Alternating wet-dry cycles rather than sulfate fertilization control pathways of methanogenesis and methane turnover in rice straw-amended paddy soil

2021 ◽  
Author(s):  
Qiong Liu ◽  
Marco Romani ◽  
Jiajia Wang ◽  
Britta Planer-Friedrich ◽  
Johanna Pausch ◽  
...  
Keyword(s):  
Rice Straw ◽  
Management Practices ◽  
Methanogenic Archaea ◽  
Paddy Soils ◽  
Effective Management ◽  
Flowering Stage ◽  
Sulfate Reducing ◽  
Hydrogenotrophic Methanogenesis ◽  
Reducing Bacteria

<p>Alternate wet-drying (AWD) and sulfate fertilization have been considered as effective management practices for lowering CH<sub>4</sub> emissions from paddy soils. However, the effects of management practices on in situ belowground CH<sub>4</sub> turnover (production and oxidation) are not yet fully understood. Here, soil CO<sub>2</sub> and CH<sub>4</sub> concentrations and their C isotope compositions were measured at three rice growing stages in straw-amended paddy soils with and without sulfate fertilization under continuously flooded conditions and two wet-dry-cycles. CH<sub>4</sub> concentration reached 51.0 mg C L<sup>-1</sup> at flowering stage under flooded conditions, while it decreased to 0.04 mg C L<sup>-1</sup> under AWD. Relative enrichment of δ<sup>13</sup>C in CH<sub>4</sub> and depletion of δ<sup>13</sup>C in CO<sub>2</sub> under AWD indicated CH<sub>4</sub> oxidation. Sulfate addition had no significant effect on CH<sub>4</sub> concentration. The ample substrate supply might have prevented sulfate-reducing bacteria from out-competing methanogenic archaea and could therefore explain the absence of a fall in CH<sub>4</sub> production. The δ<sup>13</sup>C-CO<sub>2</sub> enrichment over time (7 ‰ and 5‰ with and without sulfate fertilizer, respectively) under flooded conditions likely indicates an increasing contribution of hydrogenotrophic methanogenesis to CH<sub>4</sub> production with ongoing rice growth. Overall, the results showed that AWD could more efficiently reduce CH<sub>4</sub> production than sulfate fertilization in rice-straw-amended paddy soils.</p><p> </p>

scholarly journals Stratified Microbial Structure and Activity in Sulfide- and Methane-Producing Anaerobic Sewer Biofilms

2014 ◽  
Vol 80 (22) ◽  
pp. 7042-7052 ◽  
Author(s):  
Jing Sun ◽  
Shihu Hu ◽  
Keshab Raj Sharma ◽  
Bing-Jie Ni ◽  
Zhiguo Yuan
Keyword(s):  
Surface Layer ◽  
Methanogenic Archaea ◽  
Molecular Techniques ◽  
Content Type ◽  
Sulfate Reducing ◽  
Biofilm Model ◽  
Reducing Bacteria ◽  
Microelectrode Measurements ◽  
Good Agreement

ABSTRACTSimultaneous production of sulfide and methane by anaerobic sewer biofilms has recently been observed, suggesting that sulfate-reducing bacteria (SRB) and methanogenic archaea (MA), microorganisms known to compete for the same substrates, can coexist in this environment. This study investigated the community structures and activities of SRB and MA in anaerobic sewer biofilms (average thickness of 800 μm) using a combination of microelectrode measurements, molecular techniques, and mathematical modeling. It was seen that sulfide was mainly produced in the outer layer of the biofilm, between the depths of 0 and 300 μm, which is in good agreement with the distribution of SRB population as revealed by cryosection-fluorescencein situhybridization (FISH). SRB had a higher relative abundance of 20% on the surface layer, which decreased gradually to below 3% at a depth of 400 μm. In contrast, MA mainly inhabited the inner layer of the biofilm. Their relative abundances increased from 10% to 75% at depths of 200 μm and 700 μm, respectively, from the biofilm surface layer. High-throughput pyrosequencing of 16S rRNA amplicons showed that SRB in the biofilm were mainly affiliated with five genera,Desulfobulbus,Desulfomicrobium,Desulfovibrio,Desulfatiferula, andDesulforegula, while about 90% of the MA population belonged to the genusMethanosaeta. The spatial organizations of SRB and MA revealed by pyrosequencing were consistent with the FISH results. A biofilm model was constructed to simulate the SRB and MA distributions in the anaerobic sewer biofilm. The good fit between model predictions and the experimental data indicate that the coexistence and spatial structure of SRB and MA in the biofilm resulted from the microbial types and their metabolic transformations and interactions with substrates.

scholarly journals Integrative analysis of <i>Geobacter</i> spp. and sulfate-reducing bacteria during uranium bioremediation

2012 ◽  
Vol 9 (3) ◽  
pp. 1033-1040 ◽  
Author(s):  
M. Barlett ◽  
K. Zhuang ◽  
R. Mahadevan ◽  
D. Lovley
Keyword(s):  
Sulfate Reducing Bacteria ◽  
Field Trials ◽  
Second Phase ◽  
Sulfate Reducing ◽  
Organic Electron ◽  
Poor Understanding ◽  
Key Factor ◽  
Reducing Bacteria ◽  
The Impact

Abstract. Enhancing microbial U(VI) reduction with the addition of organic electron donors is a promising strategy for immobilizing uranium in contaminated groundwaters, but has yet to be optimized because of a poor understanding of the factors controlling the growth of various microbial communities during bioremediation. In previous field trials in which acetate was added to the subsurface, there were two distinct phases: an initial phase in which acetate-oxidizing, U(VI)-reducing Geobacter predominated and U(VI) was effectively reduced and a second phase in which acetate-oxidizing sulfate reducing bacteria (SRB) predominated and U(VI) reduction was poor. The interaction of Geobacter and SRB was investigated both in sediment incubations that mimicked in situ bioremediation and with in silico metabolic modeling. In sediment incubations, Geobacter grew quickly but then declined in numbers as the microbially reducible Fe(III) was depleted whereas the SRB grow more slowly and reached dominance after 30–40 days. Modeling predicted a similar outcome. Additional modeling in which the relative initial percentages of the Geobacter and SRB were varied indicated that there was little to no competitive interaction between Geobacter and SRB when acetate was abundant. Further simulations suggested that the addition of Fe(III) would revive the Geobacter, but have little to no effect on the SRB. This result was confirmed experimentally. The results demonstrate that it is possible to predict the impact of amendments on important components of the subsurface microbial community during groundwater bioremediation. The finding that Fe(III) availability, rather than competition with SRB, is the key factor limiting the activity of Geobacter during in situ uranium bioremediation will aid in the design of improved uranium bioremediation strategies.

Microbial ecology of sulfate-reducing bacteria in wastewater biofilms analyzed by microelectrodes and fish (fluorescent in situ hybridization) technique

1999 ◽  
Vol 39 (7) ◽  
pp. 41-47 ◽  
Author(s):  
Satoshi Okabe ◽  
Hisashi Satoh ◽  
Tsukasa Itoh ◽  
Yoshimasa Watanabe
Keyword(s):  
In Situ Hybridization ◽  
Sulfate Reduction ◽  
Sulfate Reducing Bacteria ◽  
Hybridization Technique ◽  
Concentration Profiles ◽  
Reduction Zone ◽  
Sulfate Reducing ◽  
Reducing Bacteria ◽  
Culture Dependent

The vertical distribution of sulfate-reducing bacteria (SRB) in microaerophilic wastewater biofilms grown on fully submerged rotating disk reactors (RDR) was determined by the conventional culture-dependent MPN method and in situ hybridization of fluorescently-labelled 16S rRNA-targeted oligonucleotide probes for SRB in parallel. Chemical concentration profiles within the biofilm were also measured using microelectrodes for O2, S2-, NO3- and pH. In situ hybridization revealed that the SRB probe-stained cells were distributed throughout the biofilm even in the oxic surface zone in all states from single scattered cells to clustered cells. The higher fluorescence intensity and abundance of SRB probe-stained cells were found in the middle part of the biofilm. This result corresponded well with O2 and H2S concentration profiles measured by microelectrodes, showing sulfate reduction was restricted to a narrow anaerobic zone located about 500 μm below the biofilm surface. Results of the MPN and potential sulfate reducing activity (culture-dependent approaches) indicated a similar distribution of cultivable SRB in the biofilm. The majority of the general SRB probe-stained cells were hybridized with SRB 660 probe, suggesting that one important member of the SRB in the wastewater biofilm could be the genus Desulfobulbus. An addition of nitrate forced the sulfate reduction zone deeper in the biofilm and reduced the specific sulfate reduction rate as well. The sulfate reduction zone was consequently separated from O2 and NO3- respiration zones. Anaerobic H2S oxidation with NO3- was also induced by addition of nitrate to the medium.

scholarly journals Microbial community structure with trends in methylation gene diversity and abundance in mercury-contaminated rice paddy soils in Guizhou, China

2018 ◽  
Vol 20 (4) ◽  
pp. 673-685 ◽  
Author(s):  
Tatiana A. Vishnivetskaya ◽  
Haiyan Hu ◽  
Joy D. Van Nostrand ◽  
Ann M. Wymore ◽  
Xiaohang Xu ◽  
...  
Keyword(s):  
Community Structure ◽  
Microbial Community ◽  
Microbial Community Structure ◽  
Gene Diversity ◽  
Rice Paddy ◽  
Paddy Soils ◽  
Rice Paddies ◽  
Sulfate Reducing ◽  
Rice Paddy Soils ◽  
Reducing Bacteria

Sulfate-reducing bacteria and methanogens are the primary Hg-methylators in Chinese rice paddies.

scholarly journals ANME-1 archaea drive methane accumulation and removal in estuarine sediments

2020 ◽  
Author(s):  
Richard Kevorkian ◽  
Sean Callahan ◽  
Rachel Winstead ◽  
Karen G. Lloyd
Keyword(s):  
16S Rrna ◽  
Sulfate Reducing Bacteria ◽  
Low Energy ◽  
Estuarine Sediments ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Sulfate Reducing ◽  
Hydrogenotrophic Methanogenesis ◽  
Natural Settings ◽  
Reducing Bacteria

AbstractUncultured members of the Methanomicrobia called ANME-1 perform the anaerobic oxidation of methane (AOM) through a process that uses much of the methanogenic pathway. It is unknown whether ANME-1 obligately perform AOM, or whether some of them can perform methanogenesis when methanogenesis is exergonic. Most marine sediments lack advective transport of methane, so AOM occurs in the sulfate methane transition zone (SMTZ) where sulfate-reducing bacteria consume hydrogen produced by fermenters, making hydrogenotrophic methanogenesis exergonic in the reverse direction. When sulfate is depleted deeper in the sediments, hydrogen accumulates making hydrogenotrophic methanogenesis exergonic, and methane accumulates in the methane zone (MZ). In White Oak River estuarine sediments, we found that ANME-1 comprised 99.5% of 16S rRNA genes from amplicons and 100% of 16S rRNA genes from metagenomes of the Methanomicrobia in the SMTZ and 99.9% and 98.3%, respectively, in the MZ. Each of the 16 ANME-1 OTUs (97% similarity) had peaks in the SMTZ that coincided with peaks of putative sulfate-reducing bacteria Desulfatiglans sp. and SEEP-SRB1. In the MZ, ANME-1, but no putative sulfate-reducing bacteria or cultured methanogens, increased with depth. Using publicly available data, we found that ANME-1 was the only group expressing methanogenic genes during both net AOM and net methanogenesis in an enrichment. The commonly-held belief that ANME-1 perform AOM is based on the fact that they dominate natural settings and enrichments where net AOM is measured. We found that ANME-1 also dominate natural settings and enrichment where net methanogenesis is measured, so we conclude that ANME-1 perform methane production. Alternating between AOM and methanogenesis, either in a single ANME-1 cell or between different subclades with similar 16S rRNA sequences of ANME-1, may confer a competitive advantage, explaining the predominance of low-energy adapted ANME-1 in methanogenic sediments worldwide.Abstract ImportanceLife may operate differently at very low energy levels. Natural populations of microbes that make methane survive on some of the lowest energy yields of all life. From all available data, we infer that these microbes alternate between methane production and oxidation, depending on which process is energy-yielding in the environment. This means that much of the methane produced naturally in marine sediments occurs through an organism that is also capable of destroying it under different circumstances.

scholarly journals Suspension Array Analysis of 16S rRNA from Fe- and SO42-Reducing Bacteria in Uranium-Contaminated Sediments Undergoing Bioremediation

2006 ◽  
Vol 72 (7) ◽  
pp. 4672-4687 ◽  
Author(s):  
Darrell P. Chandler ◽  
Ann E. Jarrell ◽  
Eric R. Roden ◽  
Julia Golova ◽  
Boris Chernov ◽  
...  
Keyword(s):  
16S Rrna ◽  
Total Rna ◽  
Iron Reducing Bacteria ◽  
Suspension Array ◽  
Sulfate Reducing ◽  
Subsurface Sediments ◽  
Reducing Bacteria ◽  
Bead Arrays ◽  
Microbiological Analyses

ABSTRACT A 16S rRNA-targeted tunable bead array was developed and used in a retrospective analysis of metal- and sulfate-reducing bacteria in contaminated subsurface sediments undergoing in situ U(VI) bioremediation. Total RNA was extracted from subsurface sediments and interrogated directly, without a PCR step. Bead array validation studies with total RNA derived from 24 isolates indicated that the behavior and response of the 16S rRNA-targeted oligonucleotide probes could not be predicted based on the primary nucleic acid sequence. Likewise, signal intensity (absolute or normalized) could not be used to assess the abundance of one organism (or rRNA) relative to the abundance of another organism (or rRNA). Nevertheless, the microbial community structure and dynamics through time and space and as measured by the rRNA-targeted bead array were consistent with previous data acquired at the site, where indigenous sulfate- and iron-reducing bacteria and near neighbors of Desulfotomaculum were the organisms that were most responsive to a change in injected acetate concentrations. Bead array data were best interpreted by analyzing the relative changes in the probe responses for spatially and temporally related samples and by considering only the response of one probe to itself in relation to a background (reference) environmental sample. By limiting the interpretation of the data in this manner and placing it in the context of supporting geochemical and microbiological analyses, we concluded that ecologically relevant and meaningful information can be derived from direct microarray analysis of rRNA in uncharacterized environmental samples, even with the current analytical uncertainty surrounding the behavior of individual probes on tunable bead arrays.

scholarly journals Salinity Responses of Benthic Microbial Communities in a Solar Saltern (Eilat, Israel)

2004 ◽  
Vol 70 (3) ◽  
pp. 1608-1616 ◽  
Author(s):  
Ketil Bernt S�rensen ◽  
Donald E. Canfield ◽  
Aharon Oren
Keyword(s):  
Sulfate Reduction ◽  
Reduction Rate ◽  
Sulfate Reduction Rate ◽  
Anoxygenic Phototrophs ◽  
Sulfate Reducing ◽  
Oxygen Budget ◽  
Reducing Bacteria ◽  
Increased Activity ◽  
Optimum Salinity

ABSTRACT The salinity responses of cyanobacteria, anoxygenic phototrophs, sulfate reducers, and methanogens from the laminated endoevaporitic community in the solar salterns of Eilat, Israel, were studied in situ with oxygen microelectrodes and in the laboratory in slurries. The optimum salinity for the sulfate reduction rate in sediment slurries was between 100 and 120‰, and sulfate reduction was strongly inhibited at an in situ salinity of 215‰. Nevertheless, sulfate reduction was an important respiratory process in the crust, and reoxidation of formed sulfide accounted for a major part of the oxygen budget. Methanogens were well adapted to the in situ salinity but contributed little to the anaerobic mineralization in the crust. In slurries with a salinity of 180‰ or less, methanogens were inhibited by increased activity of sulfate-reducing bacteria. Unicellular and filamentous cyanobacteria metabolized at near-optimum rates at the in situ salinity, whereas the optimum salinity for anoxygenic phototrophs was between 100 and 120‰.

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