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Effects of Spartina alterniflora invasion on the communities of methanogens and sulfate-reducing bacteria in estuarine marsh sediments.

Zeleke J, Sheng Q, Wang JG, Huang MY, Xia F, Wu JH, Quan ZX - Front Microbiol (2013)

Bottom Line: Similar trends were observed for SRB, and they were up to two orders of magnitude higher than the methanogens.Diversity indices indicated a lower diversity of methanogens in the S. alterniflora stands than the P. australis stands.The results showed that in the sediments of tidal salt marsh where S. alterniflora displaced P. australis, the abundances of methanogens and SRB increased, but the community composition of methanogens appeared to be influenced more than did the SRB.

View Article: PubMed Central - PubMed

Affiliation: Department of Microbiology and Microbial Engineering, School of Life Sciences, Fudan University Shanghai, China.

ABSTRACT
The effect of plant invasion on the microorganisms of soil sediments is very important for estuary ecology. The community structures of methanogens and sulfate-reducing bacteria (SRB) as a function of Spartina alterniflora invasion in Phragmites australis-vegetated sediments of the Dongtan wetland in the Yangtze River estuary, China, were investigated using 454 pyrosequencing and quantitative real-time PCR (qPCR) of the methyl coenzyme M reductase A (mcrA) and dissimilatory sulfite-reductase (dsrB) genes. Sediment samples were collected from two replicate locations, and each location included three sampling stands each covered by monocultures of P. australis, S. alterniflora and both plants (transition stands), respectively. qPCR analysis revealed higher copy numbers of mcrA genes in sediments from S. alterniflora stands than P. australis stands (5- and 7.5-fold more in the spring and summer, respectively), which is consistent with the higher methane flux rates measured in the S. alterniflora stands (up to 8.01 ± 5.61 mg m(-2) h(-1)). Similar trends were observed for SRB, and they were up to two orders of magnitude higher than the methanogens. Diversity indices indicated a lower diversity of methanogens in the S. alterniflora stands than the P. australis stands. In contrast, insignificant variations were observed in the diversity of SRB with the invasion. Although Methanomicrobiales and Methanococcales, the hydrogenotrophic methanogens, dominated in the salt marsh, Methanomicrobiales displayed a slight increase with the invasion and growth of S. alterniflora, whereas the later responded differently. Methanosarcina, the metabolically diverse methanogens, did not vary with the invasion of, but Methanosaeta, the exclusive acetate utilizers, appeared to increase with S. alterniflora invasion. In SRB, sequences closely related to the families Desulfobacteraceae and Desulfobulbaceae dominated in the salt marsh, although they displayed minimal changes with the S. alterniflora invasion. Approximately 11.3 ± 5.1% of the dsrB gene sequences formed a novel cluster that was reduced upon the invasion. The results showed that in the sediments of tidal salt marsh where S. alterniflora displaced P. australis, the abundances of methanogens and SRB increased, but the community composition of methanogens appeared to be influenced more than did the SRB.

No MeSH data available.


Related in: MedlinePlus

Neighbor-joining phylogenetic trees of (A) mcrA and (B) dsrB gene OTUs recovered from the Dongtan tidal salt marsh located in the Yangtze estuary. The trees were constructed based on the inferred amino acids of the OTU-representative nucleotide sequences. Percentages in the parenthesis indicate the percent of sequences included in that specific OTU. Only OTUs containing at least 0.5 and 1% of the total sequences mcrA and dsrB OTUs, respectively, are presented here.
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Figure 3: Neighbor-joining phylogenetic trees of (A) mcrA and (B) dsrB gene OTUs recovered from the Dongtan tidal salt marsh located in the Yangtze estuary. The trees were constructed based on the inferred amino acids of the OTU-representative nucleotide sequences. Percentages in the parenthesis indicate the percent of sequences included in that specific OTU. Only OTUs containing at least 0.5 and 1% of the total sequences mcrA and dsrB OTUs, respectively, are presented here.

Mentions: McrA OTUs were dominated by OTU1, 2 and 3, representing approximately 32.5, 21.5, and 16.5% of the total sequences (Figure 3A). OTU1 was closely related to the mcrA of Methanococcus, whereas OTU2 and 3 were related to the mcrA of Methanomicrobiales and Methanosarcina, respectively. Most of the mcrA gene sequences were closely related to the methanogen orders Methanomicrobiales, Methanosarcinales and Methanococcales, although other methanogens such as Methanobacteriales, ANME (1 and 3) and ZC-I were also detected in the salt marsh (Figure 3A). As the primers used in this study (mlas/mcrA-rev) can amplify mcrA and mrtA genes (Steinberg and Regan, 2009), the presence of large number of sequences (32.5%) related to Methanococcales (Luton et al., 2002), methanogens carrying mcrA and mrtA genes, might overestimate the abundance and diversity of the total methanogens. Interestingly, at both similarity cutoffs, Methanococcales was represented by a single OTU that is closely related (approximately 95% at the amino-acid level) to Methanococcus maripaludis. The occurrences of Methanomicrobiales, Methanosarcinales and Methanococcales in the mcrA sequences were also supported by the results from the analysis of archaeal 16S rRNA gene sequences where the above three methanogenic orders were also the most abundant in the phylum Euryarchaeota, which itself represented approximately 35% of the total archaeal sequences (data not shown here).


Effects of Spartina alterniflora invasion on the communities of methanogens and sulfate-reducing bacteria in estuarine marsh sediments.

Zeleke J, Sheng Q, Wang JG, Huang MY, Xia F, Wu JH, Quan ZX - Front Microbiol (2013)

Neighbor-joining phylogenetic trees of (A) mcrA and (B) dsrB gene OTUs recovered from the Dongtan tidal salt marsh located in the Yangtze estuary. The trees were constructed based on the inferred amino acids of the OTU-representative nucleotide sequences. Percentages in the parenthesis indicate the percent of sequences included in that specific OTU. Only OTUs containing at least 0.5 and 1% of the total sequences mcrA and dsrB OTUs, respectively, are presented here.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3750361&req=5

Figure 3: Neighbor-joining phylogenetic trees of (A) mcrA and (B) dsrB gene OTUs recovered from the Dongtan tidal salt marsh located in the Yangtze estuary. The trees were constructed based on the inferred amino acids of the OTU-representative nucleotide sequences. Percentages in the parenthesis indicate the percent of sequences included in that specific OTU. Only OTUs containing at least 0.5 and 1% of the total sequences mcrA and dsrB OTUs, respectively, are presented here.
Mentions: McrA OTUs were dominated by OTU1, 2 and 3, representing approximately 32.5, 21.5, and 16.5% of the total sequences (Figure 3A). OTU1 was closely related to the mcrA of Methanococcus, whereas OTU2 and 3 were related to the mcrA of Methanomicrobiales and Methanosarcina, respectively. Most of the mcrA gene sequences were closely related to the methanogen orders Methanomicrobiales, Methanosarcinales and Methanococcales, although other methanogens such as Methanobacteriales, ANME (1 and 3) and ZC-I were also detected in the salt marsh (Figure 3A). As the primers used in this study (mlas/mcrA-rev) can amplify mcrA and mrtA genes (Steinberg and Regan, 2009), the presence of large number of sequences (32.5%) related to Methanococcales (Luton et al., 2002), methanogens carrying mcrA and mrtA genes, might overestimate the abundance and diversity of the total methanogens. Interestingly, at both similarity cutoffs, Methanococcales was represented by a single OTU that is closely related (approximately 95% at the amino-acid level) to Methanococcus maripaludis. The occurrences of Methanomicrobiales, Methanosarcinales and Methanococcales in the mcrA sequences were also supported by the results from the analysis of archaeal 16S rRNA gene sequences where the above three methanogenic orders were also the most abundant in the phylum Euryarchaeota, which itself represented approximately 35% of the total archaeal sequences (data not shown here).

Bottom Line: Similar trends were observed for SRB, and they were up to two orders of magnitude higher than the methanogens.Diversity indices indicated a lower diversity of methanogens in the S. alterniflora stands than the P. australis stands.The results showed that in the sediments of tidal salt marsh where S. alterniflora displaced P. australis, the abundances of methanogens and SRB increased, but the community composition of methanogens appeared to be influenced more than did the SRB.

View Article: PubMed Central - PubMed

Affiliation: Department of Microbiology and Microbial Engineering, School of Life Sciences, Fudan University Shanghai, China.

ABSTRACT
The effect of plant invasion on the microorganisms of soil sediments is very important for estuary ecology. The community structures of methanogens and sulfate-reducing bacteria (SRB) as a function of Spartina alterniflora invasion in Phragmites australis-vegetated sediments of the Dongtan wetland in the Yangtze River estuary, China, were investigated using 454 pyrosequencing and quantitative real-time PCR (qPCR) of the methyl coenzyme M reductase A (mcrA) and dissimilatory sulfite-reductase (dsrB) genes. Sediment samples were collected from two replicate locations, and each location included three sampling stands each covered by monocultures of P. australis, S. alterniflora and both plants (transition stands), respectively. qPCR analysis revealed higher copy numbers of mcrA genes in sediments from S. alterniflora stands than P. australis stands (5- and 7.5-fold more in the spring and summer, respectively), which is consistent with the higher methane flux rates measured in the S. alterniflora stands (up to 8.01 ± 5.61 mg m(-2) h(-1)). Similar trends were observed for SRB, and they were up to two orders of magnitude higher than the methanogens. Diversity indices indicated a lower diversity of methanogens in the S. alterniflora stands than the P. australis stands. In contrast, insignificant variations were observed in the diversity of SRB with the invasion. Although Methanomicrobiales and Methanococcales, the hydrogenotrophic methanogens, dominated in the salt marsh, Methanomicrobiales displayed a slight increase with the invasion and growth of S. alterniflora, whereas the later responded differently. Methanosarcina, the metabolically diverse methanogens, did not vary with the invasion of, but Methanosaeta, the exclusive acetate utilizers, appeared to increase with S. alterniflora invasion. In SRB, sequences closely related to the families Desulfobacteraceae and Desulfobulbaceae dominated in the salt marsh, although they displayed minimal changes with the S. alterniflora invasion. Approximately 11.3 ± 5.1% of the dsrB gene sequences formed a novel cluster that was reduced upon the invasion. The results showed that in the sediments of tidal salt marsh where S. alterniflora displaced P. australis, the abundances of methanogens and SRB increased, but the community composition of methanogens appeared to be influenced more than did the SRB.

No MeSH data available.


Related in: MedlinePlus