Proof that Burkholderia strains form effective symbioses with legumes: a study of novel Mimosa-nodulating strains from South America

Twenty Mimosa-nodulating bacterial strains from Brazil and Venezuela, together with eight reference Mimosa-nodulating rhizobial strains and two other beta-rhizobial strains, were examined by amplified rRNA gene restriction analysis. They fell into 16 patterns and formed a single cluster together with the known beta-rhizobia, Burkholderia caribensis, Burkholderia phymatum, and Burkholderia tuberum. The 16S rRNA gene sequences of 15 of the 20 strains were determined, and all were shown to belong to the genus Burkholderia; four distinct clusters could be discerned, with strains isolated from the same host species usually clustering very closely. Five of the strains (MAP3-5, Br3407, Br3454, Br3461, and Br3469) were selected for further studies of the symbiosis-related genes nodA, the NodD-dependent regulatory consensus sequences (nod box), and nifH. The nodA and nifH sequences were very close to each other and to those of B. phymatum STM815, B. caribensis TJ182, and Cupriavidus taiwanensis LMG19424 but were relatively distant from those of B. tuberum STM678. In addition to nodulating their original hosts, all five strains could also nodulate other Mimosa spp., and all produced nodules on Mimosa pudica that had nitrogenase (acetylene reduction) activities and structures typical of effective N2-fixing symbioses. Finally, both wild-type and green fluorescent protein-expressing transconjugant strains of Br3461 and MAP3-5 produced N2-fixing nodules on their original hosts, Mimosa bimucronata (Br3461) and Mimosa pigra (MAP3-5), and hence this confirms strongly that Burkholderia strains can form effective symbioses with legumes.     

Monopera,a new genus of scrophulariaceae from South America

Monopera is described as a new genus in the Scrophulariaceae, subfamily Scrophularioideae, tribe Angeloneae. Two species are transferred fromAngelonia,Monopera micrantha andMonopera perennis. These species are described and illustrated, and a key is provided.     

Zameioscirpus, a new genus of Cyperaceae from South America

Systematic studies of scirpoid species in the Andes showed the necessity to exclude one species each from Scirpus and Carex. They are combined in a new genus Zameioscirpus and a third new species is described. The autonomous generic position of Zameioscirpus within the Scirpeae is supported by a phylogenetic analysis based on rbcL and trnL-F sequencing data and by conspicuous morphological similarities.     

Isolation and Characterization of a Novel Haloacid Permease from Burkholderia cepacia MBA4

Burkholderia cepacia MBA4 is a bacterium that can utilize 2-haloacids as carbon and energy sources for growth. It has been proposed that dehalogenase-associated permease mediates the uptake of haloacid. In this paper, we report the first cloning and characterization of such a haloacid permease. The structural gene, designated deh4p, was found 353 bases downstream of the dehalogenase gene deh4a. Quantitative analysis of the expression of deh4p showed that it was induced by monochloroacetate (MCA), to a level similar to the MCA-induced level of deh4a. The nucleotide sequence of deh4p was determined, and an open reading frame of 1,656 bp encoding a putative peptide of 552 amino acids was identified. Deh4p has a putative molecular weight of 59,414 and an isoelectric point of 9.88. Deh4p has the signatures of sugar transport proteins and integral membrane proteins of the major facilitator superfamily. Uptake of [¹⁴C]MCA into the cell was Deh4p dependent. Deh4p has apparent K_ms of 5.5 and 8.9 μM and V_maxs of 9.1 and 23.1 nmol mg⁻¹ min⁻¹ for acetate and MCA, respectively. A mutant with a transposon-inactivated haloacid operon failed to grow on MCA even when deh4a was provided in trans.     

Identification and Characteristics of a Novel Burkholderia Strain with Broad-Spectrum Antimicrobial Activity

A Burkholderia strain isolated from soil is capable of inhibiting the growth of bacteria, plant-pathogenic fungi, pathogenic yeasts, and protozoa. Inhibition does not involve cell contact or the presence of living cells, suggesting that at least a substantial portion of the antimicrobial activity is due to the excretion of extracellular compounds.     

Rhodothyrsus, a new genus of Euphorbiaceae from tropical South America

The new genusRhodothyrsus is proposed, based on the AmazonianSenefeldera macrophylla Ducke but also containing another newly described species,Rhodothyrsus hirsutus from northwestern Venezuela. The genus is a member of the tribe Hippomaneae of the Euphorbiaceae and apparently related toSenefeldera, but its closest relationships are still obscure, because the phylogeny of the tribe is poorly known and most of the significant characters ofRhodothyrsus are probably autapomorphies or symplesiomorphies. The restriction to tropical lowland rain forests is rare within the Hippomaneae, and several floral characters, pointing to a specialized pollination possibly by butterflies, are unique in the tribe.     

Endophytes of native grasses from South America: Biodiversity and ecology

We review and present preliminary results of studies on cool-season grass endophytes native to South America. These fungi have been studied only in Argentina, where they have been detected in 36 native grass species. The hybrid Neotyphodium tembladerae is present in an extremely wide host range found in diverse environmental conditions, but some other endophytes seem to be strictly associated with one host species in a particular environment. In host species that inhabit different environments, the incidence of endophytes is highly variable among populations and in most of the cases is clearly associated with environmental conditions. In these native grasses, Neotyphodium presents a mutualistic behaviour, conferring enhanced growth, promoting the symbiosis with arbuscular mycorrhizal fungi, and inhibiting growth of pathogenic fungi. In native forage grasses, preliminary analyses indicate that some Argentinian endophytes can produce lolines but are unlikely to produce lolitrem B or ergot alkaloids.     

The LPS O-Antigen in Photosynthetic Bradyrhizobium Strains Is Dispensable for the Establishment of a Successful Symbiosis with Aeschynomene Legumes

The photosynthetic bradyrhizobia are able to use a Nod-factor independent process to induce nitrogen-fixing nodules on some semi-aquatic Aeschynomene species. These bacteria display a unique LPS O-antigen composed of a new sugar, the bradyrhizose that is regarded as a key symbiotic factor due to its non-immunogenic character. In this study, to check this hypothesis, we isolated mutants affected in the O-antigen synthesis by screening a transposon mutant library of the ORS285 strain for clones altered in colony morphology. Over the 10,000 mutants screened, five were selected and found to be mutated in two genes, rfaL, encoding for a putative O-antigen ligase and gdh encoding for a putative dTDP-glucose 4,6-dehydratase. Biochemical analysis confirmed that the LPS of these mutants completely lack the O-antigen region. However, no effect of the mutations could be detected on the symbiotic properties of the mutants indicating that the O-antigen region of photosynthetic Bradyrhizobium strains is not required for the establishment of symbiosis with Aeschynomene.     

Licea eremophila, a new myxomycete from arid areas of South America

A new stipitate species of myxomycete of the genus Licea is described based on material from arid areas in Argentina and Chile. It was isolated from moist chamber cultures and found fruiting on field collections, usually on the same substrate, Puya sp. (Bromeliaceae). It differs from all described species in the genus in that it has stipitate sporocarps with dehiscence by defined preformed platelets and a smooth inner peridial surface. The new species has polyhedral, yellow spores with a uniform thick spore wall and dense warts except on irregularly dispersed raised bands with fewer warts, visible by SEM, an ornamentation not previously observed in the genus. Life-cycle events are described and illustrated, from germination to sporulation, based on moist chamber and agar cultures. The morphology of the myxomycete specimens was examined with scanning electron microscopy and light microscopy, and both light and SEM micrographs of relevant details are included.     

Diversity of Bacillus thuringiensis Strains from Latin America with Insecticidal Activity against Different Mosquito Species

The characterization of selected Bacillus thuringiensis strains isolated from different Latin America countries is presented. Characterization was based on their insecticidal activity against Aedes aegypti, Culex quinquefasciatus, and Anopheles albimanus larvae, scanning electron microscopy, sodium dodecyl sulfate-polyacrylamide gel electrophoresis, and plasmid profiles as well as PCR analysis using novel general and specific primers for cry and cyt genes encoding proteins active against mosquitoes (cyt1, cyt2, cry2, cry4A, cry4B, cry10, cry11, cry17, cry19, cry24, cry25, cry27, cry29, cry30, cry32, cry39, and cry40). Strains LBIT315, LBIT348, and IB604 showed threefold higher mosquitocidal activity against A. aegypti and C. quinquefasciatus larvae than B. thuringiensis subsp. israelensis and displayed high similarities with the B. thuringiensis subsp. israelensis used in this study with regard to protein and plasmid profiles and the presence of cry genes. Strain 147-8906 has activity against A. aegypti similar to that of B. thuringiensis subsp. israelensis but has different protein and plasmid profiles. This strain, harboring cry11, cry30, cyt1, and cyt2 genes, could be relevant for future resistance management interventions. Finally, the PCR screening strategy presented here led us to identify a putative novel cry11B gene.     

Estimating Effective Population Size from Temporally Spaced Samples with a Novel,Efficient Maximum-Likelihood Algorithm

The effective population size N_e is a key parameter in population genetics and evolutionary biology, as it quantifies the expected distribution of changes in allele frequency due to genetic drift. Several methods of estimating N_e have been described, the most direct of which uses allele frequencies measured at two or more time points. A new likelihood-based estimator NB^ for contemporary effective population size using temporal data is developed in this article. The existing likelihood methods are computationally intensive and unable to handle the case when the underlying N_e is large. This article tries to work around this problem by using a hidden Markov algorithm and applying continuous approximations to allele frequencies and transition probabilities. Extensive simulations are run to evaluate the performance of the proposed estimator NB^, and the results show that it is more accurate and has lower variance than previous methods. The new estimator also reduces the computational time by at least 1000-fold and relaxes the upper bound of N_e to several million, hence allowing the estimation of larger N_e. Finally, we demonstrate how this algorithm can cope with nonconstant N_e scenarios and be used as a likelihood-ratio test to test for the equality of N_e throughout the sampling horizon. An R package “NB” is now available for download to implement the method described in this article.     

Notobaetis: A New Genus of Baetidae (Ephemeroptera) from South America

A new genus and species, Notobaetis penai, n. gen., n. sp., of Baetidae (Ephemeroptera), is described based upon reared specimens collected from the Cordoba Province of Argentina. This new genus appears to be phenetically intermediate between Baetis Leach and Centroptilum Eaton while possessing a unique combination of characters and one autapomorphic character.     

The First Peopling of South America: New Evidence from Y-Chromosome Haplogroup Q

Recent progress in the phylogenetic resolution of the Y-chromosome phylogeny permits the male demographic dynamics and migratory events that occurred in Central and Southern America after the initial human spread into the Americas to be investigated at the regional level. To delve further into this issue, we examined more than 400 Native American Y chromosomes (collected in the region ranging from Mexico to South America) belonging to haplogroup Q – virtually the only branch of the Y phylogeny observed in modern-day Amerindians of Central and South America – together with 27 from Mongolia and Kamchatka. Two main founding lineages, Q1a3a1a-M3 and {"type":"entrez-protein","attrs":{"text":"Q1a3a1","term_id":"123949938","term_text":"Q1A3A1"}}Q1a3a1-L54(xM3), were detected along with novel sub-clades of younger age and more restricted geographic distributions. The first was also observed in Far East Asia while no {"type":"entrez-protein","attrs":{"text":"Q1a3a1","term_id":"123949938","term_text":"Q1A3A1"}}Q1a3a1-L54(xM3) Y chromosome was found in Asia except the southern Siberian-specific sub-clade Q1a3a1c-L330. Our data not only confirm a southern Siberian origin of ancestral populations that gave rise to Paleo-Indians and the differentiation of both Native American Q founding lineages in Beringia, but support their concomitant arrival in Mesoamerica, where Mexico acted as recipient for the first wave of migration, followed by a rapid southward migration, along the Pacific coast, into the Andean region. Although Q1a3a1a-M3 and {"type":"entrez-protein","attrs":{"text":"Q1a3a1","term_id":"123949938","term_text":"Q1A3A1"}}Q1a3a1-L54(xM3) display overlapping general distributions, they show different patterns of evolution in the Mexican plateau and the Andean area, which can be explained by local differentiations due to demographic events triggered by the introduction of agriculture and associated with the flourishing of the Great Empires.     

Titimbera,a new genus of Orthocladiinae from South and Central America (Diptera: Chironomidae)

Titimbera n. gen. is erected based on the males of three new species from South and Central America: T. amazonica n. sp. from the Amazon region, Brazil; T. titi n. sp. from Venezuela and T. laselvensis n. sp. from Costa Rica. The combination of bare eyes and wing membrane; antenna without strong apical seta; scalpellate acrostichals in mid scutum; costa strongly extended; R₄₊₅ ending opposite to M₃₊₄; Cu₁ strongly curved to slightly sinuous; anal point sitting high on tergite IX, nearly parallel-sided with bluntly rounded apex; and club-shaped to subtriangular gonostylus with distinct heel will separate the genus from all other orthoclads.     

Freshwater fishes of northern South America: a need for field guides

The efficient collection of fishes from structurally complex environments (e.g., coral reefs, kelp forests) is difficult because conventional collecting methods generally cannot be used and many of the fishes are mobile and active. We describe the design, operation, and application of a diver-propelled net for efficiently collecting many species of benthic fish that reside on coral reefs and on kelp-forested rocky reefs. The overall size of the net and mesh size of the netting can be adjusted according to the size and behavior of targeted species to minimize drag and damage to specimens. Altering these dimensions combined with proper use of the net can result in a high rate of capture success. This revised version was published online in July 2006 with corrections to the Cover Date.     

Physiological Study of Lactobacillus delbrueckii subsp. bulgaricus Strains in a Novel Chemically Defined Medium

We developed a chemically defined medium called milieu proche du lait (MPL), in which 22 Lactobacillus delbrueckii subsp. bulgaricus (L. bulgaricus) strains exhibited growth rates ranging from 0.55 to 1 h⁻¹. MPL can also be used for cultivation of other lactobacilli and Streptococcus thermophilus. The growth characteristics of L. bulgaricus in MPL containing different carbon sources were determined, including an initial characterization of the phosphotransferase system transporters involved. For the 22 tested strains, growth on lactose was faster than on glucose, mannose, and fructose. Lactose concentrations below 0.4% were limiting for growth. We isolated 2-deoxyglucose-resistant mutants from strains CNRZ397 and ATCC 11842. CNRZ397-derived mutants were all deficient for glucose, fructose, and mannose utilization, indicating that these three sugars are probably transported via a unique mannose-specific-enzyme-II-like transporter. In contrast, mutants of ATCC 11842 exhibited diverse phenotypes, suggesting that multiple transporters may exist in that strain. We also developed a protein labeling method and verified that exopolysaccharide production and phage infection can occur in MPL. The MPL medium should thus be useful in conducting physiological studies of L. bulgaricus and other lactic acid bacteria under well controlled nutritional conditions.