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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.


Relative abundance of bacteria and archaea in in situ three sediment samples. (A) Relative abundance of iron(III)-reducing bacteria as determined by Illumina sequencing according to published reviews. The left side of the figure chart represents iron(III)-reducing related bacteria at the class level, whereas its right side of the larger figure chart gives an estimate of iron(III)-reducing related bacteria as represented at the genus level. (B) Relative abundance of archaea in three sediment samples as determined by T-RFLP.
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Figure 2: Relative abundance of bacteria and archaea in in situ three sediment samples. (A) Relative abundance of iron(III)-reducing bacteria as determined by Illumina sequencing according to published reviews. The left side of the figure chart represents iron(III)-reducing related bacteria at the class level, whereas its right side of the larger figure chart gives an estimate of iron(III)-reducing related bacteria as represented at the genus level. (B) Relative abundance of archaea in three sediment samples as determined by T-RFLP.

Mentions: High-throughput Illumina sequencing was used to reveal the diversity of iron (III)-reducing microorganisms and methanogens in the iron-rich sediments of a coastal gold mining river, Jiehe River. The characteristics of the sediment samples from Jiehe River were summarized in Table 1 and the microbial diversity were shown in Figure 2, Figure S2. A total of 92,535 bacterial sequences (mean = 10,281 sequences per library; median = 10,081; maximum = 12,934; minimum = 6806) were analyzed, and the number of OTUs varied between 593 and 1426 with a 97% identity threshold. The rarefaction curves of three samples were shown in Figure S1. The overall phylum-level phylogenetic characteristics from the heatmap diagram (Figure S2A) and the 100% stacked column chart (Figure S2B) indicated that Proteobacteria, Firmicutes, Bacteroidetes, and Acidobacteria were the dominant bacteria in these sediment samples. In the Proteobacteria, Deltaprotebacteria dominated the three libraries, accounting for 0.36, 6.67, and 4.69% of the community in Jh1, Jh2, and Jh3, respectively. Within the Deltaprotebacteria, Geobacteraceae represented the highest relative abundance accounting for 2.57 and 3.67% of the community in Jh2 and Jh3 respectively. Geobacter spp., Anaeromyxobacter spp., Desulfovibrio spp. of Deltaproteobacteria, and Geothrix spp. of Acidobacteria (Figure 2A) are all known dissimilatory iron(III)-reducing microorganisms. In the Firmicutes, Bacteroidetes and Proteobacteria, the majority of the sequences belong to the genus Clostridium spp., Bacillus spp., Desulfotomaculum spp., Bacteroides, and Pseudomonas spp., Escherichia spp., Rhodobacter spp., and Thiobacillus spp. All the sequences affiliated to known dissimilatory iron(III)-reducing bacteria accounted for 6.44, 8.72, and 16.85% of the community in Jh1, Jh2, and Jh3, respectively. Remarkably, Geobacter spp. and Clostridium spp. dominated in the dissimilatory iron(III)-reducing bacteria of Jh2 and Jh3 accounting for 29.03 and 56.97%, respectively (Figure 2A). Furthermore, the results of T-RFLP showed that iron(III)-reducing bacteria in three sediment samples were accompanied by the archaea belonging to Methanosarcina, Methanobacterium/Methanosphaera, Methanosaeta, and Methanocella/Methanospirillum/Methanosphaerula (Figure 2B). Jh2 was selected as the representative sample for further experiments named as Jh.


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)

Relative abundance of bacteria and archaea in in situ three sediment samples. (A) Relative abundance of iron(III)-reducing bacteria as determined by Illumina sequencing according to published reviews. The left side of the figure chart represents iron(III)-reducing related bacteria at the class level, whereas its right side of the larger figure chart gives an estimate of iron(III)-reducing related bacteria as represented at the genus level. (B) Relative abundance of archaea in three sediment samples as determined by T-RFLP.
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Figure 2: Relative abundance of bacteria and archaea in in situ three sediment samples. (A) Relative abundance of iron(III)-reducing bacteria as determined by Illumina sequencing according to published reviews. The left side of the figure chart represents iron(III)-reducing related bacteria at the class level, whereas its right side of the larger figure chart gives an estimate of iron(III)-reducing related bacteria as represented at the genus level. (B) Relative abundance of archaea in three sediment samples as determined by T-RFLP.
Mentions: High-throughput Illumina sequencing was used to reveal the diversity of iron (III)-reducing microorganisms and methanogens in the iron-rich sediments of a coastal gold mining river, Jiehe River. The characteristics of the sediment samples from Jiehe River were summarized in Table 1 and the microbial diversity were shown in Figure 2, Figure S2. A total of 92,535 bacterial sequences (mean = 10,281 sequences per library; median = 10,081; maximum = 12,934; minimum = 6806) were analyzed, and the number of OTUs varied between 593 and 1426 with a 97% identity threshold. The rarefaction curves of three samples were shown in Figure S1. The overall phylum-level phylogenetic characteristics from the heatmap diagram (Figure S2A) and the 100% stacked column chart (Figure S2B) indicated that Proteobacteria, Firmicutes, Bacteroidetes, and Acidobacteria were the dominant bacteria in these sediment samples. In the Proteobacteria, Deltaprotebacteria dominated the three libraries, accounting for 0.36, 6.67, and 4.69% of the community in Jh1, Jh2, and Jh3, respectively. Within the Deltaprotebacteria, Geobacteraceae represented the highest relative abundance accounting for 2.57 and 3.67% of the community in Jh2 and Jh3 respectively. Geobacter spp., Anaeromyxobacter spp., Desulfovibrio spp. of Deltaproteobacteria, and Geothrix spp. of Acidobacteria (Figure 2A) are all known dissimilatory iron(III)-reducing microorganisms. In the Firmicutes, Bacteroidetes and Proteobacteria, the majority of the sequences belong to the genus Clostridium spp., Bacillus spp., Desulfotomaculum spp., Bacteroides, and Pseudomonas spp., Escherichia spp., Rhodobacter spp., and Thiobacillus spp. All the sequences affiliated to known dissimilatory iron(III)-reducing bacteria accounted for 6.44, 8.72, and 16.85% of the community in Jh1, Jh2, and Jh3, respectively. Remarkably, Geobacter spp. and Clostridium spp. dominated in the dissimilatory iron(III)-reducing bacteria of Jh2 and Jh3 accounting for 29.03 and 56.97%, respectively (Figure 2A). Furthermore, the results of T-RFLP showed that iron(III)-reducing bacteria in three sediment samples were accompanied by the archaea belonging to Methanosarcina, Methanobacterium/Methanosphaera, Methanosaeta, and Methanocella/Methanospirillum/Methanosphaerula (Figure 2B). Jh2 was selected as the representative sample for further experiments named as Jh.

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.