Structure and function of the methanogenic microbial communities in Uruguayan soils shifted between pasture and irrigated rice fields
Summary Irrigated rice fields in Uruguay are temporarily established on soils used as cattle pastures. Typically, 4 years of cattle pasture are alternated with 2 years of irrigated rice cultivation. Thus, oxic upland conditions are rotated with seasonally anoxic wetland conditions. Only the latter c...
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| Published in | Environmental microbiology Vol. 15; no. 9; pp. 2588 - 2602 |
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| Main Authors | , , , , , |
| Format | Journal Article |
| Language | English |
| Published |
Oxford
Blackwell Publishing Ltd
01.09.2013
Blackwell Wiley Subscription Services, Inc |
| Subjects | |
| Online Access | Get full text |
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| Summary: | Summary
Irrigated rice fields in Uruguay are temporarily established on soils used as cattle pastures. Typically, 4 years of cattle pasture are alternated with 2 years of irrigated rice cultivation. Thus, oxic upland conditions are rotated with seasonally anoxic wetland conditions. Only the latter conditions are suitable for the production of CH4 from anaerobic degradation of organic matter. We studied soil from a permanent pasture as well as soils from different years of the pasture‐rice rotation hypothesizing that activity and structure of the bacterial and archaeal communities involved in production of CH4 change systematically with the duration of either oxic or anoxic conditions. Soil samples were taken from drained fields, air‐dried and used for the experiments. Indeed, methanogenic archaeal gene copy numbers (16S rRNA, mcrA) were lower in soil from the permanent pasture than from the pasture‐rice alternation fields, but within the latter, there was no significant difference. Methane production started to accumulate after 16 days and 7 days of anoxic incubation in soil from the permanent pasture and the pasture‐rice alternation fields respectively. Then, CH4 production rates were slightly higher in the soils used for pasture than for rice production. Analysis of δ13C in CH4, CO2 and acetate in the presence and absence of methyl fluoride, an inhibitor of aceticlastic methanogenesis, indicated that CH4 was mainly (58–75%) produced from acetate, except in the permanent pasture soil (42%). Terminal restriction fragment length polymorphism (T‐RFLP) of archaeal 16S rRNA genes showed no difference among the soils from the pasture‐rice alternation fields with Methanocellaceae and Methanosarcinaceae as the main groups of methanogens, but in the permanent pasture soil, Methanocellaceae were relatively less abundant. T‐RFLP analysis of bacterial 16S rRNA genes allowed the distinction of permanent pasture and fields from the pasture‐rice rotation, but nevertheless with a high similarity. Pyrosequencing of bacterial 16S rRNA genes generally revealed Firmicutes as the dominant bacterial phylum, followed by Proteobacteria, Acidobacteria and Actinobacteria. We conclude that a stable methanogenic microbial community established once pastures have been turned into management by pasture‐rice alternation despite the fact that 2 years of wetland conditions were followed by 4 years of upland conditions that were not suitable for CH4 production. |
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| Bibliography: | German Research Foundation (DFG) within the Collaborative Research Center 987 Fig. S1. Summary of a preliminary experiment with soil sampled in Dec 2009 close to Treinta-y-Tres.Fig. S2. Temporal increase of the CH4 partial pressure upon incubation of soil under anoxic conditions at 25°C. The soils were from different fields with pasture-rice rotation and from a permanent pasture (UT).Fig. S3. Temporal change of the H2 partial pressure (10 ppm ≡ 1 Pa) upon incubation of soil under anoxic conditions at 25°C. The soils were from different fields with pasture-rice rotation and from a permanent pasture (UT).Fig. S4. Concentrations of (A) acetate and of (B) its δ13C at the end of incubation of soil under anoxic conditions at 25°C. The soils were from different fields with pasture-rice rotation and from a permanent pasture (UT).Fig. S5. Isotopic enrichment factor (ε) for CH4 production in soil under anoxic conditions at 25°C. The soils were from different fields with pasture-rice rotation and from a permanent pasture (UT). The values of ε were calculated from the δ13C of CH4 and CO2 measured during linear increase of CH4 partial pressures. The ε-values of the uninhibited control are apparent enrichment factors for total CH4 production, those (εCO2,CH4) in the CH3F-inhibited incubations are characteristic for hydrogenotrophic methanogenesis.Fig. S6. Cluster dendrogram of (A) bacterial and (B) archaeal communities present in different pasture and rice field soils before (b) and after (a) anoxic incubation. Hierarchical cluster analysis was performed based on Bray-Curtis distances (expressed as height) generated from T-RFLP profiles (16S rRNA gene) using Ward's method. Replicate fields are indicated by the letters A, B, C, D; before and after incubation by the letters b and a.Fig. S7. Cluster dendrogram of (A, B) bacterial and (C, D) archaeal communities present in different pasture and rice field soils (A, C) in the beginning and (B, D) the end of anoxic incubation. Hierarchical cluster analysis was performed based on Bray-Curtis distances (expressed as height) generated from T-RFLP profiles (archaeal 16S rRNA gene) using Ward's method. Replicate fields are indicated by the letters A, B, C, D.Fig. S8. Canonical correspondence analysis (CCA) ordination plot for the effect of field type (UT, UP, UR) on the composition of the bacterial community based on the relative abundance of bacterial 16S rRNA gene T-RFs in different pasture and rice field soils (A) in the beginning and (B) at the end of anoxic incubation. The eigenvalues of the first and second axes in the ordination diagrams are as follows: (A) λ1 = 0.047, λ2 = 0.019 and (B) λ1 = 0.057, λ2 = 0.050. The field type (UT, UP, UR) was used as a constraint explaining 23% and 17.8% of the total variance in plot A and B respectively (P = 0.001). Different symbols denote the different soil samples, while samples of the same field type were graphically grouped (black line).Fig. S9. Canonical correspondence analysis (CCA) ordination plot for the effect of field type (UT, UP, UR) on the composition of the archaeal community based on the relative abundance of archaeal 16S rRNA gene T-RFs in different pasture and rice field soils (A) in the beginning and (B) at the end of anoxic incubation. The eigenvalues of the first and second axes in the ordination diagrams are as follows: (A) λ1 = 0.122, λ2 = 0.016 and (B) λ1 = 0.159, λ2 = 0.014. The field type (UT, UP, UR soils) was used as a constraint explaining 42% and 46% of the total variance in plot A and B respectively (P = 0.001). Different symbols denote the different soil samples, while samples of the same field type were graphically grouped (black line).Fig. S10. Rarefaction curves of pyrosequencing of bacterial 16S rRNA genes in different soils (UT, UP1, UP4, UR2). OTUs were defined by 97% sequence similarity. The table summarizes the total number of high-quality sequences and the number of OTUs.Fig. S11. Venn diagram for the OTUs identified by pyrosequencing of bacterial 16S rRNA genes in different soils (UT, UP1, UP4, UR2).Table S1. Affiliation of archaeal 16S rRNA gene clone sequences to different T-RFs and percentage of different archaeal groups found in the clone libraries (46 clones each) prepared from four different soils. Note that the 184 bp T-RF is assigned to two different phylogenetic groups. istex:3144A801A6119AAE585E0A4F67DFB53AD6D0CCF0 ArticleID:EMI12161 ark:/67375/WNG-T557GGTZ-W ObjectType-Article-1 SourceType-Scholarly Journals-1 ObjectType-Feature-2 content type line 23 |
| ISSN: | 1462-2912 1462-2920 |
| DOI: | 10.1111/1462-2920.12161 |