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Anais Da Academia Brasileira de Ciencias Sep 2005This review covers the history on Biological Nitrogen Fixation (BNF) in Graminaceous plants grown in Brazil, and describes research progress made over the last 40 years,... (Review)
Review
This review covers the history on Biological Nitrogen Fixation (BNF) in Graminaceous plants grown in Brazil, and describes research progress made over the last 40 years, most of which was coordinated by Johanna Döbereiner. One notable accomplishment during this period was the discovery of several nitrogen-fixing bacteria such as the rhizospheric (Beijerinckia fluminensis and Azotobacter paspali), associative (Azospirillum lipoferum, A. brasilense, A. amazonense) and the endophytic (Herbaspirillum seropedicae, H. rubrisubalbicans, Gluconacetobacter diazotrophicus, Burkholderia brasilensis and B. tropica). The role of these diazotrophs in association with grasses, mainly with cereal plants, has been studied and a lot of progress has been achieved in the ecological, physiological, biochemical, and genetic aspects. The mechanisms of colonization and infection of the plant tissues are better understood, and the BNF contribution to the soil/plant system has been determined. Inoculation studies with diazotrophs showed that endophytic bacteria have a much higher BNF contribution potential than associative diazotrophs. In addition, it was found that the plant genotype influences the plant/bacteria association. Recent data suggest that more studies should be conducted on the endophytic association to strengthen the BNF potential. The ongoing genome sequencing programs: RIOGENE (Gluconacetobacter diazotrophicus) and GENOPAR (Herbaspirillum seropedicae) reflect the commitment to the BNF study in Brazil and should allow the country to continue in the forefront of research related to the BNF process in Graminaceous plants.
Topics: Brazil; Genotype; Nitrogen Fixation; Plant Roots; Poaceae; Proteobacteria
PubMed: 16127558
DOI: 10.1590/s0001-37652005000300014 -
Applied and Environmental Microbiology Mar 2002The interactions among Spartina patens and sediment microbial populations and the interactions among Phragmites australis and sediment microbial populations were studied...
The interactions among Spartina patens and sediment microbial populations and the interactions among Phragmites australis and sediment microbial populations were studied at monotypic sites in Piermont Marsh, a salt marsh of the Hudson River north of New York, N.Y., at key times during the growing season. Arbuscular mycorrhizal fungi (AMF) effectively colonized S. patens but not P. australis, and there were seasonal increases and decreases that coincided with plant growth and senescence (17 and 6% of the S. patens root length were colonized, respectively). In sediment samples from the Spartina site, the microbial community and specific bacterial populations were at least twice as large in terms of number and biomass as the microbial community and specific bacterial populations in sediment samples from the Phragmites site, and peak values occurred during reproduction. Members of the domain Bacteria, especially members of the alpha-, gamma-, and delta-subdivisions of the Proteobacteria, were the most abundant organisms at both sites throughout the growing season. The populations were generally more dynamic in samples from the Spartina site than in samples from the Phragmites site. No differences between the two sites and no differences during the growing season were observed when restriction fragment length polymorphism analyses of nifH amplicons were performed in an attempt to detect shifts in the diversity of nitrogen-fixing bacteria. Differences were observed only in the patterns generated by PCR or reverse transcription-PCR for samples from the Spartina site, suggesting that there were differences in the overall and active populations of nitrogen-fixing bacteria. Regression analyses indicated that there was a positive interaction between members of the delta-subdivision of the Proteobacteria and root biomass but not between members of the delta-subdivision of the Proteobacteria and macroorganic matter at both sites. In samples from the Spartina site, there were indications that there were bacterium-fungus interactions since populations of members of the alpha-subdivision of the Proteobacteria were negatively associated with AMF colonization and populations of members of the gamma-subdivision of the Proteobacteria were positively associated with AMF colonization.
Topics: Ecosystem; Fresh Water; Fungi; Geologic Sediments; Nitrogen Fixation; Oxidoreductases; Plant Roots; Poaceae; Proteobacteria; Seasons; Sodium Chloride
PubMed: 11872463
DOI: 10.1128/AEM.68.3.1157-1164.2002 -
Microbial Genomics Feb 2021Poly(A) polymerases (PAPs) and tRNA nucleotidyltransferases belong to a superfamily of nucleotidyltransferases and modify RNA 3'-ends. The product of the gene, PAP I,...
Poly(A) polymerases (PAPs) and tRNA nucleotidyltransferases belong to a superfamily of nucleotidyltransferases and modify RNA 3'-ends. The product of the gene, PAP I, has been characterized in a few β-, γ- and δ-. Using the PAP I signature sequence, putative PAPs were identified in bacterial species from the α- and ε- and from four other bacterial phyla (, , and ). Phylogenetic analysis, alien index and G+C content calculations strongly suggest that the PAPs in the species identified in this study arose by horizontal gene transfer from the β- and γ-.
Topics: Amino Acid Sequence; Bacterial Proteins; Base Composition; Betaproteobacteria; Evolution, Molecular; Gammaproteobacteria; Gene Transfer, Horizontal; Phylogeny; Polynucleotide Adenylyltransferase
PubMed: 33502308
DOI: 10.1099/mgen.0.000508 -
Genes & Genetic Systems 2015Soil bacterial community structures of six dominant phyla (Acidobacteria, Proteobacteria, Verrucomicrobia, Planctomycetes, Bacteroidetes and Actinobacteria) and... (Comparative Study)
Comparative Study
Soil bacterial community structures of six dominant phyla (Acidobacteria, Proteobacteria, Verrucomicrobia, Planctomycetes, Bacteroidetes and Actinobacteria) and unclassified bacteria detected in tropical Sarawakian and temperate Japanese forests were compared based on 16S rRNA gene sequence variation. The class composition in each phylum was similar among the studied forests; however, significant heterogeneities of class frequencies were detected. Acidobacteria and Proteobacteria were the most dominant phyla in all six forests, but differed in the level of bacterial species diversity, pattern of species occurrence and association pattern of species composition with physicochemical properties in soil. Species diversity among Acidobacteria was approximately half that among Proteobacteria, based on the number of clusters and the Chao1 index, even though a similar number of sequence reads were obtained for these two phyla. In contrast, species diversity within Planctomycetes and Bacteroidetes was nearly as high as within Acidobacteria, despite many fewer sequence reads. The density of species (the number of sequence reads per cluster) correlated negatively with species diversity, and species density within Acidobacteria was approximately twice that within Proteobacteria. Although the percentage of forest-specific species was high for all bacterial groups, sampling site-specific species varied among bacterial groups, indicating limited inter-forest migration and differential movement of bacteria in forest soil. For five of the seven bacterial groups, including Acidobacteria, soil pH appeared to strongly influence species composition, but this association was not observed for Proteobacterial species. Topology of UPGMA trees and pattern of NMDS plots among the forests differed among the bacterial groups, suggesting that each bacterial group has adapted and evolved independently in each forest.
Topics: Acidobacteria; Forests; Japan; Malaysia; Microbiota; Molecular Typing; Phylogeny; Proteobacteria; RNA, Bacterial; RNA, Ribosomal, 16S; Soil Microbiology
PubMed: 26399766
DOI: 10.1266/ggs.90.61 -
International Journal of Molecular... Apr 2022This study investigated the occurrence and diversity of proteobacterial XoxF-type methanol dehydrogenases (MDHs) in the microbial community that inhabits a fossil...
This study investigated the occurrence and diversity of proteobacterial XoxF-type methanol dehydrogenases (MDHs) in the microbial community that inhabits a fossil organic matter- and sedimentary lanthanide (Ln)-rich underground mine environment using a metagenomic and metaproteomic approach. A total of 8 XoxF-encoding genes (XoxF-EGs) and 14 protein sequences matching XoxF were identified. XoxF-type MDHs were produced by -, -, and represented by the four orders , , , and . The highest number of XoxF-EG- and XoxF-matching protein sequences were affiliated with and , respectively. Among the identified XoxF-EGs, two belonged to the XoxF1 clade, five to the XoxF4 clade, and one to the XoxF5 clade, while seven of the identified XoxF proteins belonged to the XoxF1 clade, four to the XoxF4 clade, and three to the XoxF5 clade. Moreover, the accumulation of light lanthanides and the presence of methanol in the microbial mat were confirmed. This study is the first to show the occurrence of XoxF in the metagenome and metaproteome of a deep microbial community colonizing a fossil organic matter- and light lanthanide-rich sedimentary environment. The presented results broaden our knowledge of the ecology of XoxF-producing bacteria as well as of the distribution and diversity of these enzymes in the natural environment.
Topics: Alcohol Oxidoreductases; Alphaproteobacteria; Bacteria; Bacterial Proteins; Gammaproteobacteria; Lanthanoid Series Elements; Methanol; Proteobacteria
PubMed: 35409305
DOI: 10.3390/ijms23073947 -
Genome Biology and Evolution Aug 2016Myxobacteria are members of δ-proteobacteria and are typified by large genomes, well-coordinated social behavior, gliding motility, and starvation-induced fruiting body...
Myxobacteria are members of δ-proteobacteria and are typified by large genomes, well-coordinated social behavior, gliding motility, and starvation-induced fruiting body formation. Here, we report the 10.33 Mb whole genome of a starch-degrading myxobacterium Sandaracinus amylolyticus DSM 53668(T) that encodes 8,962 proteins, 56 tRNA, and two rRNA operons. Phylogenetic analysis, in silico DNA-DNA hybridization and average nucleotide identity reveal its divergence from other myxobacterial species and support its taxonomic characterization into a separate family Sandaracinaceae, within the suborder Sorangiineae. Sequence similarity searches using the Carbohydrate-active enzymes (CAZyme) database help identify the enzyme repertoire of S. amylolyticus involved in starch, agar, chitin, and cellulose degradation. We identified 16 α-amylases and two γ-amylases in the S. amylolyticus genome that likely play a role in starch degradation. While many of the amylases are seen conserved in other δ-proteobacteria, we notice several novel amylases acquired via horizontal transfer from members belonging to phylum Deinococcus-Thermus, Acidobacteria, and Cyanobacteria. No agar degrading enzyme(s) were identified in the S. amylolyticus genome. Interestingly, several putative β-glucosidases and endoglucanases proteins involved in cellulose degradation were identified. However, the absence of cellobiohydrolases/exoglucanases corroborates with the lack of cellulose degradation by this bacteria.
Topics: Amylases; Bacterial Proteins; Conserved Sequence; DNA Methylation; Genome, Bacterial; Molecular Sequence Annotation; Phylogeny; Proteobacteria; RNA, Ribosomal; RNA, Transfer; Starch
PubMed: 27358428
DOI: 10.1093/gbe/evw151 -
MBio Aug 2018The role of protists and bacteriophages in bacterial predation in the microbial food web has been well studied. There is mounting evidence that and like organisms...
The role of protists and bacteriophages in bacterial predation in the microbial food web has been well studied. There is mounting evidence that and like organisms (BALOs) also contribute to bacterial mortality and, in some cases, more so than bacteriophages. A full understanding of the ecologic function of the microbial food web requires recognition of all major predators and the magnitude of each predator's contribution. Here we investigated the contribution of , one of the BALOs, and bacteriophages when incubated with their common prey, , in a seawater microcosm. We observed that was the greatest responder to the prey, increasing 18-fold with a simultaneous 4.4-log-unit reduction of at 40 h, whereas the bacteriophage population showed no significant increase. In subsequent experiments to formulate a medium that would support the predatory activities and replication of both predators, low-nutrient media favored the predation and replication of the , whereas higher-nutrient media enhanced phage growth. The greatest prey reduction and replication of both and phage were observed in media with moderate nutrient levels. Additional experiments show that the predatory activities of both predators were influenced by environmental conditions, specifically, temperature and salinity. The two predators combined exerted greater control on , a synergism that may be exploited for practical applications to reduce bacterial populations. These findings suggest that along with bacteriophage and protists, has the potential to have a prominent role in bacterial mortality and cycling of nutrients, two vital ecologic functions. Although much has been reported about the marine microbial food web and the role of micropredators, specifically viruses and protists, the contribution of -like predators has largely been ignored, posing a major gap in understanding food web processes. A complete scenario of the microbial food web cannot be developed until the roles of all major micropredators and the magnitude of their contributions to bacterial mortality, structuring of microbial communities, and cycling of nutrients are assessed. Here we show compelling evidence that , a predatory bacterium, is a significant contributor to bacterial death and, in some cases, may rival viruses as agents of bacterial mortality. These results advance current understanding of the microbial loop and top-down control on the bacterial community.
Topics: Bacteriophages; Ecosystem; Microbial Viability; Proteobacteria; Seawater
PubMed: 30087166
DOI: 10.1128/mBio.01202-18 -
Scientific Reports Jan 2021Neutrophilic Fe(II) oxidizing bacteria like Mariprofundus ferrooxydans are obligate chemolithoautotrophic bacteria that play an important role in the biogeochemical...
Neutrophilic Fe(II) oxidizing bacteria like Mariprofundus ferrooxydans are obligate chemolithoautotrophic bacteria that play an important role in the biogeochemical cycling of iron and other elements in multiple environments. These bacteria generally exhibit a singular metabolic mode of growth which prohibits comparative "omics" studies. Furthermore, these bacteria are considered non-amenable to classical genetic methods due to low cell densities, the inability to form colonies on solid medium, and production of copious amounts of insoluble iron oxyhydroxides as their metabolic byproduct. Consequently, the molecular and biochemical understanding of these bacteria remains speculative despite the availability of substantial genomic information. Here we develop the first genetic system in neutrophilic Fe(II) oxidizing bacterium and use it to engineer lithoheterotrophy in M. ferrooxydans, a metabolism that has been speculated but not experimentally validated. This synthetic biology approach could be extended to gain physiological understanding and domesticate other bacteria that grow using a single metabolic mode.
Topics: Chemoautotrophic Growth; Green Fluorescent Proteins; Heterotrophic Processes; Iron; Metabolic Engineering; Oxidation-Reduction; Plasmids; Proteobacteria; Transformation, Genetic
PubMed: 33495498
DOI: 10.1038/s41598-021-81412-3 -
Microbiome Aug 2016Although the common, silver, and bighead carps are native and sparsely distributed in Eurasia, these fish have become abundant and invasive in North America. An...
BACKGROUND
Although the common, silver, and bighead carps are native and sparsely distributed in Eurasia, these fish have become abundant and invasive in North America. An understanding of the biology of these species may provide insights into sustainable control methods. The animal-associated microbiome plays an important role in host health. Characterization of the carp microbiome and the factors that affect its composition is an important step toward understanding the biology and interrelationships between these species and their environments.
RESULTS
We compared the fecal microbiomes of common, silver, and bighead carps from wild and laboratory environments using Illumina sequencing of bacterial 16S ribosomal RNA (rRNA). The fecal bacterial communities of fish were diverse, with Shannon indices ranging from 2.3 to 4.5. The phyla Proteobacteria, Firmicutes, and Fusobacteria dominated carp guts, comprising 76.7 % of total reads. Environment played a large role in shaping fecal microbial community composition, and microbiomes among captive fishes were more similar than among wild fishes. Although differences among wild fishes could be attributed to feeding preferences, diet did not strongly affect microbial community structure in laboratory-housed fishes. Comparison of wild- and lab-invasive carps revealed five shared OTUs that comprised approximately 40 % of the core fecal microbiome.
CONCLUSIONS
The environment is a dominant factor shaping the fecal bacterial communities of invasive carps. Captivity alters the microbiome community structure relative to wild fish, while species differences are pronounced within habitats. Despite the absence of a true stomach, invasive carp species exhibited a core microbiota that warrants future study.
Topics: Animals; Base Sequence; Carps; Environment; Feces; Firmicutes; Fusobacteria; Introduced Species; Microbiota; North America; Proteobacteria; RNA, Ribosomal, 16S; Sequence Analysis, RNA
PubMed: 27514729
DOI: 10.1186/s40168-016-0190-1 -
FEMS Microbiology Ecology Dec 2013Using 454 pyrosequencing, we characterized for the first time the associated microbial community of the deep-sea carnivorous Demosponge Asbestopluma hypogea...
Using 454 pyrosequencing, we characterized for the first time the associated microbial community of the deep-sea carnivorous Demosponge Asbestopluma hypogea (Cladorhizidae). Targeting the 16S rRNA gene V3 and V6 hypervariable regions, we compared the diversity and composition of associated microbes of two individual sponges of A. hypogea freshly collected in the cave with surrounding seawater and with one sponge sample maintained 1 year in an aquarium after collection. With more than 22 961 high quality sequences from sponge samples, representing c. 800 operational taxonomic units per sponge sample at 97% sequence similarities, the phylogenetic affiliation of A. hypogea-associated microbes was assigned to 20 bacterial and two archaeal phyla, distributed into 45 classes and 95 orders. Several differences between the sponge and seawater microbes were observed, highlighting a specific and stable A. hypogea microbial community dominated by Proteobacteria and Bacteroidetes and Thaumarchaeota phyla. A high relative abundance of ammonia-oxidizing archaea and a dominance of sulfate oxidizing/reducing bacteria were observed. Our findings shed lights on the potential roles of associated microbial community in the lifestyle of A. hypogea.
Topics: Animals; Archaea; Bacteria; Bacteroidetes; Biodiversity; Caves; DNA, Bacterial; Genes, rRNA; Microbiota; Phylogeny; Porifera; Proteobacteria; RNA, Ribosomal, 16S; Seawater; Sequence Analysis, DNA
PubMed: 23845054
DOI: 10.1111/1574-6941.12178