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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 -
Astrobiology Sep 2018It is well known that dissolved salts can significantly lower the freezing point of water and thus extend habitability to subzero conditions. However, most...
It is well known that dissolved salts can significantly lower the freezing point of water and thus extend habitability to subzero conditions. However, most investigations thus far have focused on sodium chloride as a solute. In this study, we report on the survivability of the bacterial strain Planococcus halocryophilus in sodium, magnesium, and calcium chloride or perchlorate solutions at temperatures ranging from +25°C to -30°C. In addition, we determined the survival rates of P. halocryophilus when subjected to multiple freeze/thaw cycles. We found that cells suspended in chloride-containing samples have markedly increased survival rates compared with those in perchlorate-containing samples. In both cases, the survival rates increase with lower temperatures; however, this effect is more pronounced in chloride-containing samples. Furthermore, we found that higher salt concentrations increase survival rates when cells are subjected to freeze/thaw cycles. Our findings have important implications not only for the habitability of cold environments on Earth but also for extraterrestrial environments such as that of Mars, where cold brines might exist in the subsurface and perhaps even appear temporarily at the surface such as at recurring slope lineae.
Topics: Chlorides; Cold Temperature; Freezing; Microbial Viability; Osmolar Concentration; Perchlorates; Planococcus Bacteria; Salts; Water
PubMed: 29664686
DOI: 10.1089/ast.2017.1805 -
3 Biotech Jan 2018The aim of this study was to isolate bacteria from sea grass, collected from the coastal area of Jeddah, Saudi Arabia and to screen them for antifungal and enzymatic...
The aim of this study was to isolate bacteria from sea grass, collected from the coastal area of Jeddah, Saudi Arabia and to screen them for antifungal and enzymatic activities. We have isolated 162 rhizo and endophytic bacteria from soil, roots, and leaves of the sea grass. Antifungal screening of isolated bacteria revealed 19 strains (11.7%) capable to inhibit growth of four pathogenic fungi, , , and in an in vitro assay. Taxonomic and phylogenetic analyses on the basis of 16S rRNA gene sequence revealed 97-99.9% sequence identity to recognized species. , , and , within the Phylum Firmicutes, , , and (Actinobacteria), , , (α-Proteobacteria), and (γ-Proteobacteria), were isolated. Strains belong to Phylum Firmicutes remain dominant antagonistic bacteria in this study. Further hydrolytic enzyme production was determined for these antagonistic bacteria. Our results demonstrated that the sea grass represents an important source of diverse antagonistic bacteria capable of producing antifungal metabolite.
PubMed: 29354359
DOI: 10.1007/s13205-017-1066-1 -
ELife Aug 2017Gut bacteria occupy the interface between the organism and the external environment, contributing to homeostasis and disease. Yet, the causal role of the gut microbiota...
Gut bacteria occupy the interface between the organism and the external environment, contributing to homeostasis and disease. Yet, the causal role of the gut microbiota during host aging is largely unexplored. Here, using the African turquoise killifish (), a naturally short-lived vertebrate, we show that the gut microbiota plays a key role in modulating vertebrate life span. Recolonizing the gut of middle-age individuals with bacteria from young donors resulted in life span extension and delayed behavioral decline. This intervention prevented the decrease in microbial diversity associated with host aging and maintained a young-like gut bacterial community, characterized by overrepresentation of the key genera and . Our findings demonstrate that the natural microbial gut community of young individuals can causally induce long-lasting beneficial systemic effects that lead to life span extension in a vertebrate model.
Topics: Aging; Animals; Fundulidae; Gastrointestinal Microbiome; Gastrointestinal Tract; Longevity
PubMed: 28826469
DOI: 10.7554/eLife.27014 -
3 Biotech Jun 2017Microbial communities in hot springs at high elevations have been extensively studied worldwide. In this sense, the Indian Himalaya regions is valuable ecosystems for...
Microbial communities in hot springs at high elevations have been extensively studied worldwide. In this sense, the Indian Himalaya regions is valuable ecosystems for providing both the extreme 'cold' and 'hot' sites for exploring microbial diversity. In the present study, a total of 140 thermophilic bacteria were isolated from 12 samples collected from Manikaran and Yumthang hot springs of Indian Himalayas. The bacterial isolates were studied for phylogenetic profiling, growth properties at varying conditions and potential sources of extracellular thermostable hydrolytic enzymes such as protease, amylase, xylanase and cellulase. Based on production of extracellular hydrolases, 51 isolates from Manikaran (28) and Yumthang thermal springs (23) were selected and identified using 16S rRNA gene sequencing which included 37 distinct species of 14 different genera namely Anoxybacillus, Bacillus, Brevibacillus, Brevundimonas, Burkholderia, Geobacillus, Paenibacillus, Planococcus, Pseudomonas, Rhodanobacter, Thermoactinomyces, Thermobacillus, Thermonema and Thiobacillus. Out of 51 hydrolase producing bacteria, 24 isolates showed stability at wide range of temperature and pH treatments. In present investigation, three thermotolerant bacteria namely, Thermobacillus sp NBM6, Paenibacillus ehimensis NBM24 and Paenibacillus popilliae NBM68 were found to produced cellulase-free xylanase. These potential extracellular thermostable hydrolytic enzymes producing thermophilic bacteria have a great commercial prospect in various industrial, medical and agriculture applications.
PubMed: 28567630
DOI: 10.1007/s13205-017-0762-1 -
Scientific Reports Feb 2017Planococcus is a Gram-positive halotolerant bacterial genus in the phylum Firmicutes, commonly found in various habitats in Antarctica. Quorum quenching (QQ) is the...
Planococcus is a Gram-positive halotolerant bacterial genus in the phylum Firmicutes, commonly found in various habitats in Antarctica. Quorum quenching (QQ) is the disruption of bacterial cell-to-cell communication (known as quorum sensing), which has previously been described in mesophilic bacteria. This study demonstrated the QQ activity of a psychrotolerant strain, Planococcus versutus strain L10.15, isolated from a soil sample obtained near an elephant seal wallow in Antarctica. Whole genome analysis of this bacterial strain revealed the presence of an N-acyl homoserine lactonase, an enzyme that hydrolyzes the ester bond of the homoserine lactone of N-acyl homoserine lactone (AHLs). Heterologous gene expression in E. coli confirmed its functions for hydrolysis of AHLs, and the gene was designated as aidP (autoinducer degrading gene from Planococcus sp.). The low temperature activity of this enzyme suggested that it is a novel and uncharacterized class of AHL lactonase. This study is the first report on QQ activity of bacteria isolated from the polar regions.
Topics: 4-Butyrolactone; Amino Acid Sequence; Bacterial Proteins; Carboxylic Ester Hydrolases; Escherichia coli; Phylogeny; Planococcus Bacteria; Quorum Sensing; Sequence Alignment
PubMed: 28225085
DOI: 10.1038/srep42968 -
Journal of Industrial Microbiology &... Jun 2017A recently developed rapid co-composting of oil palm empty fruit bunch (OPEFB) and palm oil mill effluent (POME) anaerobic sludge is beginning to attract attention from...
A recently developed rapid co-composting of oil palm empty fruit bunch (OPEFB) and palm oil mill effluent (POME) anaerobic sludge is beginning to attract attention from the palm oil industry in managing the disposal of these wastes. However, a deeper understanding of microbial diversity is required for the sustainable practice of the co-compositing process. In this study, an in-depth assessment of bacterial community succession at different stages of the pilot scale co-composting of OPEFB-POME anaerobic sludge was performed using 454-pyrosequencing, which was then correlated with the changes of physicochemical properties including temperature, oxygen level and moisture content. Approximately 58,122 of 16S rRNA gene amplicons with more than 500 operational taxonomy units (OTUs) were obtained. Alpha diversity and principal component analysis (PCoA) indicated that bacterial diversity and distributions were most influenced by the physicochemical properties of the co-composting stages, which showed remarkable shifts of dominant species throughout the process. Species related to Devosia yakushimensis and Desemzia incerta are shown to emerge as dominant bacteria in the thermophilic stage, while Planococcus rifietoensis correlated best with the later stage of co-composting. This study proved the bacterial community shifts in the co-composting stages corresponded with the changes of the physicochemical properties, and may, therefore, be useful in monitoring the progress of co-composting and compost maturity.
Topics: Bacteria; Biodiversity; Composting; Fruit; Industrial Waste; Palm Oil; RNA, Ribosomal, 16S; Sewage
PubMed: 28197796
DOI: 10.1007/s10295-017-1916-1 -
The ISME Journal Mar 2017Mealybugs (Insecta: Hemiptera: Pseudococcidae) maintain obligatory relationships with bacterial symbionts, which provide essential nutrients to their insect hosts. Most...
Mealybugs (Insecta: Hemiptera: Pseudococcidae) maintain obligatory relationships with bacterial symbionts, which provide essential nutrients to their insect hosts. Most pseudococcinae mealybugs harbor a unique symbiosis setup with enlarged betaproteobacterial symbionts ('Candidatus Tremblaya princeps'), which themselves contain gammaproteobacterial symbionts. Here we investigated the symbiosis of the manna mealybug, Trabutina mannipara, using a metagenomic approach. Phylogenetic analyses revealed that the intrabacterial symbiont of T. mannipara represents a novel lineage within the Gammaproteobacteria, for which we propose the tentative name 'Candidatus Trabutinella endobia'. Combining our results with previous data available for the nested symbiosis of the citrus mealybug Planococcus citri, we show that synthesis of essential amino acids and vitamins and translation-related functions partition between the symbiotic partners in a highly similar manner in the two systems, despite the distinct evolutionary origin of the intrabacterial symbionts. Bacterial genes found in both mealybug genomes and complementing missing functions in both symbioses were likely integrated in ancestral mealybugs before T. mannipara and P. citri diversified. The high level of correspondence between the two mealybug systems and their highly intertwined metabolic pathways are unprecedented. Our work contributes to a better understanding of the only known intracellular symbiosis between two bacteria and suggests that the evolution of this unique symbiosis included the replacement of intrabacterial symbionts in ancestral mealybugs.
Topics: Animals; Bacteria; Betaproteobacteria; Biological Evolution; Gammaproteobacteria; Hemiptera; Symbiosis
PubMed: 27983719
DOI: 10.1038/ismej.2016.148 -
International Journal of Systematic and... Apr 2017A taxonomic study was performed on a novel Gram-stain-positive, coccus-shaped, orange-pigmented motile bacterium, designated as strain L10.15. The organism was isolated...
A taxonomic study was performed on a novel Gram-stain-positive, coccus-shaped, orange-pigmented motile bacterium, designated as strain L10.15. The organism was isolated from a soil sample collected in Lagoon Island (close to Adelaide Island, western Antarctic Peninsula) using a quorum-quenching enrichment medium. Growth occurred at 4-30 °C, pH 6-11 and at moderately high salinity (0-15 %, w/v, NaCl), with optimal growth at 26 °C, at pH 7-8 and with 6 % (w/v) NaCl. 16S rRNA gene sequence analysis showed that strain L10.15 belonged to the genus Planococcus and was closely related to Planococcus halocryophilus Or1 (99.3 % similarity), Planococcus donghaensis JH1 (99.0 %), Planococcus antarcticus DSM 14505 (98.3 %), Planococcus plakortidis AS/ASP6 (II) (97.6 %), Planococcus maritimus TF-9 (97.5 %), Planococcus salinarum ISL-6 (97.5 %) and Planococcus kocurii NCIMB 629 (97.5 %). However, the average nucleotide identity-MUMmer analysis showed low genomic relatedness values of 71.1-81.7 % to the type strains of these closely related species of the genus Planococcus. The principal fatty acids were anteiso-C15 : 0, C16 : 1ω7c and anteiso-C17 : 0, and the major menaquinones of strain L10.15 were MK-5 (48 %), MK-6 (6 %) and MK-7 (44 %). Polar lipid analysis revealed the presence of phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol and aminophospholipid. The DNA G+C content was 39.4 mol%. The phenotypic and genotypic data indicate that strain L10.15 represents a novel species of the genus Planococcus, for which the name Planococcus versutus sp. nov. is proposed. The type strain is L10.15 (=DSM 101994=KACC 18918).
Topics: Antarctic Regions; Bacterial Typing Techniques; Base Composition; DNA, Bacterial; Fatty Acids; Nucleic Acid Hybridization; Phospholipids; Phylogeny; Planococcus Bacteria; RNA, Ribosomal, 16S; Sequence Analysis, DNA; Soil Microbiology; Ubiquinone; Vitamin K 2
PubMed: 27959786
DOI: 10.1099/ijsem.0.001721 -
Frontiers in Microbiology 2016Pseudo-nitzschia blooms often occur in coastal and open ocean environments, sometimes leading to the production of the neurotoxin domoic acid that can cause severe...
Pseudo-nitzschia blooms often occur in coastal and open ocean environments, sometimes leading to the production of the neurotoxin domoic acid that can cause severe negative impacts to higher trophic levels. Increasing evidence suggests a close relationship between phytoplankton bloom and bacterial assemblages, however, the microbial composition and succession during a bloom process is unknown. Here, we investigate the bacterial assemblages before, during and after toxic and non-toxic Pseudo-nitzschia blooms to determine the patterns of bacterial succession in a natural bloom setting. Opportunistic sampling of bacterial community profiles were determined weekly at Santa Cruz Municipal Wharf by 454 pyrosequencing and analyzed together with domoic acid levels, phytoplankton community and biomass, nutrients and temperature. We asked if the bacterial communities are similar between bloom and non-bloom events and if domoic acid or the presence of toxic algal species acts as a driving force that can significantly structure phytoplankton-associated bacterial communities. We found that bacterial diversity generally increases when Pseudo-nitzschia numbers decline. Furthermore, bacterial diversity is higher when the low-DA producing P. fraudulenta dominates the algal bloom while bacterial diversity is lower when high-DA producing P. australis dominates the algal bloom, suggesting that the presence of algal toxin can structure bacterial community. We also found bloom-related succession patterns among associated bacterial groups; Gamma-proteobacteria, were dominant during low toxic P. fraudulenta blooms comprising mostly of Vibrio spp., which increased in relative abundance (6-65%) as the bloom progresses. On the other hand, Firmicutes bacteria comprising mostly of Planococcus spp. (12-86%) dominate during high toxic P. australis blooms, with the bacterial assemblage showing the same bloom-related successional patterns in three independent bloom events. Other environmental variables such as nitrate and phosphate and temperature appear to influence some low abundant bacterial groups as well. Our results suggest that phytoplankton-associated bacterial communities are strongly affected not just by phytoplankton bloom in general, but also by the type of algal species that dominates in the natural bloom.
PubMed: 27672385
DOI: 10.3389/fmicb.2016.01433