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

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.

Communities of ammonia oxidizers at different stages of Spartina alterniflora invasion in salt marshes of Yangtze River estuary

“…S1). All detailed descriptions of the sampling locations and processes as well as the characteristics of sediments were reported before (Zeleke et al, 2013). In brief, two replicate locations "a" and "b" with 60 meters apart were selected.…”

“…AOA and AOB indicate ammonia-oxidizing archaea and bacteria, respectively; TA and TB indicate the total archaea and bacteria, respectively. The copy numbers of 16S rRNA genes of TA and TB were from the work published previously (Zeleke et al, 2013).…”

“…For pyrosequencing, the primer sets that targeted the β-proteobacterial and archaeal amoA genes along with the corresponding annealing temperatures are listed in Table 1. The polymerase chain reaction (PCR) for each gene was conducted following the 2-step barcoded PCR method (Berry et al, 2011) with slight modification, as described previously (Zeleke et al, 2013). DNA from each sample was amplified in triplicate, and the PCR products were pooled.…”

“…Recently, the influence of different S. alterniflora invasion stages on the methanogen and sulfate-reducing bacterial communities in salt marshes of the Yangtze River estuary was demonstrated (Zeleke et al, 2013). The invasion of S. alterniflora notably increased the abundance of the methanogen and sulfate-reducing microbial communities and decreased the diversity of methanogens, although its effects on the ammonia-oxidizing communities have not been described.…”

The Microbial Regulation of Global Biogeochemical Cycles

“…Several submissions have highlighted the importance for plant-microbial feedbacks for the regulation of organic matter decomposition and formation Thomson et al, 2013;Churchland and Grayston, under review), the production of biogenic volatile organic compounds (Rinnan et al, 2013), and the community composition of methanogens and sulfate reducing bacteria (Zeleke et al, 2013). A very active research area in soil microbial ecology is presently how small amounts of labile carbon sources can trigger, or "prime," the decomposition of soil organic matter.…”