RESUMO
Nitrogen-fixing bacteria of the Bradyrhizobium genus are major symbionts of legume plants in American tropical forests, but little is known about the effects of deforestation and change in land use on their diversity and community structure. Forest clearing is followed by cropping of bean (Phaseolus vulgaris) and maize as intercropped plants in Los Tuxtlas tropical forest of Mexico. The identity of bean-nodulating rhizobia in this area is not known. Using promiscuous trap plants, bradyrhizobia were isolated from soil samples collected in Los Tuxtlas undisturbed forest, and in areas where forest was cleared and land was used as crop fields or as pastures, or where secondary forests were established. Rhizobia were also trapped by using bean plants. Bradyrhizobium strains were classified into genospecies by dnaK sequence analysis supported by recA, glnII and 16S-23S rDNA IGS loci analyses. A total of 29 genospecies were identified, 24 of which did not correspond to any described taxa. A reduction in Bradyrhizobium diversity was observed when forest was turned to crop fields or pastures. Diversity seemed to recover to primary forest levels in secondary forests that derived from abandoned crop fields or pastures. The shifts in diversity were not related to soil characteristics but seemingly to the density of nodulating legumes present at each land use system (LUS). Bradyrhizobium community composition in soils was dependent on land use; however, similarities were observed between crop fields and pastures but not among forest and secondary forest. Most Bradyrhizobium genospecies present in forest were not recovered or become rare in the other LUS. Rhizobium etli was found as the dominant bean-nodulating rhizobia present in crop fields and pastures, and evidence was found that this species was introduced in Los Tuxtlas forest.
Assuntos
Bradyrhizobium/crescimento & desenvolvimento , Bradyrhizobium/genética , Ecossistema , Chuva , Rhizobium etli/crescimento & desenvolvimento , Microbiologia do Solo , Árvores , Clima Tropical , Agricultura , Proteínas de Bactérias/genética , Bradyrhizobium/classificação , Bradyrhizobium/isolamento & purificação , DNA Ribossômico/genética , Agricultura Florestal , México , Filogenia , RNA Ribossômico 16S/genética , Rhizobium etli/classificação , Rhizobium etli/genética , Rhizobium etli/isolamento & purificação , Análise de Sequência de DNA , SimbioseRESUMO
Bacteria from nodules of the legume Acaciella angustissima native to the south of Mexico were characterized genetically and their nodulation and competitiveness were evaluated. Phylogenetic studies derived from rpoB gene sequences indicated that A. angustissima is nodulated by Sinorhizobium mexicanum, Rhizobium tropici, Mesorhizobium plurifarium and Agrobacterium tumefaciens and by bacteria related to Sinorhizobium americanum, Sinorhizobium terangae, Rhizobium etli and Rhizobium gallicum. A new lineage related to S. terangae is recognized based on the sequences of gyrA, nolR, recA, rpoB and rrs genes, DNA-DNA hybridization and phenotypic characteristics. The name for this new species is Sinorhizobium chiapanecum and its type strain is ITTG S70T. The symbiotic genes nodA and nifH were similar to those from S. mexicanum strains, which are Acaciella symbionts as well, with nodA gene sequences grouped within a cluster of nod genes from strains that nodulate plants from the Mimosoideae subfamily of the Leguminosae. Sinorhizobium isolates were the most frequently obtained from A. angustissima nodules and were among the best strains to promote plant growth in A. angustissima and to compete in interstrain nodule competition assays. Lateral transfer of symbiotic genes is not evident among the genera that nodulate A. angustissima (Rhizobium, Sinorhizobium and Mesorhizobium) but may occur among the sympatric and closely related sinorhizobia that nodulate Acaciella.
Assuntos
Fabaceae/microbiologia , Fixação de Nitrogênio , Rhizobium , Simbiose , Técnicas de Tipagem Bacteriana , Fabaceae/crescimento & desenvolvimento , México , Dados de Sequência Molecular , Hibridização de Ácido Nucleico , Filogenia , Rhizobium/classificação , Rhizobium/genética , Rhizobium/fisiologia , Análise de Sequência de DNA , Sinorhizobium/classificação , Sinorhizobium/genética , Sinorhizobium/fisiologia , Especificidade da Espécie , Simbiose/genéticaRESUMO
A new lineage of Ensifer nodulating the American legume Acacia angustissima in the tropical forest of Chiapas and Morelos, Mexico is described. Bacteria were identified as Ensifer with ssb or nolR specific primers. Phylogenetic analysis with partial sequences of the five chromosomal genes gyrA, nolR, recA, rpoB and rrs revealed that this new lineage is related to African Ensifer terangae. The results of total DNA-DNA hybridization and selected phenotypic tests among the A. angustissima strains and E. terangae indicated that they belong to different species. The phylogeny with the symbiotic nifH gene also separates this group as a different clade but with close affinities to bacteria belonging to the genus Ensifer isolated from American hosts. ITTG R7(T) (=CFN ER1001, HAMBI 2910, CIP 109033, ATCC BAA-1312, DSM18446) is the type strain of a new species for which the name Ensifer mexicanus sp. nov. is proposed.
Assuntos
Acacia/microbiologia , Alphaproteobacteria/classificação , Alphaproteobacteria/genética , Alphaproteobacteria/isolamento & purificação , Proteínas de Bactérias/genética , Cromossomos Bacterianos/genética , Genes Bacterianos/genética , México , Fixação de Nitrogênio/genética , Hibridização de Ácido Nucleico , Filogenia , Homologia de Sequência , Sinorhizobium/classificação , Especificidade da Espécie , SimbioseRESUMO
The Cuatro Cienegas basin in the Chihuahuan desert is a system of springs, streams, and pools. These ecosystems support >70 endemic species and abundant living stromatolites and other microbial communities, representing a desert oasis of high biodiversity. Here, we combine data from molecular microbiology and geology to document the microbial biodiversity of this unique environment. Ten water samples from locations within the Cuatro Cienegas basin and two neighboring valleys as well as three samples of wet sediments were analyzed. The phylogeny of prokaryotic populations in the samples was determined by characterizing cultured organisms and by PCR amplification and sequencing of 16S rRNA genes from total community DNA. The composition of microbial communities was also assessed by determining profiles of terminal restriction site polymorphisms of 16S rRNA genes in total community DNA. There were 250 different phylotypes among the 350 cultivated strains. Ninety-eight partial 16S rRNA gene sequences were obtained and classified. The clones represented 38 unique phylotypes from ten major lineages of Bacteria and one of Archaea. Unexpectedly, 50% of the phylotypes were most closely related to marine taxa, even though these environments have not been in contact with the ocean for tens of millions of years. Furthermore, terminal restriction site polymorphism profiles and geological data suggest that the aquatic ecosystems of Cuatro Cienegas are hydrologically interconnected with adjacent valleys recently targeted for agricultural intensification. The findings underscore the conservation value of desert aquatic ecosystems and the urgent need for study and preservation of freshwater microbial communities.
Assuntos
Biodiversidade , Microbiologia da Água , Archaea/classificação , Archaea/genética , Archaea/isolamento & purificação , Bactérias/classificação , Bactérias/genética , Bactérias/isolamento & purificação , Sequência de Bases , Clonagem Molecular , Ecossistema , Água Doce/microbiologia , Genes Arqueais , Genes Bacterianos , Fenômenos Geológicos , Geologia , México , Dados de Sequência Molecular , Polimorfismo de Fragmento de Restrição , RNA Arqueal/genética , RNA Arqueal/isolamento & purificação , RNA Bacteriano/genética , RNA Bacteriano/isolamento & purificação , RNA Ribossômico 16S/genética , RNA Ribossômico 16S/isolamento & purificaçãoRESUMO
Nitrogen fixation an ancient process that may is have originated in the archaean Eon under the primitive atmosphere anoxygenic conditions. Diazotrophy is an exclusive process of prokaryotes, only Euryarchaeota and 6 of 54 Bacteria phyla have diazotrophs lineages. Some of them coevolved with flowering plants for the establishment of molecular bases of a mutualistic symbiosis relationship. In rhizobia, the nitrogen fixation occurs inside the nodules, special structures on the roots or stems of legumes. Nodule organogenesis starts with the bacterial nodulation factors (Nod factors) codified in large plasmids or symbiotic islands in the bacterial genomes. Nodulation genes had more recent origin than the nitrogen fixation ones because the origin of the nod gene is associated with the origin of the hosts. The 16S rRNA phylogeny groups rhizobia in 7 genuses of the alpha-Proteobacteria: Bradyrhizobium, Mesorhizobium, Rhizobium, Sinorhizobium, Methylobacterium and Devosia, and two genuses recently described in f-Proteobacteria: Burkholderia and Wautersia. The phylogenies obtained with other chromosomal genes are similar at the genus level, but it is incongruent with the symbiotic gene (nif & nod) phylogeny, because horizontal gene transfer has allowed their evolution in function to the legume host fitness.
Assuntos
Evolução Biológica , Bacilos e Cocos Aeróbios Gram-Negativos/fisiologia , Nódulos Radiculares de Plantas/microbiologia , Biodiversidade , Bradyrhizobium/genética , Bradyrhizobium/fisiologia , Burkholderia/genética , Burkholderia/fisiologia , Cupriavidus/genética , Cupriavidus/fisiologia , Genes Bacterianos , Ilhas Genômicas/genética , Bacilos e Cocos Aeróbios Gram-Negativos/classificação , Bacilos e Cocos Aeróbios Gram-Negativos/genética , Magnoliopsida/microbiologia , Fixação de Nitrogênio/genética , Filogenia , Plasmídeos/genética , Plasmídeos/fisiologia , Rhizobiaceae/genética , Rhizobiaceae/fisiologia , Nódulos Radiculares de Plantas/fisiologia , Especificidade da Espécie , Simbiose/genéticaRESUMO
The sinorhizobia isolated from root nodules of Acacia species native of Mexico constitute a diverse group of bacteria on the basis of their metabolic enzyme electromorphs but share restriction patterns of the PCR products of 16S rRNA genes and a common 500 kb symbiotic plasmid. They are distinguished from other Sinorhizobium species by their levels of DNA-DNA hybridization and the sequence of 16S rRNA and nifH genes. nolR gene hybridization patterns were found useful to identify sinorhizobia and characterize species. A new species, Sinorhizobium americanus, is described and the type strain is CFNEI 156 from Acacia acatlensis.