Anaerobic ammonium oxidation coupled to iron(III) reduction (termed Feammox) with dinitrogen, nitrite, or nitrate as the end-product is a recently discovered process of nitrogen cycling. However, Feammox has not been described in paddy soils, which are rich in iron(III) oxides and subjected to intensive nitrogen fertilization. Here, evidence for Feammox in a paddy soil chronosequence with a gradient of microbially reducible iron(III) levels was obtained in Southern China using 15 N-labeled ammonium-based isotopic tracing and acetylene inhibition techniques. Our study demonstrated the occurrence of Feammox in the chronosequence, and direct dinitrogen production was shown to be the dominant Feammox pathway. Within the chronosequence, three paddy soils with higher microbially reducible iron(III) levels had higher Feammox rates (ranged from 0.17 to 0.59 mg N kg −1 d −1 ) compared to an uncultivated soil (0.04 mg N kg −1 d −1 ). It is estimated that a loss of 7.8−61 kg N ha −1 year −1 is associated with Feammox in the examined paddy soils. Overall, we discover that rice cultivation could enrich microbially reducible iron(III), accelerate Feammox reaction and thus fuel nitrogen loss from soils, and suggest that Feammox could be a potentially important pathway for nitrogen loss in paddy soils.

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 13C-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 13C-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.

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Global paddy soil is the primary source of methane, a potent greenhouse gas. It is therefore highly important to understand the carbon cycling in paddy soil. Microbial reduction of iron, which is widely found in paddy soil, is likely coupled with the oxidation of dissolved organic matter (DOM) and suppresses methanogenesis. However, little is known about the biotransformation of small molecular DOM accumulated under flooded conditions and the effect of iron reduction on the biotransformation pathway. Here, we carried out anaerobic incubation experiments using field-collected samples amended with ferrihydrite and different short-chain fatty acids. Our results showed that less than 20% of short-chain fatty acids were mineralized and released to the atmosphere. Using Fourier transform ion cyclotron resonance mass spectrometry, we further found that a large number of recalcitrant molecules were produced during microbial consumption of these short-chain fatty acids. Moreover, the biotransformation efficiency of short-chain fatty acids decreased with the increasing length of carbon chains. Ferrihydrite addition promoted microbial assimilation of short-chain fatty acids as well as enhanced the activation and biotransformation of indigenous stable carbon in the soil replenished with formate. This study demonstrates the significance of ferrihydrite in the biotransformation of labile DOM and promotes a more comprehensive understanding of the coupling of iron reduction and carbon cycling in paddy soils.

Biochar has the potential to influence methanogenesis which is a key component of global carbon cycling. However, the mechanisms governing biochar's influence on methanogenesis is not well understood, especially its effects on interspecies relationships between methanogens and anaerobic bacteria (e.g., Geobacteraceae). To understand how different types of biochar influence methanogenesis, biochars derived from rice straw (RB), wood chips (WB), and manure (MB) were added to the methanogenic enrichment culture system of a paddy soil. Compared to the nonbiochar control, RB and MB additions accelerated methanogenesis remarkably, showing 10.7 and 12.3-folds higher methane production rate, respectively; while WB had little effect on methanogenesis. Using Fourier transform infrared spectroscopy, X-ray photoelectron spectroscopy, and electrochemical methods, RB and MB also had higher redox-active properties or charging and discharging capacities than WB, and the functional groups, mainly quinones, on the biochar surface played an important role in facilitating methanogenesis. Quantitative polymerase chain reaction results demonstrated that electronic syntrophy did exist between methanogens and Geobacteraceae. RB and MB stimulate methanogenesis by facilitating direct interspecies electron transfer between methanogens and Geobacteraceae. Our findings contribute to a better understanding of the effects of biochars from different feedstocks on methanogenesis and provide new evidence to the mechanisms of stimulating methanogenesis via biochar.

Conversion of tidal wetlands into paddy soils is an ancient and prevalent agricultural practice to meet increasing demand of food in the Yangtze River Delta of China, a coastal region where paddy soils originated. However, the impacts of tidal wetland reclamation and continuous rice cultivation at long time scales on soil bacterial communities remains poorly understood. In this study, we investigated temporal dynamics of bacterial communities using 16S rRNA gene pyrosequencing to delineate the patterns and drivers of soil bacterial succession along a long-term (2000 years) chronosequence of paddy field since reclamation from tidal wetlands. The results exhibited orderly changes in soil physicochemical characteristics and bacterial community composition with increasing rice cultivation time, indicating the occurrence of paddy soil development and bacterial succession since reclamation from tidal wetlands. Soil bacterial diversity significantly increased after reclamation of tidal wetlands. Succession of bacterial community composition was primarily linked with significant decrease in the relative abundances of Gammaproteobacteria and Planctomycetes and increase in those of Alphaproteobacteria and Firmicutes. Further analysis showed that long-term rice cultivation led to the enrichment of certain populations such as Rhodospirillaceae (within the class Alphaproteobacteria) and Clostridiaceae (within the phylum Firmicutes), which are potentially beneficial to higher rice yields. Canonical correspondence analysis indicated that at the time scale of millennia, the shift of bacterial community structure was mainly driven by the changes of soil physicochemical properties, especially cation exchange capacity and pH during paddy soil development. Overall, we demonstrate an orderly shift of soil bacterial communities towards higher productivity along with a 2000-year development of paddy soils after the tidal wetland reclamation, which was primarily associated with soil physicochemical alterations with time, and suggest that such chronosequence of paddy soils can serve as a test bed to delineate the relationship between microbial community and soil functions, particularly crop productivity.

Microbes play key roles in diverse biogeochemical processes including nutrient cycling. However, responses of soil microbial community and functional genes to long-term integrated fertilization (chemical combined with organic fertilization) remain unclear. Here, we used pyrosequencing and a microarray-based GeoChip to explore the shifts of microbial community and functional genes in a paddy soil which received over 21-year fertilization with various regimes, including control (no fertilizer), rice straw (R), rice straw plus chemical fertilizer nitrogen (NR), N and phosphorus (NPR), NP and potassium (NPKR), and reduced rice straw plus reduced NPK (L-NPKR). Significant shifts of the overall soil bacterial composition only occurred in the NPKR and L-NPKR treatments, with enrichment of certain groups including Bradyrhizobiaceae and Rhodospirillaceae families that benefit higher productivity. All fertilization treatments significantly altered the soil microbial functional structure with increased diversity and abundances of genes for carbon and nitrogen cycling, in which NPKR and L-NPKR exhibited the strongest effect, while R exhibited the least. Functional gene structure and abundance were significantly correlated with corresponding soil enzymatic activities and rice yield, respectively, suggesting that the structural shift of the microbial functional community under fertilization might promote soil nutrient turnover and thereby affect yield. Overall, this study indicates that the combined application of rice straw and balanced chemical fertilizers was more pronounced in shifting the bacterial composition and improving the functional diversity toward higher productivity, providing a microbial point of view on applying a cost-effective integrated fertilization regime with rice straw plus reduced chemical fertilizers for sustainable nutrient management.

Nitrogen fertilization and returning straw to paddy soil are important factors that regulate CH 4 production. To evaluate the effect of rice straw and/or nitrate amendment on methanogens, a paddy soil was anaerobically incubated for 40 days. The results indicated that while straw addition increased CH 4 production and the abundances of mcrA genes and their transcripts, nitrate amendment showed inhibitory effects on them. The terminal restriction fragment length polymorphism (T-RFLP) analysis based on mcrA gene revealed that straw addition obviously changed methanogenic community structure. Based on mcrA gene level, straw-alone addition stimulated Methanosarcinaceaes at the early stage of incubation (first 11 days), but nitrate showed inhibitory effect. The relative abundance of Methanobacteriaceae was also stimulated by straw addition during the first 11 days. Furthermore, Methanosaetaceae were enriched by nitrate-alone addition after 11 days, while Methanocellaceae were enriched by nitrate addition especially within the first 5 days. The transcriptional methanogenic community indicated more dynamic and complicated responses to straw and/or nitrate addition. Based on mcrA transcript level, nitrate addition alone resulted in the increase of Methanocellaceae and the shift from Methanosarcinaceae to Methanosaetaceae during the first 5 days of incubation. Straw treatments increased the relative abundance of Methanobacteriaceae after 11 days. These results demonstrate that nitrate addition influences methanogens which are transcriptionally and functionally active and can alleviate CH 4 production associated with straw amendment in paddy soil incubations, presumably through competition for common substrates between nitrate-utilizing organisms and methanogens.