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Mechery J, Kumar CSP, Ambily V, Varghese A, Sylas VP. Dark fermentation of pretreated hydrolysates of pineapple fruit waste for the production of biohydrogen using bacteria isolated from wastewater sources. ENVIRONMENTAL TECHNOLOGY 2024; 45:2067-2075. [PMID: 36591897 DOI: 10.1080/09593330.2022.2164743] [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: 08/23/2022] [Accepted: 12/28/2022] [Indexed: 06/17/2023]
Abstract
In the present study, both acidic and alkaline hydrolysate of pineapple waste was utilised for the production of biohydrogen using locally isolated bacterial strains. The bacteria were isolated from different wastewater sources and were identified as Proteus mirabilis, Pseudomonas aeruginosa, Bacillus altitudinus, Bacillus subtilis, Paenibacillus alvei, and Lysinibacillus sphaericus. Experimental results showed that the highest biohydrogen yield of 836.33 ± 48.02 mL H2 was produced from alkaline hydrolysate with Bacillus altitudinis during the 96thhr of fermentation. Among the different bacterial strains, B. altitudinis showed higher H2 production. Comparatively alkaline hydrolysates exhibited a higher yield of hydrogen than acidic hydrolysates. The final pH of the experiment was found to be in acidic range. The total VFA concentration ranged between 930 ± 207.85 mg/L to 3050 ± 476.97 mg/L. Both sugar degradation and COD reduction were more than 80% in the acidic and alkaline hydrolysates while the lowest sugar degradation and COD reduction were observed for the untreated biomass. The rationale behind this study was to convert the waste biomass into energy by utilising the potential of native bacterial communities.
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Affiliation(s)
- Jerry Mechery
- School of Environmental Sciences, Mahatma Gandhi University, Kottayam, India
| | - C S Praveen Kumar
- School of Environmental Sciences, Mahatma Gandhi University, Kottayam, India
| | - V Ambily
- School of Environmental Sciences, Mahatma Gandhi University, Kottayam, India
| | - Abin Varghese
- School of Environmental Sciences, Mahatma Gandhi University, Kottayam, India
| | - V P Sylas
- School of Environmental Sciences, Mahatma Gandhi University, Kottayam, India
- Advanced Centre of Environmental Studies and Sustainable Development, Mahatma Gandhi University, Kottayam, India
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Zhong J, Chen C, Yu J, Shen Q, Liu C, Fan C. Effect of dredging and capping with clean soil on the mitigation of algae-induced black blooms in Lake Taihu, China: A simulation study. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2022; 302:114106. [PMID: 34784568 DOI: 10.1016/j.jenvman.2021.114106] [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: 07/26/2021] [Revised: 10/22/2021] [Accepted: 11/11/2021] [Indexed: 06/13/2023]
Abstract
Sediment is an important source of matter that causes blackening and odor formation in a water body. The restoration of polluted sediment can suppress algae-induced black blooms to a certain degree. In this study, we compared the control effects of sediment dredging and capping with clean soil on algae-induced black blooms in Lake Taihu using indoor simulation experiments. In addition, we explored the driving effect of temperature on algae-induced black blooms using the method of gradual warming (18, 23, and 28 °C) during the experiment. No blackening of the water body was observed in the simulation stages I (18 °C) and II (23 °C), and the blackening and odor formation occurred within 3 d when the temperature increased to 28 °C in stage III, implying that high temperature was an important driving factor for algae-induced black blooms. Dredging and capping inhibited the blackening and odor formation to some extent, and the colorimetric values in the water columns were lower in the treatment groups than in the control group. At the end of the experiment, the colorimetric values of dredging and capping treatments were 56.5% and 96.7% of the colorimetric value of the control group, respectively. The control effect of dredging on the blackening elements, i.e., Fe2+ and S2- and the main odor forming compounds, i.e., dimethyl disulfide (DMDS) and dimethyl trisulfide (DMTS) was observed in stage II (11-20 d) and stage III (21-27 d), respectively, and the inhibition ability of dredging to suppress algal-induced black blooms was superior than that of capping with clean soil.
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Affiliation(s)
- Jicheng Zhong
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, 210008, PR China.
| | - Chao Chen
- College of Environmental Sciences, Sichuan Agricultural University, Chengdu, 611130, PR China
| | - Juhua Yu
- Institute of Soil and Fertilizer, Fujian Academy of Agricultural Sciences, Fuzhou, 350013, PR China
| | - Qiushi Shen
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, 210008, PR China
| | - Cheng Liu
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, 210008, PR China
| | - Chengxin Fan
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, 210008, PR China
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Cabrol L, Marone A, Tapia-Venegas E, Steyer JP, Ruiz-Filippi G, Trably E. Microbial ecology of fermentative hydrogen producing bioprocesses: useful insights for driving the ecosystem function. FEMS Microbiol Rev 2017; 41:158-181. [DOI: 10.1093/femsre/fuw043] [Citation(s) in RCA: 154] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/05/2016] [Indexed: 11/13/2022] Open
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Bellucci M, Botticella G, Francavilla M, Beneduce L. Inoculum pre-treatment affects the fermentative activity of hydrogen-producing communities in the presence of 5-hydroxymethylfurfural. Appl Microbiol Biotechnol 2015; 100:493-504. [PMID: 26428244 DOI: 10.1007/s00253-015-7002-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2015] [Revised: 09/02/2015] [Accepted: 09/10/2015] [Indexed: 11/27/2022]
Abstract
To enhance the productivity of mixed microbial cultures for fermentative bio-hydrogen production, chemical-physical pre-treatments of the original seed are needed to suppress the activity of hydrogen (H2)-consuming microbes. This approach might influence negatively the composition and diversity of the hydrogen-producing community with consequences on the functional stability of the H2-producing systems in case of perturbations. In this study, we aimed at investigating the effect of different types of pre-treatment on the performance of hydrogen production systems in the presence of an inhibitor, such as 5-hydroxymethylfurfural (HMF). The efficiency and the microbial community structure of batch reactors amended with HMF and inoculated with non-pretreated and pretreated (acid, heat shock, and aeration) anaerobic sludge were evaluated and compared with control systems. The type of pre-treatments influenced the microbial community assembly and activity in inhibited systems, with significant effect on the performance. Cumulative H2 production tests showed that the pre-aerated systems (control and HMF inhibited) were the most efficient, while the difference of the lag phase of the pre-acidified control and HMF-added test was negligible. Analyses of the structure of the enriched microbial community in the systems through PCR-denaturing gradient gel electrophoresis (DGGE) followed by band sequencing revealed that the differences in performance were mostly related to shifts in the metabolic pathways rather than in the predominant species. In conclusion, the findings suggest that the use of specific inoculum pre-treatment could contribute to regulate the metabolic activity of the fermentative H2-producing bacteria in order to enhance the bio-energy production.
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Affiliation(s)
- Micol Bellucci
- Dipartimento di Scienze Agrarie, Alimentari ed Ambientali, Università degli Studi di Foggia, Via Napoli 25, Foggia, Italy
- STAR Agroenergy Research Group, University of Foggia, Via Gramsci, 89-91, Foggia, Italy
| | - Giuseppe Botticella
- Dipartimento di Scienze Agrarie, Alimentari ed Ambientali, Università degli Studi di Foggia, Via Napoli 25, Foggia, Italy
| | - Matteo Francavilla
- STAR Agroenergy Research Group, University of Foggia, Via Gramsci, 89-91, Foggia, Italy
| | - Luciano Beneduce
- Dipartimento di Scienze Agrarie, Alimentari ed Ambientali, Università degli Studi di Foggia, Via Napoli 25, Foggia, Italy.
- STAR Agroenergy Research Group, University of Foggia, Via Gramsci, 89-91, Foggia, Italy.
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Adlakha N, Pfau T, Ebenhöh O, Yazdani SS. Insight into metabolic pathways of the potential biofuel producer, Paenibacillus polymyxa ICGEB2008. BIOTECHNOLOGY FOR BIOFUELS 2015; 8:159. [PMID: 26413158 PMCID: PMC4583153 DOI: 10.1186/s13068-015-0338-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/23/2015] [Accepted: 09/09/2015] [Indexed: 06/05/2023]
Abstract
BACKGROUND Paenibacillus polymyxa is a facultative anaerobe known for production of hydrolytic enzymes and various important biofuel molecules. Despite its wide industrial use and the availability of its genome sequence, very little is known about metabolic pathways operative in the Paenibacillus system. Here, we report metabolic insights of an insect gut symbiont, Paenibacillus polymyxa ICGEB2008, and reveal pathways playing an important role in the production of 2,3-butanediol and ethanol. RESULT We developed a metabolic network model of P. polymyxa ICGEB2008 with 133 metabolites and 158 reactions. Flux balance analysis was employed to investigate the importance of redox balance in ICGEB2008. This led to the detection of the Bifid shunt, a pathway previously not described in Paenibacillus, which can uncouple the production of ATP from the generation of reducing equivalents. Using a combined experimental and modeling approach, we further studied pathways involved in 2,3-butanediol and ethanol production and also demonstrated the production of hydrogen by the organism. We could further show that the nitrogen source is critical for metabolite production by Paenibacillus, and correctly quantify the influence on the by-product metabolite profile of ICGEB2008. Both simulations and experiments showed that metabolic flux is diverted from ethanol to acetate production when an oxidized nitrogen source is utilized. CONCLUSION We have created a predictive model of the central carbon metabolism of P. polymyxa ICGEB2008 and could show the presence of the Bifid shunt and explain its role in ICGEB2008. An in-depth study has been performed to understand the metabolic pathways involved in ethanol, 2,3-butanediol and hydrogen production, which can be utilized as a basis for further metabolic engineering efforts to improve the efficiency of biofuel production by this P. polymyxa strain.
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Affiliation(s)
- Nidhi Adlakha
- />Synthetic Biology and Biofuels Group, International Centre for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi, India
| | - Thomas Pfau
- />Institute of Complex Systems and Mathematical Biology, University of Aberdeen, Aberdeen, UK
- />Life Sciences Research Unit, University of Luxembourg, Luxembourg City, Luxembourg
| | - Oliver Ebenhöh
- />Institute of Complex Systems and Mathematical Biology, University of Aberdeen, Aberdeen, UK
- />Cluster of Excellence on Plant Sciences (CEPLAS), Heinrich-Heine-University, Universitätsstraße 1, 40225 Düsseldorf, Germany
| | - Syed Shams Yazdani
- />Synthetic Biology and Biofuels Group, International Centre for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi, India
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Chengxin FAN. Progress and prospect in formation of black bloom in Lake Taihu: A review. ACTA ACUST UNITED AC 2015. [DOI: 10.18307/2015.0401] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/01/2022]
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Molecular and evolutionary analysis of NEAr-iron Transporter (NEAT) domains. PLoS One 2014; 9:e104794. [PMID: 25153520 PMCID: PMC4143258 DOI: 10.1371/journal.pone.0104794] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2012] [Accepted: 07/18/2014] [Indexed: 12/25/2022] Open
Abstract
Iron is essential for bacterial survival, being required for numerous biological processes. NEAr-iron Transporter (NEAT) domains have been studied in pathogenic Gram-positive bacteria to understand how their proteins obtain heme as an iron source during infection. While a 2002 study initially discovered and annotated the NEAT domain encoded by the genomes of several Gram-positive bacteria, there remains a scarcity of information regarding the conservation and distribution of NEAT domains throughout the bacterial kingdom, and whether these domains are restricted to pathogenic bacteria. This study aims to expand upon initial bioinformatics analysis of predicted NEAT domains, by exploring their evolution and conserved function. This information was used to identify new candidate domains in both pathogenic and nonpathogenic organisms. We also searched metagenomic datasets, specifically sequence from the Human Microbiome Project. Here, we report a comprehensive phylogenetic analysis of 343 NEAT domains, encoded by Gram-positive bacteria, mostly within the phylum Firmicutes, with the exception of Eggerthella sp. (Actinobacteria) and an unclassified Mollicutes bacterium (Tenericutes). No new NEAT sequences were identified in the HMP dataset. We detected specific groups of NEAT domains based on phylogeny of protein sequences, including a cluster of novel clostridial NEAT domains. We also identified environmental and soil organisms that encode putative NEAT proteins. Biochemical analysis of heme binding by a NEAT domain from a protein encoded by the soil-dwelling organism Paenibacillus polymyxa demonstrated that the domain is homologous in function to NEAT domains encoded by pathogenic bacteria. Together, this study provides the first global bioinformatics analysis and phylogenetic evidence that NEAT domains have a strong conservation of function, despite group-specific differences at the amino acid level. These findings will provide information useful for future projects concerning the structure and function of NEAT domains, particularly in pathogens where they have yet to be studied.
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Gadelle D, Krupovic M, Raymann K, Mayer C, Forterre P. DNA topoisomerase VIII: a novel subfamily of type IIB topoisomerases encoded by free or integrated plasmids in Archaea and Bacteria. Nucleic Acids Res 2014; 42:8578-91. [PMID: 24990376 PMCID: PMC4117785 DOI: 10.1093/nar/gku568] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2014] [Revised: 06/10/2014] [Accepted: 06/11/2014] [Indexed: 11/14/2022] Open
Abstract
Type II DNA topoisomerases are divided into two families, IIA and IIB. Types IIA and IIB enzymes share homologous B subunits encompassing the ATP-binding site, but have non-homologous A subunits catalyzing DNA cleavage. Type IIA topoisomerases are ubiquitous in Bacteria and Eukarya, whereas members of the IIB family are mostly present in Archaea and plants. Here, we report the detection of genes encoding type IIB enzymes in which the A and B subunits are fused into a single polypeptide. These proteins are encoded in several bacterial genomes, two bacterial plasmids and one archaeal plasmid. They form a monophyletic group that is very divergent from archaeal and eukaryotic type IIB enzymes (DNA topoisomerase VI). We propose to classify them into a new subfamily, denoted DNA topoisomerase VIII. Bacterial genes encoding a topoisomerase VIII are present within integrated mobile elements, most likely derived from conjugative plasmids. Purified topoisomerase VIII encoded by the plasmid pPPM1a from Paenibacillus polymyxa M1 had ATP-dependent relaxation and decatenation activities. In contrast, the enzyme encoded by mobile elements integrated into the genome of Ammonifex degensii exhibited DNA cleavage activity producing a full-length linear plasmid and that from Microscilla marina exhibited ATP-independent relaxation activity. Topoisomerases VIII, the smallest known type IIB enzymes, could be new promising models for structural and mechanistic studies.
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Affiliation(s)
- Danièle Gadelle
- Université Paris-Sud, CNRS UMR8621, Institut de Génétique Microbiologie, 91405 Orsay Cedex, France
| | - Mart Krupovic
- Institut Pasteur, Unité de Biologie moléculaire du gène chez les extrêmophiles, Département de Microbiologie, F-75015 Paris, France
| | - Kasie Raymann
- Institut Pasteur, Unité de Biologie moléculaire du gène chez les extrêmophiles, Département de Microbiologie, F-75015 Paris, France
| | - Claudine Mayer
- Institut Pasteur, Unité de Microbiologie structurale, Département de Biologie structurale et Chimie, F-75015 Paris, France CNRS, UMR3528, F-75015 Paris, France Université Paris Diderot, Sorbonne Paris Cité, Cellule Pasteur, rue du Dr Roux 75015 Paris, France
| | - Patrick Forterre
- Université Paris-Sud, CNRS UMR8621, Institut de Génétique Microbiologie, 91405 Orsay Cedex, France Institut Pasteur, Unité de Biologie moléculaire du gène chez les extrêmophiles, Département de Microbiologie, F-75015 Paris, France
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Complete Genome Sequence of Paenibacillus polymyxa SQR-21, a Plant Growth-Promoting Rhizobacterium with Antifungal Activity and Rhizosphere Colonization Ability. GENOME ANNOUNCEMENTS 2014; 2:2/2/e00281-14. [PMID: 24723719 PMCID: PMC3983308 DOI: 10.1128/genomea.00281-14] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Here we report the complete genome sequence of a plant growth-promoting rhizobacterium (PGPR), Paenibacillus polymyxa SQR-21, which consists of one circular chromosome of 5,828,438 bp with 5,024 coding sequences (CDS). The data presented highlight multiple sets of functional genes associated with its plant-beneficial characteristics.
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Complete Genome Sequence of Paenibacillus polymyxa CR1, a Plant Growth-Promoting Bacterium Isolated from the Corn Rhizosphere Exhibiting Potential for Biocontrol, Biomass Degradation, and Biofuel Production. GENOME ANNOUNCEMENTS 2014; 2:2/1/e01218-13. [PMID: 24459277 PMCID: PMC3900909 DOI: 10.1128/genomea.01218-13] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Here we report the complete genome sequence of the bacterium Paenibacillus polymyxa CR1 (accession no. CP006941), which consists of one circular chromosome of 6,024,666 bp with 5,283 coding sequences (CDS), 87 tRNAs, and 12 rRNA operons. Data presented will allow for further insights into the mechanisms underpinning agriculturally and industrially relevant processes.
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