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ABSTRACT. The microbiota of the Amazon River basin has been little studied. We compared the structure of bacterial communities of the Solimões and Negro Rivers, the main Amazon River tributaries, based on analysis of 16S rRNA gene sequences. Water was sampled with a 3-L Van Dorn collection bottle; samples were collected at nine different points/depths totaling 27 L of water from each river. Total DNA was extracted from biomass retained by a 0.22-μm filter after sequential filtration of the water through 0.8-and 0.22-μm filters. The 16S rRNA gene was amplified by PCR, cloned and sequenced, and the sequences were analyzed with the PHYLIP and DOTUR programs to obtain the operational taxonomic units (OTUs) and to calculate the diversity and richness indices using the SPADE program. Taxonomic affiliation was determined using the naive Bayesian rRNA Classifier of the RDP II (Ribosomal Database Project). We recovered 158 sequences from the Solimões River grouped into 103 OTUs, and 197 sequences from the Negro River library grouped into 90 OTUs by the DOTUR program. The Solimões River was found to have a greater diversity of bacterial genera, and greater estimated richness of 446 OTUs, compared with 242 OTUs from the Negro River, as calculated by ACE estimator. The Negro River has less bacterial diversity, but more 16S rRNA gene sequences belonging to the bacterial genus Polynucleobacter were detected; 56 sequences from this genus were found (about 30% of the total sequences). We suggest that a more in-depth investigation be made to elucidate the role played by these bacteria in the river environment. These differences in bacterial diversity between Solimões and Negro Rivers could be explained by differences in organic matter content and pH of the rivers.

The phyllosphere -the aerial parts of plants -is an important microbial habitat that is home to diverse microbial communities. The spatial organization of bacterial cells on leaf surfaces is non-random, and correlates with leaf microscopic features. Yet, the role of microscale interactions between bacterial cells therein is not well understood. Here, we ask how interactions between immigrant bacteria and resident microbiota affect the spatial organization of the combined community. By means of live imaging in a simplified in vitro system, we studied the spatial organization, at the micrometer scale, of the bio-control agent Pseudomonas fluorescens A506 and the plant pathogen P. syringae B728a when introduced to pear and bean leaf microbiota (the corresponding native plants of these strains). We found significant co-localization of immigrant and resident microbial cells at distances of a few micrometers, for both strains. Interestingly, this co-localization was in part due to preferential attachment of microbiota cells near newly formed P. fluorescens aggregates. Our results indicate that two-way immigrant bacteria -resident microbiota interactions affect the leaf's microscale spatial organization, and possibly that of other surface-related microbial communities..

Summary Methylated amines are ubiquitous in the environment and play a role in regulating the earth's climate via a set of complex biological and chemical reactions. Microbial degradation of these compounds is thought to be a major sink. Recently we isolated a facultative methylotroph, Gemmobacter sp. LW‐1, an isolate from the unique environment Movile Cave, Romania, which is capable of methylated amine utilization as a carbon source. Here, using a comparative genomics approach, we investigate how widespread methylated amine utilization is within members of the bacterial genus Gemmobacter. Seven genomes of different Gemmobacter species isolated from diverse environments, such as activated sludge, fresh water, sulphuric cave waters (Movile Cave) and the marine environment were available from the public repositories and used for the analysis. Our results indicate that methylamine utilization is a distinctive feature of selected members of the genus Gemmobacter, namely G. aquatilis, G. lutimaris, G. sp. HYN0069, G. caeni and G. sp. LW‐1 have the genetic potential while others (G. megaterium and G. nectariphilus) have not.

Functional screening of metagenomic libraries is an effective approach for identification of novel enzymes. A Caatinga biome goat rumen metagenomic library was screened using esculin as a substrate, and a gene from an unknown bacterium encoding a novel GH3 enzyme, BGL11, was identified. None of the BGL11 closely related genes have been previously characterized. Recombinant BGL11 was obtained and kinetically characterized. Substrate specificity of the purified protein was assessed using seven synthetic aryl substrates. Activity towards nitrophenyl-β-D-glucopyranoside (pNPG), 4-nitrophenyl-β-D-xylopyranoside (pNPX) and 4-nitrophenyl-β-D-cellobioside (pNPC) suggested that BGL11 is a multifunctional enzyme with β-glucosidase, β-xylosidase, and cellobiohydrolase activities. However, further testing with five natural substrates revealed that, although BGL11 has multiple substrate specificity, it is most active towards xylobiose. Thus, in its native goat rumen environment, BGL11 most likely functions as an extracellular β-xylosidase acting on hemicellulose. Biochemical characterization of BGL11 showed an optimal pH of 5.6, and an optimal temperature of 50°C. Enzyme stability, an important parameter for industrial application, was also investigated. At 40°C purified BGL11 remained active for more than 15 hours without reduction in activity, and at 50°C, after 7 hours of incubation, BGL11 remained 60% active. The enzyme kinetic parameters of Km and Vmax using xylobiose were determined to be 3.88 mM and 38.53 μmol.min-1.mg-1, respectively, and the Kcat was 57.79 s-1. In contrast to BLG11, most β-xylosidases kinetically studied belong to the GH43 family and have been characterized only using synthetic substrates. In industry, β-xylosidases can be used for plant biomass deconstruction, and the released sugars can be fermented into valuable bio-products, ranging from the biofuel ethanol to the sugar substitute xylitol.

Strain K001 was isolated from a cyanobacterial culture derived from Abrolhos, a reef bank microbial mat (South Atlantic Ocean-Brazil). Cells of K001 are Gram stain-negative, catalase and oxidase-positive, non-motile, rod-shaped, and with or without appendages. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain K001 belongs to the genus Muricauda. The highest strain K001 16S rRNA gene identity, ANI, and dDDH, respectively, are with M. aquimarina (98.90%, 79.23, 21.60%), M. ruestringensis (98.20%, 80.82, 23.40%), and M. lutimaris (97.86%, 79.23, 22.70%). The strain grows at 15-37°C and between 0.5 and 10% NaCl. The major fatty acids of strain K001 are iso-C 15:0 , iso-C 15:1 G, iso-C 17:0 3-OH, and summed feature 3 (C 16:1 ω6c and/or C 16:1 ω7c). The polar lipids are represented by phosphatidylethanolamine, three unidentified aminolipids, and three unidentified polar lipids. The major respiratory quinone is MK-6. The G+C content of the DNA of strain K001 is 41.62 mol%. Based on polyphasic analysis of strain K001, it was identified as a novel representative of the genus Muricauda and was named Muricauda brasiliensis sp. nov. The type strain is K001 (=CBMAI 2315 T = CBAS 752 T). Keywords Flavobacteriaceae. Muricauda brasiliensis. Cyanobacterial culture. Abrolhos reef bank In order to investigate heterotrophic bacteria associated with cyanobacterial cultures from Abrolhos reef bank (South Atlantic Ocean-17°57′ S, 38°42′ W), several strains were isolated. The strain K001 was selected for further analysis in part due to its potential for pigment production. Based on 16S rRNA gene sequence analyses, strain K001 belongs to the genus

The phyllosphere -the aerial parts of plants -is an important microbial habitat that is home to diverse microbial communities. The spatial organization of bacterial cells on leaf surfaces is non-random and correlates with leaf microscopic features. Yet the role of microscale interactions between cells therein is not well-understood. Here, we ask how interactions between immigrant bacteria and resident microbiota affect the spatial organization of the combined population. By means of live imaging on a simplified in vitro system, we studied the microscale spatial organization of the plant pathogen Pseudomonas syringae B728a and the bio-control agent P. fluorescens A506 when introduced to both native and non-native leaf microbiota (bean and pear). We revealed that both strains preferentially attach to the surface in locations adjacent to microbiota aggregates. Interestingly, preferential attachment of microbiota cells near newly formed P. fluorescens aggregates was also observed. Our results indicate that twoway immigrant bacteria -resident microbiota interactions affect the microscale spatial organization of leaf microbial communities; and that preferential attachmentpreviously suggested as a general strategy that increases fitness under periodic stressis a common surface colonization strategy. The implications of this study are likely relevant to other surface-associated microbial habitats. DiscussionIn summary, through live imaging and spatial analyses at microscale, we show that immigrant bacteria display a non-random spatial colonization pattern with respect to the spatial organization of natural resident leaf microbiota cells. This non-random organization is not necessarily observable by eye, but was revealed by a rigorous image and spatial analysis. As our simplified system excludes the heterogeneity of

We report the genome sequence of a polyethylene-degrading bacterial strain identified as Stenotrophomonas maltophilia strain PE591, which was isolated from plastic debris found in savanna soil. The genome was assembled in 16 scaffolds with a length of 4,751,236 bp, a GC content of 66.5%, and 4,432 predicted genes.