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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

Proportions of the dominant orders of SRB analyzed from 16S rRNA gene sequences of Bacteria. The samples were collected from P. australis (P), S. alterniflora (S) and transition (T) stands. The sample names are as described in Figure 1.
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Figure 7: Proportions of the dominant orders of SRB analyzed from 16S rRNA gene sequences of Bacteria. The samples were collected from P. australis (P), S. alterniflora (S) and transition (T) stands. The sample names are as described in Figure 1.

Mentions: Among the SRB, the variations among the proportions of OTUs were very low. For instance, the most dominant 70% similarity OTUs (OTU 1, 2, and 3) represented approximately 7, 6 and 6% of the total sequences, respectively (Figure 3B). Phylogenetic analysis indicated that more than 85% of the sequences were related to Deltaproteobacteria, suggesting their significant role in the marsh. In the dsrB gene sequences, the most frequently detected families of SRB appeared to be Desulfobacteraceae (49.2 ± 8.5%) and Desulfobulbaceae (29.6 ± 7.8%), whereas sequences related to Desulfovibrionaceae, Peptococcaceae, Syntrophaceae and Syntrophobacteraceae were detected, but at much lower proportions (total <8%), The dominance of Desulfobacteraceae was mainly contributed to by three dominant dsrB OTUs that were either closely related to the genus Desulfosarcina or uncultured family members (Figure 3B). Interestingly, we detected relatively a large proportion of OTUs (11.3 ± 5.1%) clustered distinctly from the previously isolated dsrB phylotypes. This novel cluster formed a distinct deep branch between Desulfobulbaceae (with approximately 56.6% amino-acid sequence similarities) and Syntrophobacteraceae (with approximately 61% amino-acid sequence similarities) (Figure 3B). An analysis of the total bacterial 16S rRNA gene sequences indicated consistent results with the dsrB gene sequence results in that sequences related to the order Desulfobacterales were dominant (Figure 7).


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)

Proportions of the dominant orders of SRB analyzed from 16S rRNA gene sequences of Bacteria. The samples were collected from P. australis (P), S. alterniflora (S) and transition (T) stands. The sample names are as described in Figure 1.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Figure 7: Proportions of the dominant orders of SRB analyzed from 16S rRNA gene sequences of Bacteria. The samples were collected from P. australis (P), S. alterniflora (S) and transition (T) stands. The sample names are as described in Figure 1.
Mentions: Among the SRB, the variations among the proportions of OTUs were very low. For instance, the most dominant 70% similarity OTUs (OTU 1, 2, and 3) represented approximately 7, 6 and 6% of the total sequences, respectively (Figure 3B). Phylogenetic analysis indicated that more than 85% of the sequences were related to Deltaproteobacteria, suggesting their significant role in the marsh. In the dsrB gene sequences, the most frequently detected families of SRB appeared to be Desulfobacteraceae (49.2 ± 8.5%) and Desulfobulbaceae (29.6 ± 7.8%), whereas sequences related to Desulfovibrionaceae, Peptococcaceae, Syntrophaceae and Syntrophobacteraceae were detected, but at much lower proportions (total <8%), The dominance of Desulfobacteraceae was mainly contributed to by three dominant dsrB OTUs that were either closely related to the genus Desulfosarcina or uncultured family members (Figure 3B). Interestingly, we detected relatively a large proportion of OTUs (11.3 ± 5.1%) clustered distinctly from the previously isolated dsrB phylotypes. This novel cluster formed a distinct deep branch between Desulfobulbaceae (with approximately 56.6% amino-acid sequence similarities) and Syntrophobacteraceae (with approximately 61% amino-acid sequence similarities) (Figure 3B). An analysis of the total bacterial 16S rRNA gene sequences indicated consistent results with the dsrB gene sequence results in that sequences related to the order Desulfobacterales were dominant (Figure 7).

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