RESUMO
We present new genomes from the bacterial symbiont Candidatus Dactylopiibacterium carminicum obtained from non-domesticated carmine cochineals belonging to the scale insect Dactylopius (Hemiptera: Coccoidea: Dactylopiidae). As Dactylopiibacterium has not yet been cultured in the laboratory, metagenomes and metatranscriptomics have been key in revealing putative symbiont functions. Dactylopiibacterium is a nitrogen-fixing beta-proteobacterium that may be vertically transmitted and shows differential gene expression inside the cochineal depending on the tissue colonized. Here we found that all cochineal species tested had Dactylopiibacterium carminicum which has a highly conserved genome. All Dactylopiibacterium genomes analyzed had genes involved in nitrogen fixation and plant polymer degradation. Dactylopiibacterium genomes resemble those from free-living plant bacteria, some found as endophytes. Notably, we found here a new putative novel function where the bacteria may protect the insect from viruses, since all Dactylopiibacterium genomes contain CRISPRs with a spacer matching nucleopolyhedrovirus that affects insects.
Assuntos
Sistemas CRISPR-Cas , Genoma Bacteriano , Hemípteros , Simbiose , Hemípteros/microbiologia , Hemípteros/virologia , Animais , Genoma Bacteriano/genética , Genômica , Filogenia , Fixação de NitrogênioRESUMO
Symbiotic Paraburkholderia have been increasingly studied in the past 20 years, especially when associated with Mimosa; however, studies with native/endemic species are still scarce. In this study, thirty strains were isolated from root nodules of native Mimosa paranapiacabae and M. micropteris in two locations of the Campos Gerais. The BOX-PCR fingerprinting revealed high genomic diversity, and the 16S rRNA phylogeny clustered the strains in three distinct groups (GI, GII, GIII), with one strain occupying an isolated position. Phylogenetic analysis with four concatenated housekeeping genes (atpD + gltB + gyrB + recA) confirmed the same clusters of 16S rRNA, and the closest species were P. nodosa BR 3437T and P. guartelaensis CNPSo 3008T; this last one isolated from another Mimosa species of the Campos Gerais. The phylogenies of the symbiotic genes nodAC and nifH placed all strains in a well-supported branch with the other species of the symbiovar mimosae. The phylogenetic analyses indicated that the strains represent novel lineages of sv. mimosae and that endemic Mimosa coevolved with indigenous Paraburkholderia in their natural environments.
Assuntos
Mimosa , Rhizobium , DNA Bacteriano/genética , Filogenia , RNA Ribossômico 16S/genética , Rhizobium/genética , Nódulos Radiculares de Plantas , Análise de Sequência de DNA , SimbioseRESUMO
The scale insect Dactylopius coccus produces high amounts of carminic acid, which has historically been used as a pigment by pre-Hispanic American cultures. Nowadays carmine is found in food, cosmetics, and textiles. Metagenomic approaches revealed that Dactylopius spp. cochineals contain two Wolbachia strains, a betaproteobacterium named Candidatus Dactylopiibacterium carminicum and Spiroplasma, in addition to different fungi. We describe here a transcriptomic analysis indicating that Dactylopiibacterium is metabolically active inside the insect host, and estimate that there are over twice as many Dactylopiibacterium cells in the hemolymph than in the gut, with even fewer in the ovary. Albeit scarce, the transcripts in the ovaries support the presence of Dactylopiibacterium in this tissue and a vertical mode of transmission. In the cochineal, Dactylopiibacterium may catabolize plant polysaccharides, and be active in carbon and nitrogen provisioning through its degradative activity and by fixing nitrogen. In most insects, nitrogen-fixing bacteria are found in the gut, but in this study they are shown to occur in the hemolymph, probably delivering essential amino acids and riboflavin to the host from nitrogen substrates derived from nitrogen fixation.
RESUMO
Floristic surveys performed in "Campos Gerais" (Paraná, Brazil), an ecotone of Mata Atlântica and Cerrado biomes, highlights the richness and relative abundance of the family Fabaceae and point out the diversity and endemism of Mimosa spp. Our study reports the genetic diversity of rhizobia isolated from root nodules of native/endemic Mimosa gymnas Barneby in three areas of Guartelá State Park, an important conservation unit of "Campos Gerais". Soils of the sample areas were characterized as sandy, acid, poor in nutrients and organic matter. The genetic variability among the isolates was revealed by BOX-PCR genomic fingerprinting. Phylogeny based on 16S rRNA gene grouped the strains in a large cluster including Paraburkholderia nodosa and P. bannensis, while recA-gyrB phylogeny separated the strains in two groups: one including P. nodosa and the other without any described Paraburkholderia species. MLSA confirmed the separate position of this second group of strains within the genus Paraburkholderia and the nucleotide identity of the five concatened housekeeping genes was 95.9% in relation to P. nodosa BR 3437T. Phylogram based on symbiosis-essential nodC gene was in agreement with 16S rRNA analysis. Our molecular phylogenetic analysis support that Paraburkholderia are the main symbionts of native Mimosa in specific edaphic conditions found in South America and reveal the importance of endemic/native leguminous plants as reservoirs of novel rhizobial species.
Assuntos
Betaproteobacteria/genética , Mimosa/genética , Rhizobium/genética , Brasil , DNA Bacteriano/genética , Fabaceae/genética , Variação Genética/genética , Filogenia , Raízes de Plantas/genética , RNA Ribossômico 16S/genética , Análise de Sequência de DNA , Solo/química , SimbioseRESUMO
Our comprehension of the dynamics and diversity of freshwater planktonic bacterial communities is far from complete concerning the Brazilian Amazonian region. Therefore, reference studies are urgently needed. We mapped bacterial communities present in the planktonic communities of a freshwater artificial reservoir located in the western Amazonian basin. Two samples were obtained from rainy and dry seasons, the periods during which water quality and plankton diversity undergo the most significant changes. Hypervariable 16S rRNA and shotgun sequencing were performed to describe the first reference of a microbial community in an Amazonian lentic system. Microbial composition consisted mainly of Betaproteobacteria, Cyanobacteria, Alphaproteobacteria, and Actinobacteria in the dry period. The bacteria distribution in the rainy period was notably absent of Cyanobacteria. Microcystis was observed in the dry period in which the gene cluster for cyanotoxins was found. Iron acquisition gene group was higher in the sample from the rainy season. This work mapped the first inventory of the planktonic microbial community of a large water reservoir in the Amazon, providing a reference for future functional studies and determining other communities and how they interact.
Assuntos
Actinobacteria/isolamento & purificação , Alphaproteobacteria/isolamento & purificação , Betaproteobacteria/isolamento & purificação , Cianobactérias/isolamento & purificação , Microbiota/genética , Plâncton/classificação , Actinobacteria/classificação , Actinobacteria/genética , Alphaproteobacteria/classificação , Alphaproteobacteria/genética , Betaproteobacteria/classificação , Betaproteobacteria/genética , Biodiversidade , Brasil , Cianobactérias/classificação , Cianobactérias/genética , Lagos/microbiologia , Plâncton/microbiologia , RNA Ribossômico 16S/genética , Chuva/microbiologia , Estações do AnoRESUMO
Groundwater reservoirs constitute important freshwater resources. However, these ecosystems are highly vulnerable to contamination and have to rely on the resident microbiota to attenuate the impact of this contamination. Nitrate is one of the main contaminants found in groundwater, and denitrification is the main process that removes the compound. In this study, the response to nutrient load on indigenous microbial communities in groundwater from a low impacted aquifer in Uruguay was evaluated. Denitrification rates were measured in groundwater samples from three different sites with nitrate, acetate and pyrite amendments. Results showed that denitrification is feasible under in situ nitrate and electron donor concentrations, although the lack of readily available organic energy source would limit the attenuation of higher nitrate concentrations. DNA-stable isotope probing, combined with amplicon sequencing of 16S rRNA, nirS and nirK genes, was used to identify the active denitrifiers. Members of the phylum Betaproteobacteria were the dominant denitrifiers in two of three sites, with different families being observed; members of the genus Vogesella (Neisseriaceae) were key denitrifiers at one site, while the genera Dechloromonas (Rhodocyclaceae) and Comamonas (Comamonadaceae) were the main denitrifiers detected at the other sites.
Assuntos
Comamonadaceae/metabolismo , Desnitrificação/fisiologia , Água Subterrânea/química , Água Subterrânea/microbiologia , Neisseriaceae/metabolismo , Nitratos/análise , Nitratos/metabolismo , Rhodocyclaceae/metabolismo , Acetatos/metabolismo , Comamonadaceae/classificação , Comamonadaceae/genética , DNA , Sondas de DNA , Ferro/metabolismo , Marcação por Isótopo , Isótopos , Neisseriaceae/classificação , Neisseriaceae/genética , RNA Ribossômico 16S/genética , Rhodocyclaceae/classificação , Rhodocyclaceae/genética , Sulfetos/metabolismo , UruguaiRESUMO
Betaproteobacteria were the most common isolates from the water-filled tank of a Costa Rican bromeliad. Isolates included eight species from the orders Neisseriales and Burkholderiales, with close relatives recovered previously from tropical soils, wetlands, freshwater, or in association with plants. Compared to close relatives, the isolates displayed high temperature and comparatively low pH optima, reflecting the tropical, acidic nature of the bromeliad tank. Bromeliad-associated bacteria most closely related to Chromobacterium, Herbaspirillum, and Aquitalea were all isolated exclusively at pH 6, while Ralstonia, Cupriavidus, and three species of Burkholderia were isolated mostly at pH 4. Activity profiles for the isolates suggest pervasive capabilities for the breakdown of plant-sourced organics, including d-galacturonic acid, mannitol, d-xylose, and l-phenylalanine, also reflecting a niche dominated by decomposition of leaves from the overlying canopy, which become entrained in the tanks. Metabolic activity profiles were overlapping between the Burkholderiales, isolated at pH 4, and the Neisseriales, isolated at pH 6, suggesting that plant material decomposition, which is presumably the underlying process sustaining the tank community and possibly the plant itself, occurs in the tanks at both pH extremes. These results suggest that bromeliad-associated betaproteobacteria may play an important role in the cycling of carbon in this unusual aquatic habitat.
Assuntos
Betaproteobacteria/genética , Betaproteobacteria/metabolismo , Bromeliaceae/metabolismo , Bromeliaceae/microbiologia , Betaproteobacteria/classificação , Betaproteobacteria/isolamento & purificação , Biodiversidade , Ciclo do Carbono/fisiologia , Costa Rica , Temperatura Alta , Concentração de Íons de Hidrogênio , RNA Ribossômico 16S/genética , Solo/química , Microbiologia do Solo , Termotolerância/genética , Termotolerância/fisiologia , Clima Tropical , Microbiologia da ÁguaRESUMO
BACKGROUND AND AIMS: The large monophyletic genus Mimosa comprises approx. 500 species, most of which are native to the New World, with Central Brazil being the main centre of radiation. All Brazilian Mimosa spp. so far examined are nodulated by rhizobia in the betaproteobacterial genus Burkholderia. Approximately 10 Mya, transoceanic dispersal resulted in the Indian subcontinent hosting up to six endemic Mimosa spp. The nodulation ability and rhizobial symbionts of two of these, M. hamata and M. himalayana, both from north-west India, are here examined, and compared with those of M. pudica, an invasive species. METHODS: Nodules were collected from several locations, and examined by light and electron microscopy. Rhizobia isolated from them were characterized in terms of their abilities to nodulate the three Mimosa hosts. The molecular phylogenetic relationships of the rhizobia were determined by analysis of 16S rRNA, nifH and nodA gene sequences. KEY RESULTS: Both native Indian Mimosa spp. nodulated effectively in their respective rhizosphere soils. Based on 16S rRNA, nifH and nodA sequences, their symbionts were identified as belonging to the alphaproteobacterial genus Ensifer, and were closest to the 'Old World' Ensifer saheli, E. kostiensis and E. arboris. In contrast, the invasive M. pudica was predominantly nodulated by Betaproteobacteria in the genera Cupriavidus and Burkholderia. All rhizobial strains tested effectively nodulated their original hosts, but the symbionts of the native species could not nodulate M. pudica. CONCLUSIONS: The native Mimosa spp. in India are not nodulated by the Burkholderia symbionts of their South American relatives, but by a unique group of alpha-rhizobial microsymbionts that are closely related to the 'local' Old World Ensifer symbionts of other mimosoid legumes in north-west India. They appear not to share symbionts with the invasive M. pudica, symbionts of which are mostly beta-rhizobial.