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Scientifica 2018The identification of potential hydrocarbon utilizing bacteria is an essential requirement in microbial enhanced oil recovery (MEOR). Molecular approaches like proteomic...
The identification of potential hydrocarbon utilizing bacteria is an essential requirement in microbial enhanced oil recovery (MEOR). Molecular approaches like proteomic and genomic characterization of the isolates are replacing the traditional method of identification with systemic classification. Genotypic profiling of the isolates includes fingerprint or pattern-based technique and sequence-based technique. Understanding community structure and dynamics is essential for studying diversity profiles and is challenging in the case of microbial analysis. The present study aims to understand the bacterial community composition from different heavy oil contaminated soil samples collected from geographically related oil well areas in Oman and to identify spore-forming hydrocarbon utilizing cultivable bacteria. V4 region of 16S rDNA gene was the target for Ion PGM™. A total of 825081 raw sequences were obtained from Ion torrent from all the 10 soil samples. The species richness and evenness were found to be moderate in all the samples with four main phyla, Firmicutes, Bacteroidetes, Proteobacteria, and Actinobacteria, the most abundant being Firmicutes. sp. ubiquitously dominated in all samples followed by , which was followed by , , and . Principal Coordinate Analysis (PCoA) and UPGMA dendrogram clustered the 10 soil samples into four main groups. Weighted UniFrac significance test determined that there was significant difference in the communities present in soil samples examined. It can be concluded that the microbial community was different in all the 10 soil samples with and sp. as predominating genus. The 16S rDNA sequencing of cultivable spore-forming bacteria identified the hydrocarbon utilizing bacteria as and sp. and the nucleotide sequences were submitted to NCBI GenBank under accession numbers KP119097-KP119115. and sp., which were relatively abundant in the oil fields, can be recommended to be chosen as candidates for hydrocarbon utilization study.
PubMed: 29755805
DOI: 10.1155/2018/9230143 -
Microorganisms Dec 2021Marine bacterial biomineralisation by CaCO precipitation provides natural limestone structures, like beachrocks and stromatolites. Calcareous deposits can also be...
Marine bacterial biomineralisation by CaCO precipitation provides natural limestone structures, like beachrocks and stromatolites. Calcareous deposits can also be abiotically formed in seawater at the surface of steel grids under cathodic polarisation. In this work, we showed that this mineral-rich alkaline environment harbours bacteria belonging to different genera able to induce CaCO precipitation. We previously isolated 14 biocalcifying marine bacteria from electrochemically formed calcareous deposits and their immediate environment. By microscopy and µ-Raman spectroscopy, these bacterial strains were shown to produce calcite-type CaCO. Identification by 16S rDNA sequencing provided between 98.5 and 100% identity with genera and . All 14 strains produced carbonic anhydrase, and six were urease positive. Both proteins are major enzymes involved in the biocalcification process. However, this does not preclude that one or more other metabolisms could also be involved in the process. In the presence of urea, CD6 exhibited the most efficient precipitation of CaCO. However, the urease pathway has the disadvantage of producing ammonia, a toxic molecule. We showed herein that different marine bacteria could induce CaCO precipitation without urea. These bacteria could then be used for eco-friendly applications, e.g., the formation of bio-cements to strengthen dikes and delay coastal erosion.
PubMed: 35056526
DOI: 10.3390/microorganisms10010076 -
PeerJ 2024Plastic waste is a global environmental issue that impacts the well-being of humans, animals, plants, and microorganisms. Microplastic contamination has been previously...
BACKGROUND
Plastic waste is a global environmental issue that impacts the well-being of humans, animals, plants, and microorganisms. Microplastic contamination has been previously reported at Kung Wiman Beach, located in Chanthaburi province along with the Eastern Gulf of Thailand. Our research aimed to study the microbial population of the sand and plastisphere and isolate microorganisms with potential plastic degradation activity.
METHODS
Plastic and sand samples were collected from Kung Wiman Beach for microbial isolation on agar plates. The plastic samples were identified by Fourier-transform infrared spectroscopy. Plastic degradation properties were evaluated by observing the halo zone on mineral salts medium (MSM) supplemented with emulsified plastics, including polystyrene (PS), polylactic acid (PLA), polyvinyl chloride (PVC), and bis (2-hydroxyethyl) terephthalate (BHET). Bacteria and fungi were identified by analyzing nucleotide sequence analysis of the 16S rRNA and internal transcribed spacer (ITS) regions, respectively. 16S and ITS microbiomes analysis was conducted on the total DNA extracted from each sample to assess the microbial communities.
RESULTS
Of 16 plastic samples, five were identified as polypropylene (PP), four as polystyrene (PS), four as polyethylene terephthalate (PET), two as high-density polyethylene (HDPE), and one sample remained unidentified. Only 27 bacterial and 38 fungal isolates were found to have the ability to degrade PLA or BHET on MSM agar. However, none showed degradation capabilities for PS or PVC on MSM agar. Notably, sp. PP5 showed the highest hydrolysis capacity of 1.64 ± 0.12. The 16S rRNA analysis revealed 13 bacterial genera, with seven showing plastic degradation abilities: , , , , , , and . This study reports, for the first time of the BHET-degrading properties of the genera and . Additionally, The ITS analysis identified nine fungal genera, five of which demonstrated plastic degradation abilities: , , , , and . Microbial community composition analysis and linear discriminant analysis effect size revealed certain dominant microbial groups in the plastic and sand samples that were absent under culture-dependent conditions. Furthermore, 16S and ITS amplicon microbiome analysis revealed microbial groups were significantly different in the plastic and sand samples collected.
CONCLUSIONS
We reported on the microbial communities found on the plastisphere at Kung Wiman Beach and isolated and identified microbes with the capacity to degrade PLA and BHET.
Topics: Actinomycetales; Agar; Bacteria; Microbiota; Plastics; Polyesters; Polystyrenes; RNA, Ribosomal, 16S; Sand
PubMed: 38590706
DOI: 10.7717/peerj.17165 -
PeerJ 2020Numerous bacteria entered the viable but non-culturable state due to the stresses of dry and salt in soils. YeaZ of Gram-negative bacteria is a resuscitation promoting...
Numerous bacteria entered the viable but non-culturable state due to the stresses of dry and salt in soils. YeaZ of Gram-negative bacteria is a resuscitation promoting factor (Rpf) homologous protein could resuscitate bacteria of natural environment in VBNC state. To investigate the promoting effect of YeaZ on the isolation of viable but non-culturable (VBNC) bacteria from soil samples in extreme environments, the recombinant YeaZ of was prepared and added to the soil samples from volcanic soil and saline soil in Northwest China. The study has shown that YeaZ can promote the recovery and growth of soil microorganisms, and the number of cultivable bacteria in volcanic and saline soil has increased from 0.17 × 10 and 2.03 × 10 cfu⋅ml to 1.00 × 10 and 5.55 × 10 cfu⋅ml, respectively. The 16S rDNA gene sequencing and phylogenetic analysis showed that YeaZ played an essential role in the increase of composition and diversity of bacteria. A total of 13 bacterial strains were isolated from the volcanic soil samples, which belong to phyla Actinobacteria, Firmicutes and Gamma-proteobacteria. Four species, including , , and were found in the control group, while , , , , and were isolated from the treatment groups (addition of YeaZ). Twenty-one strains were isolated from the saline soil samples, including eight species from the control group and thirteen species from the treatment groups, among which nine species were only found, including , , , , , , , and . The results suggest that addition of YeaZ to soil samples can promote the recovery of VBNC. This method has the implications for the discovery of VBNC bacteria that have potential environmental functions.
PubMed: 33391864
DOI: 10.7717/peerj.10342 -
Scientific Reports Mar 2021Dwarf bunt of wheat, which is caused by Tilletia controversa J.G. Kühn, is a soil-borne disease which may lead up to an 80% loss of yield together with degradation of...
Dwarf bunt of wheat, which is caused by Tilletia controversa J.G. Kühn, is a soil-borne disease which may lead up to an 80% loss of yield together with degradation of the quality of the wheat flour by production of a fishy smell. In this study, high-throughput sequencing technology was employed to characterize the microbial composition of wheat tissues (roots, spikes, first stem under the ear, and stem base) and rhizosphere soil of wheat varieties that are resistant and susceptible to T. controversa. We observed that the soil fungal community abundance and diversity were higher in resistant varieties than in susceptible varieties in both inoculated and uninoculated wheat, and the abundances of Sordariomycetes and Mortierellomycetes increased in the resistant varieties infected with T. controversa, while the abundances of Dothideomycetes and Bacteroidia increased in the susceptible varieties. Regarding the bacteria present in wheat tissues, the abundances of Chloroflexi, Bacteroidetes, Gemmatimonadetes, Verrucomicrobia and Acidobacteria in the ear and the first stem under the ear were higher than those in other tissues. Our results indicated that the abundances of Sordariomycetes, Mortierellomycetes, Leotiomycetes, Chryseobacterium and Massilia were higher in T. controversa-infected resistant varieties than in their controls, that Dothideomycetes, Bacteroidia, Nocardioides and Pseudomonas showed higher abundances in T. controversa-infected susceptible varieties, and that Curtobacterium, Exiguobacterium, Planococcus, and Pantoea may have higher abundances in both T. controversa-infected susceptible and resistant varieties than in their own controls.
Topics: Bacteria; Biodiversity; Endophytes; Fungi; Microbiota; Plant Diseases; Plant Leaves; Plant Roots; Plant Stems; Principal Component Analysis; Rhizosphere; Sequence Analysis, DNA; Soil Microbiology; Triticum
PubMed: 33707584
DOI: 10.1038/s41598-021-85281-8 -
International Journal of Systematic and... Mar 2024A novel bacterial strain, APC 4016, was previously isolated from the skin of a snub-nosed spiny eel, , from a depth of 1000 m in the northern Atlantic Ocean. Cells...
A novel bacterial strain, APC 4016, was previously isolated from the skin of a snub-nosed spiny eel, , from a depth of 1000 m in the northern Atlantic Ocean. Cells were aerobic, cocci, motile, Gram-positive to Gram-variable staining, and gave rise to orange-pigmented colonies. Growth occurred at 4-40 °C (optimum, 25-28 °C), pH 5.5-12 (optimum, pH 7-7.5), and 0-12 % (w/v) NaCl (optimum, 1 %). 16S rRNA gene phylogenetic analysis confirmed that strain APC 4016 belonged to the genus and was most closely related to IFO 12536 (98.98 % 16S similarity). However, digital DNA-DNA hybridization and average nucleotide identity values between these two strains were low, at 20.1 and 83.8 %, respectively. Major (>10 %) cellular fatty acids of strain APC 4016 were iso-C, anteiso-C and C-ω-Alc. The predominant respiratory quinones were menaquinones 5, 6, 7 and 8. The major cellular polar lipids were phosphatidylglycerol, diphosphatidylglycerol and phosphatidylethanolamine, and three unknown lipids were also present. The draft genome sequence is 3.6 Mb with a G+C content of 45.25 mol%. This strain was previously shown to have antimicrobial activity and to encode bacteriocin and secondary metabolite biosynthetic gene clusters. Based on the phylogenetic analysis and its distinct phenotypic characteristics, strain APC 4016 is deemed to represent a novel species of the genus , and for which the name sp. nov. is proposed. The type strain of this species is APC 4016 (=DSM 115753=NCIMB 15463).
Topics: Animals; Fatty Acids; Phospholipids; Phylogeny; RNA, Ribosomal, 16S; Sequence Analysis, DNA; Base Composition; Bacterial Typing Techniques; DNA, Bacterial; Planococcus Bacteria; Eels
PubMed: 38512752
DOI: 10.1099/ijsem.0.006298 -
International Journal of Environmental... Apr 2022Taking into consideration the essential contribution of farming, it is of rising importance to add knowledge regarding bacterial species occurrence in water samples...
Taking into consideration the essential contribution of farming, it is of rising importance to add knowledge regarding bacterial species occurrence in water samples from aquaculture zones from the point of view of both the organism and public health. In the present study, we investigated the bacterial community existing in water samples from six aquaculture areas in the Thermaikos gulf, northern Greece, that may provoke toxicity in aquatic organisms and humans and may indicate environmental pollution in mussel production as well as algal blooms. Bacterial species were identified molecularly by sequencing of a partial 16s rRNA segment and were analyzed phylogenetically for the confirmation of the bacterial taxonomy. The results obtained revealed the presence of four bacterial genera ( sp., sp., sp., and sp.). Members of the and genera have been isolated from highly polluted sites, bacteria have been identified in samples derived directly from plastic debris, and bacteria are in line with microcystin detection. In this context, the monitoring of the bacteria community in mussel aquaculture water samples from the Thermaikos gulf, the largest mussel cultivation area in Greece, represents an indicator of water pollution, microplastics presence, algal blooms, and toxin presence.
Topics: Animals; Cyanobacteria; Greece; Humans; Mytilus; Plastics; RNA, Ribosomal, 16S; Water; Water Pollution
PubMed: 35564680
DOI: 10.3390/ijerph19095285 -
International Journal of Microbiology 2023Zambia has seen rapid development in aquaculture, and in recent years, the industry has experienced disease outbreaks where fish have increasingly become a potential...
Zambia has seen rapid development in aquaculture, and in recent years, the industry has experienced disease outbreaks where fish have increasingly become a potential contributor to emerging bacterial zoonotic diseases. The aim of this study was to identify bacterial pathogens with zoonotic potential in apparently healthy fish and water from their habitat. A total of sixty-three fish were sampled, and fifty-nine water samples were collected from the habitats of these fish. Bacteria were cultured from the internal organs of fish and water, and these were identified through standard bacteriological methods comprising morphological characterization, Gram-staining, and a panel of biochemical tests. The following bacterial pathogens with zoonotic potential were identified at a farm prevalence of (13.2%), (2.1%), (2.1%), (0.7%), (6.9%), (2.1%), (0.7%), (18.1%), and (0.7). Other bacteria with varying significance as fish pathogens identified included (2.1%), (1.4%), (1.4%), (2.1%), (10.4%), (3.5%), (1.4%), (1.4%), (2.1%), (4.2%), (6.9%), (1.4%), (1.4%), (6.3%), (1.4%), (1.4%), (0.7%), and (0.7%). The current study provides baseline information for future reference and the implementation of public health guidelines with regard to potential zoonotic diseases in fish.
PubMed: 37333886
DOI: 10.1155/2023/6650378 -
Biotechnology Reports (Amsterdam,... Mar 2019Carotenoids are isoprenoid pigments used by pharmaceutical, cosmetic, food and feed industry as antioxidants and colorants. Although traditional sources of carotenoids...
Carotenoids are isoprenoid pigments used by pharmaceutical, cosmetic, food and feed industry as antioxidants and colorants. Although traditional sources of carotenoids are fruits, vegetables and chemical synthesis, prospecting for alternative sinks of common and/or unusual carotenoids is important for the development of natural carotenoid industry. In this work, 30 pigmented bacterial strains from Fildes Peninsula in King George Island, Antarctica, were isolated and identified by 16S rRNA gene sequencing and classified in three phyla, Bacteroidetes, Firmicutes and Actinobacteria. After cells extraction, ten different carotenoids were identified based on the chromatographic and spectroscopic characteristic obtained by HPLC-PDA and HPLC-PDA-APCI-MS analyses. Strains assigned to Bacteroidetes affiliated to and genera, presented a pigment profile composed of zeaxanthin, β-cryptoxanthin and β-carotene. Firmicutes strains of genus produced a C50 carotenoid, identified as C.p. 450 glucoside. Actinobacteria isolates were mainly assigned to genus, and few to and genera. strains produced C50 carotenoids such as decaprenoxanthin and its glucosylated derivatives, as well as some C40 carotenoids such as lycopene which is used as synthesis precursors of the C50 carotenoids. and genera produced C.p. 450 free form and its glucosylated derivatives. Although most isolates produce carotenoids similar in diversity and quantity than those already reported in the literature, novel sources for C50 carotenoids results from this work. According to their carotenoid content, all isolates could be promising candidates for carotenoids production.
PubMed: 30705834
DOI: 10.1016/j.btre.2019.e00306 -
MicrobiologyOpen Jun 2020Strain Y74 was an isolate from the sandy soil in the town of Huatugou, Qinghai-Tibet Plateau, China. An analysis of this strain's phenotypic, chemotaxonomic, and genomic...
Strain Y74 was an isolate from the sandy soil in the town of Huatugou, Qinghai-Tibet Plateau, China. An analysis of this strain's phenotypic, chemotaxonomic, and genomic characteristics established the relationship of the isolate with the genus Planococcus. Strain Y74 was able to grow between 4 and 42°C (with an optimum temperature of 28°C) at pH values of 6-8.5 and in 0%-7% (w/v) NaCl. The dominant quinones were MK-8 and MK-7. The polar lipids were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, and an unknown phospholipid. The majority of the fatty acid content was anteiso-C (28.8%) followed by C ω7c alcohol (20.9%) and iso-C (13.4%). The 16S rRNA gene sequence similarity analysis demonstrated a stable branch formed by strain Y74 and Planococcus halotolerans SCU63 (99.66%). The digital DNA-DNA hybridization between these two strains was 57.2%. The G + C content in the DNA of Y74 was 44.5 mol%. In addition, the morphological, physiological, and chemotaxonomic pattern clearly differentiated the isolates from their known relatives. In conclusion, the strain Y74 (=JCM 32826 = CICC24461 ) represents a novel member of the genus Planococcus, for which the name Planococcus antioxidans sp. nov. is proposed. Strain Y74 was found to have potent antioxidant activity via its hydrogen peroxide tolerance and its 1,1-diphenyl-2-picrylhydrazyl (DPPH) radical-scavenging activity. The DPPH radical-scavenging activity was determined to be 40.2 ± 0.7%. The genomic analysis indicated that six peroxidases genes, one superoxide dismutase gene, and one dprA (DNA-protecting protein) are present in the genome of Y74 .
Topics: Antioxidants; Bacterial Typing Techniques; Base Composition; DNA, Bacterial; Fatty Acids; Genome, Bacterial; Planococcus Bacteria; Sequence Analysis, DNA; Soil Microbiology; Tibet; Whole Genome Sequencing
PubMed: 32162498
DOI: 10.1002/mbo3.1028