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The potentials for sequential reduction of inorganic electron acceptors and production of methane have been examined in sixteen rice soils obtained from China, the Philippines, and Italy. Methane, CO2, Fe(II), NO3-, SO42-, pH, Eh, H2 and acetate were monitored duringanaerobic incubation at 30 deg. C for 120 days. Based on the accumulation patterns of CO2 and CH4, the reduction process was divided into three distinct phases: (1) an initial reduction phase during which most of the inorganic electron acceptors were depleted and CO2 production was at its maximum, (2) a methanogenic phase during which CH4 production was initiated andreached its highest rate, and (3) a steady state phase with constantproduction rates of CH4 and CO2. The reductionphases lasted for 19 to 75 days with maximum CO2 production of 2.3 to 10.9 micromol d-1 g-1 dry soil. Methane production started after 2 to 87 days and became constant afterabout 38-68 days (one soil > 120 days). The maximum CH4 production rates ranged between 0.01 and 3.08 micromol d-1 g-1. During steady state the constant CH4 and CO2 production rates varied from 0.07 to 0.30 micromol d-1 g-1 and 0.02 and 0.28 micromol d-1 g-1, respectively. Within the 120 d of anaerobic incubationonly 6-17% of the total soil organic carbon was released into the gas phase. The gaseous carbon released consisted of 61-100% CO2, <0.1-35% CH4, and <5% nonmethane hydrocarbons. Associated with the reduction of available Fe(III) most of the CO2 was produced during the reduction phase. The electron transfer wasbalanced between total CO2 produced and both CH4 formed and Fe(III), sulfate and nitrate reduced. Maximum CH4 p [ABSTRACT FROM AUTHOR]

Methane is an important greenhouse gas and acetate is the most important intermediate (average 70%) of the carbon flow to CH 4 in paddy fields. Sulfate (e.g., gypsum) application can reduce CH 4 emissions up to 70%. However, the effect of gypsum application on acetate degradation and the microbial communities involved are unclear. Therefore, we studied acetate-dependent sulfate reduction in anoxic microcosms of Italian rice paddy soil, combining profiling of 16S rRNA and dissimilatory sulfite reductase (dsrB) genes and transcripts and rRNA based stable isotope probing (SIP) analysis. Methane production was completely inhibited by gypsum in the absence of exogenous acetate. Amended acetate (either 13 C labelled or non-labelled) was stoichiometrically coupled to sulfate reduction or CH 4 production. With methyl fluoride in the presence of sulfate, added propionate and butyrate were incompletely oxidized to acetate, which transiently accumulated. After the depletion of propionate and butyrate the accumulated acetate was rapidly consumed. The relative abundance of dsrB and 16S rRNA genes and transcripts from Syntrophobacteraceae (Desulfovirga spp., Syntrophobacter spp. and unclassified Syntrophobacteraceae) increased upon addition of gypsum and acetate. Simultaneously, Syntrophobacteraceae affiliated species were significantly labelled with 13 C. In addition, minor groups like Desulforhabdus spp., Desulfobacca spp. and Desulfotomaculum spp. substantially incorporated 13 C into their nucleic acids. The relative abundance of Desulfovibrio spp. slightly increased upon gypsum amendments. However, 13 C labelling of Desulfovibrio spp. was only moderate. In summary, Syntrophobacteraceae affiliated species were identified as the major acetotrophic sulfate reducers (SRB) in Italian paddy soil. The identification of these SRB as dominant acetate degraders well explained the scenarios of competition between SRB and acetoclastic methanogens as observed in rice paddy soil., (© 2017 Society for Applied Microbiology and John Wiley & Sons Ltd.)

Microorganisms associated with the roots of plants have an important function in plant growth and in soil carbon sequestration. Rice cultivation is the second largest anthropogenic source of atmospheric CH4, which is a significant greenhouse gas. Up to 60% of fixed carbon formed by photosynthesis in plants is transported below ground, much of it as root exudates that are consumed by microorganisms. A stable isotope probing (SIP) approach was used to identify microorganisms using plant carbon in association with the roots and rhizosphere of rice plants. Rice plants grown in Italian paddy soil were labeled with (13)CO2 for 10 days. RNA was extracted from root material and rhizosphere soil and subjected to cesium gradient centrifugation followed by 16S rRNA amplicon pyrosequencing to identify microorganisms enriched with (13)C. Thirty operational taxonomic units (OTUs) were labeled and mostly corresponded to Proteobacteria (13 OTUs) and Verrucomicrobia (8 OTUs). These OTUs were affiliated with the Alphaproteobacteria, Betaproteobacteria, and Deltaproteobacteria classes of Proteobacteria and the "Spartobacteria" and Opitutae classes of Verrucomicrobia. In general, different bacterial groups were labeled in the root and rhizosphere, reflecting different physicochemical characteristics of these locations. The labeled OTUs in the root compartment corresponded to a greater proportion of the 16S rRNA sequences (∼20%) than did those in the rhizosphere (∼4%), indicating that a proportion of the active microbial community on the roots greater than that in the rhizosphere incorporated plant-derived carbon within the time frame of the experiment., (Copyright © 2015, American Society for Microbiology. All Rights Reserved.)

The impact of environmental perturbation (e.g., nitrogenous fertilizers) on the dynamics of methane fluxes from soils and wetland systems is poorly understood. Results of fertilizer studies are often contradictory, even within similar ecosystems. In the present study the hypothesis of whether these contradictory results may be explained by the composition of the methane-consuming microbial community and hence whether methanotrophic diversity affects methane fluxes was investigated. To this end, rice field and forest soils were incubated in microcosms and supplemented with different nitrogenous fertilizers and methane concentrations. By labeling the methane with 13C, diversity and function could be coupled by analyses of phospholipid-derived fatty acids (PLFA) extracted from the soils at different time points during incubation. In both rice field and forest soils, the activity as well as the growth rate of methane-consuming bacteria was affected differentially. For type I methanotrophs, fertilizer application stimulated the consumption of methane and the subsequent growth, while type II methanotrophs were generally inhibited. Terminal restriction fragment length polymorphism analyses of the pmoA gene supported the PLFA results. Multivariate analyses of stable-isotope-probing PLFA profiles indicated that in forest and rice field soils, Methylocystis (type II) species were affected by fertilization. The type I methanotrophs active in forest soils (Methylomicrobium/Methylosarcina related) differed from the active species in rice field soils (Methylobacter/Methylomonas related). Our results provide a case example showing that microbial community structure indeed matters, especially when assessing and predicting the impact of environmental change on biodiversity loss and ecosystem functioning.

We designed a PCR assay specific for the 16S rRNA genes of members of the class Actinobacteria, and created a clone library using the amplification product of total community DNA extracted from anoxic Italian rice field soil. Eighteen out of 27 randomly sequenced clones were affiliated with Actinobacteria, i.e. Frankineae, Corynebacterineae, Micrococcineae, the bacterium candidatus "Microthrix parvicella" and a novel taxonomically undefined cluster.