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Applied and Environmental Microbiology Aug 2021Poly-3-hydroxyalkanoic acids (PHAs) are bacterial storage polymers commonly used in bioplastic production. Halophilic bacteria are industrially interesting organisms, as...
Poly-3-hydroxyalkanoic acids (PHAs) are bacterial storage polymers commonly used in bioplastic production. Halophilic bacteria are industrially interesting organisms, as their salinity tolerance and psychrophilic nature lowers sterility requirements and subsequent production costs. We investigated PHA synthesis in two bacterial strains, sp. 363 and sp. 392, isolated from Southern Ocean sea ice and elucidated the related PHA biopolymer accumulation and composition with various approaches, such as transcriptomics, microscopy, and chromatography. We show that both bacterial strains produce PHAs at 4°C when the availability of nitrogen and/or oxygen limited growth. The genome of sp. 363 carries three synthase genes and transcribes genes along three PHA pathways (I to III), whereas sp. 392 carries only one gene and transcribes genes along one pathway (I). Thus, sp. 363 has a versatile repertoire of genes and pathways enabling production of both short- and medium-chain-length PHA products. Plastic pollution is one of the most topical threats to the health of the oceans and seas. One recognized way to alleviate the problem is to use degradable bioplastic materials in high-risk applications. PHA is a promising bioplastic material as it is nontoxic and fully produced and degraded by bacteria. Sea ice is an interesting environment for prospecting novel PHA-producing organisms, since traits advantageous to lower production costs, such as tolerance for high salinities and low temperatures, are common. We show that two sea-ice bacteria, sp. 363 and sp. 392, are able to produce various types of PHA from inexpensive carbon sources. sp. 363 is an especially interesting PHA-producing organism, since it has three different synthesis pathways to produce both short- and medium-chain-length PHAs.
Topics: Bacterial Proteins; Cold Temperature; Genome, Bacterial; Halomonas; Ice Cover; Paracoccus; Phylogeny; Polyhydroxyalkanoates; Seawater; Temperature
PubMed: 34160268
DOI: 10.1128/AEM.00929-21 -
FEMS Microbiology Letters Mar 2018In oxygen-limited environments, denitrifying bacteria can switch from oxygen-dependent respiration to nitrate (NO3-) respiration in which the NO3- is sequentially... (Review)
Review
In oxygen-limited environments, denitrifying bacteria can switch from oxygen-dependent respiration to nitrate (NO3-) respiration in which the NO3- is sequentially reduced via nitrite (NO2-), nitric oxide (NO) and nitrous oxide (N2O) to dinitrogen (N2). However, atmospheric N2O continues to rise, a significant proportion of which is microbial in origin. This implies that the enzyme responsible for N2O reduction, nitrous oxide reductase (NosZ), does not always carry out the final step of denitrification either efficiently or in synchrony with the rest of the pathway. Despite a solid understanding of the biochemistry underpinning denitrification, there is a relatively poor understanding of how environmental signals and respective transcriptional regulators control expression of the denitrification apparatus. This minireview describes the current picture for transcriptional regulation of denitrification in the model bacterium, Paracoccus denitrificans, highlighting differences in other denitrifying bacteria where appropriate, as well as gaps in our understanding. Alongside this, the emerging role of small regulatory RNAs in regulation of denitrification is discussed. We conclude by speculating how this information, aside from providing a better understanding of the denitrification process, can be translated into development of novel greenhouse gas mitigation strategies.
Topics: Bacteria; Bacterial Proteins; Denitrification; Environment; Gene Expression Regulation, Bacterial; Nitrous Oxide; Oxidoreductases; Oxygen; Paracoccus denitrificans; RNA, Small Untranslated
PubMed: 29272423
DOI: 10.1093/femsle/fnx277 -
Antonie Van Leeuwenhoek May 2024A Gram-stain-negative, aerobic, non-motile, catalase- and oxidase-positive, pale orange, rod-shaped strain EF6, was isolated from a natural wetland reserve in Hebei...
A Gram-stain-negative, aerobic, non-motile, catalase- and oxidase-positive, pale orange, rod-shaped strain EF6, was isolated from a natural wetland reserve in Hebei province, China. The strain grew at 25-37 °C (optimum, 30 °C), pH 5-9 (optimum, pH 7), and in the presence of 1.0-4.0% (w/v) NaCl (optimum, 2%). A phylogenetic analysis based on 16S rRNA gene sequence revealed that strain EF6 belongs to the genus Paracoccus, and the closest members were Paracoccus shandongensis wg2 with 98.1% similarity, Paracoccus fontiphilus MVW-1 (97.9%), Paracoccus everestensis S8-55 (97.7%), Paracoccus subflavus GY0581 (97.6%), Paracoccus sediminis CMB17 (97.3%), Paracoccus caeni MJ17 (97.0%), and Paracoccus angustae E6 (97.0%). The genome size of strain EF6 was 4.88 Mb, and the DNA G + C content was 65.3%. The digital DNA-DNA hybridization, average nucleotide identity, and average amino acid identity values between strain EF6 and the reference strains were all below the threshold limit for species delineation (< 32.8%, < 88.0%, and < 86.7%, respectively). The major fatty acids (≥ 5.0%) were summed feature 8 (86.3%, C ω6c and/or C ω7c) and C (5.0%) and the only isoprenoid quinone was Q-10. The polar lipids consisted of diphosphatidylglycerol, phosphatidylglycerol, two unidentified glycolipids, five unidentified phospholipids, and an unidentified aminolipid. Strain EF6 displays notable resistance to benzoate and selenite, with higher tolerance levels (25 g/L for benzoate and 150 mM for selenite) compared to the closely related species. Genomic analysis identified six benzoate resistance genes (acdA, pcaF, fadA, pcaC, purB, and catA) and twenty selenite resistance and reduction-related genes (iscR, ssuB, ssuD, selA, selD and so on). Additionally, EF6 possesses unique genes (catA, ssuB, and ssuC) absent in the closely related species for benzoate and selenite resistance. Its robust resistance to benzoate and selenite, coupled with its genomic makeup, make EF6 a promising candidate for the remediation of both organic and inorganic pollutants. It is worth noting that the specific resistance phenotypes described above were not reported in other novel species in Paracoccus. Based on the results of biochemical, physiological, phylogenetic, and chemotaxonomic analyses, combined with comparisons of the 16S rRNA gene sequence and the whole genome sequence, strain EF6 is considered to represent a novel species of the genus Paracoccus within the family Rhodobacteraceae, for which the name Paracoccus benzoatiresistens sp. nov. is proposed. The type strain is EF6 (= GDMCC 1.3400 = JCM 35642 = MCCC 1K08702).
Topics: Wetlands; Phylogeny; Paracoccus; RNA, Ribosomal, 16S; Fatty Acids; Base Composition; DNA, Bacterial; China; Sodium Selenite; Bacterial Typing Techniques; Phospholipids; Sequence Analysis, DNA; Nucleic Acid Hybridization; Oxidation-Reduction; Drug Resistance, Bacterial
PubMed: 38777900
DOI: 10.1007/s10482-024-01969-7 -
PloS One 2021Despite the formation of biofilms on catheters for extracorporeal membrane oxygenation (ECMO), some patients do not show bacteremia. To elucidate the specific linkage...
Despite the formation of biofilms on catheters for extracorporeal membrane oxygenation (ECMO), some patients do not show bacteremia. To elucidate the specific linkage between biofilms and bacteremia in patients with ECMO, an improved understanding of the microbial community within catheter biofilms is necessary. Hence, we aimed to evaluate the biofilm microbiome of ECMO catheters from adults with (n = 6) and without (n = 15) bacteremia. The microbiomes of the catheter biofilms were evaluated by profiling the V3 and V4 regions of bacterial 16s rRNA genes using the Illumina MiSeq sequencing platform. In total, 2,548,172 reads, with an average of 121,341 reads per sample, were generated. Although alpha diversity was slightly higher in the non-bacteremic group, the difference was not statistically significant. In addition, there was no difference in beta diversity between the two groups. We found 367 different genera, of which 8 were present in all samples regardless of group; Limnohabitans, Flavobacterium, Delftia, Massilia, Bacillus, Candidatus, Xiphinematobacter, and CL0-1 showed an abundance of more than 1% in the sample. In particular, Arthrobacter, SMB53, Neisseria, Ortrobactrum, Candidatus Rhabdochlamydia, Deefgae, Dyella, Paracoccus, and Pedobacter were highly abundant in the bacteremic group. Network analysis indicated that the microbiome of the bacteremic group was more complex than that of the non-bacteremic group. Flavobacterium and CL0.1, which were abundant in the bacteremic group, were considered important genera because they connected different subnetworks. Biofilm characteristics in ECMO catheters varied according to the presence or absence of bacteremia. There were no significant differences in diversity between the two groups, but there were significant differences in the community composition of the biofilms. The biofilm-associated community was dynamic, with the bacteremic group showing very complex network connections within the microbiome.
Topics: Arthrobacter; Bacteremia; Bacteria; Biofilms; Catheter-Related Infections; Extracorporeal Membrane Oxygenation; Female; Humans; Male; Microbiota; Middle Aged; Neisseria; RNA, Ribosomal, 16S; Retrospective Studies
PubMed: 34529734
DOI: 10.1371/journal.pone.0257449 -
Current Microbiology Dec 2021A novel strain, wg2, was isolated from activated sludge obtained from wastewater treatment plant in Shandong province, China. The bacterium was Gram-strain-negative,...
A novel strain, wg2, was isolated from activated sludge obtained from wastewater treatment plant in Shandong province, China. The bacterium was Gram-strain-negative, aerobic, rod-shaped, non-flagellated and non-gliding. This bacterium was characterized to determine its taxonomic position using the polyphasic approach. Strain wg2 grew at 25-45 °C (optimum, 30 °C), at salinities of 0-7.0% (w/v) NaCl (optimum, 0-2.0%) and at pH 7-9 (optimum, pH 7.0). Phylogenetic analysis based on 16S rRNA gene sequence showed that strain wg2 clustered with species of genus Paracoccus and shares high similarities with Paracoccus sediminis DSM 26170 (98.1%) and Paracoccus fontiphilus MVW-1 (97.7%), respectively. The genome size of strain wg2 was 3.93 Mbp and the DNA G + C content was 66.05%. The dDDH values and ANI between strain wg2 and each of reference strains P. sediminis DSM 26170, P. fontiphilus MVW-1 and P. denitrificans DSM 413 were 18.3, 12.5, 24.5% and 85.3, 87.0, 78.4%, respectively. The major respiratory quinone was found to be Q-10 and the major fatty acid was C ω7c. The polar lipids consisted of aminoglycolipid (AGL), phosphatidylcholine (PC), glycolipid (GL), phosphatidylserine (PS), phosphatidylglycerol phosphate (PGP), aminophospholipids (APL). Combining above descriptions, strain wg2 should represent a novel species of genus Paracoccus, for which the name Paracoccus shandongensis sp. nov., is proposed. The type strain is wg2 (= KCTC 72862 = CCTCC AB 2019401).
Topics: Bacterial Typing Techniques; China; DNA, Bacterial; Fatty Acids; Paracoccus; Phospholipids; Phylogeny; RNA, Ribosomal, 16S; Sequence Analysis, DNA; Sewage
PubMed: 34905098
DOI: 10.1007/s00284-021-02705-4 -
PloS One 2023The genus Paracoccus capable of inhabiting a variety of different ecological niches both, marine and terrestrial, is globally distributed. In addition, Paracoccus is...
The genus Paracoccus capable of inhabiting a variety of different ecological niches both, marine and terrestrial, is globally distributed. In addition, Paracoccus is taxonomically, metabolically and regarding lifestyle highly diverse. Until now, little is known on how Paracoccus can adapt to such a range of different ecological niches and lifestyles. In the present study, the genus Paracoccus was phylogenomically analyzed (n = 160) and revisited, allowing species level classification of 16 so far unclassified Paracoccus sp. strains and detection of five misclassifications. Moreover, we performed pan-genome analysis of Paracoccus-type strains, isolated from a variety of ecological niches, including different soils, tidal flat sediment, host association such as the bluespotted cornetfish, Bugula plumosa, and the reef-building coral Stylophora pistillata to elucidate either i) the importance of lifestyle and adaptation potential, and ii) the role of the genomic equipment and niche adaptation potential. Six complete genomes were de novo hybrid assembled using a combination of short and long-read technologies. These Paracoccus genomes increase the number of completely closed high-quality genomes of type strains from 15 to 21. Pan-genome analysis revealed an open pan-genome composed of 13,819 genes with a minimal chromosomal core (8.84%) highlighting the genomic adaptation potential and the huge impact of extra-chromosomal elements. All genomes are shaped by the acquisition of various mobile genetic elements including genomic islands, prophages, transposases, and insertion sequences emphasizing their genomic plasticity. In terms of lifestyle, each mobile genetic elements should be evaluated separately with respect to the ecological context. Free-living genomes, in contrast to host-associated, tend to comprise (1) larger genomes, or the highest number of extra-chromosomal elements, (2) higher number of genomic islands and insertion sequence elements, and (3) a lower number of intact prophage regions. Regarding lifestyle adaptations, free-living genomes share genes linked to genetic exchange via T4SS, especially relevant for Paracoccus, known for their numerous extrachromosomal elements, enabling adaptation to dynamic environments. Conversely, host-associated genomes feature diverse genes involved in molecule transport, cell wall modification, attachment, stress protection, DNA repair, carbon, and nitrogen metabolism. Due to the vast number of adaptive genes, Paracoccus can quickly adapt to changing environmental conditions.
Topics: Paracoccus; DNA Transposable Elements; Genomics; Genomic Islands; Phylogeny; Genome, Bacterial
PubMed: 38117845
DOI: 10.1371/journal.pone.0287947 -
Archives of Microbiology May 2022Bacteria are important participants in sulfur cycle of the extremely haloalkaline environment, e.g. soda lake. The effects of physicochemical factors on the composition...
Bacteria are important participants in sulfur cycle of the extremely haloalkaline environment, e.g. soda lake. The effects of physicochemical factors on the composition of sulfide-oxidizing bacteria (SOB) and sulfate-reducing bacteria (SRB) in soda lake have remained elusive. Here, we surveyed the community structure of total bacteria, SOB and SRB based on 16S rRNA, soxB and dsrB gene sequencing, respectively, in five soda lakes with different physicochemical factors. The results showed that the dominant bacteria belonged to the phyla Proteobacteria, Bacteroidetes, Halanaerobiaeota, Firmicutes and Actinobacteria. SOB and SRB were widely distributed in lakes with different physicochemical characteristics, and the community composition were different. In general, salinity and inorganic nitrogen sources (NH-N, NO-N) were the most significant factors. Specifically, the communities of SOB, mainly including Thioalkalivibrio, Burkholderia, Paracoccus, Bradyrhizobium, and Hydrogenophaga genera, were remarkably influenced by the levels of NH-N and salinity. Yet, for SRB communities, including Desulfurivibrio, Candidatus Electrothrix, Desulfonatronospira, Desulfonatronum, Desulfonatronovibrio, Desulfonatronobacter and so on, the most significant determinants were salinity and NO-N. Besides, Rhodoplanes played a significant role in the interaction between SOB and SRB. From our results, the knowledge regarding the community structures of SOB and SRB in extremely haloalkaline environment was extended.
Topics: Bacteria; Desulfovibrio; Humans; Lakes; Oxidation-Reduction; Phylogeny; RNA, Ribosomal, 16S; Salinity; Sulfides; Sulfur
PubMed: 35567694
DOI: 10.1007/s00203-022-02925-7 -
Frontiers in Immunology 2021Microbiota acquired during labor and through the first days of life contributes to the newborn's immune maturation and development. Mother provides probiotics and... (Observational Study)
Observational Study
Microbiota acquired during labor and through the first days of life contributes to the newborn's immune maturation and development. Mother provides probiotics and prebiotics factors through colostrum and maternal milk to shape the first neonatal microbiota. Previous works have reported that immunoglobulin A (IgA) secreted in colostrum is coating a fraction of maternal microbiota. Thus, to better characterize this IgA-microbiota association, we used flow cytometry coupled with 16S rRNA gene sequencing (IgA-Seq) in human colostrum and neonatal feces. We identified IgA bound bacteria (IgA+) and characterized their diversity and composition shared in colostrum fractions and neonatal fecal bacteria. We found that IgA2 is mainly associated with , , and , among other genera shared in colostrum and neonatal fecal samples. We found that metabolic pathways related to epithelial adhesion and carbohydrate consumption are enriched within the IgA2+ fecal microbiota. The association of IgA2 with specific bacteria could be explained because these antibodies recognize common antigens expressed on the surface of these bacterial genera. Our data suggest a preferential targeting of commensal bacteria by IgA2, revealing a possible function of maternal IgA2 in the shaping of the fecal microbial composition in the neonate during the first days of life.
Topics: Antigens; Bacteria; Colostrum; Feces; Female; Gastrointestinal Microbiome; Humans; Immunoglobulin A; Infant, Newborn; Linear Models; Longitudinal Studies; Pregnancy; Prospective Studies; RNA, Ribosomal, 16S
PubMed: 34804008
DOI: 10.3389/fimmu.2021.712130 -
Archives of Microbiology Aug 2021A gram-stain-negative, non-motile and rod-shaped strain, designated wg1, was isolated from activated sludge obtained from wastewater treatment plant in Binzhou (Shandong...
A gram-stain-negative, non-motile and rod-shaped strain, designated wg1, was isolated from activated sludge obtained from wastewater treatment plant in Binzhou (Shandong province, PR China). Growth of strain wg1 occurred at 25-45 °C (optimum, 37 °C), at pH 7.0-9.0 (optimum growth at pH 8.0) and at a salinity range of 0-4% (optimum, 1%). The chemotaxonomic, phenotypic and genomic traits were investigated. The 16S rRNA gene sequence analysis showed that strain wg1 belonged to the genus Paracoccus. The species with highest similarity to strain wg1 was Paracoccus communis VKM B-2787 (98.27%), followed by Paracoccus kondratievae VKM B-2222 (98.25%). The isoprenoid quinone was Q-10. Major cellular fatty acids were summed feature 8, C and C. The major polar lipids were diphosphatidylglycerol (DPG), phosphatidylethanolamine (PE), aminoglycolipid (AGL), phosphatidylglycerol (PG), phosphatidylcholine (PC), aminolipid (AL), one unidentified lipid (L) and one unidentified phospholipid (PL). The genome size was 4,834,448 bp with a G+C content of 67.67 mol%. The prediction result of secondary metabolites based on genome has shown that the strain wg1 contained 12 clusters, and the gene involved in primary metabolism showed differences in the comparison between wg1 and reference strains. The dDDH values of strain wg1 with P. communis VKM B-2787, P. kondratievae VKM B-2222 and P. denitrificans DSM 413 were 45.30, 30.60 and 39.50%, respectively. Based on its physiological properties, chemotaxonomic characteristics and low ANI and dDDH results, strain wg1 is considered to represent a novel species for which the name Paracoccus binzhouensis sp. nov., is proposed. The type strain is wg1 (= KCTC 72861 = CCTCC AB 2019400).
Topics: Bacterial Typing Techniques; China; DNA, Bacterial; Fatty Acids; Paracoccus; Phospholipids; Phylogeny; RNA, Ribosomal, 16S; Sequence Analysis, DNA; Sewage; Species Specificity
PubMed: 33774710
DOI: 10.1007/s00203-021-02286-7 -
Microscopy Research and Technique Jul 2022The participation of numerous physicochemical and biological functions maintains the evolution and expansion of the remarkable nature. Due to its vast applicability in...
The participation of numerous physicochemical and biological functions maintains the evolution and expansion of the remarkable nature. Due to its vast applicability in several engineering disciplines, naturally occurring bio-mineralization or microbially induced calcium carbonate (MICP) precipitation is attracting more interest. Cave bacteria contribute to the precipitation of calcium carbonate (CaCO ). In the present study, soil sediments were collected from Kashmir cave, KPK, Pakistan, and plated on B4 specific nutrients limited medium for bacterial isolation and the viable bacterial count was calculated. Three bacterial strains named GSN-11, TFSN-14, and TFSN-15 were capable of precipitating CaCO . These bacterial isolates were identified through 16S rRNA gene sequencing and strain GSN-11 was identified as Bacillus toyonensis, TFSN-14 as Paracoccus limosus and TFSN-15 as Brevundimonas diminuta. Enhanced CaCO precipitation potential of these bacteria strains was observed at 25°C and pH 5. The precipitated CaCO was confirmed by scanning electron microscopy, X-ray powder diffraction, and Fourier transform infra-red spectroscopy. The findings showed that the precipitates were dominated by calcite, aragonite, and nanosize vaterite. Current research suggests that precipitation of CaCO by proteolytic cave bacteria is widespread in Kashmir cave and these bacterial communities can actively contribute to the formation of CaCO by enhancing the pH of the microenvironment. RESEARCH HIGHLIGHTS: Kashmir cave inhabit potentially active bacteria in terms of biogeochemical processes. Cave bacteria significantly precipitated CaCO . Calcite, aragonite, and nanosize vaterite were dominant in precipitates.
Topics: Bacteria; Calcium Carbonate; Chemical Precipitation; Pakistan; RNA, Ribosomal, 16S
PubMed: 35388567
DOI: 10.1002/jemt.24105