Siderophore production confers to bacteria competitive advantages to colonize plant tissues and to exclude other microorganisms from the same ecological niche. This work shows that the community of endophytic siderophore-producing bacteria (SPB) associated to Oryza sativa cultivated in Uruguayan soils is dynamic and diverse. These bacteria were present in grains, roots, and leaves, and their density fluctuated between log(10) 3.44 and log(10) 5.52 cfu g(-1) fresh weight (fw) during the plant growth. Less than 10% of the heterotrophic bacteria produced siderophores in roots and leaves of young plants, but most of the heterotrophic bacteria were siderophore-producers in mature plants. According to their amplified restriction DNA ribosomal analysis (ARDRA) pattern, 54 of the 109 endophytic SPB isolated from different plant tissues or growth stages from replicate plots, were unique. Bacteria belonging to the genera Sphingomonas, Pseudomonas, Burkholderia, and Enterobacter alternated during plant growth, but the genus Pantoea was predominant in roots at tillering and in leaves at subsequent stages. Pantoea ananatis was the SPB permanently associated to any of the plant tissues, but the genetic diversity within this species-revealed by BOX-PCR fingerprinting- showed that different strains were randomly distributed along time and plant tissue, suggesting that a common trait of the species P. ananatis determined the interaction with the rice plant. Several isolates were stronger IAA producers than Azospirillum brasilense or Herbaspirillum seropedicae. In vitro inhibition assays showed that SPB of the genus Burkholderia were good antagonists of pathogenic fungi and that only one SPB isolate of the genus Pseudomonas was able to inhibit A. brasilense and H. seropedicae. These results denoted that SPB were selected into the rice plant. P. ananatis was the permanent and dominant associated species which was unable to inhibit two of the relevant plant growth-promoting bacteria.

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Lonar Lake is a unique saline and alkaline ecosystem formed by meteor impact in the Deccan basalts in India around 52 000 years ago. To investigate the role of methylotrophy in the cycling of carbon in this unusual environment, stable-isotope probing (SIP) was carried out using the onecarbon compounds methane, methanol and methylamine. Denaturing gradient gel electrophoresis fingerprinting analyses performed with heavy 13 C-labelled DNA retrieved from sediment microcosms confirmed the enrichment and labelling of active methylotrophic communities. Clone libraries were constructed using PCR primers targeting 16S rRNA genes and functional genes. Methylomicrobium, Methylophaga and Bacillus spp. were identified as the predominant active methylotrophs in methane, methanol and methylamine SIP microcosms, respectively. Absence of mauA gene amplification in the methylamine SIP heavy fraction also indicated that methylamine metabolism in Lonar Lake sediments may not be mediated by the methylamine dehydrogenase enzyme pathway. Many gene sequences retrieved in this study were not affiliated with extant methanotrophs or methylotrophs. These sequences may represent hitherto uncharacterized novel methylotrophs or heterotrophic organisms that may have been cross-feeding on methylotrophic metabolites or biomass. This study represents an essential first step towards understanding the relevance of methylotrophy in the soda lake sediments of an unusual impact crater structure.

Flooding impacts soil microbial communities, but its effect on endophytic communities has rarely been explored. This work addresses the effect of flooding on the abundance and diversity of endophytic diazotrophic communities on rice plants established in a greenhouse experiment. The nifH gene was significantly more abundant in roots after flooding, whereas the nifH gene copy numbers in leaves were unaffected and remained low. The PCA (principal component analysis) of T-RFLP (terminal restriction fragment length polymorphism) profiles indicated that root communities of replicate plots were more similar and diverse after flooding than before flooding. The nifH libraries obtained by cloning and 454 pyrosequencing consistently showed a remarkable shift in the diazotrophic community composition after flooding. Gammaproteobacteria (66-98%), mainly of the genus Stenotrophomonas, prevailed in roots before flooding, whereas Betaproteobacteria was the dominant class (26-34%) after flooding. A wide variety of aerotolerant and anaerobic diazotrophic bacteria (e.g. Dechloromonas, Rhodopseudomonas, Desulfovibrio, Geobacter, Chlorobium, Spirochaeta, Selenomonas and Dehalobacter) with diverse metabolic traits were retrieved from flooded rice roots. These findings suggest that endophytic communities could be significantly impacted by changes in plant-soil conditions derived from flooding during rice cropping.

Aims:  To combine molecular and cultivation techniques to characterize the methanotrophic community in the soil–water interface (SWI) and rhizospheric soil from flooded rice fields in Uruguay, a temperate region in South America. Methods and Results:  A novel type I, related to the genus Methylococcus, and three type II methanotrophs were isolated from the highest positive dilution steps from the most probable number (MPN) counts. Potential methane oxidation activities measured in slurried samples were higher in the rhizospheric soil compared to the SWI and were stimulated by N‐fertilization. PmoA (particulate methane monooxygenase) clone libraries were constructed for both rice microsites. SWI clones clustered in six groups related to cultivated and uncultivated members from different ecosystems of the genera Methylobacter, Methylomonas, Methylococcus and a novel type I sublineage while cultivation and T‐RFLP (terminal restriction fragment length polymorphism) analysis confirmed the presence of type II methanotrophs. Conclusions:  Cultivation techniques, cloning analysis and T‐RFLP fingerprinting of the pmoA gene revealed a diverse methanotrophic community in the rice rhizospheric soil and SWI. Significance and Impact of the Study:  This study reports, for the first time, the analysis of the methanotrophic diversity in rice SWI and this diversity may be exploited in reducing methane emissions.

The endophytic bacterial communities of the three most important rice varieties cultivated in Uruguay were compared by a multiphasic approach. Leaves of mature plants grown in field experiments for two consecutive crop seasons were studied. No significant differences were found in the heterotrophic bacterial density for the three varieties. Pantoea ananatis and Pseudomonas syringae constituted 51% of the total of the isolates. These species were always present regardless of the variety or the season. Molecular analysis based on the 16S rRNA gene was performed by terminal restriction fragment length polymorphism (T-RFLP) and cloning. T-RFLP analysis revealed that bacterial communities grouped according to the variety, although the three varieties presented communities that showed 74% or higher similarities. Brevundimonas, the dominant genus in the clone library (18% of the clones), which might be present in all varieties according to T-RFLP profiles, was not recovered by cultivation. Conversely, bacteria from the genus Pseudomonas were not detected in the clone library. These results indicate that communities established in leaves of physiologically different rice varieties were highly similar and composed by a reduced group of strongly associated and persistent bacteria that were partially recovered by cultivation.

Methylogaea oryzae gen. nov., sp. nov., a mesophilic methanotroph isolated from a rice paddy field Aerobic methane-oxidizing bacteria (MOB) are a highly specialized and important group of ubiquitous bacteria that are capable of utilizing methane as the sole source of carbon and energy and, therefore, represent the largest global methane sink. They inhabit environments where both methane and oxygen are present, such as soils, wetlands, freshwater and marine systems, lakes and sediments (Bowman, 2006).Based on their phylogeny, chemotaxonomy, internal ultrastructure and metabolic pathways, MOB can be split into two major subgroups (Hanson & Hanson, 1996). The type I MOB include members of the genera Methylobacter, Methylomicrobium, Methylomonas, Methylosphaera, Methylosarcina, Methylohalobius, Methylosoma, Methylovulum, Methylothermus, Methylocaldum and Methylococcus, which belong to the class Gammaproteobacteria. The type II MOB include members of the genera Methylosinus, Methylocystis, Methylocella and Methylocapsa, which are assigned to the class Alphaproteobacteria. In addition, two filamentous Gammaproteobacteria, Crenothrix polyspora and 'Clonothrix fusca', are now considered to be type I methanotrophs based on 16S rRNA analysis (Stoecker et al., 2006;Vigliotta et al., 2007). Extreme methane oxidation by acidophilic bacteria belonging to the phylum Verrucomicrobia has also been reported (Op den Camp et al., 2009).In wetland rice fields, MOB play a vital role functioning as a bio-filter, oxidizing methane produced in anaerobic environments by the methanogenic Archaea and thus decreasing the release of methane into the atmosphere. In a previous study, a novel bacterial strain, designated E10 T , was isolated from the soil-water interface of a flooded Uruguayan rice field and was found to be moderately related to the Methylococcus-Methylocaldum group (Ferrando & Tarlera, 2009). To our knowledge, this is the first reported case of the isolation of a type I MOB from a rice paddy. Here, strain E10T is formally described and assigned an accurate taxonomic rank. Strain E10T was isolated from the soil-water interface of a flooded rice field in Treinta y Tres, South-east Uruguay (32 u 559 S 54 u 509 W) from most probable number (MPN) counts of methanotrophs followed by repeated dilution in liquid nitrate mineral salts (NMS) medium (Whittenbury et al., 1970), with added methane to achieve a 25 % (v/v) Abbreviations: MOB, methane-oxidizing bacteria; MPN, most probable number; pMMO, particulate methane monoxygenase; sMMO, soluble methane monoxygenase.

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