10, Bandung 40132, Indonesia; (H.H.); (D.I.A.); (S.P.P.)
| | - Sastia Prama Putri
- School of Life Sciences and Technology, Institut Teknologi Bandung, Jalan Ganesha No.10, Bandung 40132, Indonesia; (H.H.); (D.I.A.); (S.P.P.)
- Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan; (A.S.); (E.F.)
- Industrial Biotechnology Initiative Division, Institute for Open and Transdisciplinary Research Initiatives, Osaka University, Osaka 565-0871, Japan
| | - Arisa Sato
- Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan; (A.S.); (E.F.)
| | - Walter A. Laviña
- Microbiology Division, Institute of Biological Sciences, University of the Philippines Los Baños, Los Baños, Laguna 4031, Philippines;
| | - Eiichiro Fukusaki
- Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan; (A.S.); (E.F.)
- Industrial Biotechnology Initiative Division, Institute for Open and Transdisciplinary Research Initiatives, Osaka University, Osaka 565-0871, Japan
- Osaka University-Shimadzu Omics Innovation Research Laboratories, Osaka University, Osaka 565-0871, Japan
| | - Pingkan Aditiawati
- School of Life Sciences and Technology, Institut Teknologi Bandung, Jalan Ganesha No.10, Bandung 40132, Indonesia; (H.H.); (D.I.A.); (S.P.P.)
- Correspondence: ; Tel.: +62-22-251-1575 or +62-22-250-0258
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12
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A biogeographic 16S rRNA survey of bacterial communities of ureolytic biomineralization from California public restrooms. PLoS One 2022; 17:e0262425. [PMID: 35030221 PMCID: PMC8759634 DOI: 10.1371/journal.pone.0262425] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Accepted: 12/24/2021] [Indexed: 11/29/2022] Open
Abstract
In this study, we examined the total bacterial community associated with ureolytic biomineralization from urine drainage systems. Biomineral samples were obtained from 11 California Department of Transportation public restrooms fitted with waterless, low-flow, or conventional urinals in 2019. Following high throughput 16S rRNA Illumina sequences processed using the DADA2 pipeline, the microbial diversity assessment of 169 biomineral and urine samples resulted in 3,869 reference sequences aggregated as 598 operational taxonomic units (OTUs). Using PERMANOVA testing, we found strong, significant differences between biomineral samples grouped by intrasystem sampling location and urinal type. Biomineral microbial community profiles and alpha diversities differed significantly when controlling for sampling season. Observational statistics revealed that biomineral samples obtained from waterless urinals contained the largest ureC/16S gene copy ratios and were the least diverse urinal type in terms of Shannon indices. Waterless urinal biomineral samples were largely dominated by the Bacilli class (86.1%) compared to low-flow (41.3%) and conventional samples (20.5%), and had the fewest genera that account for less than 2.5% relative abundance per OTU. Our findings are useful for future microbial ecology studies of urine source-separation technologies, as we have established a comparative basis using a large sample size and study area.
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13
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Martin G, Sharma S, Ryan W, Srinivasan NK, Senko JM. Identification of Microbiological Activities in Wet Flue Gas Desulfurization Systems. Front Microbiol 2021; 12:675628. [PMID: 34262541 PMCID: PMC8273512 DOI: 10.3389/fmicb.2021.675628] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Accepted: 06/07/2021] [Indexed: 11/18/2022] Open
Abstract
Thermoelectric power generation from coal requires large amounts of water, much of which is used for wet flue gas desulfurization (wFGD) systems that minimize sulfur emissions, and consequently, acid rain. The microbial communities in wFGDs and throughout thermoelectric power plants can influence system performance, waste processing, and the long term stewardship of residual wastes. Any microorganisms that survive in wFGD slurries must tolerate high total dissolved solids concentrations (TDS) and temperatures (50–60°C), but the inocula for wFGDs are typically from fresh surface waters (e.g., lakes or rivers) of low TDS and temperatures, and whose activity might be limited under the physicochemically extreme conditions of the wFGD. To determine the extents of microbiological activities in wFGDs, we examined the microbial activities and communities associated with three wFGDs. O2 consumption rates of three wFGD slurries were optimal at 55°C, and living cells could be detected microscopically, indicating that living and active communities of organisms were present in the wFGD and could metabolize at the high temperature of the wFGD. A 16S rRNA gene-based survey revealed that the wFGD-associated microbial communities included taxa attributable to both thermophilic and mesophilic lineages. Metatranscriptomic analysis of one of the wFGDs indicated an abundance of active Burholderiaceae and several Gammaproteobacteria, and production of transcripts associated with carbohydrate metabolism, osmotic stress response, as well as phage, prophages, and transposable elements. These results illustrate that microbial activities can be sustained in physicochemically extreme wFGDs, and these activities may influence the performance and environmental impacts of thermoelectric power plants.
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Affiliation(s)
- Gregory Martin
- Department of Biology, The University of Akron, Akron, OH, United States
| | - Shagun Sharma
- Department of Biology, The University of Akron, Akron, OH, United States.,Integrated Bioscience Program, The University of Akron, Akron, OH, United States
| | - William Ryan
- Department of Biology, The University of Akron, Akron, OH, United States
| | | | - John M Senko
- Department of Biology, The University of Akron, Akron, OH, United States.,Integrated Bioscience Program, The University of Akron, Akron, OH, United States.,Department of Geosciences, The University of Akron, Akron, OH, United States
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14
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Sun H, Cui X, Stinner W, Zhang L, Ju X, Guo J, Dong R. Ensiling excessively wilted maize stover with biogas slurry: Effects on storage performance and subsequent biogas potential. BIORESOURCE TECHNOLOGY 2020; 305:123042. [PMID: 32105847 DOI: 10.1016/j.biortech.2020.123042] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/03/2020] [Revised: 02/16/2020] [Accepted: 02/17/2020] [Indexed: 06/10/2023]
Abstract
This study evaluated the ensiling performance of excessively wilted maize stover (EWMS) with biogas slurries and the effect on the subsequent biomethane potential. Chicken and pig manure biogas slurries with or without solid-liquid separation were used to amend the stover humidity before ensiling for 60 d. The hetero-lactic-acid fermentative bacteria Atopostipes and Lactobacillus were enriched by the biogas slurry regardless of the solid-liquid separation. Significant increases in the total organic-acid content were observed in silages with chicken (41%) and pig (15%) manure biogas slurries without solid-liquid separation, which was not the case for treatments with solid-liquid separation. During the ensiling process, more lignocellulose was degraded under the high buffer-capacity provided by the ammonia-nitrogen in the biogas slurry. An increase of 7.1%-9.6% was observed for the specific methane yieldmeasured, which offset a storage loss of 5.0%-7.3%. Ensiling EWMS with biogas slurry therefore provides a viable strategy for biogas production.
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Affiliation(s)
- Hui Sun
- College of Engineering (Key Laboratory for Clean Renewable Energy Utilization Technology, Ministry of Agriculture), China Agricultural University, Beijing 100083, PR China
| | - Xian Cui
- College of Engineering (Key Laboratory for Clean Renewable Energy Utilization Technology, Ministry of Agriculture), China Agricultural University, Beijing 100083, PR China
| | - Walter Stinner
- German Biomass Research Center, Deutsches Biomasseforschungszentrum gemeinnützige GmbH, Torgauer Str. 116, 04347 Leipzig, Germany; Sino-German Biomass Research Center Anhui, Hefei University, Jinxiu Dadao 99, 230601 Hefei, PR China
| | - Leping Zhang
- College of Engineering (Key Laboratory for Clean Renewable Energy Utilization Technology, Ministry of Agriculture), China Agricultural University, Beijing 100083, PR China
| | - Xinxin Ju
- Yantai Institute, China Agricultural University, Yantai 264032, Shandong, PR China
| | - Jianbin Guo
- College of Engineering (Key Laboratory for Clean Renewable Energy Utilization Technology, Ministry of Agriculture), China Agricultural University, Beijing 100083, PR China.
| | - Renjie Dong
- College of Engineering (Key Laboratory for Clean Renewable Energy Utilization Technology, Ministry of Agriculture), China Agricultural University, Beijing 100083, PR China; Yantai Institute, China Agricultural University, Yantai 264032, Shandong, PR China
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15
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Geomicrobial Investigations of Colored Outer Coatings from an Ethiopian Rock Art Gallery. COATINGS 2020. [DOI: 10.3390/coatings10060536] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
The open rock shelter of Yabelo in Ethiopia hosts diverse Holocene paintings of great cultural importance. The paintings are characterized by the presence of different mineral coatings, whose features have not been studied yet. Our goal was to understand whether different rock samples from the Yabelo paintings collected in close proximity may reveal coatings with different minerology and biology. Thus, elemental analyses combined with microscopic and molecular investigations were performed on two coatings, one whitish (sample 1) and one reddish (sample 2). Although both samples were dominated by heterotrophic bacteria, the two coatings showed distinct mineralogical and microbiological characteristics. Sample 1 contained higher amounts of Ca and P than sample 2, which was likely related to the presence of organic matter. Sample 1 hosted bacterial genera that are potentially involved in biomineralization processes, metal redox cycles and metal resistance. In contrast, sample 2 showed mainly pathogenic and commensal bacteria that are characteristic of animal and human microbiota, and other microorganisms that are involved in nitrogen and metal biogeochemical cycles. Overall, our results indicated that the bacterial communities were particular to the coating mineralogy, suggesting a potential role of the biological components in the crust genesis.
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16
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Im S, Petersen SO, Lee D, Kim DH. Effects of storage temperature on CH 4 emissions from cattle manure and subsequent biogas production potential. WASTE MANAGEMENT (NEW YORK, N.Y.) 2020; 101:35-43. [PMID: 31586875 DOI: 10.1016/j.wasman.2019.09.036] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/10/2019] [Revised: 09/18/2019] [Accepted: 09/24/2019] [Indexed: 06/10/2023]
Abstract
CH4 is one of the main greenhouse gases (GHGs) generated from agricultural sector, and a significant amount of it is emitted during the storage of livestock manure. To mitigate the CH4 emissions, strong acid addition to the manure was attempted, which is only applicable to slurry-type manure. On the other hand, lowering the storage temperature could be an effective method to reduce the CH4 emissions, particularly applicable to solid-type manure. In this study, cattle manure (CM) with a high-solid content (TS > 30%) was stored at different temperatures (15-35 °C) for 80 d. The highest CH4 emissions of 375.1 kg CO2 eq./ton VS was observed at 35 °C, and this was reduced to less than half at ≤20 °C. Like the difference in CH4 emissions, the degradation of organic matter showed a similar trend. The maximum VS reduction of 29% was observed at 35 °C, while only 8% reduction was observed at 15 °C. Results from microbial community analyses and specific methanogenic activity tests indicated that hydrogenotrophic methanogens were the dominant indigenous CH4-producers, and the abundance of psychrophilic methanogens increased with decreasing temperature. The conservation of organic matter at low temperature led to an increase in biogas production potential from 25 to 43 L CH4/kg CM. It was calculated that the GHGs emissions from electricity consumption for cooling CM below 25 °C can be offset by mitigating CH4 emissions during storage but increasing in subsequent biogas production potential of CM. Compared at 35 °C, 91.6 kg CO2 eq./ton CM of GHGs reduction can be attained at 15 °C.
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Affiliation(s)
- Seongwon Im
- Department of Civil Engineering, Inha University, Inha-ro 100, Nam-gu, Incheon 22212, Republic of Korea
| | - Søren O Petersen
- Department of Agroecology, Aarhus University, Blichers Allé 20, 8830 Tjele, Denmark
| | - Dongjin Lee
- Environmental Resources Research Department, National Institute of Environmental Research, Hwangyeong-ro 42, Seo-gu, Incheon 22689, Republic of Korea
| | - Dong-Hoon Kim
- Department of Civil Engineering, Inha University, Inha-ro 100, Nam-gu, Incheon 22212, Republic of Korea.
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17
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A time travel story: metagenomic analyses decipher the unknown geographical shift and the storage history of possibly smuggled antique marble statues. ANN MICROBIOL 2019. [DOI: 10.1007/s13213-019-1446-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
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18
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Liu Y, Wang W, Xu J, Xue H, Stanford K, McAllister TA, Xu W. Evaluation of compost, vegetable and food waste as amendments to improve the composting of NaOH/NaClO-contaminated poultry manure. PLoS One 2018; 13:e0205112. [PMID: 30307982 PMCID: PMC6181338 DOI: 10.1371/journal.pone.0205112] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2018] [Accepted: 09/19/2018] [Indexed: 11/20/2022] Open
Abstract
Regular usage of NaOH/NaClO disinfectants results in high sodium salt and alkalinity of poultry manure. This study compared three amendments: vegetable waste (V), food waste (F) and mature compost (C) for their ability to improve the composting of NaOH/NaClO-contaminated poultry manure. C compost resulted in the highest compost temperatures (p<0.001) and greatest reduction in OM, TC, TN and NH4-N (p<0.05). C and V composts were more efficient at lowering extractable-Na (ext-Na) and electrical conductivity (EC) than F (p<0.05). Maturity was primarily indicated by NH4-N, EC and ext-Na. Bacterial dynamics was profoundly influenced by NH4-N, EC and TC, with the decrease leading to discriminate genera shift from Sinibacillus and Thiopseudomonas to Brevbacterium, Brachybacterium, and Microbacterium. These findings suggest that mature compost was more desirable amendment than vegetable and food waste in the composting of NaOH/NaClO-contaminated poultry manure, and the decrease of ext-Na indicated compost maturity but did not influence bacterial dynamics.
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Affiliation(s)
- Yuting Liu
- School of Food and Environment, Dalian University of Technology, Panjin campus, Panjin, China
| | - Wenxia Wang
- School of Food and Environment, Dalian University of Technology, Panjin campus, Panjin, China
| | - Jianqiang Xu
- School of Life Science and Medicine, Dalian University of Technology, Panjin campus, Panjin, China
- Panjin Industrial Technology Institute of Dalian University of Technology, Panjin, China
| | - Hongyu Xue
- School of Life Science and Medicine, Dalian University of Technology, Panjin campus, Panjin, China
| | - Kim Stanford
- Alberta Agriculture and Forestry, Agriculture Centre, Lethbridge, Alberta, Canada
| | - Tim A. McAllister
- Agriculture and Agri-Food Canada, Lethbridge Research Centre, Lethbridge, Alberta, Canada
| | - Weiping Xu
- School of Food and Environment, Dalian University of Technology, Panjin campus, Panjin, China
- Panjin Industrial Technology Institute of Dalian University of Technology, Panjin, China
- * E-mail:
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19
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Barbosa SG, Peixoto L, Soares OS, Pereira MFR, Heijne AT, Kuntke P, Alves MM, Pereira MA. Influence of carbon anode properties on performance and microbiome of Microbial Electrolysis Cells operated on urine. Electrochim Acta 2018. [DOI: 10.1016/j.electacta.2018.02.083] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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20
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Xu S, Lu W, Liu Y, Ming Z, Liu Y, Meng R, Wang H. Structure and diversity of bacterial communities in two large sanitary landfills in China as revealed by high-throughput sequencing (MiSeq). WASTE MANAGEMENT (NEW YORK, N.Y.) 2017; 63:41-48. [PMID: 27515184 DOI: 10.1016/j.wasman.2016.07.047] [Citation(s) in RCA: 81] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/19/2016] [Revised: 07/11/2016] [Accepted: 07/31/2016] [Indexed: 05/21/2023]
Abstract
Landfill disposal has been considered as a very economically viable management practice for municipal solid waste in mainland China. However, insufficient knowledge of the bacterial community structure and diversity in landfills hampers effectively landfill disposal. In this study, the structure and diversity of bacterial communities in two large sanitary landfills in northern and western parts of China were examined by high-throughput sequencing via a MiSeq platform. Nearly 1million effective sequences (981,575) were obtained from the 20 samples collected from four independent sites with different deposit depths (up to 18m). These sequences contained high amount of operational taxonomic units (OTUs), 2511-9955 OTUs at a cutoff level of 3% and a sequencing depth of 23,928. Firmicutes, Bacteroidetes and Proteobacteria were the most abundant phyla in the samples. Clear geographical differences between the sampling sites were revealed by nonmetric multidimensional scaling. Most of the samples from the same sampling site could be clustered together. Thus, the heterogeneity of the bacterial community structures was more significantly affected by the sampling site than by sampling depth. Redundancy analysis results suggested that seven physicochemical attributes, namely NH4+-N, NO2--N, moisture, pH, dissolved organic carbon (DOC), SO42- and total Cu element, significantly affected the bacterial community structures (P<0.001) based on variance inflation factor selection. Among these attributes, NH4+-N, NO2--N, moisture, pH and DOC were the most important parameters influencing the bacterial community structures (P<0.05). This study elucidated the structure and diversity of bacterial communities in landfills and discerned the relationships between bacterial community structures and physicochemical attributes. To the best of our knowledge, this study is among the first to characterize bacterial community structures in landfills by using this novel high-throughput sequencing approach.
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Affiliation(s)
- Sai Xu
- School of Environment, Tsinghua University, Beijing 100084, China
| | - Wenjing Lu
- School of Environment, Tsinghua University, Beijing 100084, China; Key Laboratory for Solid Waste Management and Environment Safety (Tsinghua University), Ministry of Education of China, Tsinghua University, Beijing 100084, China.
| | - Yanting Liu
- School of Environment, Tsinghua University, Beijing 100084, China
| | - Zhongyuan Ming
- School of Environment, Tsinghua University, Beijing 100084, China
| | - Yanjun Liu
- School of Environment, Tsinghua University, Beijing 100084, China
| | - Ruihong Meng
- School of Environment, Tsinghua University, Beijing 100084, China
| | - Hongtao Wang
- School of Environment, Tsinghua University, Beijing 100084, China; Key Laboratory for Solid Waste Management and Environment Safety (Tsinghua University), Ministry of Education of China, Tsinghua University, Beijing 100084, China.
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21
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Stanisavljević S, Lukić J, Momčilović M, Miljković M, Jevtić B, Kojić M, Golić N, Mostarica Stojković M, Miljković D. Gut-associated lymphoid tissue, gut microbes and susceptibility to experimental autoimmune encephalomyelitis. Benef Microbes 2016; 7:363-73. [PMID: 26839070 DOI: 10.3920/bm2015.0159] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Gut microbiota and gut-associated lymphoid tissue have been increasingly appreciated as important players in pathogenesis of various autoimmune diseases, including multiple sclerosis. Experimental autoimmune encephalomyelitis (EAE) is an animal model of multiple sclerosis that can be induced with an injection of spinal cord homogenate emulsified in complete Freund's adjuvant in Dark Agouti (DA) rats, but not in Albino Oxford (AO) rats. In this study, mesenteric lymph nodes (MLN), Peyer's patches (PP) and gut microbiota were analysed in these two rat strains. There was higher proportion of CD4(+) T cells and regulatory T cells in non-immunised DA rats in comparison to AO rats. Also, DA rat MLN and PP cells were higher producers of pro-inflammatory cytokines interferon-γ and interleukin-17. Finally, microbial analyses showed that uncultivated species of Turicibacter and Atopostipes genus were exclusively present in AO rats, in faeces and intestinal tissue, respectively. Thus, it is clear that in comparison of an EAE-susceptible with an EAE-resistant strain of rats, various discrepancies at the level of gut associated lymphoid tissue, as well as at the level of gut microbiota can be observed. Future studies should determine if the differences have functional significance for EAE pathogenesis.
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Affiliation(s)
- S Stanisavljević
- 1 Department of Immunology, Institute for Biological Research 'Siniša Stanković', University of Belgrade, Despota Stefana 142, 11000 Belgrade, Serbia
| | - J Lukić
- 2 Laboratory for Molecular Microbiology, Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Vojvode Stepe 444a, 11010 Belgrade, Serbia
| | - M Momčilović
- 1 Department of Immunology, Institute for Biological Research 'Siniša Stanković', University of Belgrade, Despota Stefana 142, 11000 Belgrade, Serbia
| | - M Miljković
- 2 Laboratory for Molecular Microbiology, Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Vojvode Stepe 444a, 11010 Belgrade, Serbia
| | - B Jevtić
- 1 Department of Immunology, Institute for Biological Research 'Siniša Stanković', University of Belgrade, Despota Stefana 142, 11000 Belgrade, Serbia
| | - M Kojić
- 2 Laboratory for Molecular Microbiology, Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Vojvode Stepe 444a, 11010 Belgrade, Serbia
| | - N Golić
- 2 Laboratory for Molecular Microbiology, Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Vojvode Stepe 444a, 11010 Belgrade, Serbia
| | - M Mostarica Stojković
- 3 Institute for Microbiology and Immunology, School of Medicine, University of Belgrade, dr. Subotica 1, 11000 Belgrade, Serbia
| | - D Miljković
- 1 Department of Immunology, Institute for Biological Research 'Siniša Stanković', University of Belgrade, Despota Stefana 142, 11000 Belgrade, Serbia
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22
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Cho S, Hwang O, Park S. Effect of Dietary Protein Levels on Composition of Odorous Compounds and Bacterial Ecology in Pig Manure. ASIAN-AUSTRALASIAN JOURNAL OF ANIMAL SCIENCES 2015; 28:1362-70. [PMID: 26194219 PMCID: PMC4554878 DOI: 10.5713/ajas.15.0078] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/29/2015] [Revised: 03/23/2015] [Accepted: 04/03/2015] [Indexed: 01/10/2023]
Abstract
This study was performed to investigate the effect of different levels of dietary crude protein (CP) on composition of odorous compounds and bacterial communities in pig manure. A total of 48 male pigs (average initial body weight 45 kg) fed diets containing three levels of dietary CP (20%, 17.5%, and 15%) and their slurry samples were collected from the pits under the floor every week for one month. Changes in composition of odorous compounds and bacterial communities were analyzed by gas chromatography and 454 FLX titanium pyrosequencing systems, respectively. Levels of phenols, indoles, short chain fatty acid and branched chain fatty acid were lowest (p<0.05) in CP 15% group among three CP levels. Relative abundance of Bacteroidetes phylum and bacterial genera including Leuconostoc, Bacillus, Atopostipes, Peptonphilus, Ruminococcaceae_uc, Bacteroides, and Pseudomonas was lower (p<0.05) in CP 15% than in CP 20% group. There was a positive correlation (p<0.05) between odorous compounds and bacterial genera: phenol, indole, iso-butyric acid, and iso-valeric acid with Atopostipes, p-cresol and skatole with Bacteroides, acetic acid and butyric acid with AM982595_g of Porphyromonadaceae family, and propionic acid with Tissierella. Taken together, administration of 15% CP showed less production of odorous compounds than 20% CP group and this result might be associated with the changes in bacterial communities especially whose roles in protein metabolism.
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Affiliation(s)
- Sungback Cho
- Department of Food Science and Technology, Sejong University, Seoul 143-747, Korea
| | - Okhwa Hwang
- Department of Food Science and Technology, Sejong University, Seoul 143-747, Korea
| | - Sungkwon Park
- Department of Food Science and Technology, Sejong University, Seoul 143-747, Korea
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23
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Da Silva MLB, Cantão ME, Mezzari MP, Ma J, Nossa CW. Assessment of bacterial and archaeal community structure in Swine wastewater treatment processes. MICROBIAL ECOLOGY 2015; 70:77-87. [PMID: 25432577 DOI: 10.1007/s00248-014-0537-8] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/10/2014] [Accepted: 11/12/2014] [Indexed: 05/27/2023]
Abstract
Microbial communities from two field-scale swine wastewater treatment plants (WWTPs) were assessed by pyrosequencing analyses of bacterial and archaeal 16S ribosomal DNA (rDNA) fragments. Effluent samples from secondary (anaerobic covered lagoons and upflow anaerobic sludge blanket [UASB]) and tertiary treatment systems (open-pond natural attenuation lagoon and air-sparged nitrification-denitrification tank followed by alkaline phosphorus precipitation process) were analyzed. A total of 56,807 and 48,859 high-quality reads were obtained from bacterial and archaeal libraries, respectively. Dominant bacterial communities were associated with the phylum Firmicutes, Bacteroidetes, Proteobacteria, or Actinobacteria. Bacteria and archaea diversity were highest in UASB effluent sample. Escherichia, Lactobacillus, Bacteroides, and/or Prevotella were used as indicators of putative pathogen reduction throughout the WWTPs. Satisfactory pathogen reduction was observed after the open-pond natural attenuation lagoon but not after the air-sparged nitrification/denitrification followed by alkaline phosphorus precipitation treatment processes. Among the archaeal communities, 80% of the reads was related to hydrogeno-trophic methanogens Methanospirillum. Enrichment of hydrogenotrophic methanogens detected in effluent samples from the anaerobic covered lagoons and UASB suggested that CO2 reduction with H2 was the dominant methanogenic pathway in these systems. Overall, the results served to improve our current understanding of major microbial communities' changes downgradient from the pen and throughout swine WWTP as a result of different treatment processes.
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24
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Savagea faecisuis gen. nov., sp. nov., a tylosin- and tetracycline-resistant bacterium isolated from a swine-manure storage pit. Antonie van Leeuwenhoek 2015; 108:151-61. [DOI: 10.1007/s10482-015-0473-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/21/2014] [Accepted: 05/06/2015] [Indexed: 10/23/2022]
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25
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Zhou X, Qu Y, Kim BH, Du Y, Wang H, Li H, Dong Y, He W, Liu J, Feng Y. Simultaneous current generation and ammonia recovery from real urine using nitrogen-purged bioelectrochemical systems. RSC Adv 2015. [DOI: 10.1039/c5ra11556f] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Ammonia could be recovered from human urine through combination of bioelectrochemical systems and nitrogen purging, with concomitant mitigation of ammonia inhibition of anode electroactivity.
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Affiliation(s)
- Xiangtong Zhou
- State Key Laboratory of Urban Water Resource and Environment
- Harbin Institute of Technology
- Harbin
- China
| | - Youpeng Qu
- School of Life Science and Biotechnology
- Harbin Institute of Technology
- Harbin
- China
| | - Byung Hong Kim
- State Key Laboratory of Urban Water Resource and Environment
- Harbin Institute of Technology
- Harbin
- China
- Bioelectrochemistry Laboratory
| | - Yue Du
- State Key Laboratory of Urban Water Resource and Environment
- Harbin Institute of Technology
- Harbin
- China
| | - Haiman Wang
- State Key Laboratory of Urban Water Resource and Environment
- Harbin Institute of Technology
- Harbin
- China
| | - Henan Li
- State Key Laboratory of Urban Water Resource and Environment
- Harbin Institute of Technology
- Harbin
- China
| | - Yue Dong
- State Key Laboratory of Urban Water Resource and Environment
- Harbin Institute of Technology
- Harbin
- China
| | - Weihua He
- State Key Laboratory of Urban Water Resource and Environment
- Harbin Institute of Technology
- Harbin
- China
| | - Jia Liu
- State Key Laboratory of Urban Water Resource and Environment
- Harbin Institute of Technology
- Harbin
- China
| | - Yujie Feng
- State Key Laboratory of Urban Water Resource and Environment
- Harbin Institute of Technology
- Harbin
- China
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26
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Recommended minimal standards for description of new taxa of the genera Bifidobacterium, Lactobacillus and related genera. Int J Syst Evol Microbiol 2014; 64:1434-1451. [DOI: 10.1099/ijs.0.060046-0] [Citation(s) in RCA: 77] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Minimal standards for the description of new cultivable strains that represent novel genera and species belonging to the genera
Bifidobacterium
,
Lactobacillus
and related genera are proposed in accordance with Recommendation 30b of the Bacteriological Code (1990 Revision): the description of novel species should be based on phenotypic, genotypic and ecological characteristics to ensure a rich polyphasic characterization. Concerning genotypic characterization, in addition to DNA G+C content (mol%) data, the description should be based on DNA–DNA hybridization (DDH), 16S rRNA gene sequence similarities and at least two housekeeping gene (e.g. hsp60 and recA) sequence similarities. DDH might not be needed if the 16S rRNA gene sequence similarity to the closest known species is lower than 97 %. This proposal has been endorsed by members of the Subcommittee on the Taxonomy of
Bifidobacterium
,
Lactobacillus
and related organisms of the International Committee on the Systematics of Prokaryotes.
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Petri RM, Schwaiger T, Penner GB, Beauchemin KA, Forster RJ, McKinnon JJ, McAllister TA. Characterization of the core rumen microbiome in cattle during transition from forage to concentrate as well as during and after an acidotic challenge. PLoS One 2013; 8:e83424. [PMID: 24391765 PMCID: PMC3877040 DOI: 10.1371/journal.pone.0083424] [Citation(s) in RCA: 251] [Impact Index Per Article: 22.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2013] [Accepted: 11/05/2013] [Indexed: 11/21/2022] Open
Abstract
This study investigated the effect of diet and host on the rumen bacterial microbiome and the impact of an acidotic challenge on its composition. Using parallel pyrosequencing of the V3 hypervariable region of 16S rRNA gene, solid and liquid associated bacterial communities of 8 heifers were profiled. Heifers were exclusively fed forage, before being transitioned to a concentrate diet, subjected to an acidotic challenge and allowed to recover. Samples of rumen digesta were collected when heifers were fed forage, mixed forage, high grain, during challenge (4 h and 12 h) and recovery. A total of 560,994 high-quality bacterial sequences were obtained from the solid and liquid digesta. Using cluster analysis, prominent bacterial populations differed (P≤0.10) in solid and liquid fractions between forage and grain diets. Differences among hosts and diets were not revealed by DGGE, but real time qPCR showed that several bacteria taxon were impacted by changes in diet, with the exception of Streptococcus bovis. Analysis of the core rumen microbiome identified 32 OTU's representing 10 distinct bacterial taxa including Bacteroidetes (32.8%), Firmicutes (43.2%) and Proteobacteria (14.3%). Diversity of OTUs was highest with forage with 38 unique OTUs identified as compared to only 11 with the high grain diet. Comparison of the microbial profiles of clincial vs. subclinical acidotic heifers found a increases in the relative abundances of Acetitomaculum, Lactobacillus, Prevotella, and Streptococcus. Increases in Streptococcus and Lactobacillus likely reflect the tolerance of these species to low pH and their ability to proliferate on surplus fermentable carbohydrate. The acetogen, Acetitomaculum may thereforeplay a role in the conversion of lactate to acetate in acidotic animals. Further profiling of the bacterial populations associated with subclinical and clinical acidosis could establish a microbial fingerprint for these disorders and provide insight into whether there are causative microbial populations that could potentially be therapeutically manipulated.
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Affiliation(s)
- Renee M. Petri
- Lethbridge Research Centre, Agriculture and Agri-Food Canada, Lethbridge, Alberta, Canada
- Department of Animal and Poultry Science, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - Tyler Schwaiger
- Lethbridge Research Centre, Agriculture and Agri-Food Canada, Lethbridge, Alberta, Canada
- Department of Animal and Poultry Science, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - Greg B. Penner
- Department of Animal and Poultry Science, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - Karen A. Beauchemin
- Lethbridge Research Centre, Agriculture and Agri-Food Canada, Lethbridge, Alberta, Canada
| | - Robert J. Forster
- Lethbridge Research Centre, Agriculture and Agri-Food Canada, Lethbridge, Alberta, Canada
| | - John J. McKinnon
- Department of Animal and Poultry Science, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - Tim A. McAllister
- Lethbridge Research Centre, Agriculture and Agri-Food Canada, Lethbridge, Alberta, Canada
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Microbial community structure of a pilot-scale thermophilic anaerobic digester treating poultry litter. Appl Microbiol Biotechnol 2013; 98:2321-34. [PMID: 23989973 DOI: 10.1007/s00253-013-5144-y] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2013] [Revised: 07/17/2013] [Accepted: 07/19/2013] [Indexed: 10/26/2022]
Abstract
The microbial community structure of a stable pilot-scale thermophilic continuous stirred tank reactor digester stabilized on poultry litter was investigated. This 40-m(3) digester produced biogas with 57% methane, and chemical oxygen demand removal of 54%. Bacterial and archaeal diversity were examined using both cloning and pyrosequencing that targeted 16S rRNA genes. The bacterial community was dominated by phylum Firmicutes, constituting 93% of the clones and 76% of the pyrotags. Of the Firmicutes, class Clostridia (52% pyrotags) was most abundant followed by class Bacilli (13% pyrotags). The bacterial libraries identified 94 operational taxonomic units (OTUs) and pyrosequencing identified 577 OTUs at the 97% minimum similarity level. Fifteen OTUs were dominant (≥2% abundance), and nine of these were novel unclassified Firmicutes. Several of the dominant OTUs could not be classified more specifically than Clostridiales, but were most similar to plant biomass degraders, including Clostridium thermocellum. Of the rare pyrotag OTUs (<0.5% abundance), 75% were Firmicutes. The dominant methanogen was Methanothermobacter which has hydrogenotrophic metabolism, and accounted for >99% of the archaeal clones. Based on the primary methanogen, as well as digester chemistry (high VA and ammonia levels), we propose that bacterial acetate oxidation is the primary pathway in this digester for the control of acetate levels.
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29
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Wadud S, Michaelsen A, Gallagher E, Parcsi G, Zemb O, Stuetz R, Manefield M. Bacterial and fungal community composition over time in chicken litter with high or low moisture content. Br Poult Sci 2013; 53:561-9. [PMID: 23281748 DOI: 10.1080/00071668.2012.723802] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
1. Changes in bacterial and fungal communities in chicken litter with high and low moisture content over a five week period during a single chicken grow out cycle in a poultry shed in subtropical Australia were investigated to study the association between specific microbes and odour production. 2. Microbial biomass, as indicated by DNA yields, was higher and community composition was more dynamic over time in moist compared with dry chicken litter. 3. Bacillus, Atopostipes and Aspergillus species increased in relative abundance in moist chicken litter samples over time reflecting the relatively high fitness and hence activity of these specific bacteria and this specific fungus in this environment.
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Affiliation(s)
- S Wadud
- School of Biotechnology and Biomolecular Sciences, Centre for Marine BioInnovation, University of New South Wales, Sydney, Australia
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30
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Jeong JY, Park HD, Lee KH, Weon HY, Ka JO. Microbial community analysis and identification of alternative host-specific fecal indicators in fecal and river water samples using pyrosequencing. J Microbiol 2011; 49:585-94. [PMID: 21887641 DOI: 10.1007/s12275-011-0530-6] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2010] [Accepted: 03/31/2011] [Indexed: 01/15/2023]
Abstract
It is important to know the comprehensive microbial communities of fecal pollution sources and receiving water bodies for microbial source tracking. Pyrosequencing targeting the V1-V3 hypervariable regions of the 16S rRNA gene was used to investigate the characteristics of bacterial and Bacteroidales communities in major fecal sources and river waters. Diversity analysis indicated that cow feces had the highest diversities in the bacterial and Bacteroidales group followed by the pig sample, with human feces having the lowest value. The Bacteroidales, one of the potential fecal indicators, totally dominated in the fecal samples accounting for 31%-52% of bacterial sequences, but much less (0.6%) in the river water. Clustering and Venn diagram analyses showed that the human sample had a greater similarity to the pig sample in the bacterial and Bacteroidales communities than to samples from other hosts. Traditional fecal indicators, i.e., Escherichia coli, were detected in the human and river water samples at very low rates and Clostridium perfringens and enterococci were not detected in any samples. Besides the Bacteroidales group, some microorganisms detected in the specific hosts, i.e., Parasutterella excrementihominis, Veillonella sp., Dialister invisus, Megamonas funiformis, and Ruminococcus lactaris for the human and Lactobacillus amylovorus and Atopostipes sp. for the pig, could be used as potential host-specific fecal indicators. These microorganisms could be used as multiple fecal indicators that are not dependent on the absence or presence of a single indicator. Monitoring for multiple indicators that are highly abundant and host-specific would greatly enhance the effectiveness of fecal pollution source tracking.
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Affiliation(s)
- Ju-Yong Jeong
- Department of Water Quality Research, Gyeonggi-do Institute of Health and Environment, Suwon 440-290, Republic of Korea
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31
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Iino T, Suzuki KI, Harayama S. Lacticigenium naphtae gen. nov., sp. nov., a halotolerant and motile lactic acid bacterium isolated from crude oil. Int J Syst Evol Microbiol 2009; 59:775-80. [DOI: 10.1099/ijs.0.003293-0] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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32
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Watanabe K, Nagao N, Toda T, Kurosawa N. Changes in bacterial communities accompanied by aggregation in a fed-batch composting reactor. Curr Microbiol 2008; 56:458-67. [PMID: 18231830 DOI: 10.1007/s00284-008-9107-y] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2007] [Accepted: 11/26/2007] [Indexed: 11/30/2022]
Abstract
The contents of fed-batch composting (FBC) reactors often aggregate after prolonged operation. This process leads to irreversible breakdown of the decomposition reaction and possible alteration of the bacterial communities. We compared the structures of bacterial communities in reactors under aggregate and optimal conditions. The results of 16S rRNA gene clone analysis showed that populations of the family Bacillaceae (such as Bacillus spp., Cerasibacillus spp., Gracilibacillus spp.), which dominate (98%) under optimal condition, were significantly decreased under aggregate condition. In contrast, populations of the family Staphylococcaceae considerably increased after aggregation and accounted for 53% of the total. Phylogenetic analysis also showed that anaerobes or facultative anaerobes related to Tetragenococcus halophilus, Atopostipes suicloacalis, Jeotgalicoccus pinnipedialis, and Staphylococcus spp. were dominant in the aggregates. These results suggested that aerobic Gram-positive bacteria mainly contributed to organic degradation and that aggregation created some anaerobic environment, which promoted the growth of bacterial communities usually not found in well-functioning FBC reactors.
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Affiliation(s)
- Keiko Watanabe
- Graduate School of Engineering, Soka University, 1-236, Tangi-cho, Hachioji, Tokyo 192-8577, Japan.
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33
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Lovanh N, Cook KL, Rothrock MJ, Miles DM, Sistani K. Spatial Shifts in Microbial Population Structure Within Poultry Litter Associated with Physicochemical Properties. Poult Sci 2007; 86:1840-9. [PMID: 17704369 DOI: 10.1093/ps/86.9.1840] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Microbial populations within poultry litter have been largely ignored with the exception of potential human or livestock pathogens. A better understanding of the community structure and identity of the microbial populations within poultry litter could aid in the development of management practices that would reduce populations responsible for toxic air emissions and pathogen incidence. In this study, poultry litter air and physical properties were correlated to shifts in microbial community structure as analyzed by principal component analysis (PCA) and measured by denaturing gradient gel electrophoresis (DGGE). Litter samples were taken in a 36-point grid pattern at 5 m across and 12 m down a 146 m x 12.8 m chicken house. At each sample point, physical parameters such as litter moisture, pH, air and litter temperature, and relative humidity were recorded, and samples were taken for molecular analysis. The DGGE analysis showed that the banding pattern of samples from the back and water/feeder areas of poultry house were distinct from those of samples from other areas. There were distinct clusters of banding patterns corresponding to the front, middle front, middle back, back, and waterer/feeder areas. The PCA analysis showed similar cluster patterns, but with more distinct separation of the front and midhouse samples. The PCA analysis also showed that moisture content and litter temperature (accounting for 51.5 and 31.5% of the separation of samples, respectively) play a major role in spatial diversity of microbial community in the poultry house. Based on analysis of DGGE fingerprints and cloned DGGE band sequences, there appear to be differences in the types of microorganisms over the length of the house, which correspond to differences in the physical properties of the litter.
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Affiliation(s)
- N Lovanh
- USDA-ARS, Animal Waste Management Research Unit, Bowling Green, KY 42104, USA.
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Validation of publication of new names and new combinations previously effectively published outside the IJSEM. Int J Syst Evol Microbiol 2005; 54:1425-1426. [PMID: 15388689 DOI: 10.1099/ijs.0.63444-0] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The purpose of this announcement is to effect the valid publication of the following new names and new combinations under the procedure described in the Bacteriological Code (1990 Revision). Authors and other individuals wishing to have new names and/or combinations included in future lists should send three copies of the pertinent reprint or photocopies thereof to the IJSEM Editorial Office for confirmation that all of the other requirements for valid publication have been met. It is also a requirement of IJSEM and the ICSP that authors of new species, new subspecies and new combinations provide evidence that types are deposited in two recognized culture collections in two different countries (i.e. documents certifying deposition and availability of type strains). It should be noted that the date of valid publication of these new names and combinations is the date of publication of this list, not the date of the original publication of the names and combinations. The authors of the new names and combinations are as given below, and these authors' names will be included in the author index of the present issue and in the volume author index. Inclusion of a name on these lists validates the publication of the name and thereby makes it available in bacteriological nomenclature. The inclusion of a name on this list is not to be construed as taxonomic acceptance of the taxon to which the name is applied. Indeed, some of these names may, in time, be shown to be synonyms, or the organisms may be transferred to another genus, thus necessitating the creation of a new combination.
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