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Co-occurrence of Methanosarcina mazei and Geobacteraceae in an iron (III)-reducing enrichment culture.

Zheng S, Zhang H, Li Y, Zhang H, Wang O, Zhang J, Liu F - Front Microbiol (2015)

Bottom Line: First, iron (III) reducers including Geobacteraceae were successfully enriched by 3-months successive culture on amorphous Fe(III) oxides as electron acceptor and acetate as electron donor.Remarkably, aggregates were successively formed in the enrichments after three transfers.The results revealed by RNA-based analysis demonstrate that the co-occurrence of Methanosarcina mazei and Geobacteraceae in an iron (III)-reducing enrichment culture.

View Article: PubMed Central - PubMed

Affiliation: Key Laboratory of Coastal Environmental Processes and Ecological Remediation, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences Yantai, China ; Key Laboratory of Coastal Biology and Biological Resources Utilization, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences Yantai, China.

ABSTRACT
Methanosaeta harundinacea and Methanosarcina barkeri, known as classic acetoclastic methanogens, are capable of directly accepting electrons from Geobacter metallireducens for the reduction of carbon dioxide to methane, having been revealed as direct interspecies electron transfer (DIET) in the laboratory co-cultures. However, whether their co-occurrences are ubiquitous in the iron (III)-reducing environments and the other species of acetoclastic methanogens such as Methanosarcina mazei are capable of DIET are still unknown. Instead of initiating the co-cultures with pure cultures, two-step cultivation was employed to selectively enrich iron (III)-reducing microorganisms in a coastal gold mining river, Jiehe River, with rich iron content in the sediments. First, iron (III) reducers including Geobacteraceae were successfully enriched by 3-months successive culture on amorphous Fe(III) oxides as electron acceptor and acetate as electron donor. High-throughput Illumina sequencing, terminal restriction fragment length polymorphism (T-RFLP) and clone library analysis based on 16S rRNA genes revealed that the enrichment cultures actively contained the bacteria belong to Geobacteraceae and Bacilli, exclusively dominated by the archaea belong to Methanosarcinaceae. Second, the enrichment cultures including methanogens and Geobacteraceae were transferred with ethanol as alternative electron donor. Remarkably, aggregates were successively formed in the enrichments after three transfers. The results revealed by RNA-based analysis demonstrate that the co-occurrence of Methanosarcina mazei and Geobacteraceae in an iron (III)-reducing enrichment culture. Furthermore, the aggregates, as close physical contact, formed in the enrichment culture, indicate that DIET could be a possible option for interspecies electron transfer in the aggregates.

No MeSH data available.


Community characteristics of bacteria and archaea in the sediments before and after the enrichment incubations, as revealed by T-RFLP and clone libraries of 16S rRNA genes. (A) Relative abundance of different bacterial T-RFs from DNA and RNA extracted from in situ sediments and enrichment cultures (with or without Fe(III) oxides treatment). T-RF fingerprints were generated using Msp I restriction enzyme. Bac-Bacillus; Geo-Geobater; Uni-Unidentified; Ali-Alishewanella; Aci/Dia-Acidovorax/Diaphorobacter. (B) Relative abundance of different archaeal T-RFs from DNA and RNA extracted from in situ sediments and enrichment cultures. T-RF fingerprints were generated using Taq I restriction enzyme. Mb/Ms-Methanobacterium/Methanosphaera; Msr-Methanosarcina; Msa-Methanosaeta; Mce/Msp-Methanocella/Methanospirillum/Methanosphaerula. T-RF size in base pairs. BDJh, Bacterial DNA extracted from sediment Jh; BeRJh, Bacterial RNA extracted from enriched sediment Jh; ADJh, Archaeal DNA extracted from sediment Jh; AeRJh, Archaeal RNA extracted from enriched sediment Jh. Relative T-RF abundance of rDNA and rRNA were presented from triplicate DNA and RNA extractions for each sample.
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Figure 4: Community characteristics of bacteria and archaea in the sediments before and after the enrichment incubations, as revealed by T-RFLP and clone libraries of 16S rRNA genes. (A) Relative abundance of different bacterial T-RFs from DNA and RNA extracted from in situ sediments and enrichment cultures (with or without Fe(III) oxides treatment). T-RF fingerprints were generated using Msp I restriction enzyme. Bac-Bacillus; Geo-Geobater; Uni-Unidentified; Ali-Alishewanella; Aci/Dia-Acidovorax/Diaphorobacter. (B) Relative abundance of different archaeal T-RFs from DNA and RNA extracted from in situ sediments and enrichment cultures. T-RF fingerprints were generated using Taq I restriction enzyme. Mb/Ms-Methanobacterium/Methanosphaera; Msr-Methanosarcina; Msa-Methanosaeta; Mce/Msp-Methanocella/Methanospirillum/Methanosphaerula. T-RF size in base pairs. BDJh, Bacterial DNA extracted from sediment Jh; BeRJh, Bacterial RNA extracted from enriched sediment Jh; ADJh, Archaeal DNA extracted from sediment Jh; AeRJh, Archaeal RNA extracted from enriched sediment Jh. Relative T-RF abundance of rDNA and rRNA were presented from triplicate DNA and RNA extractions for each sample.

Mentions: Analysis of the relative abundance of the bacterial terminal restriction fragments (T-RF) after an incubation period is shown in Figure 4A. For rRNA (enrichment cultures of 30 days) with Fe(III) oxides treatment and acetate as the electron donor, the T-RF of 162 bp was exclusively predominant in enrichment cultures. After 3-months successive culture, rRNA with Fe(III) oxides treatment and ethanol as the electron donor, the T-RF of 162 and 487 bp were predominant in enrichment cultures. For rRNA without Fe(III) oxides treatment (enrichment cultures of 30 days), the T-RF of 152 and 162 bp were predominant in enrichment cultures with acetate or ethanol as the electron donor. For rDNA without Fe(III) oxides treatment, the T-RF of 162, 477, and 487 bp were predominant in sediments.


Co-occurrence of Methanosarcina mazei and Geobacteraceae in an iron (III)-reducing enrichment culture.

Zheng S, Zhang H, Li Y, Zhang H, Wang O, Zhang J, Liu F - Front Microbiol (2015)

Community characteristics of bacteria and archaea in the sediments before and after the enrichment incubations, as revealed by T-RFLP and clone libraries of 16S rRNA genes. (A) Relative abundance of different bacterial T-RFs from DNA and RNA extracted from in situ sediments and enrichment cultures (with or without Fe(III) oxides treatment). T-RF fingerprints were generated using Msp I restriction enzyme. Bac-Bacillus; Geo-Geobater; Uni-Unidentified; Ali-Alishewanella; Aci/Dia-Acidovorax/Diaphorobacter. (B) Relative abundance of different archaeal T-RFs from DNA and RNA extracted from in situ sediments and enrichment cultures. T-RF fingerprints were generated using Taq I restriction enzyme. Mb/Ms-Methanobacterium/Methanosphaera; Msr-Methanosarcina; Msa-Methanosaeta; Mce/Msp-Methanocella/Methanospirillum/Methanosphaerula. T-RF size in base pairs. BDJh, Bacterial DNA extracted from sediment Jh; BeRJh, Bacterial RNA extracted from enriched sediment Jh; ADJh, Archaeal DNA extracted from sediment Jh; AeRJh, Archaeal RNA extracted from enriched sediment Jh. Relative T-RF abundance of rDNA and rRNA were presented from triplicate DNA and RNA extractions for each sample.
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Related In: Results  -  Collection

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Figure 4: Community characteristics of bacteria and archaea in the sediments before and after the enrichment incubations, as revealed by T-RFLP and clone libraries of 16S rRNA genes. (A) Relative abundance of different bacterial T-RFs from DNA and RNA extracted from in situ sediments and enrichment cultures (with or without Fe(III) oxides treatment). T-RF fingerprints were generated using Msp I restriction enzyme. Bac-Bacillus; Geo-Geobater; Uni-Unidentified; Ali-Alishewanella; Aci/Dia-Acidovorax/Diaphorobacter. (B) Relative abundance of different archaeal T-RFs from DNA and RNA extracted from in situ sediments and enrichment cultures. T-RF fingerprints were generated using Taq I restriction enzyme. Mb/Ms-Methanobacterium/Methanosphaera; Msr-Methanosarcina; Msa-Methanosaeta; Mce/Msp-Methanocella/Methanospirillum/Methanosphaerula. T-RF size in base pairs. BDJh, Bacterial DNA extracted from sediment Jh; BeRJh, Bacterial RNA extracted from enriched sediment Jh; ADJh, Archaeal DNA extracted from sediment Jh; AeRJh, Archaeal RNA extracted from enriched sediment Jh. Relative T-RF abundance of rDNA and rRNA were presented from triplicate DNA and RNA extractions for each sample.
Mentions: Analysis of the relative abundance of the bacterial terminal restriction fragments (T-RF) after an incubation period is shown in Figure 4A. For rRNA (enrichment cultures of 30 days) with Fe(III) oxides treatment and acetate as the electron donor, the T-RF of 162 bp was exclusively predominant in enrichment cultures. After 3-months successive culture, rRNA with Fe(III) oxides treatment and ethanol as the electron donor, the T-RF of 162 and 487 bp were predominant in enrichment cultures. For rRNA without Fe(III) oxides treatment (enrichment cultures of 30 days), the T-RF of 152 and 162 bp were predominant in enrichment cultures with acetate or ethanol as the electron donor. For rDNA without Fe(III) oxides treatment, the T-RF of 162, 477, and 487 bp were predominant in sediments.

Bottom Line: First, iron (III) reducers including Geobacteraceae were successfully enriched by 3-months successive culture on amorphous Fe(III) oxides as electron acceptor and acetate as electron donor.Remarkably, aggregates were successively formed in the enrichments after three transfers.The results revealed by RNA-based analysis demonstrate that the co-occurrence of Methanosarcina mazei and Geobacteraceae in an iron (III)-reducing enrichment culture.

View Article: PubMed Central - PubMed

Affiliation: Key Laboratory of Coastal Environmental Processes and Ecological Remediation, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences Yantai, China ; Key Laboratory of Coastal Biology and Biological Resources Utilization, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences Yantai, China.

ABSTRACT
Methanosaeta harundinacea and Methanosarcina barkeri, known as classic acetoclastic methanogens, are capable of directly accepting electrons from Geobacter metallireducens for the reduction of carbon dioxide to methane, having been revealed as direct interspecies electron transfer (DIET) in the laboratory co-cultures. However, whether their co-occurrences are ubiquitous in the iron (III)-reducing environments and the other species of acetoclastic methanogens such as Methanosarcina mazei are capable of DIET are still unknown. Instead of initiating the co-cultures with pure cultures, two-step cultivation was employed to selectively enrich iron (III)-reducing microorganisms in a coastal gold mining river, Jiehe River, with rich iron content in the sediments. First, iron (III) reducers including Geobacteraceae were successfully enriched by 3-months successive culture on amorphous Fe(III) oxides as electron acceptor and acetate as electron donor. High-throughput Illumina sequencing, terminal restriction fragment length polymorphism (T-RFLP) and clone library analysis based on 16S rRNA genes revealed that the enrichment cultures actively contained the bacteria belong to Geobacteraceae and Bacilli, exclusively dominated by the archaea belong to Methanosarcinaceae. Second, the enrichment cultures including methanogens and Geobacteraceae were transferred with ethanol as alternative electron donor. Remarkably, aggregates were successively formed in the enrichments after three transfers. The results revealed by RNA-based analysis demonstrate that the co-occurrence of Methanosarcina mazei and Geobacteraceae in an iron (III)-reducing enrichment culture. Furthermore, the aggregates, as close physical contact, formed in the enrichment culture, indicate that DIET could be a possible option for interspecies electron transfer in the aggregates.

No MeSH data available.