RESUMEN
South Florida (USA) has a subtropical to tropical climate with an extensive and diverse coastline that supports the growth of benthic cyanobacterial mats (BCMs). These BCMs are widespread and potentially house numerous bioactive compounds; however, the extent of the cyanobacterial diversity within these mats remains largely unknown. To elucidate this diversity, BCMs from select locations in South Florida were sampled and isolated into unicyanobacterial cultures for morphological and molecular studies. Phylogenetic relationships of isolated taxa were assessed using the markers 16S rRNA and 16S-23S rRNA ITS by both maximum likelihood and Bayesian inference. We propose Affixifilum gen. nov. based on morphological characteristics and the 16S rRNA phylogeny. Two species are included: Affixifilum granulosum comb nov. (=Neolyngbya granulosa) found in Brazil and Florida (USA) and A. floridanum sp. nov. Several other features, including pair-wise distance of 16S rRNA and 16S-23S rRNA ITS, 16S-23S rRNA ITS secondary structure, morphology, and ecology, provide support for Affixifilum. We also propose the transfer of Lyngbya regalis to Neolyngbya as N. regalis comb. nov. and include the description of one novel species, N. biscaynensis sp. nov.
Asunto(s)
Cianobacterias , ADN Bacteriano , Filogenia , Teorema de Bayes , Brasil , Florida , ARN Ribosómico 16S/genética , Análisis de Secuencia de ADNRESUMEN
Bacteria of the genus Paenibacillus are relevant to humans, animals and plants. The species Paenibacillus massiliensis and Paenibacillus panacisoli are Gram-stain-positive and endospore-forming bacilli isolated from a blood culture of a leukemia patient and from soil of a ginseng field, respectively. Comparative analyses of their 16S rRNA genes revealed that the two Paenibacillus species could be synonyms (99.3% sequence identity). In the present study we performed different genomic analyses in order to evaluate the phylogenetic relationship of these micro-organisms. Paenibacillus massiliensis DSM 16942T and P. panacisoli DSM 21345T presented a difference in their G+C content lower than 1âmol%, overall genome relatedness index values higher than the species circumscription thresholds (average nucleotide identity, 95.57â%; genome-wide ANI, =96.51â%; and orthologous ANI, 96.25â%), and a monophyletic grouping pattern in the phylogenies of the 16S rRNA gene and the proteome core. Considering that these strains present differential biochemical capabilities and that their computed digital DNA-DNA hybridization value is lower than the cut-off for bacterial subspecies circumscription, we suggest that each of them form different subspecies of P. massiliensis, Paenibacillus massiliensis subsp. panacisoli subsp. nov. (type strain DSM 21345T) and Paenibacillus massiliensis subsp. massiliensis subsp. nov. (type strain DSM 16942T).
Asunto(s)
Paenibacillus/clasificación , Filogenia , Técnicas de Tipificación Bacteriana , Composición de Base , ADN Bacteriano/genética , Genes Bacterianos , Hibridación de Ácido Nucleico , ARN Ribosómico 16S/genética , Análisis de Secuencia de ADNRESUMEN
Three facultatively anaerobic endospore-forming bacteria were isolated from the rhizosphere of sunflowers grown in fields of Rio Grande do Sul State, Brazil. The designated type strain P26ET was previously identified as a sunflower growth promoting bacterium and is able to fix nitrogen and to excrete ammonia. According to analyses of 16S rRNA gene sequences, P26ET presented similarity values above 98.8% in relation to Paenibacillus azotifigens NF2-4-5T, Paenibacillus graminis RSA19T, Paenibacillus jilunlii Be17T, Paenibacillus salinicaeni LAM0A28T, and Paenibacillus sonchi X19-5T. Phylogenetic reconstructions based on 16S rRNA gene and core proteome data showed that the strains P26ET, P3E and P32E form a distinct clade, which did not include any type strain of the currently described Paenibacillus species. Also, genomic comparisons using average nucleotide identity (ANI), Orthologous ANI and in silico DNA-DNA hybridization revealed similarity ranges below the recommended thresholds when the three isolates from sunflower were compared to their close relatives. The DNA G + C content of strain P26ET was determined to be 49.4 mol%. The major cellular fatty acids are anteiso-C15:0 and iso-C15:0, representing about 58 and 14% of the total fatty acids in P26ET, respectively. Based on different taxonomic genomic metrics, phylogeny, and phenotypic data, we propose that strain P26ET (= DSM 102269 = BR10509) represents a novel species within the genus Paenibacillus, for which the name Paenibacillus helianthi sp. nov. is proposed.
Asunto(s)
ADN Bacteriano/genética , Helianthus/microbiología , Fijación del Nitrógeno/fisiología , Paenibacillus/genética , Filogenia , ARN Ribosómico 16S/genética , Anaerobiosis/fisiología , Técnicas de Tipificación Bacteriana , Composición de Base , Brasil , Ácidos Grasos/biosíntesis , Genotipo , Nitrógeno/metabolismo , Paenibacillus/clasificación , Paenibacillus/aislamiento & purificación , Paenibacillus/metabolismo , Fenotipo , Rizosfera , Esporas Bacterianas/fisiologíaRESUMEN
The Amazon Rainforest holds great tropical biodiversity, mainly because of its favourable climatic conditions. The high temperatures, luminosity and humidity coupled with the nutritional simplicity of cyanobacteria allow undiscovered diversity to flourish within this group of microorganisms. Some efforts to reveal this diversity have been attempted; however, most were focused on the microscopic observation of environmental samples without any genetic information. Very few studies focusing on morphological, ecological and molecular criteria have been conducted, and none have been devoted to homocytous cyanobacteria forms in Amazonia region. Therefore, the genetic relationships amongst strains retrieved from this ecosystem with regard to other environments from Brazil and the world have not been tested and, consequently, the Amazonian strains would naturally be assumed as novel to science. To examine these relationships, cultured homocytous cyanobacteria isolated from two Amazonian rivers (Amazonas and Solimões) were evaluated using a phylogenetic perspective, considering the 16S rRNA gene sequence. A total of eleven homocytous cyanobacterial strains were isolated. Morphologically, they were identified as Pseudanabaena, Leptolyngbya, Planktothrix and Phormidium, but genetically they were included in the typical clusters of Planktothrix, Pseudanabaena, Cephalothrix, Pantanalinema and Alkalinema. These three latter genera have been detected in other Brazilian ecosystems only (Pantanal, Atlantic Rainforest and Pampa), while those remaining have been extensively found in many parts of the world. The data provided here indicate that Amazonian rivers support a homocytous cyanobacterial diversity previously reported from other geographical and ecological environments.
Asunto(s)
Biodiversidad , Cianobacterias/clasificación , Filogenia , Ríos/microbiología , Secuencia de Bases , Brasil , Cianobacterias/genética , Cianobacterias/crecimiento & desarrollo , Cianobacterias/aislamiento & purificación , ADN Bacteriano/genética , ADN Espaciador Ribosómico/genética , Geografía , Concentración de Iones de Hidrógeno , Funciones de Verosimilitud , Conformación de Ácido Nucleico , ARN Ribosómico 16S/genéticaRESUMEN
A strictly anaerobic Gram-stain positive, spore-forming, rod-shaped bacterium designated NE08V(T), was isolated from a fecal sample of an individual residing in a remote Amazonian community in Peru. Phylogenetic analysis based on the 16S rRNA gene sequence showed the organism belonged to the genus Clostridium and is most closely related to Clostridium vulturis (97.4% sequence similarity) and was further characterized using biochemical and chemotaxonomic methods. The major cellular fatty acids were anteiso C13:0 and C16:0 with a genomic DNA G + C content of 31.6 mol%. Fermentation products during growth with PYG were acetate and butyrate. Based on phylogenetic, phenotypic and chemotaxonomic information, strain NE08V was identified as representing a novel species of the genus Clostridium, for which the name Clostridium amazonense sp. nov. is proposed. The type strain is NE08V(T) (DSM 23598(T) = CCUG 59712(T)).
Asunto(s)
Clostridium/clasificación , Clostridium/aislamiento & purificación , Heces/microbiología , Técnicas de Tipificación Bacteriana , Composición de Base , Análisis por Conglomerados , Citosol/química , ADN Bacteriano/química , ADN Bacteriano/genética , ADN Ribosómico/química , ADN Ribosómico/genética , Ácidos Grasos/análisis , Humanos , Datos de Secuencia Molecular , Perú , Filogenia , Grupos de Población , ARN Ribosómico 16S/genética , Población Rural , Análisis de Secuencia de ADNRESUMEN
A novel Gram-stain positive, non-motile, non-sporeforming coccus-shaped, obligately anaerobic bacterium was isolated from a fecal sample of an individual residing in a traditional Peruvian community. The organism was characterized using biochemical, chemotaxonomic and phylogenetic methods. Comparative 16S rRNA gene sequence analyses and phenotypic characteristics demonstrated that the organism was biochemically and phenotypically related, but distinct, from a group of organisms referred to as the Gram-stain positive anaerobic cocci (GPAC). The major cellular fatty acids of the novel isolate were determined to be C16:0 (18.3%), C18:1ω9c (39.8%), C18:2ω6,9c/C18:0 ANTE (13.2%). Fermentation end products from PYG are acetate and formate. Cell-wall peptidoglycan was found to be A4α (L-Lys-L-Ala-L-Glu) and the G + C content was determined to be 38.4 mol%. Based on the phenotypic, chemotaxonomic, and phylogenetic results, Ezakiella peruensis gen. nov., sp. nov., is now proposed. The type strain is M6.X2(T) (DSM 27367(T) = NBRC 109957 (T) = CCUG 64571(T)).