Dataset Information

Long-term nitrogen fertilization of paddy soil shifts iron-reducing microbial community revealed by RNA-(13)C-acetate probing coupled with pyrosequencing.

ABSTRACT: Iron reduction is an important biogeochemical process in paddy soils, yet little is known about the microbial coupling between nitrogen and iron reduction. Here, we investigated the shift of acetate-metabolizing iron-reducers under long-term nitrogen fertilization using (13)C-acetate-based ribosomal RNA (rRNA)-stable isotope probing (SIP) and pyrosequencing in an incubation experiment, and the shift of putative iron-reducers in original field samples were investigated by 16S rRNA gene-based pyrosequencing. During SIP incubations, in the presence of iron(III) oxyhydroxides, more iron(II) formation and less methane production were detected in nitrogen-fertilized (N) compared with non-fertilized (NF) soil. In (13)C-rRNA from microcosms amended with ferrihydrite (FER), Geobacter spp. were the important active iron-reducers in both soils, and labeled to a greater extent in N (31% of the bacterial classified sequences) than NF soils (11%). Pyrosequencing of the total 16S rRNA transcripts from microcosms at the whole community level further revealed hitherto unknown metabolisms of potential FER reduction by microorganisms including Pseudomonas and Solibacillus spp. in N soil, Dechloromonas, Clostridium, Bacillus and Solibacillus spp. in NF soil. Goethite (GOE) amendment stimulated Geobacter spp. to a lesser extent in both soils compared with FER treatment. Pseudomonas spp. in the N soil and Clostridium spp. in the NF soil may also be involved in GOE reduction. Pyrosequencing results from field samples showed that Geobacter spp. were the most abundant putative iron-reducers in both soils, and significantly stimulated by long-term nitrogen fertilization. Overall, for the first time, we demonstrate that long-term nitrogen fertilization promotes iron(III) reduction and modulates iron-reducing bacterial community in paddy soils.

SUBMITTER: Ding LJ

PROVIDER: S-EPMC4331580 | biostudies-literature | 2015 Mar

REPOSITORIES: biostudies-literature

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Long-term nitrogen fertilization of paddy soil shifts iron-reducing microbial community revealed by RNA-(13)C-acetate probing coupled with pyrosequencing.

Ding Long-Jun LJ Su Jian-Qiang JQ Xu Hui-Juan HJ Jia Zhong-Jun ZJ Zhu Yong-Guan YG

The ISME journal 20140829 3

Iron reduction is an important biogeochemical process in paddy soils, yet little is known about the microbial coupling between nitrogen and iron reduction. Here, we investigated the shift of acetate-metabolizing iron-reducers under long-term nitrogen fertilization using (13)C-acetate-based ribosomal RNA (rRNA)-stable isotope probing (SIP) and pyrosequencing in an incubation experiment, and the shift of putative iron-reducers in original field samples were investigated by 16S rRNA gene-based pyro ...[more]

PMID: 25171335

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Project description:Long-term livestock over-grazing causes nitrogen outputs to exceed inputs in Inner Mongolia, suggesting that low levels of nitrogen fertilization could help restore grasslands degraded by overgrazing. However, the effectiveness of such an approach depends on the response of production and species composition to the interactive drivers of nitrogen and water availability. We conducted a five-year experiment manipulating precipitation (NP: natural precipitation and SWP: simulated wet year precipitation) and nitrogen (0, 25 and 50 kg N ha(-1) yr(-1)) addition in Inner Mongolia. We hypothesized that nitrogen fertilization would increase forage production when water availability was relatively high. However, the extent to which nitrogen would co-limit production under average or below average rainfall in these grasslands was unknown.Aboveground net primary production (ANPP) increased in response to nitrogen when precipitation was similar to or higher than the long-term average, but not when precipitation was below average. This shift in limitation was also reflected by water and nitrogen use efficiency. Belowground live biomass significantly increased with increasing water availability, but was not affected by nitrogen addition. Under natural precipitation (NP treatment), the inter-annual variation of ANPP was 3-fold greater than with stable water availability (CV(ANPP) = 61±6% and 17±3% for NP and SWP treatment, respectively) and nitrogen addition increased CV(ANPP) even more (89±14%). This occurred in part because fertilizer nitrogen left in the soil in dry years remained available for uptake during wet years and because of high production by unpalatable annual species in wet years in the NP treatment. In summary, plant growth by residual fertilizer nitrogen could lead to sufficient yields to offset lack of additional production in dry years. However, the utility of fertilization for restoration may be constrained by shifts in species composition and the lack of response by belowground biomass, which reduces replacement of soil carbon and nitrogen.

Project description:Soil microbiome responses to short-term nitrogen (N) inputs remain uncertain when compared with previous research that has focused on long-term fertilization responses. Here, we examined soil bacterial/archaeal and fungal communities pre- and post-N fertilization in an 8 year-old switchgrass field, in which twenty-four plots received N fertilization at three levels (0, 100, and 200 kg N ha-1 as NH4NO3) for the first time since planting. Soils were collected at two depths, 0-5 and 5-15 cm, for DNA extraction and amplicon sequencing of 16S rRNA genes and ITS regions for assessment of microbial community composition. Baseline assessments prior to fertilization revealed no significant pre-existing divergence in either bacterial/archaeal or fungal communities across plots. The one-time N fertilizations increased switchgrass yields and tissue N content, and the added N was nearly completely removed from the soil of fertilized plots by the end of the growing season. Both bacterial/archaeal and fungal communities showed large spatial (by depth) and temporal variation (by season) within each plot, accounting for 17 and 12-22% of the variation as calculated from the Sq. root of PERMANOVA tests for bacterial/archaeal and fungal community composition, respectively. While N fertilization effects accounted for only ~4% of overall variation, some specific microbial groups, including the bacterial genus Pseudonocardia and the fungal genus Archaeorhizomyces, were notably repressed by fertilization at 200 kg N ha-1. Bacterial groups varied with both depth in the soil profile and time of sampling, while temporal variability shaped the fungal community more significantly than vertical heterogeneity in the soil. These results suggest that short-term effects of N fertilization are significant but subtle, and other sources of variation will need to be carefully accounted for study designs including multiple intra-annual sampling dates, rather than one-time "snapshot" analyses that are common in the literature. Continued analyses of these trends over time with fertilization and management are needed to understand how these effects may persist or change over time.

Dataset Information

Long-term nitrogen fertilization of paddy soil shifts iron-reducing microbial community revealed by RNA-(13)C-acetate probing coupled with pyrosequencing.

Publications

Long-term nitrogen fertilization of paddy soil shifts iron-reducing microbial community revealed by RNA-(13)C-acetate probing coupled with pyrosequencing.

Similar Datasets

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