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Applied and Environmental Microbiology May 2020Most freshwater bacterial communities are characterized by a few dominant taxa that are often ubiquitous across freshwater biomes worldwide. Our understanding of the...
Most freshwater bacterial communities are characterized by a few dominant taxa that are often ubiquitous across freshwater biomes worldwide. Our understanding of the genomic diversity within these taxonomic groups is limited to a subset of taxa. Here, we investigated the genomic diversity that enables , a freshwater genus key in funneling carbon from primary producers to higher trophic levels, to achieve abundance and ubiquity. We reconstructed eight putative metagenome-assembled genomes (MAGs) from stations located along broad environmental gradients existing in Lake Michigan, part of Earth's largest surface freshwater system. strain inference analysis resolved a total of 23 strains from these MAGs, which strongly partitioned into two habitat-specific clusters with cooccurring strains from different lineages. The largest number of strains belonged to the abundant LimB lineage, for which robust strain delineation had not previously been achieved. Our data show that temperature and nutrient levels may be important environmental parameters associated with microdiversification within the genus. In addition, strains predominant in low- and high-phosphorus conditions had larger genomic divergence than strains abundant under different temperatures. Comparative genomics and gene expression analysis yielded evidence for the ability of LimB populations to exhibit cellular motility and chemotaxis, a phenotype not yet associated with available isolates. Our findings broaden historical marker gene-based surveys of microdiversification and provide evidence of genome diversity and its functional implications across freshwater gradients. is an important bacterial taxonomic group for cycling carbon in freshwater ecosystems worldwide. Here, we examined the genomic diversity of different lineages. We focused on the LimB lineage of this genus, which is globally distributed and often abundant, and its abundance has shown to be largely invariant to environmental change. Our data show that the LimB lineage is actually comprised of multiple cooccurring populations for which the composition and genomic characteristics are associated with variations in temperature and nutrient levels. The gene expression profiles of this lineage suggest the importance of chemotaxis and motility, traits that had not yet been associated with the genus, in adapting to environmental conditions.
Topics: Comamonadaceae; Gene Expression; Genes, Bacterial; Genetic Variation; Lakes; Michigan; Microbiota; Nutrients; Temperature
PubMed: 32169939
DOI: 10.1128/AEM.00140-20 -
Scientific Reports Jul 2019Microbial communities have not been studied using molecular approaches at high elevations on the African continent. Here we describe the diversity of microbial...
Microbial communities have not been studied using molecular approaches at high elevations on the African continent. Here we describe the diversity of microbial communities from ice and periglacial soils from near the summit of Mt. Kilimanjaro by using both Illumina and Sanger sequencing of 16S and 18S rRNA genes. Ice and periglacial soils contain unexpectedly diverse and rich assemblages of Bacteria and Eukarya indicating that there may be high rates of dispersal to the top of this tropical mountain and/or that the habitat is more conducive to microbial life than was previously thought. Most bacterial OTUs are cosmopolitan and an analysis of isolation by geographic distance patterns of the genus Polaromonas emphasized the importance of global Aeolian transport in the assembly of bacterial communities on Kilimanjaro. The eukaryotic communities were less diverse than the bacterial communities and showed more evidence of dispersal limitations and apparent endemism. Cercozoa dominated the 18S communities, including a high abundance of testate amoebae and a high diversity of endemic OTUs within the Vampyrellida. These results argue for more intense study of this unique high-elevation "island of the cryosphere" before the glaciers of Kilimanjaro disappear forever.
Topics: Biodiversity; Comamonadaceae; Ecosystem; Eukaryota; Ice Cover; Microbiota; RNA, Ribosomal, 16S; RNA, Ribosomal, 18S; Soil Microbiology; Tanzania
PubMed: 31337772
DOI: 10.1038/s41598-019-46521-0 -
Genome Biology and Evolution Apr 2021Schlegelella thermodepolymerans is a moderately thermophilic bacterium capable of producing polyhydroxyalkanoates-biodegradable polymers representing an alternative to...
Schlegelella thermodepolymerans is a moderately thermophilic bacterium capable of producing polyhydroxyalkanoates-biodegradable polymers representing an alternative to conventional plastics. Here, we present the first complete genome of the type strain S. thermodepolymerans DSM 15344 that was assembled by hybrid approach using both long (Oxford Nanopore) and short (Illumina) reads. The genome consists of a single 3,858,501-bp-long circular chromosome with GC content of 70.3%. Genome annotation identified 3,650 genes in total, whereas 3,598 open reading frames belonged to protein-coding genes. Functional annotation of the genome and division of genes into clusters of orthologous groups revealed a relatively high number of 1,013 genes with unknown function or unknown clusters of orthologous groups, which reflects the fact that only a little is known about thermophilic polyhydroxyalkanoates-producing bacteria on a genome level. On the other hand, 270 genes involved in energy conversion and production were detected. This group covers genes involved in catabolic processes, which suggests capability of S. thermodepolymerans DSM 15344 to utilize and biotechnologically convert various substrates such as lignocellulose-based saccharides, glycerol, or lipids. Based on the knowledge of its genome, it can be stated that S. thermodepolymerans DSM 15344 is a very interesting, metabolically versatile bacterium with great biotechnological potential.
Topics: Base Composition; Comamonadaceae; Genome, Bacterial; Molecular Sequence Annotation; Sequence Analysis, DNA; Whole Genome Sequencing
PubMed: 33432323
DOI: 10.1093/gbe/evab007 -
Journal of Bacteriology Jun 2006In Comamonas testosteroni strain BR6020, metabolism of isovanillate (iVan; 3-hydroxy-4-methoxybenzoate), vanillate (Van; 4-hydroxy-3-methoxybenzoate), and veratrate...
In Comamonas testosteroni strain BR6020, metabolism of isovanillate (iVan; 3-hydroxy-4-methoxybenzoate), vanillate (Van; 4-hydroxy-3-methoxybenzoate), and veratrate (Ver; 3,4-dimethoxybenzoate) proceeds via protocatechuate (Pca; 3,4-dihydroxybenzoate). A 13.4-kb locus coding for the catabolic enzymes that channel the three substrates to Pca was cloned. O demethylation is mediated by the phthalate family oxygenases IvaA (converts iVan to Pca and Ver to Van) and VanA (converts Van to Pca and Ver to iVan). Reducing equivalents from NAD(P)H are transferred to the oxygenases by the class IA oxidoreductase IvaB. Studies using whole cells, cell extracts, and reverse transcriptase PCR showed that degradative activity and expression of vanA, ivaA, and ivaB are inducible. In succinate- and Pca-grown cells, there is negligible degradative activity towards Van, Ver, and iVan and little to no expression of vanA, ivaA, and ivaB. Growth on Van or Ver results in production of oxygenases with activity towards Van, Ver, and iVan and expression of vanA, ivaA, and ivaB. With iVan-grown cultures, ivaA and ivaB are expressed, and in assays with whole cells, production of the iVan oxygenase is observed, but there is little activity towards Van or Ver. In cell extracts, though, Ver metabolism is observed, which suggests that the system mediating iVan uptake in whole cells does not mediate Ver uptake.
Topics: Comamonas testosteroni; DNA Primers; Genotype; Hydroxybenzoates; Kinetics; Molecular Sequence Data; Open Reading Frames; Phenotype; Polymerase Chain Reaction; Restriction Mapping; Vanillic Acid
PubMed: 16707678
DOI: 10.1128/JB.01675-05 -
Environmental Science and Pollution... Sep 2020The primary aims of this present study were to evaluate the effect of oxygen limitation on the bacterial community structure of enrichment cultures degrading either...
Effect of oxygen limitation on the enrichment of bacteria degrading either benzene or toluene and the identification of Malikia spinosa (Comamonadaceae) as prominent aerobic benzene-, toluene-, and ethylbenzene-degrading bacterium: enrichment, isolation and whole-genome analysis.
The primary aims of this present study were to evaluate the effect of oxygen limitation on the bacterial community structure of enrichment cultures degrading either benzene or toluene and to clarify the role of Malikia-related bacteria in the aerobic degradation of BTEX compounds. Accordingly, parallel aerobic and microaerobic enrichment cultures were set up and the bacterial communities were investigated through cultivation and 16S rDNA Illumina amplicon sequencing. In the aerobic benzene-degrading enrichment cultures, the overwhelming dominance of Malikia spinosa was observed and it was abundant in the aerobic toluene-degrading enrichment cultures as well. Successful isolation of a Malikia spinosa strain shed light on the fact that this bacterium harbours a catechol 2,3-dioxygenase (C23O) gene encoding a subfamily I.2.C-type extradiol dioxygenase and it is able to degrade benzene, toluene and ethylbenzene under clear aerobic conditions. While quick degradation of the aromatic substrates was observable in the case of the aerobic enrichments, no significant benzene degradation, and the slow degradation of toluene was observed in the microaerobic enrichments. Despite harbouring a subfamily I.2.C-type C23O gene, Malikia spinosa was not found in the microaerobic enrichments; instead, members of the Pseudomonas veronii/extremaustralis lineage dominated these communities. Whole-genome analysis of M. spinosa strain AB6 revealed that the C23O gene was part of a phenol-degrading gene cluster, which was acquired by the strain through a horizontal gene transfer event. Results of the present study revealed that bacteria, which encode subfamily I.2.C-type extradiol dioxygenase enzyme, will not be automatically able to degrade monoaromatic hydrocarbons under microaerobic conditions.
Topics: Benzene; Benzene Derivatives; Biodegradation, Environmental; Comamonadaceae; Oxygen; Pseudomonas; Toluene; Xylenes
PubMed: 32474783
DOI: 10.1007/s11356-020-09277-z -
IET Nanobiotechnology Jun 2019In the present study sp. Shakibaie, Forootanfar, and Ghazanfari (SFG), was applied for preparation of biogenic Bi nanoparticles (BiNPs) and antibacterial and...
In the present study sp. Shakibaie, Forootanfar, and Ghazanfari (SFG), was applied for preparation of biogenic Bi nanoparticles (BiNPs) and antibacterial and anti-biofilm activities of the purified BiNPs were investigated by microdilution and disc diffusion methods. Transmission electron micrographs showed that the produced nanostructures were spherical with a size range of 40-120 nm. The measured minimum inhibitory concentration of both the Bi subnitrate and BiNPs against three biofilms producing bacterial pathogens of , , and were found to be above 1280 µg/ml. Addition of BiNPs (1000 µg/disc) to antibiotic discs containing tobramycin, nalidixic acid, ceftriaxone, bacitracin, cefalexin, amoxicillin, and cefixime significantly increased the antibacterial effects against methicillin-resistant (MRSA) in comparison with Bi subnitrate ( < 0.05). Furthermore, the biogenic BiNPs decreased the biofilm formation of , , and to 55, 85, and 15%, respectively. In comparison to Bi subnitrate, BiNPs indicated significant anti-biofilm activity against ( < 0.05) while the anti-biofilm activity of BiNPs against and was similar to that of Bi subnitrate. To sum up, the attained results showed that combination of biogenic BiNPs with commonly used antibiotics relatively enhanced their antibacterial effects against MRSA.
Topics: Anti-Bacterial Agents; Bacteria; Biofilms; Bismuth; Delftia; Microbial Sensitivity Tests; Nanoparticles; Plant Extracts
PubMed: 31171741
DOI: 10.1049/iet-nbt.2018.5102 -
Genes Jul 2020Polyhydroxyalkanoates (PHAs), the intracellular polymers produced by various microorganisms as carbon and energy storage, are of great technological potential as...
Polyhydroxyalkanoates (PHAs), the intracellular polymers produced by various microorganisms as carbon and energy storage, are of great technological potential as biodegradable versions of common plastics. PHA-producing microbes are therefore in great demand and a plethora of different environments, especially extreme habitats, have been probed for the presence of PHA-accumulators. However, the polar region has been neglected in this regard, probably due to the low accessibility of the sampling material and unusual cultivation regime. Here, we present the results of a screening procedure involving 200 bacterial strains isolated from 25 habitats of both polar regions. Agar-based tests, microscopy, and genetic methods were conducted to elucidate the biodiversity and potential of polar-region PHA-accumulators. Microscopic observation of Nile Red stained cells proved to be the most reliable screening method as it allowed to confirm the characteristic bright orange glow of the Nile Red-PHA complex as well as the typical morphology of the PHA inclusions. Psychrophilic PHA-producers belonged mostly to the family (Betaproteobacteria) although actinobacterial PHA synthesizers of the families, and also featured prominently. Glacial and postglacial habitats as well as developed polar region soils, were evaluated as promising for PHA-producer bioprospection. This study highlights the importance of psychrophiles as biodiverse and potent polyhydroxyalkanoate sources for scientific and application-aimed research.
Topics: Arctic Regions; Comamonadaceae; Microbiota; Micrococcaceae; Phylogeny; Polyhydroxyalkanoates; Polymorphism, Genetic; Seawater; Soil Microbiology
PubMed: 32752049
DOI: 10.3390/genes11080873 -
F1000Research 2020, a green micro-alga can be grown at the lab heterotrophically or photo-heterotrophically in Tris-Phosphate-Acetate (TAP) medium which contains acetate as the sole...
Isolation and characterization of a novel bacterial strain from a Tris-Acetate-Phosphate agar medium plate of the green micro-alga that can utilize common environmental pollutants as a carbon source.
, a green micro-alga can be grown at the lab heterotrophically or photo-heterotrophically in Tris-Phosphate-Acetate (TAP) medium which contains acetate as the sole carbon source. When grown in TAP medium, can utilize the exogenous acetate in the medium for gluconeogenesis using the glyoxylate cycle, which is also present in many bacteria and higher plants. A novel bacterial strain, LMJ, was isolated from a contaminated TAP medium plate of . We present our work on the isolation and physiological and biochemical characterizations of LMJ. Several microbiological tests were conducted to characterize LMJ, including its sensitivity to four antibiotics. We amplified and sequenced partially the 16S rRNA gene of LMJ. We tested if LMJ can utilize cyclic alkanes, aromatic hydrocarbons, poly-hydroxyalkanoates, and fresh and combusted car motor oil as the sole carbon source on Tris-Phosphate (TP) agar medium plates for growth. LMJ is a gram-negative rod, oxidase-positive, mesophilic, non-enteric, pigmented, salt-sensitive bacterium. LMJ can ferment glucose, is starch hydrolysis-negative, and is very sensitive to penicillin and chloramphenicol. Preliminary spectrophotometric analyses indicate LMJ produces pyomelanin. NCBI-BLAST analyses of the partial 16S rRNA gene sequence of LMJ showed that it matched to that of an uncultured bacterium clone LIB091_C05_1243. The nearest genus relative of LMJ is an sp. strain. LMJ was able to use alkane hydrocarbons, fresh and combusted car motor oil, poly-hydroxybutyrate, phenanthrene, naphthalene, benzoic acid and phenyl acetate as the sole carbon source for growth on TP-agar medium plates. LMJ has 99.14% sequence identity with the sp. strain A16OP12 whose genome has not been sequenced yet. LMJ's ability to use chemicals that are common environmental pollutants makes it a promising candidate for further investigation for its use in bioremediation and, provides us with an incentive to sequence its genome.
Topics: Acetates; Agar; Bacteria; Carbon; Chlamydomonas reinhardtii; Comamonadaceae; Environmental Pollutants; Phosphates; RNA, Ribosomal, 16S
PubMed: 32855811
DOI: 10.12688/f1000research.24680.1 -
MicrobiologyOpen Apr 2018The proteobacteria Variovorax sp. WDL1, Comamonas testosteroni WDL7, and Hyphomicrobium sulfonivorans WDL6 compose a triple-species consortium that synergistically...
The proteobacteria Variovorax sp. WDL1, Comamonas testosteroni WDL7, and Hyphomicrobium sulfonivorans WDL6 compose a triple-species consortium that synergistically degrades and grows on the phenylurea herbicide linuron. To acquire a better insight into the interactions between the consortium members and the underlying molecular mechanisms, we compared the transcriptomes of the key biodegrading strains WDL7 and WDL1 grown as biofilms in either isolation or consortium conditions by differential RNAseq analysis. Differentially expressed pathways and cellular systems were inferred using the network-based algorithm PheNetic. Coculturing affected mainly metabolism in WDL1. Significantly enhanced expression of hylA encoding linuron hydrolase was observed. Moreover, differential expression of several pathways involved in carbohydrate, amino acid, nitrogen, and sulfur metabolism was observed indicating that WDL1 gains carbon and energy from linuron indirectly by consuming excretion products from WDL7 and/or WDL6. Moreover, in consortium conditions, WDL1 showed a pronounced stress response and overexpression of cell to cell interaction systems such as quorum sensing, contact-dependent inhibition, and Type VI secretion. Since the latter two systems can mediate interference competition, it prompts the question if synergistic linuron degradation is the result of true adaptive cooperation or rather a facultative interaction between bacteria that coincidentally occupy complementary metabolic niches.
Topics: Aniline Compounds; Biodegradation, Environmental; Biofilms; Comamonadaceae; Gene Expression Regulation, Bacterial; Herbicides; Hydrolases; Hyphomicrobium; Linuron; Transcriptome; Type VI Secretion Systems
PubMed: 29314727
DOI: 10.1002/mbo3.559 -
Research in Microbiology 2021Bdellovibrio bacteriovorus, a Gram-negative predatory bacterium belonging to the Bdellovibrio and like organisms (BALOs), predates on Gram-negative bacteria. BALO...
Bdellovibrio bacteriovorus, a Gram-negative predatory bacterium belonging to the Bdellovibrio and like organisms (BALOs), predates on Gram-negative bacteria. BALO strains differ in prey range but so far, the genetic basis of resistance against BALO predation is hardly understood. We developed a loss-of-function approach to screen for sensitive mutants in a library of strain M6, a predation-resistant strain of the plant pathogen Acidovorax citrulli. The screen is based on tracking the growth of a B. bacteriovorus strain expressing the fluorescent reporter Tdtomato in mutant pools to reveal predation-sensitive variants. Two independent loci were identified in mutant strains exhibiting significant levels of susceptibility to the predator. Genes in the two loci were analysed using both protein sequence homology and protein structure modeling. Both were secretion-related proteins and thus associated to the bacterial cell wall. Successful complementation of gspK, a gene encoding for a minor pseudopilin protein confirmed the involvement of the type II secretion system in A. citrulli M6 resistance. This proof of concept study shows that our approach can identify key elements of the BALO-prey interaction, and it validates the hypothesis that mutational changes in a single gene can drastically impact prey resistance to BALO predation.
Topics: Bacterial Proteins; Bdellovibrio bacteriovorus; Comamonadaceae; Genes, Bacterial; Microbial Interactions; Mutagenesis, Insertional; Mutation; Type II Secretion Systems
PubMed: 34492337
DOI: 10.1016/j.resmic.2021.103878