scholarly journals Exploring the Bacterial Communities of Infernaccio Waterfalls: A Phenotypic and Molecular Characterization of Acinetobacter and Pseudomonas Strains Living in a Red Epilithic Biofilm

Diversity ◽  
2019 ◽  
Vol 11 (10) ◽  
pp. 175 ◽  
Author(s):  
Carolina Chiellini ◽  
Sofia Chioccioli ◽  
Alberto Vassallo ◽  
Stefano Mocali ◽  
Elisangela Miceli ◽  
...  
Keyword(s):  
Heavy Metals ◽  
Bacterial Communities ◽  
High Throughput Sequencing ◽  
Rapd Analysis ◽  
Environmental Pollutants ◽  
Biotechnological Applications ◽  
Bacterial Strains ◽  
Bacterial Composition ◽  
Cultivable Bacteria

Acquarossa river (Viterbo, Italy) was the site of a prospering Etruscan civilization thanks to metallurgical activity around 625–550 B.C. This caused the spread of heavy metals throughout the area. Rocks along the river probably act as a filter for these elements and they are covered by two different biofilms (epilithons). They differ for both color and bacterial composition. One is red and is enriched with Pseudomonas strains, while the other one is black and Acinetobacter is the most represented genus. Along the river lay the Infernaccio waterfalls, whose surrounding rocks are covered only by the red epilithon. The bacterial composition of this biofilm was analyzed through high throughput sequencing and compared to those ones of red and black epilithons of Acquarossa river. Moreover, cultivable bacteria were isolated and their phenotype (i.e., resistance against antibiotics and heavy metals) was studied. As previously observed in the case of Acquarossa river, characterization of bacterial composition of the Infernaccio red epilithon revealed that the two most represented genera were Acinetobacter and Pseudomonas. Nonetheless, these strains differed from those isolated from Acquarossa, as revealed by RAPD analysis. This work, besides increasing knowledge about the ecological properties of this site, allowed to isolate new bacterial strains, which could potentially be exploited for biotechnological applications, because of their resistance against environmental pollutants.

scholarly journals New Insights on the Zeugodacus cucurbitae (Coquillett) Bacteriome

2021 ◽  
Vol 9 (3) ◽  
pp. 659
Author(s):  
Elias Asimakis ◽  
Panagiota Stathopoulou ◽  
Apostolis Sapounas ◽  
Kanjana Khaeso ◽  
Costas Batargias ◽  
...  
Keyword(s):  
Relative Abundance ◽  
Bacterial Communities ◽  
High Throughput Sequencing ◽  
Mutual Exclusion ◽  
Bacterial Composition ◽  
Operational Taxonomic Units ◽  
Host Diet ◽  
Dominant Bacteria ◽  
High Degree

Various factors, including the insect host, diet, and surrounding ecosystem can shape the structure of the bacterial communities of insects. We have employed next generation, high-throughput sequencing of the 16S rRNA to characterize the bacteriome of wild Zeugodacus (Bactrocera) cucurbitae (Coquillett) flies from three regions of Bangladesh. The tested populations developed distinct bacterial communities with differences in bacterial composition, suggesting that geography has an impact on the fly bacteriome. The dominant bacteria belonged to the families Enterobacteriaceae, Dysgomonadaceae and Orbaceae, with the genera Dysgonomonas, Orbus and Citrobacter showing the highest relative abundance across populations. Network analysis indicated variable interactions between operational taxonomic units (OTUs), with cases of mutual exclusion and copresence. Certain bacterial genera with high relative abundance were also characterized by a high degree of interactions. Interestingly, genera with a low relative abundance like Shimwellia, Gilliamella, and Chishuiella were among those that showed abundant interactions, suggesting that they are also important components of the bacterial community. Such knowledge could help us identify ideal wild populations for domestication in the context of the sterile insect technique or similar biotechnological methods. Further characterization of this bacterial diversity with transcriptomic and metabolic approaches, could also reveal their specific role in Z. cucurbitae physiology.

Isolation and characterization of heavy metal tolerant Gram-positive bacteria with bioremedial properties from municipal waste rich soil of Kestopur canal (Kolkata), West Bengal, India

Biologia ◽  
2012 ◽  
Vol 67 (5) ◽  
Author(s):  
Kamala Gupta ◽  
Chitrita Chatterjee ◽  
Bhaskar Gupta
Keyword(s):  
Heavy Metals ◽  
Heavy Metal ◽  
Metal Tolerance ◽  
Environmental Pollutants ◽  
Heavy Metal Tolerance ◽  
Antibiotic Sensitivity ◽  
Bacterial Strains ◽  
High Concentration ◽  
Isolation And Characterization ◽  
Bacillus Weihenstephanensis

AbstractThe present study was conducted to determine the culturable bacterial profile from Kestopur canal (Kolkata, India) and analyze their heavy metal tolerance. In addition to daily sewage including solid and soluble wastes, a considerable load of toxic metals are released into this water body from industries, tanneries and agriculture, household as well as health sectors. Screening out microbes from such an environment was done keeping in mind their multifunctional application especially for bioremediation. Heavy metals are major environmental pollutants when present in high concentration in soil and show potential toxic effects on growth and development in plants and animals. Some edible herbs growing in the canal vicinity, and consumed by people, were found to harbour these heavy metals at sub-toxic levels. The bioconcentration factor of these plants being <1 indicates that they probably only absorb but not accumulate heavy metals. All the thirteen Grampositive bacteria isolated from these plants rhizosphere were found to tolerate high concentration of heavy metals like Co, Ni, Pb, Cr, Fe. Phylogenetic analysis of their 16S rDNA genes revealed that they belonged to one main taxonomic group — the Firmicutes. Seven of them were found to be novel with 92–95% sequence homology with known bacterial strains. Further microbiological analyses show that the alkaliphilic Bacillus weihenstephanensis strain IA1 and Exiguobacterium aestuarii strain CE1, with selective antibiotic sensitivity along with high Ni2+ and Cr6+ removal capabilities, respectively, can be prospective candidates for bioremediation.

scholarly journals Culture-independent analysis of the bacterial communities in Chinese fermented vegetables and genomic analysis of lactic acid bacteria

2021 ◽  
Author(s):  
Jianming Zhang ◽  
Hye Seon Song ◽  
Chengcheng Zhang ◽  
Yeon Bee Kim ◽  
Seong Woon Roh ◽  
...  
Keyword(s):  
Lactic Acid ◽  
Lactic Acid Bacteria ◽  
Bacterial Communities ◽  
High Throughput Sequencing ◽  
Rrna Gene ◽  
Bacterial Strains ◽  
Whole Genome Analysis ◽  
Sequencing Platform ◽  
Tuber Mustard ◽  
Fermented Vegetables

Abstract Six different fermented vegetables were collected from Zhejiang Province, China, to explore the associated bacterial communities using a high-throughput sequencing platform. A total of 24 phyla, 274 families and 569 genera were identified from six samples. Firmicutes and Proteobacteria were the main phyla in all of samples. Meanwhile, Brevibacterium was the major genus in Xiaoshan pickled radish. Lactobacillus-related genera and Vibrio were the major genera in fermented potherb mustard and its brine. Enterobacter and Cobetia were the major genera in fermented radish and its brine. Chromohalobacter was the major genus in the tuber mustard. These results indicated there were clear differences between the bacterial genera present in Xiaoshan pickled radish, fermented potherb mustard, fermented radish, and tuber mustard. This demonstrated the possible influences of raw materials and manufacturing processes. Furthermore, a large number of lactic acid bacteria were isolated and identified by culture-dependent and 16S rRNA gene sequence analysis, which accounted for more than 68% of all the isolates. In addition, whole genome analysis of Lactobacillus suantsaii, Lactobacillus sakei subsp. sakei, and Weissella cibaria showed they had large numbers of genes associated with carbohydrate metabolism. This may explain why these three bacterial strains can grow in fermented vegetable environments.

scholarly journals Cultivatable bacterial community at a fresh water nullah contaminated with household sewage and industrial waste is more diverse and populated compared to non-polluted water

2021 ◽  
Author(s):  
Wishal Khan ◽  
Sobia Yaseen ◽  
Abdul Waheed ◽  
Zuhair Hasnain ◽  
Zahra Jabeen ◽  
...  
Keyword(s):  
Heavy Metals ◽  
Bacterial Community ◽  
Bacterial Community Composition ◽  
Environmental Pollutants ◽  
Oxygen Demand ◽  
Polluted Water ◽  
Rrna Gene ◽  
Bacterial Strains ◽  
Broth Microdilution Method ◽  
Acinetobacter Guillouiae

The effect of environmental pollutants on living organisms can be assessed by studying the changes in the indigenous microbial community. Therefore, in the present study, cultivatable bacterial community in non-polluted as well as household sewage and industrially polluted water of Lai Nullah flowing through Islamabad-Rawalpindi, Pakistan was analysed. Bacterial community composition and population present in the polluted water was significantly different from the non-polluted water (P < 0.05). Non-polluted water had much fewer species and population of bacteria compared to polluted water. Sequence analysis of bacterial 16S rRNA gene revealed that Citrobacter freundii, Klebsiella pneumoniae, Escherichia coli, Lactobacillus plantarum, Geobacillus stearothermophilus, Enterococcus faecalis, Acinetobacter guillouiae, Ralstonia sp., Comamonas sp. and Stenotrophomonas maltophilia were specific to the polluted water. On the other hand, Aeromonas veronii, Exiguobacterium sp. and Lysinibacillus macroides were only found in the non-polluted water. Among measured physicochemical parameters, higher colony count in the polluted water was best correlated with higher biological oxygen demand, phosphate, sodium and chloride values (Spearman's rho = 0.85). Concentration of heavy metals such as cadmium, chromium, copper, nickel and lead were below 0.03μg/mL at all the study sites. During plate assay, bacterial strains found at polluted sites showed resistance to selected heavy metals with highest minimum inhibitory concentration for lead (8mM) followed by copper (5mM), nickel (3mM) and cadmium (1mM). All the bacterial isolates also showed various levels of resistance against antibiotics ampicillin, tetracycline, ciprofloxacin and vancomycin using broth microdilution method. Current research provides new insight into the effect of household sewage and industrially polluted water of Lai Nullah on the indigenous bacteria".

scholarly journals Characterization of Bacterial Communities in Mexican Artisanal Raw Milk “Bola de Ocosingo” Cheese by High-Throughput Sequencing

2018 ◽  
Vol 9 ◽  
Author(s):  
Alejandro Aldrete-Tapia ◽  
Claudia Meyli Escobar-Ramírez ◽  
Mark L. Tamplin ◽  
Montserrat Hernández-Iturriaga
Keyword(s):  
High Throughput ◽  
Bacterial Communities ◽  
High Throughput Sequencing ◽  
Raw Milk

scholarly journals Effects of a Bioprocessed Soybean Meal Ingredient on the Intestinal Microbiota of Hybrid Striped Bass, Morone chrysops x M. saxatilis

2021 ◽  
Vol 9 (5) ◽  
pp. 1032
Author(s):  
Emily Celeste Fowler ◽  
Prakash Poudel ◽  
Brandon White ◽  
Benoit St-Pierre ◽  
Michael Brown
Keyword(s):  
Striped Bass ◽  
Soybean Meal ◽  
Bacterial Communities ◽  
High Throughput Sequencing ◽  
Rrna Gene ◽  
Hybrid Striped Bass ◽  
Bacterial Composition ◽  
Morone Chrysops ◽  
Fish Diets ◽  
Significant Difference

The hybrid striped bass (Morone chrysops x M. saxatilis) is a carnivorous species and a major product of US aquaculture. To reduce costs and improve resource sustainability, traditional ingredients used in fish diets are becoming more broadly replaced by plant-based products; however, plant meals can be problematic for carnivorous fish. Bioprocessing has improved nutritional quality and allowed higher inclusions in fish diets, but these could potentially affect other systems such as the gut microbiome. In this context, the effects of bioprocessed soybean meal on the intestinal bacterial composition in hybrid striped bass were investigated. Using high-throughput sequencing of amplicons targeting the V1–V3 region of the 16S rRNA gene, no significant difference in bacterial composition was observed between fish fed a control diet, and fish fed a diet with the base bioprocessed soybean meal. The prominent Operational Taxonomic Unit (OTU) in these samples was predicted to be a novel species affiliated to Peptostreptococcaceae. In contrast, the intestinal bacterial communities of fish fed bioprocessed soybean meal that had been further modified after fermentation exhibited lower alpha diversity (p < 0.05), as well as distinct and more varied composition patterns, with OTUs predicted to be strains of Lactococcus lactis, Plesiomonas shigelloides, or Ralstonia pickettii being the most dominant. Together, these results suggest that compounds in bioprocessed soybean meal can affect intestinal bacterial communities in hybrid striped bass.

scholarly journals Bacterial diversity in high Andean grassland soils disturbed with Lepidium meyenii crops evaluated by metagenomics

2022 ◽  
Vol 82 ◽  
Author(s):  
F. Huaraca-Meza ◽  
M. Custodio ◽  
R. Peñaloza ◽  
J. Alvarado-Ibañez ◽  
R. Paredes ◽  
...  
Keyword(s):  
Bacterial Diversity ◽  
Bacterial Communities ◽  
Specific Pattern ◽  
Metagenomic Sequencing ◽  
Grassland Soils ◽  
Bacterial Composition ◽  
Lepidium Meyenii ◽  
Crop Development ◽  
Poverty Indicators

Abstract Soil quality is usually determined by its physical-chemical characteristics without taking into account the bacterial communities that play a fundamental role in the chemical decomposition of plant nutrients. In this context, the objective of the study was to evaluate bacterial diversity in high Andean grassland soils disturbed with Lepidium meyenii cultivation under different gradients of use (first, second and third use) and crop development (pre-sowing, hypocotyl development and post-harvest). The sampling was carried out in the Bombón plateau in the central Andes of Peru, during the rainy and low water seasons, by the systematic method based on a specific pattern assigned in a geometric rectangular shape at a depth of 0 - 20 cm. The characterization of the bacterial communities was carried out through the metagenomic sequencing of the 16S rRNA. 376 families of bacteria were reported, of which it was determined that there was a significant change in bacterial composition and distribution in relation to use pressure. There were no major changes due to the development of Lepidium meyenii. The families most sensitive to use pressure and soil poverty indicators were Verrucomicrobiaceae, Acidobacteraceae and Aakkermansiaceae.

scholarly journals Variations in gut bacterial communities of hooded crane (Grus monacha) over spatial-temporal scales

PeerJ ◽  
2019 ◽  
Vol 7 ◽  
pp. e7045 ◽  
Author(s):  
Yuanqiu Dong ◽  
Xingjia Xiang ◽  
Guanghong Zhao ◽  
Yunwei Song ◽  
Lizhi Zhou
Keyword(s):  
Bacterial Community ◽  
Bacterial Communities ◽  
Seasonal Changes ◽  
High Throughput Sequencing ◽  
Bacterial Composition ◽  
Gut Microbe ◽  
Host Life ◽  
Internal And External Factors ◽  
Gut Microbial Community ◽  
Grus Monacha

BackgroundMicrobes have been recognized as important symbionts to regulate host life. The animal gut harbors abundance and diverse bacteria. Numerous internal and external factors influence intestinal bacterial communities, including diet, seasonal fluctuations and habitat sites. However, the factors that influence the gut bacterial communities of wild bird is poorly characterized.MethodsBy high-throughput sequencing and statistical analysis, we investigated the variations in gut bacterial communities of the hooded cranes at three wintering stages in Caizi (CZL) and Shengjin Lake (SJL), which are two shallow lakes in the middle and lower Yangtze River floodplain.ResultsOur results revealed significant differences in gut bacterial community structure and diversity among different sampling sites and wintering stages. Seasonal changes have a significant impact on the gut microbe composition of hooded cranes in the two lakes. ANOSIM analysis demonstrated that the samples in CZL had greater differences in the gut bacterial composition than that in SJL. Our data showed strong evidence that the host’s gut filtering might be an important factor in shaping bacterial community according to mean nearest taxon distance (MNTD). The PICRUSt analysis showed that the predicted metagenomes associated with the gut microbiome were carbohydrate metabolism, amino acid metabolism and energy metabolism over the entire wintering period at the two lakes.ConclusionsThe results demonstrated that both seasonal changes and habitat sites have significant impact on the gut bacterial communities of hooded cranes. In addition, predictive function of gut microbes in hooded cranes varied over time. These results provide new insights into the gut microbial community of the cranes, which serves as a foundation for future studies.

scholarly journals Antibiotic and metal resistance of cultivable bacteria in the Antarctic sea urchin

2016 ◽  
Vol 28 (4) ◽  
pp. 261-268 ◽  
Author(s):  
M. González-Aravena ◽  
R. Urtubia ◽  
K. Del Campo ◽  
P. Lavín ◽  
C.M.V.L. Wong ◽  
...  
Keyword(s):  
Heavy Metals ◽  
Antibiotic Resistance ◽  
Sea Urchin ◽  
Sea Urchins ◽  
Antibiotic Resistance Genes ◽  
Metal Resistance ◽  
Coelomic Fluid ◽  
Bacterial Strains ◽  
Cultivable Bacteria ◽  
The Antarctic

AbstractIn this paper we report the first characterization of cultivable bacteria obtained from the Antarctic sea urchinSterechinus neumayeri. The coelomic fluid was obtained from a pool of sea urchins which was plated onto different media to isolate the bacteria. A total of 42 isolates of psychrotrophic and aerobic γ-Proteobacteria (59.5%), Flavobacteria (33.3%) and Actinomycetes (7.2%) were isolated and sequenced. These bacteria were exposed to heavy metals and antibiotics, where 38 strains were analysed by the minimal inhibitory concentration method. Antibiotic resistance was detected in 44% of cultivable strains, and a further 13% presented co-resistance to antibiotics and heavy metals. The genera of bacteria that showed an increased resistance and co-resistance to metals and antibiotics wereFlavobacterium,PsychrobacterandPseudomonas. Additionally, 30.9% of isolated bacterial strains contained plasmids, which are probably related to resistance and co-resistance to metals. These results indicate that sea urchin-associated bacteria could be reservoirs for antibiotic resistance genes.

Sign in / Sign up

Export Citation Format

Share Document