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Yin L, Zhou A, Wei Y, Varrone C, Li D, Luo J, He Z, Liu W, Yue X. Deep insights into the roles and microbial ecological mechanisms behind waste activated sludge digestion triggered by persulfate oxidation activated through multiple modes. ENVIRONMENTAL RESEARCH 2024; 252:118905. [PMID: 38604480 DOI: 10.1016/j.envres.2024.118905] [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: 02/14/2024] [Revised: 03/23/2024] [Accepted: 04/08/2024] [Indexed: 04/13/2024]
Abstract
Persulfate oxidation (PS) is widely employed as a promising alternative for waste activated sludge pretreatment due to the capability of generating free radicals. The product differences and microbiological mechanisms by which PS activation triggers WAS digestion through multiple modes need to be further investigated. This study comprehensively investigated the effects of persulfate oxidation activated through multiple modes, i.e., ferrous, zero-valent iron (ZVI), ultraviolet (UV) and heat, on the performance of sludge digestion. Results showed that PS_ZVI significantly accelerated the methane production rate to 12.02 mL/g VSS. By contrast, PS_Heat promoted the sludge acidification and gained the maximum short-chain fatty acids (SCFAs) yield (277.11 ± 7.81 mg COD/g VSS), which was 3.41-fold compared to that in PS_ZVI. Moreover, ferrous and ZVI activated PS achieved the oriented conversion of acetate, the proportions of which took 73% and 78%, respectively. MiSeq sequencing results revealed that PS_Heat and PS_UV evidently enriched anaerobic fermentation bacteria (AFB) (i.e., Macellibacteroides and Clostridium XlVa). However, PS_Ferrous and PS_ZVI facilitated the enrichment of Woesearchaeota and methanogens. Furthermore, molecular ecological network and mantel test revealed the intrinsic interactions among the multiple functional microbes and environmental variables. The homo-acetogens and sulfate-reducing bacterial had potential cooperative and symbiotic relationships with AFB, while the nitrate-reducing bacteria displayed distinguishing ecological niches. Suitable activation modes for PS pretreatments resulted in an upregulation of genes expression responsible for digestion. This study established a scientific foundation for the application of sulfate radical-based oxidation on energy or high value-added chemicals recovery from waste residues.
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Affiliation(s)
- Lijiao Yin
- College of Environmental Science and Engineering, Taiyuan University of Technology, Taiyuan, 030024, China
| | - Aijuan Zhou
- College of Environmental Science and Engineering, Taiyuan University of Technology, Taiyuan, 030024, China; Shanxi-Zheda Institute of Advanced Materials and Chemical Engineering, Taiyuan, 030000, China.
| | - Yaoli Wei
- College of Environmental Science and Engineering, Taiyuan University of Technology, Taiyuan, 030024, China
| | - Cristiano Varrone
- Department of Chemistry and BioScience, Aalborg University, Copenhagen, Denmark
| | - Dengfei Li
- College of Environmental Science and Engineering, Taiyuan University of Technology, Taiyuan, 030024, China
| | - Jingyang Luo
- College of Environment, Hohai University, Nanjing, 210098, China
| | - Zhangwei He
- Shaanxi Key Laboratory of Environmental Engineering, School of Environmental and Municipal Engineering, Xi'an University of Architecture and Technology, Xi'an, 710055, China
| | - Wenzong Liu
- School of Civil and Environmental Engineering, Harbin Institute of Technology Shenzhen, Shenzhen, 518005, China
| | - Xiuping Yue
- College of Environmental Science and Engineering, Taiyuan University of Technology, Taiyuan, 030024, China; Shanxi-Zheda Institute of Advanced Materials and Chemical Engineering, Taiyuan, 030000, China; Shanxi Engineer Research Institute of Sludge Disposition and Resources, Taiyuan University of Technology, Taiyuan, 030024, China
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Miyazaki U, Mizutani D, Hashimoto Y, Tame A, Sawayama S, Miyazaki J, Takai K, Nakagawa S. Helicovermis profundi gen. nov., sp. nov., a novel mesophilic, asporogenous bacterium within the Clostridia isolated from a deep-sea hydrothermal vent chimney. Antonie Van Leeuwenhoek 2024; 117:24. [PMID: 38217723 DOI: 10.1007/s10482-023-01919-9] [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: 08/18/2023] [Accepted: 12/12/2023] [Indexed: 01/15/2024]
Abstract
A novel mesophilic bacterial strain, designated S502T, was isolated from a deep-sea hydrothermal vent at Suiyo Seamount, Japan. Cells were Gram-positive, asporogenous, motile, and curved rods, measuring 1.6-5.6 µm in length. The strain was an obligate anaerobe that grew fermentatively on complex substrates such as yeast extract and Bacto peptone. Elemental sulfur stimulated the growth of the strain, and was reduced to hydrogen sulfide. The strain grew within a temperature range of 10-23 °C (optimum at 20 °C), pH range of 4.8-8.3 (optimum at 7.4), and a NaCl concentration range of 1.0-4.0% (w/v) (optimum at 3.0%, w/v). Phylogenetic analysis based on the 16S rRNA gene sequence revealed that the isolate was a member of the class Clostridia, with Fusibacter paucivorans strain SEBR 4211T (91.1% sequence identity) being its closest relative. The total size of the genome of the strain was 3.12 Mbp, and a G + C content was 28.2 mol%. The highest values for average nucleotide identity (ANI), average amino acid identity (AAI), and digital DNA-DNA hybridization (dDDH) value of strain S502T with relatives were 67.5% (with Marinisporobacter balticus strain 59.4MT), 51.5% (with M. balticus strain 59.4MT), and 40.9% (with Alkaliphilus serpentinus strain LacTT), respectively. Based on a combination of phylogenetic, genomic, and phenotypic characteristics, we propose strain S502T to represent a novel genus and species, Helicovermis profundi gen. nov., sp. nov., with the type strain S502T (= DSM 112048T = JCM 39167T).
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Affiliation(s)
- Urara Miyazaki
- Laboratory of Marine Environmental Microbiology, Division of Applied Biosciences, Graduate School of Agriculture, Kyoto University, Oiwake-Cho, Kitashirakawa, Sakyo-Ku, Kyoto, 606-8502, Japan
| | - Daiki Mizutani
- Laboratory of Marine Environmental Microbiology, Division of Applied Biosciences, Graduate School of Agriculture, Kyoto University, Oiwake-Cho, Kitashirakawa, Sakyo-Ku, Kyoto, 606-8502, Japan
| | - Yurina Hashimoto
- Laboratory of Marine Environmental Microbiology, Division of Applied Biosciences, Graduate School of Agriculture, Kyoto University, Oiwake-Cho, Kitashirakawa, Sakyo-Ku, Kyoto, 606-8502, Japan
| | - Akihiro Tame
- Depertment of Marine and Earth Sciences, Marine Works Japan Ltd, 3-54-1 Oppamahigashi, Yokosuka, 237-0063, Japan
- General Affairs Department, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), 2-15 Natsushima-Cho, Yokosuka, 237-0061, Japan
| | - Shigeki Sawayama
- Laboratory of Marine Environmental Microbiology, Division of Applied Biosciences, Graduate School of Agriculture, Kyoto University, Oiwake-Cho, Kitashirakawa, Sakyo-Ku, Kyoto, 606-8502, Japan
| | - Junichi Miyazaki
- Institute for Extra-Cutting-Edge Science and Technology Avant-Garde Research (X-Star), Japan Agency for Marine-Earth Science & Technology (JAMSTEC), 2-15 Natsushima-Cho, Yokosuka, 237-0061, Japan
| | - Ken Takai
- Institute for Extra-Cutting-Edge Science and Technology Avant-Garde Research (X-Star), Japan Agency for Marine-Earth Science & Technology (JAMSTEC), 2-15 Natsushima-Cho, Yokosuka, 237-0061, Japan
- Section for Exploration of Life in Extreme Environments, Exploratory Research Center On Life and Living Systems (ExCELLS), National Institute of Natural Sciences, 5-1 Higashiyama, Myodaiji-Cho, Okazaki, 444-8787, Japan
| | - Satoshi Nakagawa
- Laboratory of Marine Environmental Microbiology, Division of Applied Biosciences, Graduate School of Agriculture, Kyoto University, Oiwake-Cho, Kitashirakawa, Sakyo-Ku, Kyoto, 606-8502, Japan.
- Institute for Extra-Cutting-Edge Science and Technology Avant-Garde Research (X-Star), Japan Agency for Marine-Earth Science & Technology (JAMSTEC), 2-15 Natsushima-Cho, Yokosuka, 237-0061, Japan.
- Section for Exploration of Life in Extreme Environments, Exploratory Research Center On Life and Living Systems (ExCELLS), National Institute of Natural Sciences, 5-1 Higashiyama, Myodaiji-Cho, Okazaki, 444-8787, Japan.
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Brioukhanov AL, Kadnikov VV, Beletsky AV, Savvichev AS. Aerotolerant Thiosulfate-Reducing Bacterium Fusibacter sp. Strain WBS Isolated from Littoral Bottom Sediments of the White Sea-Biochemical and Genome Analysis. Microorganisms 2023; 11:1642. [PMID: 37512815 PMCID: PMC10386464 DOI: 10.3390/microorganisms11071642] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Revised: 06/19/2023] [Accepted: 06/20/2023] [Indexed: 07/30/2023] Open
Abstract
The strain WBS, an anaerobic, psychro- and halotolerant bacterium belonging to the genus Fusibacter, was isolated from the littoral bottom sediments of the White Sea, Arctic, Russia. Fusibacter bizertensis WBS grew at temperatures between 8 and 32 °C (optimum growth at 18-20 °C), pH between 5.2 and 8.3 (optimum growth at pH 7.2), and at NaCl concentrations between 0 and 70 g L-1 (optimum growth at 32 g L-1). It reduced sulfate, thiosulfate, and elemental sulfur into sulfide, and, probably, the strain is able to disproportionate thiosulfate. The strain also utilized a wide range of substrates as it is a chemoorganotrophic bacterium. Analysis of the sequenced genome revealed genes for all enzymes involved in the Embden-Meyerhof glycolytic pathway as well as genes for the non-oxidative stage of the pentose phosphate pathway. The presence of genes encoding aldehyde dehydrogenases and alcohol dehydrogenases also suggests that, in addition to acetate, alcohols can also be the fermentation products. The strain possessed superoxide dismutase and peroxidase activities and the ability to consume O2, which is in full accordance with the presence of corresponding genes of antioxidant defense in the genome. The phylogenetic analysis suggested that the strain WBS is the closest relative of Fusibacter bizertensis LTF Kr01T (16S rRNA gene sequence similarity 98.78%). Based on biochemical and genomic characteristics, the strain WBS is proposed to represent a novel aero-, halo- and psychrotolerant strain from the genus Fusibacter, isolated for the first time among its members from cold oxygenated marine bottom sediments.
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Affiliation(s)
| | - Vitaly V Kadnikov
- Skryabin Institute of Bioengineering, Research Center of Biotechnology, Russian Academy of Sciences, 117312 Moscow, Russia
| | - Alexey V Beletsky
- Skryabin Institute of Bioengineering, Research Center of Biotechnology, Russian Academy of Sciences, 117312 Moscow, Russia
| | - Alexander S Savvichev
- Winogradsky Institute of Microbiology, Research Center of Biotechnology, Russian Academy of Sciences, 117312 Moscow, Russia
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Chang CC, Li SL, Wu ZX, Yu CP. Developing a novel computer numerical control-fabricated laminar-flow microfluidic microbial fuel cells as the bioelectrochemical sensor and power source: Enrichment, operation, and Cr(VI) detection. Biosens Bioelectron 2023; 226:115119. [PMID: 36764128 DOI: 10.1016/j.bios.2023.115119] [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: 11/06/2022] [Revised: 01/20/2023] [Accepted: 02/01/2023] [Indexed: 02/07/2023]
Abstract
By introducing the computer numerical control (CNC) engraving technology, this study fabricated the reusable CNC-fabricated membrane-less laminar flow microfluidic MFC (LMMFC) to develop the bioelectrochemical sensor and power source simultaneously. To verify its applicability, optimization of electroactive bacteria (EAB) cultivation and laminar-flow formation, performance of power density and long-term operation, and detection of Cr(VI) were evaluated. Results of EAB optimization showed under lower external resistance, shorter start-up time of current production, larger oxidation current, denser microbial distribution, and a higher percentage of Geobacter spp. were observed. Results of the laminar-flow operation indicated that increasing the density difference between two solutions and raising the anode flow velocity can minimize the interference of the diffusion zone. The power output of LMMFC could reach 2085 mW m-2 and achieve long-term stability for current production (∼150 h). Regarding the detection of Cr(VI), low-concentration (0.1∼1 ppm) and high-concentration (1-10 ppm) ranges reached the linear coefficient of determination of 0.98 and 0.97, respectively. Overall, these results suggest that an LMMFC which can both act as the power source and biosensor was successfully developed, showing potential for future self-power application.
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Affiliation(s)
- Chao-Chin Chang
- Graduate Institute of Environmental Engineering, National Taiwan University, No. 1, Sec. 4, Roosevelt Rd, Taipei, 10617, Taiwan, ROC
| | - Shiue-Lin Li
- Environmental Science and Engineering, TungHai University, No. 1727, Sec. 4, Taiwan Boulevard, Xitun District, Taichung, 407224, Taiwan, ROC
| | - Zhong-Xian Wu
- Graduate Institute of Environmental Engineering, National Taiwan University, No. 1, Sec. 4, Roosevelt Rd, Taipei, 10617, Taiwan, ROC
| | - Chang-Ping Yu
- Graduate Institute of Environmental Engineering, National Taiwan University, No. 1, Sec. 4, Roosevelt Rd, Taipei, 10617, Taiwan, ROC.
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Zhang K, Zhu Z, Peng M, Tian L, Chen Y, Zhu J, Gan M. Enhancement of Cr(VI) reduction by indigenous bacterial consortia using natural pyrite: A detailed study to elucidate the mechanisms involved in the highly efficient and possible sustainable system. CHEMOSPHERE 2022; 308:136228. [PMID: 36041522 DOI: 10.1016/j.chemosphere.2022.136228] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Revised: 07/28/2022] [Accepted: 08/24/2022] [Indexed: 06/15/2023]
Abstract
Pyrite was applied to Cr(VI) bioremediation as an inorganic electron donor due to the ability to provide electrons, while the role of pyrite in Cr(VI) bioremediation where organics as electron donors remains unknown. Herein a pyrite-based Cr(VI) bioreduction process in the sediment system containing lactate was demonstrated to be effective to detoxify Cr(VI): over 2200 mg L-1 Cr(VI) was continuously removed within 210 h with high reactivity (10.5 mg/(L·h)) all along. High-throughput 16S rDNA gene sequencing indicated that the pyrite could shape a functioning community that electrochemically active bacteria dominated (such as Fusibacter sp. and Rhodobacteraceae) instead of iron-oxidizing bacteria and sulfur-oxidizing bacteria. Mineralogy analysis results indicated that Fe(III), S22- and S0 formed on the pyrite surface after the oxidation of Cr(VI) might serve as the electron acceptor of microflora, then the S2- and Fe(II) with strong Cr(VI) reduction ability were formed by microbial reduction to enhance the removal of Cr(VI). This study provides new insights into thoroughly understanding the role of pyrite in the practical application of Cr(VI) bioreduction.
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Affiliation(s)
- Ke Zhang
- School of Minerals Processing and Bioengineering, Key Laboratory of Biohydrometallurgy of Ministry of Education, Central South University, Changsha, 410083, China
| | - Zhenyu Zhu
- Faculty of Agriculture, Forestry and Food Engineering, Yibin University, Yibin, 644000, China
| | - Mingxian Peng
- School of Minerals Processing and Bioengineering, Key Laboratory of Biohydrometallurgy of Ministry of Education, Central South University, Changsha, 410083, China
| | - Luyan Tian
- School of Minerals Processing and Bioengineering, Key Laboratory of Biohydrometallurgy of Ministry of Education, Central South University, Changsha, 410083, China
| | - Yaozong Chen
- School of Minerals Processing and Bioengineering, Key Laboratory of Biohydrometallurgy of Ministry of Education, Central South University, Changsha, 410083, China
| | - Jianyu Zhu
- School of Minerals Processing and Bioengineering, Key Laboratory of Biohydrometallurgy of Ministry of Education, Central South University, Changsha, 410083, China.
| | - Min Gan
- School of Minerals Processing and Bioengineering, Key Laboratory of Biohydrometallurgy of Ministry of Education, Central South University, Changsha, 410083, China.
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Acosta-Grinok M, Vázquez S, Guiliani N, Marín S, Demergasso C. Looking for the mechanism of arsenate respiration of Fusibacter sp. strain 3D3, independent of ArrAB. Front Microbiol 2022; 13:1029886. [PMID: 36532432 PMCID: PMC9751042 DOI: 10.3389/fmicb.2022.1029886] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2022] [Accepted: 11/08/2022] [Indexed: 12/02/2022] Open
Abstract
The literature has reported the isolation of arsenate-dependent growing microorganisms which lack a canonical homolog for respiratory arsenate reductase, ArrAB. We recently isolated an arsenate-dependent growing bacterium from volcanic arsenic-bearing environments in Northern Chile, Fusibacter sp. strain 3D3 (Fas) and studied the arsenic metabolism in this Gram-positive isolate. Features of Fas deduced from genome analysis and comparative analysis with other arsenate-reducing microorganisms revealed the lack of ArrAB coding genes and the occurrence of two arsC genes encoding for putative cytoplasmic arsenate reductases named ArsC-1 and ArsC-2. Interestingly, ArsC-1 and ArsC-2 belong to the thioredoxin-coupled family (because of the redox-active disulfide protein used as reductant), but they conferred differential arsenate resistance to the E. coli WC3110 ΔarsC strain. PCR experiments confirmed the absence of arrAB genes and results obtained using uncouplers revealed that Fas growth is linked to the proton gradient. In addition, Fas harbors ferredoxin-NAD+ oxidoreductase (Rnf) and electron transfer flavoprotein (etf) coding genes. These are key molecular markers of a recently discovered flavin-based electron bifurcation mechanism involved in energy conservation, mainly in anaerobic metabolisms regulated by the cellular redox state and mostly associated with cytoplasmic enzyme complexes. At least three electron-bifurcating flavoenzyme complexes were evidenced in Fas, some of them shared in conserved genomic regions by other members of the Fusibacter genus. These physiological and genomic findings permit us to hypothesize the existence of an uncharacterized arsenate-dependent growth metabolism regulated by the cellular redox state in the Fusibacter genus.
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Affiliation(s)
| | - Susana Vázquez
- Cátedra de Biotecnología, Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires, Buenos Aires, Argentina,Instituto de Nanobiotecnología (NANOBIOTEC), Universidad de Buenos Aires (UBA) - Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | - Nicolás Guiliani
- Departamento de Biología, Facultad de Ciencias, Universidad de Chile, Antofagasta, Chile
| | - Sabrina Marín
- Biotechnology Center, Universidad Católica del Norte, Antofagasta, Chile
| | - Cecilia Demergasso
- Biotechnology Center, Universidad Católica del Norte, Antofagasta, Chile,Nucleus for the Study of Cancer at a Basic, Applied, and Clinical Level, Universidad Católica del Norte, Antofagasta, Chile,*Correspondence: Cecilia Demergasso,
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Perinatal Propionate Supplementation Protects Adult Male Offspring from Maternal Chronic Kidney Disease-Induced Hypertension. Nutrients 2022; 14:nu14163435. [PMID: 36014941 PMCID: PMC9412881 DOI: 10.3390/nu14163435] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Revised: 08/17/2022] [Accepted: 08/19/2022] [Indexed: 12/13/2022] Open
Abstract
Emerging evidence supports that early-life disturbance of gut microbiota has an impact on adult disease in later life. Offspring hypertension can be programmed by maternal chronic kidney disease (CKD). Conversely, perinatal use of gut microbiota-targeted therapy has been implemented to reverse programming processes and prevent hypertension. Short-chain fatty acids (SCFAs), the major gut microbiota-derived metabolites, can be applied as postbiotics. Propionate, one of predominant SCFAs, has been shown to have antihypertensive property. We examined whether perinatal propionate supplementation can prevent offspring hypertension induced by maternal CKD. CKD was induced by chow supplemented with 0.5% adenine for 3 weeks before pregnancy. Propionate (P) was supplemented at 200 mmol/L in drinking water during pregnancy and lactation. Male offspring were divided into four groups (n = 7–8/group): control, CKD, control+propionate (CP), and CKD+propionate (CKDP). Maternal CKD-induced offspring hypertension was reversed by perinatal propionate supplementation. The protective effects of perinatal propionate treatment were related to increased propionate-generating bacteria Clostridium spp. and plasma propionate level, increased expression of renal G protein-coupled receptor 41 (GPR41, a SCFA receptor), augmentation of α-diversity, and shifts in gut microbiota composition. In summary, our results highlight that maternal CKD-induced offspring hypertension can be prevented by the use of gut microbial metabolite SCFAs in early life, which could shed light on the prevention of the current hypertension pandemic.
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Zou Z, Yang H, Zhang S, Chi W, Wang X, Liu Z. Nitrogen removal performance and microbial community analysis of immobilized biological fillers in rare earth mine wastewater. Biochem Eng J 2022. [DOI: 10.1016/j.bej.2022.108559] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
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9
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DNA- and RNA-based bacterial communities and geochemical zonation under changing sediment porewater dynamics on the Aldabra Atoll. Sci Rep 2022; 12:4257. [PMID: 35277525 PMCID: PMC8917147 DOI: 10.1038/s41598-022-07980-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Accepted: 02/28/2022] [Indexed: 11/26/2022] Open
Abstract
The remote Aldabra Atoll, Seychelles, provides the rare opportunity to study bacterial communities in pristine carbonate sediments across an entire biome. The four sampled sites cover sand with high porewater exchange, bioturbated silt and mud with intermediate exchange, as well as a seasonally and episodically desiccated landlocked pool. As sediments harbour dead cells and environmental DNA alongside live cells, we used bacterial 16S rRNA gene and transcript analysis to distinguish between past and present inhabitants. Previously described laminated sediments mirroring past conditions in the Cerin, France could not be retrieved. Thus, the aim was adjusted to determine whether bacterial community composition and diversity follow typical geochemical zonation patterns at different locations of the atoll. Our data confirm previous observations that diversity decreases with depth. In the lagoon, the bacterial community composition changed from Pseudomonas dominating in the sand to diverse mixed surface and sulphate reduction zones in the anaerobic mud with strongly negative Eh. The latter correlated with high total alkalinity, ammonia, and total sulphide, alongside a decrease in SO42−/Cl− and high relative abundances of sulphate reducing (Halo-) Desulfovibrio, sulphur oxidizing Arcobacteraceae, photo(hetero)troph Cyanobacteria, Alphaproteobacteria, and fermenting Propionigenium. In contrast to expectations, deeper mud and pool sediments harboured high abundances of Halomonas or Alphaproteobacteria alongside high C/N and increased salinity. We believe that this atypical community shift may be driven by a change in the complexity of available organic matter.
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Qiu D, Zeng X, Zeng L, Li G, Shao Z. Fusibacter ferrireducens sp. nov., an anaerobic, Fe(Ⅲ)- and sulphur-reducing bacterium isolated from mangrove sediment. Int J Syst Evol Microbiol 2021; 71. [PMID: 34739363 DOI: 10.1099/ijsem.0.004952] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
An anaerobic, alkaliphilic, halotolerant, Gram-stain-positive and rod-shaped bacterium, designated Q10-2T, was isolated from mangrove sediment sampled at the Jiulong river estuary, PR China. The cells of strain Q10-2T were motile and 0.5×2-4 µm in size. Strain Q10-2T grew at 8-45 °C (optimum, 32 °C), at pH 7.0-10.5 (optimum, pH 8.5) and in the presence of 0-6 % (w/v) NaCl (optimum, 3 %). It could use complex organic compounds and carbohydrates including d-fructose, d-galactose, d-glucose, d-mannitol, d-xylose, trehalose, lactose, maltose, sucrose and starch as carbon sources and electron donors. It could reduce sulphate, thiosulphate and elemental sulphur to sulphide, but not sulphite. Fe (Ⅲ) citrate, ferrihydrite, haematite and goethite in the presence of glucose as the electron donor were also reduced. Acetate, butyrate, ethanol, CO2 and H2 were end products of glucose fermentation. The predominant cellular fatty acids were composed of C14 : 0, C16 : 0 and summed features containing C16 : 1 ω7c and/or iso-C15 : 0 2-OH and iso-C17 : 1 and/or anteiso-C17 : 1 B. Phylogenetic analysis based on 16S rRNA gene sequences indicated that the novel strain was most closely related to Fusibacter paucivorans DSM 12116T (95.5 % sequence similarity). The genome size of strain Q10-2T was 5.0 Mb, with a G+C content of 37.4 mol%. The average nucleotide identity and digital DNA-DNA hybridization values between strain Q10-2T and F. paucivorans DSM 12116T were 69.1 and 21.8 %, respectively. The combined genotypic and phenotypic data showed that strain Q10-2T represents a novel species of the genus Fusibacter, for which the name Fusibacter ferrireducens sp. nov. is proposed. The type strain is Q10-2T (=MCCC 1A16257T=KCTC 15906T).
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Affiliation(s)
- Donghua Qiu
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen 361005, PR China.,State Key Laboratory Breeding Base of Marine Genetic Resources, Fujian Key Laboratory of Marine Genetic Resource, Xiamen 361005, PR China
| | - Xiang Zeng
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen 361005, PR China.,State Key Laboratory Breeding Base of Marine Genetic Resources, Fujian Key Laboratory of Marine Genetic Resource, Xiamen 361005, PR China
| | - Lingyu Zeng
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen 361005, PR China.,State Key Laboratory Breeding Base of Marine Genetic Resources, Fujian Key Laboratory of Marine Genetic Resource, Xiamen 361005, PR China
| | - Guangyu Li
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen 361005, PR China.,State Key Laboratory Breeding Base of Marine Genetic Resources, Fujian Key Laboratory of Marine Genetic Resource, Xiamen 361005, PR China
| | - Zongze Shao
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen 361005, PR China.,State Key Laboratory Breeding Base of Marine Genetic Resources, Fujian Key Laboratory of Marine Genetic Resource, Xiamen 361005, PR China.,Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai 519000, PR China
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11
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Ruen-Pham K, Graham LE, Satjarak A. Spatial Variation of Cladophora Epiphytes in the Nan River, Thailand. PLANTS (BASEL, SWITZERLAND) 2021; 10:2266. [PMID: 34834629 PMCID: PMC8622721 DOI: 10.3390/plants10112266] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Revised: 10/19/2021] [Accepted: 10/20/2021] [Indexed: 11/16/2022]
Abstract
Cladophora is an algal genus known to be ecologically important. It provides habitats for microorganisms known to provide ecological services such as biosynthesis of cobalamin (vitamin B12) and nutrient cycling. Most knowledge of microbiomes was obtained from studies of lacustrine Cladophora species. However, whether lotic freshwater Cladophora microbiomes are as complex as the lentic ones or provide similar ecological services is not known. To illuminate these issues, we used amplicons of 16S rDNA, 18S rDNA, and ITS to investigate the taxonomy and diversity of the microorganisms associated with replicate Cladophora samples from three sites along the Nan River, Thailand. Results showed that the diversity of prokaryotic and eukaryotic members of Cladophora microbiomes collected from different sampling sites was statistically different. Fifty percent of the identifiable taxa were shared across sampling sites: these included organisms belonging to different trophic levels, decomposers, and heterotrophic bacteria. These heterogeneous assemblages of bacteria, by functional inference, have the potential to perform various ecological functions, i.e., cellulose degradation, cobalamin biosynthesis, fermentative hydrogen production, ammonium oxidation, amino acid fermentation, dissimilatory reduction of nitrate to ammonium, nitrite reduction, nitrate reduction, sulfur reduction, polyphosphate accumulation, denitrifying phosphorus-accumulation, and degradation of aromatic compounds. Results suggested that river populations of Cladophora provide ecologically important habitat for microorganisms that are key to nutrient cycling in lotic ecosystems.
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Affiliation(s)
- Karnjana Ruen-Pham
- Plants of Thailand Research Unit, Department of Botany, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand;
| | - Linda E. Graham
- Department of Botany, University of Wisconsin-Madison, 430 Lincoln Drive, Madison, WI 53706, USA;
| | - Anchittha Satjarak
- Plants of Thailand Research Unit, Department of Botany, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand;
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12
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Leng Q, Mu J, Yang G. Efficient anaerobic bioremediation of high-concentration benzo[a]pyrene in marine environments. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2021; 284:117210. [PMID: 33932831 DOI: 10.1016/j.envpol.2021.117210] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/08/2020] [Revised: 04/05/2021] [Accepted: 04/20/2021] [Indexed: 06/12/2023]
Abstract
Benzo[a]pyrene (BaP), a persistent organic pollutant that may accumulate in sea sediments after oil spill or BaP chemical leakage accidents, considerably harms marine ecosystems and human health. Previous studies have been predominantly focused on its degradation at low concentrations, while the remediation of BaP pollution with high concentrations was neglected. Additionally, the metabolic pathways associated with its anaerobic degradation remain unclear. As a first attempt, super-efficient systems for BaP anaerobic degradation were established, and the corresponding metabolic pathways were elucidated in this study. The results showed that the BaP removal rate in BaP-only system with initial concentrations of 200 mg/L reached 3.09 mg/(L·d) within 45 days. Co-solvent, acetone promoted anaerobic BaP degradation (4.252 mg/(L·d)), while dichloromethane showed a newly-discovered co-metabolic effect. In the system with 500 mg/L of BaP and dichloromethane addition, the removal rate increased drastically (14.64 mg/(L·d)) at 400 mg/L turn point of BaP. Additionally, the corresponding microbial community-level metabolic network was firstly proposed.
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Affiliation(s)
- Qingxue Leng
- School of Marine Science & Technology, Zhejiang Ocean University, Zhoushan, Zhejiang, 316022, China
| | - Jun Mu
- School of Ecological & Environment, Hainan Tropical Ocean University, Sanya, Hainan, 572022, China.
| | - Guangfeng Yang
- School of Marine Science & Technology, Zhejiang Ocean University, Zhoushan, Zhejiang, 316022, China
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13
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Valkanas MM, Rosso T, Packard JE, Trun NJ. Limited carbon sources prevent sulfate remediation in circumneutral abandoned mine drainage. FEMS Microbiol Ecol 2021; 97:6070647. [PMID: 33417684 DOI: 10.1093/femsec/fiaa262] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2020] [Accepted: 12/31/2020] [Indexed: 01/04/2023] Open
Abstract
Passive remediation systems (PRS) use both biotic and abiotic processes to precipitate contaminants from abandoned mine drainage (AMD) so that the contaminants do not spread into local watersheds. PRS are efficient at removing heavy metals but sulfate remediation frequently does not occur. To understand the reasons for the lack of sulfate remediation, we studied four PRS that treat circumneutral AMD and one raw mine drainage discharge. Using 16S sequencing analysis, microbial community composition revealed a high relative abundance of bacterial families with sulfur cycling genera. Anaerobic abiotic studies showed that sulfide was quickly geochemically oxidized in the presence of iron hydroxides, leading to a buildup of sulfur intermediates. Supplementation of laboratory grown microbes from the PRS with lactate demonstrated the ability of actively growing microbes to overcome this abiotic sulfide oxidation by increasing the rate of sulfate reduction. Thus, the lack of carbon sources in the PRS contributes to the lack of sulfate remediation. Bacterial community analysis of 16S rRNA gene revealed that while the microbial communities in different parts of the PRS were phylogenetically distinct, the contaminated environments selected for communities that shared similar metabolic capabilities.
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Affiliation(s)
- Michelle M Valkanas
- Department of Biological Sciences, Duquesne University, 256 Mellon Hall, 600 Forbes Ave, Pittsburgh, PA 15282, USA
| | - Taylor Rosso
- Department of Biological Sciences, Duquesne University, 256 Mellon Hall, 600 Forbes Ave, Pittsburgh, PA 15282, USA
| | - Jessica E Packard
- Department of Biological Sciences, Duquesne University, 256 Mellon Hall, 600 Forbes Ave, Pittsburgh, PA 15282, USA
| | - Nancy J Trun
- Department of Biological Sciences, Duquesne University, 256 Mellon Hall, 600 Forbes Ave, Pittsburgh, PA 15282, USA
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14
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Liu Z, Zhou A, Wang S, Cheng S, Yin X, Yue X. Quorum sensing shaped microbial consortia and enhanced hydrogen recovery from waste activated sludge electro-fermentation on basis of free nitrous acid treatment. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 766:144348. [PMID: 33418258 DOI: 10.1016/j.scitotenv.2020.144348] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Revised: 12/01/2020] [Accepted: 12/02/2020] [Indexed: 06/12/2023]
Abstract
In this study, the feasibility of free nitrous acid (FNA) pretreatment coupled with quorum sensing (QS) was investigated to enhance hydrogen recovery from waste activated sludge (WAS) via electro-fermentation (EF). 3-oxo-hexanoyl-homoserine lactone (3OC6-HSL), as the signal molecule, was only added in the first three cycles of sludge inoculation at the phase of microbial electrolysis cells (MECs) startup. Results showed that QS combined FNA (AHL-FMEC) enabled highest hydrogen yield and current (4.3 mg/g VSS and 4.5 mA), while that generated from sole FNA/QS treated WAS (FMEC/AHL-RMEC) were only 3.5/3.0 mg/g VSS and 1.5/1.5 mA, respectively. Fourier transform infrared (FT-IR) spectra illustrated the effective conversion of organics in AHL-FMEC, the utilization efficiencies of proteins and carbohydrates achieved to 75.0% and 79.7%, respectively. Besides, the internal resistance decreased from 34.5 Ω (FMEC) to 22.9 Ω (AHL-RMEC), further to 18.0 Ω, indicating the promoted bioelectrochemical activity of electroactive bacteria (EAB) in AHL-FMEC. Correspondingly, both EAB (21.7%), e.g., Geobacter (9.3%) and Pseudomonas (3.2%) and anaerobic fermentation bacteria (AFB, 28.6%), e.g., Proteiniclasticum (14.2%) and Petrimonas (3.6%) enriched to peaks in AHL-FMEC. Moreover, molecular ecological network (MEN) analysis revealed the underling relationships among AFB, EAB and homo-acetogen in EF system, suggesting the possible cooperative QS has been constructed. The results obtained in this study may provide a new insight for efficient hydrogen recovery from electro-fermentation of WAS.
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Affiliation(s)
- Zhihong Liu
- College of Environmental Science and Engineering, Taiyuan University of Technology, Taiyuan, China
| | - Aijuan Zhou
- College of Environmental Science and Engineering, Taiyuan University of Technology, Taiyuan, China; State Key Laboratory of Pollution Control and Resource Reuse, Tongji University, Shanghai 200092, China.
| | - Sufang Wang
- College of Environmental Science and Engineering, Taiyuan University of Technology, Taiyuan, China.
| | - Shuanglan Cheng
- College of Environmental Science and Engineering, Taiyuan University of Technology, Taiyuan, China
| | - Xiaoyun Yin
- College of Environmental Science and Engineering, Taiyuan University of Technology, Taiyuan, China
| | - Xiuping Yue
- College of Environmental Science and Engineering, Taiyuan University of Technology, Taiyuan, China; Shanxi Engineer Research Institute of Sludge Disposition and Resources, Taiyuan, China.
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15
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Philippon T, Tian J, Bureau C, Chaumont C, Midoux C, Tournebize J, Bouchez T, Barrière F. Denitrifying bio-cathodes developed from constructed wetland sediments exhibit electroactive nitrate reducing biofilms dominated by the genera Azoarcus and Pontibacter. Bioelectrochemistry 2021; 140:107819. [PMID: 33894567 DOI: 10.1016/j.bioelechem.2021.107819] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Revised: 03/24/2021] [Accepted: 04/01/2021] [Indexed: 10/21/2022]
Abstract
To limit the nitrate contamination of ground and surface water, stimulation of denitrification by electrochemical approach is an innovative way to be explored. Two nitrate reducing bio-cathodes were developed under constant polarization (-0.5 V vs SCE) using sediments and water from a constructed wetland (Rampillon, Seine-et-Marne, France). The bio-cathodes responded to nitrate addition on chronoamperometry through an increase of the reductive current. The denitrification efficiency of the pilots increased by 47% compared to the negative controls without electrodes after polarization. 16S rRNA gene sequencing of the biofilms and sediments evidenced the significant and discriminating presence of the Azoarcus and Pontibacter genera in the biofilms from biocathodes active for nitrate reduction. Our study shows the possibility to promote the development of efficient Azoarcus-dominated biocathodes from freshwater sediment to enhance nitrate removal from surface waters.
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Affiliation(s)
- Timothé Philippon
- Univ Rennes, CNRS, Institut des Sciences Chimiques de Rennes, 35042 Rennes, France.
| | - Jianghao Tian
- Université Paris-Saclay, INRAE, UR PROSE, 92160 Antony, France
| | | | - Cédric Chaumont
- Université Paris-Saclay, INRAE, UR HYCAR, 92160 Anthony, France
| | - Cédric Midoux
- Université Paris-Saclay, INRAE, UR PROSE, 92160 Antony, France
| | | | | | - Frédéric Barrière
- Univ Rennes, CNRS, Institut des Sciences Chimiques de Rennes, 35042 Rennes, France.
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16
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Clark DE, Pilditch CA, Pearman JK, Ellis JI, Zaiko A. Environmental DNA metabarcoding reveals estuarine benthic community response to nutrient enrichment - Evidence from an in-situ experiment. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2020; 267:115472. [PMID: 32891048 DOI: 10.1016/j.envpol.2020.115472] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Revised: 07/27/2020] [Accepted: 08/19/2020] [Indexed: 06/11/2023]
Abstract
Nutrient loading is a major threat to estuaries and coastal environments worldwide, therefore, it is critical that we have good monitoring tools to detect early signs of degradation in these ecologically important and vulnerable ecosystems. Traditionally, bottom-dwelling macroinvertebrates have been used for ecological health assessment but recent advances in environmental genomics mean we can now characterize less visible forms of biodiversity, offering a more holistic view of the ecosystem and potentially providing early warning signals of disturbance. We carried out a manipulative nutrient enrichment experiment (0, 150 and 600 g N fertilizer m-2) in two estuaries in New Zealand to assess the effects of nutrient loading on benthic communities. After seven months of enrichment, environmental DNA (eDNA) metabarcoding was used to examine the response of eukaryotic (18S rRNA), diatom only (rbcL) and bacterial (16S rRNA) communities. Multivariate analyses demonstrated changes in eukaryotic, diatom and bacterial communities in response to nutrient enrichment at both sites, despite differing environmental conditions. These patterns aligned with changes in macrofaunal communities identified using traditional morphological techniques, confirming concordance between disturbance indicators detected by eDNA and current monitoring approaches. Clear shifts in eukaryotic and bacterial indicator taxa were seen in response to nutrient loading while changes in diatom only communities were more subtle. Community changes were discernible between 0 and 150 g N m-2 treatments, suggesting that estuary health assessment tools could be developed to detect early signs of degradation. Increasing variation in community structure associated with nutrient loading could also be used as an indicator of stress or approaching tipping points. This work represents a first step towards the development of molecular-based estuary monitoring tools, which could provide a more holistic and standardized approach to ecosystem health assessment with faster turn-around times and lower costs.
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Affiliation(s)
- D E Clark
- Cawthron Institute, Private Bag 2, Nelson, 7042, New Zealand; University of Waikato, Gate 1, Knighton Rd, Hamilton, 3240, New Zealand.
| | - C A Pilditch
- University of Waikato, Gate 1, Knighton Rd, Hamilton, 3240, New Zealand
| | - J K Pearman
- Cawthron Institute, Private Bag 2, Nelson, 7042, New Zealand
| | - J I Ellis
- University of Waikato, Private Bag 3105, Tauranga, 3110, New Zealand
| | - A Zaiko
- Cawthron Institute, Private Bag 2, Nelson, 7042, New Zealand; Institute of Marine Science, University of Auckland, Private Bag 349, Warkworth, 0941, New Zealand
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17
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Moopantakath J, Imchen M, Siddhardha B, Kumavath R. 16s rRNA metagenomic analysis reveals predominance of Crtl and CruF genes in Arabian Sea coast of India. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 743:140699. [PMID: 32679495 DOI: 10.1016/j.scitotenv.2020.140699] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/03/2020] [Revised: 06/25/2020] [Accepted: 07/01/2020] [Indexed: 06/11/2023]
Abstract
Microbial communities perform crucial biogeochemical cycles in distinct ecosystems. Halophilic microbial communities are enriched in the saline areas. Hence, haloarchaea have been primarily studied in salterns and marine biosystems with the aim to harness haloarcheal carotenoids biosynthesis. In this study, sediment from several distinct biosystems (mangrove, seashore, estuary, river, lake, salt pan and island) across the Arabian coastal region of India were collected and analyzed though 16s rRNA metagenomic and whole genome approach to elucidated the dominant representative genre, haloarcheal diversity, and the prevalence of Crtl and CruF genes. We found that the microbial diversity in mangrove sediment (794 OTUs) was highest and lowest in lake and river (558-560 OTUs). Moreover, the bacterial domain dominated in all biosystems (96.00-99.45%). Top 10 abundant genera were involved in biochemical cycles such as sulfur, methane, ammonia, hydrocarbon degradation, and antibiotics production. The Archaea was mainly composed of Haloarchaea, Methanobacteria, Methanococci, Methanomicrobia and Crenarchaeota. Carotenoid gene, Crtl, was observed in a major portion (abundance 60%; diversity 45%) of microbial community. Interestingly, we found that all species under haloarcheal class that were represented in fresh as well as marine biosystems encodes CruF gene (bacterioruberin carotenoid). Our study demonstrates the high microbial diversity in various ecosystems, enrichment of Crtl gene, and also shows that Crtl and CruF genes are highly abundant in haloarcheal genera. The finding of ecosystems specific Crtl and CruF encoding genera opens up a promising area in bioprospecting the carotenoid derivatives from the wide range of natural biosystems.
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Affiliation(s)
- Jamseel Moopantakath
- Department of Genomic Science, Central University of Kerala, Tejaswini Hills, Periya, Kasaragod 671320, Kerala, India
| | - Madangchanok Imchen
- Department of Genomic Science, Central University of Kerala, Tejaswini Hills, Periya, Kasaragod 671320, Kerala, India
| | - Busi Siddhardha
- Department of Microbiology, School of Life Sciences, Pondicherry University, Puducherry 605014, India
| | - Ranjith Kumavath
- Department of Genomic Science, Central University of Kerala, Tejaswini Hills, Periya, Kasaragod 671320, Kerala, India.
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18
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Wang S, Zhi L, Shan W, Lu H, Xu Q, Li J. Correlation of extracellular polymeric substances and microbial community structure in denitrification biofilm exposed to adverse conditions. Microb Biotechnol 2020; 13:1889-1903. [PMID: 32700468 PMCID: PMC7533329 DOI: 10.1111/1751-7915.13633] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2020] [Accepted: 07/01/2020] [Indexed: 01/24/2023] Open
Abstract
Microbial community may respond to different adverse conditions and result in the variation of extracellular polymeric substances (EPS) in denitrification biofilm; this study discovered the role of EPS in accordance with the analysis of cyclic diguanylate (c-di-GMP) and electron equilibrium (EE) under low organic loading rate, shock organic loading rate and low temperature conditions. Good nitrate removal performance could be achieved under shock organic loading rate and low temperature conditions; however, owing to the low organic loading rate, the carbon source was preferentially utilized for biomass growth. Tightly bound EPS (TB-EPS) contents progressively increased and facilitated cell adhesion and biofilm formation. The stable TB protein (TB-PN) content in TB-EPS built a cross-linked network to maintain internal biofilm structure and led to the rapid biosynthesis of polysaccharides, which could further enhance microbial adhesion and improve nitrate removal. C-di-GMP played an important role in biomass retention and biofilm formation, based on the correlation analysis of c-di-GMP and EPS. TB polysaccharide (TB-PS) contents presented a significant positive correlation with c-di-GMP content, microbial adhesion and biofilm stabilization was further enhanced through c-di-GMP regulation. In addition, a remarkable negative correlation between electron deletion rate (EDR) and TB-PN and TB-PS was discovered, and TB-PS was required to serve as energy source to enhance denitrification according to EE analysis. Surprisingly, dynamic microbial community was observed due to the drastic community succession under low temperature conditions, and the discrepancy between the dominant species for denitrification was found under shock organic loading rate and low temperature conditions. The notable increase in bacterial strains Simlicispira, Pseudomonas and Chryseobacterium was conducive to biofilm formation and denitrification under shock organic loading rate, while Dechloromonas and Zoogloea dramatically enriched for nitrate removal under low temperature conditions. The high abundance of Dechloromonas improved the secretion of EPS through the downstream signal transduction, and the c-di-GMP conserved in Pseudomonas concurrently facilitated to enhance exopolysaccharide production to shock organic loading rate and low temperature conditions.
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Affiliation(s)
- Shuo Wang
- Jiangsu Key Laboratory of Anaerobic BiotechnologySchool of Environment and Civil EngineeringJiangnan UniversityWuxi214122China
- Jiangsu Engineering Laboratory for Biomass Energy and Carbon Reduction TechnologyJiangnan UniversityWuxi214122China
- Jiangsu College of Water Treatment Technology and Material Collaborative Innovation CenterSuzhou215009China
- Department of Civil EngineeringSchulich School of EngineeringUniversity of CalgaryCalgaryT2N 1N4Canada
| | - Liling Zhi
- Jiangsu Key Laboratory of Anaerobic BiotechnologySchool of Environment and Civil EngineeringJiangnan UniversityWuxi214122China
| | - Wei Shan
- Jiangsu Key Laboratory of Anaerobic BiotechnologySchool of Environment and Civil EngineeringJiangnan UniversityWuxi214122China
| | - Hui Lu
- School of Environmental Science and EngineeringSun Yat‐sen UniversityGuangzhou510006China
| | - Qiao Xu
- Jiangsu Key Laboratory of Anaerobic BiotechnologySchool of Environment and Civil EngineeringJiangnan UniversityWuxi214122China
| | - Ji Li
- Jiangsu Key Laboratory of Anaerobic BiotechnologySchool of Environment and Civil EngineeringJiangnan UniversityWuxi214122China
- Jiangsu Engineering Laboratory for Biomass Energy and Carbon Reduction TechnologyJiangnan UniversityWuxi214122China
- Jiangsu College of Water Treatment Technology and Material Collaborative Innovation CenterSuzhou215009China
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19
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van Grinsven S, Sinninghe Damsté JS, Villanueva L. Assessing the Effect of Humic Substances and Fe(III) as Potential Electron Acceptors for Anaerobic Methane Oxidation in a Marine Anoxic System. Microorganisms 2020; 8:E1288. [PMID: 32846903 PMCID: PMC7564286 DOI: 10.3390/microorganisms8091288] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Revised: 08/06/2020] [Accepted: 08/17/2020] [Indexed: 12/13/2022] Open
Abstract
Marine anaerobic methane oxidation (AOM) is generally assumed to be coupled to sulfate reduction, via a consortium of anaerobic methane-oxidizing archaea (ANME) and sulfate-reducing bacteria (SRB). ANME-1 are, however, often found as single cells, or only loosely aggregated with SRB, suggesting they perform a form of AOM independent of sulfate reduction. Oxidized metals and humic substances have been suggested as potential electron acceptors for ANME, but up to now, AOM linked to reduction of these compounds has only been shown for the ANME-2 and ANME-3 clades. Here, the effect of the electron acceptors anthraquinone-disulfonate (AQDS), a humic acids analog, and Fe3+ on anaerobic methane oxidation were assessed by incubation experiments with anoxic Black Sea water containing ANME-1b. Incubation experiments with 13C-methane and AQDS showed a stimulating effect of AQDS on methane oxidation. Fe3+ enhanced the ANME-1b abundance but did not substantially increase methane oxidation. Sodium molybdate, which was added as an inhibitor of sulfate reduction, surprisingly enhanced methane oxidation, possibly related to the dominant abundance of Sulfurospirillum in those incubations. The presented data suggest the potential involvement of ANME-1b in AQDS-enhanced anaerobic methane oxidation, possibly via electron shuttling to AQDS or via interaction with other members of the microbial community.
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Affiliation(s)
- Sigrid van Grinsven
- Department of Marine Microbiology and Biogeochemistry, NIOZ Royal Netherlands Institute for Sea Research, Utrecht University, 1797 SZ ’t Horntje, Texel, The Netherlands; (J.S.S.D.); (L.V.)
| | - Jaap S. Sinninghe Damsté
- Department of Marine Microbiology and Biogeochemistry, NIOZ Royal Netherlands Institute for Sea Research, Utrecht University, 1797 SZ ’t Horntje, Texel, The Netherlands; (J.S.S.D.); (L.V.)
- Department of Earth Sciences, Faculty of Geosciences, Utrecht University, 3584 CB Utrecht, The Netherlands
| | - Laura Villanueva
- Department of Marine Microbiology and Biogeochemistry, NIOZ Royal Netherlands Institute for Sea Research, Utrecht University, 1797 SZ ’t Horntje, Texel, The Netherlands; (J.S.S.D.); (L.V.)
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20
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Effects of Hydraulic Retention Time and Influent Nitrate-N Concentration on Nitrogen Removal and the Microbial Community of an Aerobic Denitrification Reactor Treating Recirculating Marine Aquaculture System Effluent. WATER 2020. [DOI: 10.3390/w12030650] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
The effects of hydraulic retention time (HRT) and influent nitrate-N concentration on nitrogen removal and the microbial community composition of an aerobic denitrification reactor treating recirculating marine aquaculture system effluent were evaluated. Results showed that over 98% of nitrogen was removed and ammonia-N and nitrite-N levels were below 1 mg/L when influent nitrate-N was below 150 mg/L and HRT over 5 h. The maximum nitrogen removal efficiency and nitrogen removal rate were observed at HRT of 6 or 7 h when influent nitrate-N was 150 mg/L. High-throughput DNA sequencing analysis revealed that the microbial phyla Proteobacteria and Bacteroidetes were predominant in the reactor, with an average relative total abundance above 70%. The relative abundance of denitrifying bacteria of genera Halomonas and Denitratisoma within the reactor decreased with increasing influent nitrate-N concentrations. Our results show the presence of an aerobically denitrifying microbial consortium with both expected and unexpected members, many of them relatively new to science. Our findings provide insights into the biological workings and inform the design and operation of denitrifying reactors for marine aquaculture systems.
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21
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Novotnik B, Zorz J, Bryant S, Strous M. The Effect of Dissimilatory Manganese Reduction on Lactate Fermentation and Microbial Community Assembly. Front Microbiol 2019; 10:1007. [PMID: 31156573 PMCID: PMC6531920 DOI: 10.3389/fmicb.2019.01007] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2018] [Accepted: 04/18/2019] [Indexed: 12/30/2022] Open
Abstract
Fermentation and dissimilatory manganese (Mn) reduction are inter-related metabolic processes that microbes can perform in anoxic environments. Fermentation is less energetically favorable and is often not considered to compete for organic carbon with dissimilatory metal reduction. Therefore, the aim of our study was to investigate the outcome of the competition for lactate between fermentation and Mn oxide (birnessite) reduction in a mixed microbial community. A birnessite reducing enrichment culture was obtained from activated sludge with lactate and birnessite as the substrates. This enrichment was further used to test how various birnessite activities (0, 10, 20, and 40 mM) affected the rates of fermentation and metal reduction, as well as community composition. Increased birnessite activity led to a decrease of lactate consumption rate. Acetate and propionate were the main products. With increasing birnessite activity, the propionate/acetate ratio decreased from 1.4 to 0.47. Significant CO2 production was detected only in the absence of birnessite. In its presence, CO2 concentrations remained close to the background since most of the CO2 produced in these experiments was recovered as MnCO3. The Mn reduction efficiency (Mn(II) produced divided by birnessite added) was the highest at 10 mM birnessite added, where about 50% of added birnessite was reduced to Mn(II), whereas at 20 and 40 mM approximately 21 and 16% was reduced. The decreased birnessite reduction efficiency at higher birnessite activities points to inhibition by terminal electron acceptors and/or its toxicity which was also indicated by retarded lactate oxidation and decreased concentrations of microbial metabolites. Birnessite activity strongly affected microbial community structure. Firmicutes and Bacteroidetes were the most abundant phyla at 0 mM of birnessite. Their abundance was inversely correlated with birnessite concentration. The relative sequence abundance of Proteobacteria correlated with birnessite concentrations. Most of the enriched populations were involved in lactate/acetate or amino acid fermentation and the only previously known metal reducing genus detected was related to Shewanella sp. The sequencing data confirmed that lactate consumption coupled to metal reduction was only one of the processes occurring and did not outcompete fermentation processes.
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Affiliation(s)
- Breda Novotnik
- Department of Geoscience, University of Calgary, Calgary, AB, Canada
| | - Jackie Zorz
- Department of Geoscience, University of Calgary, Calgary, AB, Canada
| | - Steven Bryant
- Department of Chemical and Petroleum Engineering, University of Calgary, Calgary, AB, Canada
| | - Marc Strous
- Department of Geoscience, University of Calgary, Calgary, AB, Canada
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22
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Dos Passos VF, Marcilio R, Aquino-Neto S, Santana FB, Dias ACF, Andreote FD, de Andrade AR, Reginatto V. Hydrogen and electrical energy co-generation by a cooperative fermentation system comprising Clostridium and microbial fuel cell inoculated with port drainage sediment. BIORESOURCE TECHNOLOGY 2019; 277:94-103. [PMID: 30660066 DOI: 10.1016/j.biortech.2019.01.031] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/12/2018] [Revised: 01/03/2019] [Accepted: 01/08/2019] [Indexed: 06/09/2023]
Abstract
This research work has succeeded in recovering energy from glucose by generating H2 with the aid of a Clostridium beijerinckii strain and obtaining electrical energy from compounds present in the H2 fermentation effluent in a microbial fuel cell (MFC) seeded with native port drainage sediment. In the fermentation step, 49.5% of the initial glucose concentration (56 mmol/L) was used to produce 104 mmol/L H2; 5, 33, 3, and 1 mmol/L acetate, butyrate, lactate, and ethanol also emerged, respectively. MFC tests by feeding the anodic compartment with acetate, butyrate, lactate (individually or as a mixture), or the H2 fermentation effluent provided power density values ranging between 0.6 and 1.2 W/m2. Acetate furnished the highest power density with a nanowire-rich biofilm despite the lowest anode bacterial concentration (1012 16S gene copies/g of sediment). Non-conventional exoelectrogenic microbial communities were observed in the acetate-fed MFC; e.g., Pseudomonadaceae (Pseudomonas) and Clostridia (Acidaminobacter, Fusibacter).
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Affiliation(s)
- Vinícius Fabiano Dos Passos
- Department of Chemistry, Faculty of Philosophy, Sciences and Letters of Ribeirão Preto, University of São Paulo, Ribeirão Preto, SP, Brazil
| | - Rafaella Marcilio
- Department of Chemistry, Faculty of Philosophy, Sciences and Letters of Ribeirão Preto, University of São Paulo, Ribeirão Preto, SP, Brazil
| | - Sidney Aquino-Neto
- Department of Chemistry, Faculty of Philosophy, Sciences and Letters of Ribeirão Preto, University of São Paulo, Ribeirão Preto, SP, Brazil
| | | | | | - Fenando Dini Andreote
- Luiz de Queiroz College of Agriculture - Department of Soil Science, University of São Paulo, Piracicaba, SP, Brazil
| | - Adalgisa Rodrigues de Andrade
- Department of Chemistry, Faculty of Philosophy, Sciences and Letters of Ribeirão Preto, University of São Paulo, Ribeirão Preto, SP, Brazil
| | - Valeria Reginatto
- Department of Chemistry, Faculty of Philosophy, Sciences and Letters of Ribeirão Preto, University of São Paulo, Ribeirão Preto, SP, Brazil.
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Hatam I, Petticrew EL, French TD, Owens PN, Laval B, Baldwin SA. The bacterial community of Quesnel Lake sediments impacted by a catastrophic mine tailings spill differ in composition from those at undisturbed locations - two years post-spill. Sci Rep 2019; 9:2705. [PMID: 30804448 PMCID: PMC6389986 DOI: 10.1038/s41598-019-38909-9] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2018] [Accepted: 12/31/2018] [Indexed: 11/17/2022] Open
Abstract
The West Basin of Quesnel Lake (British Columbia, Canada) suffered a catastrophic disturbance event in August 2014 when mine tailings and scoured natural material were deposited into the lake’s West Basin due to an impoundment failure at the adjacent Mount Polley copper-gold mine. The deposit covered a significant portion of the West Basin floor with a thick layer of material. Since lake sediments host bacterial communities that play key roles in the geochemical cycling in lacustrine environments, it is important to understand which groups inhabit the newly deposited material and what this implies for the ecological function of the West Basin. Here we report a study conducted two years post-spill, comparing the bacterial communities from sediments of both disturbed and undisturbed sites. Our results show that sediments from disturbed sites differed in physical and chemical properties than those in undisturbed sites (e.g. higher pH, particle size and Cu concentration). Furthermore, bacterial communities from the disturbed sites appeared to be legacy communities from the tailings impoundment, with metabolic potential revolving mainly around the cycling of S and metals, whereas the ones from the undisturbed sites were associated with the cycling of N.
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Affiliation(s)
- I Hatam
- Department of Chemical and Biological Engineering, University of British Columbia, Vancouver, British Columbia, V6T1Z3, Canada.
| | - E L Petticrew
- Geography Program and Quesnel River Research Centre, University of Northern British Columbia, Prince George, British Columbia, V2N4Z9, Canada
| | - T D French
- Geography Program and Quesnel River Research Centre, University of Northern British Columbia, Prince George, British Columbia, V2N4Z9, Canada.,Environmental Science Program and Quesnel River Research Centre, University of Northern British Columbia, Prince George, British Columbia, V2N4Z9, Canada
| | - P N Owens
- Environmental Science Program and Quesnel River Research Centre, University of Northern British Columbia, Prince George, British Columbia, V2N4Z9, Canada
| | - B Laval
- Department of Civil Engineering, University of British Columbia, Vancouver, British Columbia, V6T1Z3, Canada
| | - S A Baldwin
- Department of Chemical and Biological Engineering, University of British Columbia, Vancouver, British Columbia, V6T1Z3, Canada.
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24
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Aromokeye DA, Richter-Heitmann T, Oni OE, Kulkarni A, Yin X, Kasten S, Friedrich MW. Temperature Controls Crystalline Iron Oxide Utilization by Microbial Communities in Methanic Ferruginous Marine Sediment Incubations. Front Microbiol 2018; 9:2574. [PMID: 30425692 PMCID: PMC6218420 DOI: 10.3389/fmicb.2018.02574] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2018] [Accepted: 10/09/2018] [Indexed: 11/13/2022] Open
Abstract
Microorganisms can use crystalline iron minerals for iron reduction linked to organic matter degradation or as conduits for direct interspecies electron transfer (mDIET) to syntrophic partners, e.g., methanogens. The environmental conditions that lead either to reduction or conduit use are so far unknown. We investigated microbial community shifts and interactions with crystalline iron minerals (hematite and magnetite) in methanic ferruginous marine sediment incubations during organic matter (glucose) degradation at varying temperatures. Iron reduction rates increased with decreasing temperature from 30°C to 4°C. Both hematite and magnetite facilitated iron reduction at 4°C, demonstrating that microorganisms in the methanic zone of marine sediments can reduce crystalline iron oxides under psychrophilic conditions. Methanogenesis occurred, however, at higher rates with increasing temperature. At 30°C, both hematite and magnetite accelerated methanogenesis onset and maximum process rates. At lower temperatures (10°C and 4°C), hematite could still facilitate methanogenesis but magnetite served more as an electron acceptor for iron reduction than as a conduit. Different temperatures selected for different key microorganisms: at 30°C, members of genus Orenia, Halobacteroidaceae, at 10°C, Photobacterium and the order Clostridiales, and at 4°C Photobacterium and Psychromonas were enriched. Members of the order Desulfuromonadales harboring known dissimilatory iron reducers were also enriched at all temperatures. Our results show that crystalline iron oxides predominant in some natural environments can facilitate electron transfer between microbial communities at psychrophilic temperatures. Furthermore, temperature has a critical role in determining the pathway of crystalline iron oxide utilization in marine sediment shifting from conduction at 30°C to predominantly iron reduction at lower temperatures.
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Affiliation(s)
- David A Aromokeye
- Microbial Ecophysiology Group, Faculty of Biology/Chemistry, University of Bremen, Bremen, Germany.,MARUM, Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany.,International Max Planck Research School for Marine Microbiology, Max-Planck-Institute for Marine Microbiology, Bremen, Germany
| | - Tim Richter-Heitmann
- Microbial Ecophysiology Group, Faculty of Biology/Chemistry, University of Bremen, Bremen, Germany
| | - Oluwatobi E Oni
- Microbial Ecophysiology Group, Faculty of Biology/Chemistry, University of Bremen, Bremen, Germany.,MARUM, Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany
| | - Ajinkya Kulkarni
- Microbial Ecophysiology Group, Faculty of Biology/Chemistry, University of Bremen, Bremen, Germany.,MARUM, Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany.,International Max Planck Research School for Marine Microbiology, Max-Planck-Institute for Marine Microbiology, Bremen, Germany
| | - Xiuran Yin
- Microbial Ecophysiology Group, Faculty of Biology/Chemistry, University of Bremen, Bremen, Germany.,MARUM, Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany.,International Max Planck Research School for Marine Microbiology, Max-Planck-Institute for Marine Microbiology, Bremen, Germany
| | - Sabine Kasten
- MARUM, Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany.,Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Bremerhaven, Germany.,Faculty of Geosciences, University of Bremen, Bremen, Germany
| | - Michael W Friedrich
- Microbial Ecophysiology Group, Faculty of Biology/Chemistry, University of Bremen, Bremen, Germany.,MARUM, Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany
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25
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Wu L, Tang B, Bin L, Chen G, Huang S, Li P, Fu F. Heterogeneity of the diverse aerobic sludge granules self-cultivated in a membrane bioreactor with enhanced internal circulation. BIORESOURCE TECHNOLOGY 2018; 263:297-305. [PMID: 29753931 DOI: 10.1016/j.biortech.2018.05.004] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/18/2018] [Revised: 04/28/2018] [Accepted: 05/01/2018] [Indexed: 06/08/2023]
Abstract
The present work revealed the heterogeneity of the sludge granules formed in a membrane bioreactor with enhanced internal circulation, and also contributed to better understanding of their forming mechanisms. By continuously carrying out an experiment lasting for more than 3 months with the floc sludge from a local municipal wastewater treatment plant as inoculation sludge, diverse aerobic sludge granules were found to be successfully self-cultivated within the reactor. The results of scanning electron microscopy, fluorescence microscope and high-throughput sequencing measurement indicated that the obtained diverse granules exhibited quite obvious heterogeneity in their basic physico-chemical and microbial properties, and filamentous bacteria actually acted as a main skeleton to keep the self-cultivated sludge granules stable in both their structure and morphology. Furthermore, stable and high COD and TN removal achieved, over 85% and 60%, respectively, which confirmed its usefulness in wastewater treatment.
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Affiliation(s)
- Luying Wu
- School of Environmental Science and Engineering and Institute of Environmental Health and Pollution Control, Guangdong University of Technology, Guangzhou Key Laboratory of Environmental Catalysis and Pollution Control, Guangzhou 510006, PR China
| | - Bing Tang
- School of Environmental Science and Engineering and Institute of Environmental Health and Pollution Control, Guangdong University of Technology, Guangzhou Key Laboratory of Environmental Catalysis and Pollution Control, Guangzhou 510006, PR China.
| | - Liying Bin
- School of Environmental Science and Engineering and Institute of Environmental Health and Pollution Control, Guangdong University of Technology, Guangzhou Key Laboratory of Environmental Catalysis and Pollution Control, Guangzhou 510006, PR China
| | - Guangpeng Chen
- School of Environmental Science and Engineering and Institute of Environmental Health and Pollution Control, Guangdong University of Technology, Guangzhou Key Laboratory of Environmental Catalysis and Pollution Control, Guangzhou 510006, PR China
| | - Shaosong Huang
- School of Environmental Science and Engineering and Institute of Environmental Health and Pollution Control, Guangdong University of Technology, Guangzhou Key Laboratory of Environmental Catalysis and Pollution Control, Guangzhou 510006, PR China
| | - Ping Li
- School of Environmental Science and Engineering and Institute of Environmental Health and Pollution Control, Guangdong University of Technology, Guangzhou Key Laboratory of Environmental Catalysis and Pollution Control, Guangzhou 510006, PR China
| | - Fenglian Fu
- School of Environmental Science and Engineering and Institute of Environmental Health and Pollution Control, Guangdong University of Technology, Guangzhou Key Laboratory of Environmental Catalysis and Pollution Control, Guangzhou 510006, PR China
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26
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Serrano AE, Escudero LV, Tebes-Cayo C, Acosta M, Encalada O, Fernández-Moroso S, Demergasso C. First draft genome sequence of a strain from the genus Fusibacter isolated from Salar de Ascotán in Northern Chile. Stand Genomic Sci 2017; 12:43. [PMID: 28770028 PMCID: PMC5525254 DOI: 10.1186/s40793-017-0252-4] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2017] [Accepted: 07/12/2017] [Indexed: 11/18/2022] Open
Abstract
Fusibacter sp. 3D3 (ATCC BAA-2418) is an arsenate-reducing halotolerant strain within the Firmicutes phylum, isolated from the Salar de Ascotán, a hypersaline salt flat in Northern Chile. This high-Andean closed basin is an athalassohaline environment located at the bottom of a tectonic basin surrounded by mountain range, including some active volcanoes. This landscape can be an advantageous system to explore the effect of salinity on microorganisms that mediate biogeochemical reactions. Since 2000, microbial reduction of arsenic has been evidenced in the system, and the phylogenetic analysis of the original community plus the culture enrichments has revealed the predominance of Firmicutes phylum. Here, we describe the first whole draft genome sequence of an arsenic-reducing strain belonging to the Fusibacter genus showing the highest 16S rRNA gene sequence similarity (98%) with Fusibacter sp. strain Vns02. The draft genome consists of 57 contigs with 5,111,250 bp and an average G + C content of 37.6%. Out of 4780 total genes predicted, 4700 genes code for proteins and 80 genes for RNAs. Insights from the genome sequence and some microbiological features of the strain 3D3 are available under Bioproject accession PRJDB4973 and Biosample SAMD00055724. The release of the genome sequence of this strain could contribute to the understanding of the arsenic biogeochemistry in extreme environments.
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Affiliation(s)
- Antonio E Serrano
- Centro de Biotecnología, Universidad Católica del Norte, Antofagasta, Chile
| | - Lorena V Escudero
- Centro de Biotecnología, Universidad Católica del Norte, Antofagasta, Chile.,Centro de Investigación Científica y Tecnológica para la Minería, Antofagasta, Chile
| | - Cinthya Tebes-Cayo
- Centro de Biotecnología, Universidad Católica del Norte, Antofagasta, Chile
| | - Mauricio Acosta
- Centro de Biotecnología, Universidad Católica del Norte, Antofagasta, Chile
| | - Olga Encalada
- Centro de Biotecnología, Universidad Católica del Norte, Antofagasta, Chile
| | | | - Cecilia Demergasso
- Centro de Biotecnología, Universidad Católica del Norte, Antofagasta, Chile.,Centro de Investigación Científica y Tecnológica para la Minería, Antofagasta, Chile
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27
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Ren Y, Niu J, Huang W, Peng D, Xiao Y, Zhang X, Liang Y, Liu X, Yin H. Comparison of microbial taxonomic and functional shift pattern along contamination gradient. BMC Microbiol 2016; 16:110. [PMID: 27301322 PMCID: PMC4908767 DOI: 10.1186/s12866-016-0731-6] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2015] [Accepted: 06/06/2016] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The interaction mechanism between microbial communities and environment is a key issue in microbial ecology. Microbial communities usually change significantly under environmental stress, which has been studied both phylogenetically and functionally, however which method is more effective in assessing the relationship between microbial communities shift and environmental changes still remains controversial. RESULTS By comparing the microbial taxonomic and functional shift pattern along heavy metal contamination gradient, we found that both sedimentary composition and function shifted significantly along contamination gradient. For example, the relative abundance of Geobacter and Fusibacter decreased along contamination gradient (from high to low), while Janthinobacterium and Arthrobacter increased their abundances. Most genes involved in heavy metal resistance (e.g., metc, aoxb and mer) showed higher intensity in sites with higher concentration of heavy metals. Comparing the two shift patterns, there were correlations between them, because functional and phylogenetic β-diversities were significantly correlated, and many heavy metal resistance genes were derived from Geobacter, explaining their high abundance in heavily contaminated sites. However, there was a stronger link between functional composition and environmental drivers, while stochasticity played an important role in formation and succession of phylogenetic composition demonstrated by null model test. CONCLUSIONS Overall our research suggested that the responses of functional traits depended more on environmental changes, while stochasticity played an important role in formation and succession of phylogenetic composition for microbial communities. So profiling microbial functional composition seems more appropriate to study the relationship between microbial communities and environment, as well as explore the adaptation and remediation mechanism of microbial communities to heavy metal contamination.
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Affiliation(s)
- Youhua Ren
- School of Minerals Processing and Bioengineering, Central South University, Changsha, 410083, China.,Key laboratory of Biometallurgy, Ministry of Education, Changsha, 410083, China.,College of Food Science and Technology, Hunan Agricultural University, Changsha, 410083, China
| | - Jiaojiao Niu
- School of Minerals Processing and Bioengineering, Central South University, Changsha, 410083, China.,Key laboratory of Biometallurgy, Ministry of Education, Changsha, 410083, China
| | - Wenkun Huang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Deliang Peng
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Yunhua Xiao
- School of Minerals Processing and Bioengineering, Central South University, Changsha, 410083, China.,Key laboratory of Biometallurgy, Ministry of Education, Changsha, 410083, China
| | - Xian Zhang
- School of Minerals Processing and Bioengineering, Central South University, Changsha, 410083, China.,Key laboratory of Biometallurgy, Ministry of Education, Changsha, 410083, China
| | - Yili Liang
- School of Minerals Processing and Bioengineering, Central South University, Changsha, 410083, China.,Key laboratory of Biometallurgy, Ministry of Education, Changsha, 410083, China
| | - Xueduan Liu
- School of Minerals Processing and Bioengineering, Central South University, Changsha, 410083, China.,Key laboratory of Biometallurgy, Ministry of Education, Changsha, 410083, China
| | - Huaqun Yin
- School of Minerals Processing and Bioengineering, Central South University, Changsha, 410083, China. .,Key laboratory of Biometallurgy, Ministry of Education, Changsha, 410083, China.
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