Phyllosphere Metaproteomes of Trees from the Brazilian Atlantic Forest Show High Levels of Functional Redundancy.

The phyllosphere of the Brazilian Atlantic Forest has been estimated to contain several million bacterial species that are associated with approximately 20000 plant species. Despite the high bacterial diversity in the phyllosphere, the function of these microorganisms and the mechanisms driving their community assembly are largely unknown. In this study, we characterized the bacterial communities in the phyllospheres of four tree species of the Atlantic Forest (Mollinedia schottiana, Ocotea dispersa, Ocotea teleiandra, and Tabebuia serratifolia) and their metaproteomes to examine the basic protein functional groups expressed in the phyllosphere. Bacterial community analyses using 16S rRNA gene sequencing confirmed prior observations that plant species harbor distinct bacterial communities and that plants of the same taxon have more similar communities than more distantly related taxa. Using LC-ESI-Q-TOF, we identified 216 nonredundant proteins, based on 3503 peptide mass spectra. Most protein families were shared among the phyllosphere communities, suggesting functional redundancy despite differences in the species compositions of the bacterial communities. Proteins involved in glycolysis and anaerobic carbohydrate metabolism, solute transport, protein metabolism, cell motility, stress and antioxidant responses, nitrogen metabolism, and iron homeostasis were among the most frequently detected. In contrast to prior studies on crop plants and Arabidopsis, a low abundance of OTUs related to Methylobacterium and no proteins associated with the metabolism of one-carbon molecules were detected in the phyllospheres of the tree species studied here. Our data suggest that even though the phyllosphere bacterial communities of different tree species are phylogenetically diverse, their metaproteomes are functionally convergent with respect to traits required for survival on leaf surfaces.

Bacterial and archaeal communities in bleached mottles of tropical podzols.

Podzols frequently show bleached mottles depleted in organic matter, most readily visible in the Bh horizons. Even though the process of bleached mottles development is not understood, it has been suggested that the selective degradation of organic matter by soil microorganisms has a major contribution. In this study, we examined the bacterial and archaeal communities along three Brazilian coastal podzol profiles, as well as in bleached mottles and their immediate vicinity, using 16S rRNA gene profiling. Our results showed that the bacterial and archaeal community structures in the studied podzols varied with depth and that the bacterial communities in the bleached mottles were significantly different from that in their immediate vicinity. In contrast, the archaeal communities in bleached mottles were significantly different from their vicinity only in the Bertioga (BT) profile, based on sequencing of amplicons of the 16S rRNA gene. Redundancy analyses showed that the bacterial community structures in the bleached mottles of BT were negatively associated mostly with the levels of organic carbon, exchangeable-aluminum (Al), exchangeable potassium, and Al-saturation, whereas in the surrounding soil, the opposite was observed. In the Ilha Comprida (IC) profiles, no such relationships were observed, suggesting distinct drivers of the bacterial community structures in bleached mottles of different podzols. In the bleached mottles of the BT profile, operational taxonomic units (OTUs) phylogenetically related to Pseudomonas were the most abundant Bacteria, whereas in the IC profiles, OTUs related to Acidobacteria were predominant. Thermoprotei (Crenarchaeota) were the most abundant Archaea in the bleached mottles and in their immediate vicinity. Based on the diverse metabolic capabilities of Pseudomonas and Acidobacteria, our data suggest that these groups of bacteria may be involved in the development of bleached mottles in the podzols studied and that the selection of specific bacterial populations in the bleached mottles may depend on the local edaphic conditions.

Proteome changes in Oncidium sphacelatum (Orchidaceae) at different trophic stages of symbiotic germination.

Mutualistic symbioses between plants and fungi are a widespread phenomenon in nature. Particularly in orchids, association with symbiotic fungi is required for seed germination and seedling development. During the initial stages of symbiotic germination, before the onset of photosynthesis, orchid protocorms are fully mycoheterotrophic. The molecular mechanisms involved in orchid symbiotic germination and development are largely unknown, but it is likely that changes in plant energy metabolism and defense-related responses play a central role in these processes. We have used 2D-LC-MS/MS coupled to isobaric tagging for relative and absolute quantification to identify proteins with differential accumulation in Oncidium sphacelatum at different stages of mycorrhizal protocorm development (achlorophyllous and green protocorms) after seed inoculation with a Ceratobasidium sp. isolate. We identified and quantified 88 proteins, including proteins putatively involved in energy metabolism, cell rescue and defense, molecular signaling, and secondary metabolism. Quantitative analysis showed that the expected changes in carbon metabolism in green protocorms were accompanied by enhanced accumulation of proteins involved in the modulation of reactive oxygen species homeostasis, defense-related responses, and phytoalexins and carotenoid biosynthesis. Our results suggest profound metabolic changes in orchid protocorms during the switch from the fully mycoheterotrophic to the photosynthetic stage. Part of these changes may be also related to the obligatory nature of the interaction with the endomycorrhizal fungus.

Bacterial and archaeal communities in the acid pit lake sediments of a chalcopyrite mine.

Bacterial and archaeal community structures and diversity of three different sedimentary environments (BH1A, BH2A and BH3A) in the acid pit lake of a chalcopyrite mine at Touro (Spain) were determined by 16S rRNA gene PCR-DGGE and sequencing of clone libraries. DGGE of bacterial and archaeal amplicons showed that the sediments harbor different communities. Bacterial 16S rRNA gene sequences were assigned to Acidobacteria, Actinobacteria, Cyanobacteria, Planctomycetes, Proteobacteria, Chloroflexi and uncultured bacteria, after clustering into 42 operational taxonomic units (OTUs). OTU 2 represented approximately 37, 42 and 37 % of all sequences from sediments BH1A, BH2A and BH3A, respectively, and was phylogenetically related to uncultured Chloroflexi. Remaining OTUs were phylogenetically related to heterotrophic bacteria, including representatives of Ferrithrix and Acidobacterium genera. Archaeal 16S rRNA gene sequences were clustered into 54 OTUs. Most of the sequences from the BH1A sediment were assigned to Euryarchaeota, whereas those from BH2A sediment were assigned to Crenarchaeota. The majority of the sequences from BH3A sediment were assigned to unclassified Archaea, and showed similarities to uncultured and unclassified environmental clones. No sequences related to Acidithiobacillus and Leptospirillum, commonly associated with acid mine drainage, were detected in this study.

A genomic approach to the understanding of Xylella fastidiosa pathogenicity.

Xylella fastidiosa is a fastidious, xylem-limited bacterium that causes several economically important plant diseases, including citrus variegated chlorosis (CVC). X. fastidiosa is the first plant pathogen to have its genome completely sequenced. In addition, it is probably the least previously studied of any organism for which the complete genome sequence is available. Several pathogenicity-related genes have been identified in the X. fastidiosa genome by similarity with other bacterial genes involved in pathogenesis in plants, as well as in animals. The X. fastidiosa genome encodes different classes of proteins directly or indirectly involved in cell-cell interactions, degradation of plant cell walls, iron homeostasis, anti-oxidant responses, synthesis of toxins, and regulation of pathogenicity. Neither genes encoding members of the type III protein secretion system nor avirulence-like genes have been identified in X. fastidiosa.

Intestinal bacterial community and growth performance of chickens fed diets containing antibiotics.

This study was conducted to relate the performance of broiler chickens fed diets containing growth-promoting antibiotics to changes in the intestinal microbiota. The technique of denaturing gradient gel electrophoresis (DGGE) of amplicons of the region V3 of 16S rDNA was used to characterize the microbiota. Two experiments were conducted, one with broilers raised in battery cages and the other with broilers raised in floor pens. Antibiotics improved the performance of the chickens raised in floor pens only. Avilamycin, bacitracin methylene disalicylate, and enramycin induced changes in the composition of the intestinal bacterial community of the birds in both experiments. The number of bacterial genotypes found in the intestinal tract of chickens was not reduced by the antibiotics supplemented in either environment. However, the changes in the composition of the intestinal bacterial community induced by antibiotics may be related to improvement in growth performance. This was indicated by the suppression of 6 amplicons and the presence of 4 amplicons exclusive to the treatment that had the best performance in the floor pen experiment.

Antioxidant responses in bean (Phaseolus vulgaris) roots colonized by arbuscular mycorrhizal fungi.

• Degradation of reactive oxygen species in arbuscular mycorrhizas (AM) may be an efficient mechanism to attenuate the activation of plant defenses. Here, we evaluated the activities of superoxide dismutase (SOD), guaiacol-peroxidase (GPX) and catalase (CAT) in bean (Phaseolus vulgaris) mycorrhizal roots at different conditions and stages of symbiosis development. • Bean plants were inoculated with Glomus clarum (Gc) or G. intraradices (Gi), under low (LP) and high P (HP) concentrations, and grown under glasshouse conditions. In a second experiment, bean seeds were treated with formononetin and inoculated with Gc under LP and HP conditions. The activities of SOD, GPX and CAT were evaluated. • SOD was induced only in roots colonized by Gc, at a late stage of the symbiosis development under LP, and at an early stage under HP. GPX was induced in roots colonized by Gc at an early time point and suppressed later under LP. In general, CAT was induced in roots colonized by Gc under LP. CAT activities in roots were dependent on P and formononetin treatment. • The possible roles of SOD, GPX and CAT in AM are discussed.

Bacterial diversity in tree canopies of the Atlantic forest.

We found an extraordinary level of bacterial biodiversity in the tree leaf canopy of a tropical Atlantic forest by using culture-independent molecular methods. Our survey suggests that each tree species selects for a distinct microbial community. Analysis of the bacterial 16S ribosomal RNA gene sequences revealed that about 97% of the bacteria were unknown species and that the phyllosphere of any one tree species carries at least 95 to 671 bacterial species. The tree canopies of tropical forests likely represent a large reservoir of unexplored microbial diversity.