Assessment Of Bacterial Diversity Research Articles

Staphylococcus aureus Isolated From Traditional Artisanal Raw Milk Cheese from Southern Brazil: Diversity, Virulence, and Antimicrobial Resistance Profile

Staphylococcus aureus is one of the primary pathogenic agents found in cheeses produced with raw milk. Some strains of S. aureus are enterotoxigenic, possessing the ability to produce toxins responsible for staphylococcal food poisoning when present in contaminated foods. This study aimed to genotypically characterize, assess the antimicrobial resistance profile, and examine the enterotoxigenic potential of strains of S. aureus isolated from artisanal colonial cheese. Additionally, a bacterial diversity assessment in the cheeses was conducted by sequencing the 16S rRNA gene. The metataxomic profile revealed the presence of 68 distinct species in the cheese samples. Fifty-seven isolates of S. aureus were identified, with highlighted resistance to penicillin in 33% of the isolates, followed by clindamycin (28%), erythromycin (26%), and tetracycline (23%). The evaluated strains also exhibited inducible resistance to clindamycin, with nine isolates considered multidrug-resistant (MDR). The agr type I was the most prevalent (62%) among the isolates, followed by agr type II (24%). Additionally, ten spa types were identified. Although no enterotoxins and their associated genes were detected in the samples and isolates, respectively, the Panton-Valentine leukocidin gene (lukS-lukF) was found in 39% of the isolates. The presence of MDR pathogens in the artisanal raw milk cheese production chain underscores the need for quality management to prevent the contamination and dissemination of S. aureus strains.

The assessment of bacterial diversity in CO2 treated and untreated raw milk during cold storage using high‐throughput sequencing technology

SummaryCarbon dioxide (CO2) has the potential to extend the storage time of raw milk, but its industrial application in this regard has not been thoroughly explored. This study aimed to investigate the microflora of CO2‐treated and untreated raw milk from South China using Illumina sequencing. The sequencing results confirmed the presence of Delftia, Pseudomonas and Serratia as the main spoilage species in raw cow milk from South China. However, CO2 treatment was found to selectively inhibit the growth of these spoilage bacteria. Principal coordinate analysis revealed differences in the microbiota structures of samples collected from the Fuyi and Guanyuan sites. Additionally, a total of 119 and 120 bacterial species were identified in the Fuyi and Guanyuan samples, respectively. The spoilage of raw milk from the Fuyi and Guanyuan was delayed by 7 and 19 days, respectively, with the application of CO2 treatment. Conversely, the samples without CO2 treatment were found to be contaminated with Pseudomonas fluorescens and Serratia. Moreover, the CO2‐treated samples from the Fuyi and Guanyuan ranches exhibited a different composition of spoilage bacteria, with a significant increase in the number of lactic acid bacteria (LAB) compared to the control samples. This study suggests that LAB have a remarkable tolerance to CO2, which is consistent with their selection in fruit, vegetable and meat products stored in CO2‐enriched modified atmosphere packaging. The findings of this study provide a foundation for further exploration of the potential application of CO2 treatment in raw milk processing.

Assessment of bacterial diversity in the chicken litter: A potent risk to environmental health

Using chicken litter as an organic fertilizer on land is the most common, cheapest and environmentally safest way to manage the latter generated swiftly from the poultry industry. Raw chicken litter has been applied to field soils where various vegetables are cropped to increase yield or productivity. However, the chicken litter frequently come in contact with different environments, such as water, soil, microbes and vegetation. When chickens defecate, their litters, in a few countries, are particularly reused for the next flock, potentially causing cross-contamination. Due to various contact points in the environment, a high probability of bacterial transmission is predicted, which could lead to infection spread in animals and humans. Consumption of contaminated water, food, and meat could lead to the transmission of deadly infections. Microbes in the chicken litter also affect the grazing animals while feeding on fields duly applied with chicken litter as manure. The maximum permissible limits (MPLs) in the chicken litter for land application should not exceed 106-108 CFU/g for Coliform bacteria. Antibiotics are regularly mixed in the diet or drinking water of chicken grown in marketable poultry farms for treating bacterial diseases. Rampant usage of antimicrobials also results in resistant bacteria's survival in animal excreta. Herein, we surveyed the literature to identify the major bacterial genus harboured in the fields applied with chicken manure to increase soil fertility. Our detailed survey identified different bacterial pathogens from chicken litter samples from different investigations. Most studies showed the prevalence of Campylobacter, Salmonella, Enterococcus, E. coli, Bacillus, Comamonas, Proteus and Citrobacter, including many other bacterial species in the chicken litter samples. This article suggested that chicken litter does not meet the standard parameters for direct application as organic fertilizer in the fields. Before being applied to the ground, chicken litter should be treated to lessen the danger of polluting crops or water supplies by reducing the prevalence of harmful bacteria carrying antibiotic-resistance genes.

Comparative assessment of bacterial diversity and composition in arsenic hyperaccumulator, Pteris vittata L. and non-accumulator, Pteris ensiformis Burm

The use of arsenic (As) for various industrial and agricultural applications has led to worldwide environmental contamination. Phytoremediation using hyperaccumulators is a sustainable soil As mitigation strategy. Microbial processes play an important role in the tolerance and uptake of trace elements such as in plants. The rhizospheric and endophytic microbial communities are responsible for accelerating the mobility of trace elements around the roots and the production of plant growth-promoting compounds and enzymes. Several studies have reported that the As hyperaccumulator, Pteris vittata L. (PV) influences the microbial community in its rhizosphere and roots. Deciphering the differences in the microbiomes of hyperaccumulators and non-accumulators is crucial in understanding the mechanism of hyperaccumulation. We hypothesized that there are significant differences in the microbiome of roots, rhizospheric soil, and bulk soil between the hyperaccumulator PV and a non-accumulator of the same genus, Pteris ensiformis Burm. (PE), and that the differential recruitment of bacterial communities provides PV with an advantage in As contaminated soil. We compared root endophytic, rhizospheric, and bulk soil microbial communities between PV and PE species grown in As-contaminated soil in a greenhouse setting. There was a significant difference (p < 0.001) in the microbiome of the three compartments between the ferns. Differential abundance analysis showed 328 Amplicon Sequence Variants (ASVs) enriched in PV compared to 172 in PE. The bulk and rhizospheric soil of both ferns were abundant in As-resistant genera. However, As-tolerant root endophytic genera were present in PV but absent in PE. Our findings show that there is a difference between the bacterial composition of an As hyperaccumulator and a non-accumulator species grown in As-contaminated soil. These differences need to be further explored to develop strategies for improving the efficiency of metal uptake in plants growing in As polluted soil.

Organic Farming Favors phoD-Harboring Rhizospheric Bacterial Community and Alkaline Phosphatase Activity in Tropical Agroecosystem

The bacteria harboring phoD encodes alkaline phosphatase (ALP), a secretory enzyme that hydrolyzes organic phosphorous (P) to a usable form in the soil. The impact of farming practices and crop types on phoD bacterial abundance and diversity in tropical agroecosystems is largely unknown. In this research, the aim was to study the effect of farming practices (organic vs. conventional) and crop types on the phoD-harboring bacterial community. A high-throughput amplicon (phoD gene) sequencing method was employed for the assessment of bacterial diversity and qPCR for phoD gene abundance. Outcomes revealed that soils treated for organic farming have high observed OTUs, ALP activity, and phoD population than soils managed under conventional farming with the trend of maize > chickpea > mustard > soybean vegetated soils. The relative abundance of Rhizobiales exhibited dominance. Ensifer, Bradyrhizobium, Streptomyces, and Pseudomonas were observed as dominant genera in both farming practices. Overall, the study demonstrated that organic farming practice favors the ALP activity, phoD abundance, and OTU richness which varied across crop types with maize crops showing the highest OTUs followed by chickpea, mustard, and least in soybean cropping.

Amplicon-based assessment of bacterial diversity and community structure in three tropical forest soils in Kenya

Forest soils provide a multitude of habitats for diverse communities of bacteria. In this study, we selected three tropical forests in Kenya to determine the diversity and community structure of soil bacteria inhabiting these regions. Kakamega and Irangi are rainforests, whereas Gazi Bay harbors mangrove forests. The three natural forests occupy different altitudinal zones and differ in their environmental characteristics. Soil samples were collected from a total of 12 sites and soil physicochemical parameters for each sampling site were analyzed. We used an amplicon-based Illumina high-throughput sequencing approach. Total community DNA was extracted from individual samples using the phenol-chloroform method. The 16S ribosomal RNA gene segment spanning the V4 region was amplified using the Illumina MiSeq platform. Diversity indices, rarefaction curves, hierarchical clustering, principal component analysis (PCA), and non-metric multidimensional scaling (NMDS) analyses were performed in R software. A total of 13,410 OTUs were observed at 97% sequence similarity. Bacterial communities were dominated by Proteobacteria, Bacteroidetes, Firmicutes, Actinobacteria, and Acidobacteria in both rainforest and mangrove sampling sites. Alpha diversity indices and species richness were higher in Kakamega and Irangi rainforests compared to mangroves in Gazi Bay. The composition of bacterial communities within and between the three forests was also significantly differentiated (R = 0.559, p = 0.007). Clustering in both PCA and NMDS plots showed that each sampling site had a distinct bacterial community profile. The NMDS analysis also indicated that soil EC, sodium, sulfur, magnesium, boron, and manganese contributed significantly to the observed variation in the bacterial community structure. Overall, this study demonstrated the presence of diverse taxa and heterogeneous community structures of soil bacteria inhabiting three tropical forests of Kenya. Our results also indicated that variation in soil chemical parameters was the major driver of the observed bacterial diversity and community structure in these forests.

Comparison of Three DNA Extraction Kits for Assessment of Bacterial Diversity in Activated Sludge, Biofilm, and Anaerobic Digestate

Direct DNA analysis is the most widely used approach for microorganism characterization in natural and built environments; therefore, reliable and effective methods of nucleic acid extraction for samples from particular types of environments are needed. In this study, we compared three commercial kits for metagenomic DNA extraction from three types of biomass: activated sludge, biofilm, and anaerobic digestate. The yield, purity, and quality of DNA were measured, and the effect that the DNA kit had on the subsequent microbial community analysis was assessed with amplified ribosomal intergenic spacer analysis (ARISA). Amplicons were analyzed automatically utilizing capillary electrophoresis. For the activated sludge and digestate, the suggested kit is FastDNA™ Spin Kit for Soil (MP Biomedicals). This kit allowed the highest DNA yield to be obtained and provided the highest biodiversity. For biofilm with a high content of extracellular polymeric substances, the FavorPrep™ Soil DNA Isolation Mini Kit (FAVORGEN) is recommended. This kit allowed to obtain the highest biodiversity and provided the most reliable results of genetic distance assessment in this type of biomass.

Assessment of Bacterial Diversity of Industrial Poultry Wastewater by Denaturing Gradient Gel Electrophoresis (DGGE) and the Cultivation Method in Order to Inform Its Reuse in Agriculture.

Effluents discharged by poultry meat industries are heavily polluted with raw materials, such as fat, blood residues, and proteins. Thus, untreated effluents directly discharged into the environment may constitute a public health threat. This study aims to evaluate the bacterial diversity of three water qualities: industrial poultry wastewater (PWW), tap water (TW), and PWW diluted with TW (50 : 50) (V/V) (TWPWW) by the combination of culture-independent and culture-dependent approaches. The total bacterial DNA was extracted using phenol/chloroform method. The hypervariable 16S rRNA region V3-V5 was amplified by PCR using universal primers. The amplicons were separated by vertical electrophoresis on a polyacrylamide gel of increasing denaturing gradient according to their richness in GC bases. Selected bands were reamplified and sequenced. Pure isolated bacteria from nutrient agar medium were characterized according to their morphological and biochemical characteristics. Genomic DNA from pure strains was extracted by boiling method, and a molecular amplification of the 16S–23S ITS region of the 16S rRNA gene was performed using the universal primers. Selected isolates were identified by sequencing. Results showed a high bacterial load and diversity in PWW in comparison with TW and TWPWW. A collection of 44 strains was obtained, and 25 of them were identified by sequencing. Proteobacteria represented 76% of isolated bacteria Gamma-Proteobacteria was the predominate isolate (68%). Other isolates were Firmicutes (8%), Bacteroidetes (12%), and Actinobacteria (8%). These isolates belong to different genera, namely, Pseudomonas, Acinetobacter, Proteus, Empedobacter, Corynebacterium, Enterobacter, Comamonas, Frondibacter, Leclercia, Staphylococcus, Atlantibacter, Klebsiella, and Microbacterium.

Assessment of bacterial diversity associated with assisted reproductive technologies through next-generation sequencing

BackgroundTo assess bacterial diversity in infertile couples with their biochemical pregnancy outcomes. Using a retrospective case-control study design, participants were recruited for collection of vaginal swab, follicular fluid, endometrial fluid, and semen samples. The microbial composition was analyzed by 16S ribosomal RNA (rRNA) gene amplification with (MinION) Oxford Nanopore Ltd.ResultsOur findings revealed that age and endometrial thickness had a significant impact on the pregnancy success rate of pregnant (P) and non-pregnant (NP) patients receiving IVF, with high levels of luteinizing hormone, estrogen, and progesterone in the P group. In addition, the partial least squares discriminant analysis (PLS-DA) revealed a difference in microbial composition between the P and NP groups, as well as a higher microbial abundance in non-pregnant patients compared to pregnant patients. After comparison between pregnant patients and non-pregnant patients, pregnant patients had a higher abundance of Firmicutes and Proteobacteria and a lower abundance of Actinobacteria, Fusobacterium, and Bacteroidetes at the phylum level. Non-pregnant patients had a lower abundance of the probiotics lactobacillus and a higher abundance of infections Prevotella and Gardnerella at the genus level. As a result, a disordered microbiota in non-pregnant patients, characterized by a decrease in probiotics and an increase in pathogens, could be used as a possible marker for a higher IVF failure rate.ConclusionAlteration of the microbiota of the reproductive tract or the presence of certain microbes, regardless of the degree of pathogenicity that can affect fertilization, as well as implantation and subsequent embryonic development. This could result in failed fertility treatments and a lower live birth (LBR) rate.

Oral Microbiome Transmission and Infant Feeding Habits.

ABSTRACTTransmission of oral microbiota from mother to infant is a highly relevant and, so far, understudied topic due to lack of mainstream high-throughput methods for the assessment of bacterial diversity at a strain level. In their recent article in mBio, S. Kageyama, M. Furuta, T. Takeshita, J. Ma, et al. (mBio 13:e03452-21, 2021, https://doi.org/10.1128/mbio.03452-21) evaluated oral microbial transmission from mothers to their infants by using full-length analysis of the 16S rRNA gene and demonstrated the applicability of this method for assessment of transmission of oral bacteria at the single-nucleotide-difference level. By analyzing different metadata of the mother-infant pairs, they discovered that the presence of maternal oral bacteria was higher in formula-fed infants compared to infants who were breastfed or received mixed feeding. This interesting finding suggests that breastfeeding may prevent early maturation of infant’s oral microbiome. The physiological role of this phenomenon still needs to be elucidated.

Influence of Human Age on the Prebiotic Effect of Pectin-Derived Oligosaccharides Obtained from Apple Pomace

The aim of this study was to evaluate the prebiotic effect of pectin-derived oligosaccharides (POS) obtained from apple pomace on the growth and metabolism of microbiota from the human gastrointestinal tract as a function of the age of the host. The counts of major bacterial groups Bifidobacterium sp., lactobacilli, Clostridium sp., Bacteroides sp., Enterococcus sp. and Enterobacteria were assessed during long-term in vitro fermentation of mixed cultures in a prebiotic medium. Comparative assessment of bacterial diversity in the human fecal microbiota was performed relative to the age of the host, from childhood to old age, through younger years and middle age. The age group of the host was found to be an important factor that determined the prebiotic effect of POS, which was related to both the qualitative and quantitative composition of fecal microbiota and its metabolism. In contrast to the microbiota of elderly subjects, the child-derived intestinal microbiota underwent significantly different alterations in terms of the proportion and composition of lactic acid bacteria, leading to a more favorable pattern of short-chain fatty acids (SCFA) and lactic acid levels.

Bacterial diversity assessment of world's largest sewage-fed fish farms with special reference to water quality: a Ramsar site.

Bacterial community structure is one of the essential components of aquaculture dynamics and plays an important role in maintaining wetland health. The present work is an effort to study the structure of bacterial communities in the world's largest sewage-fed fish farms, the East Kolkata Wetlands (EKWs), along with their predicted functional metabolic pathways and correlation with environmental variables. Sequencing data analysis revealed the abundance of genera such as Arcobacter (0-50%), Pseudomonas (0-15%), Sulfurospirillum (0-9%), Cloacibacterium (0-6%), hgcI clade (7-29%), C39 (0-9%), V6 (3-36%), Fluiivicola (1-6%) and Cyanobium (3-8%) in the EKWs. Further, water quality analysis of three treatment groups, i.e. Sewage, Sewage F-1 and Sewage F-2, revealed that dissolved oxygen (DO), biochemical oxygen demand (BOD) and chemical oxygen demand (COD) differed significantly and violated the standard prescribed norms (Central Pollution Control Board, CPCB, New Delhi) for fishery propagation and irrigation in India. Further, the correlation matrix analysis between the abundance of bacterial genera and environmental variables indicated that DO, BOD and COD were mainly responsible for bacterial community structure and their proliferation in the EKWs. Our results indicated that the abundance of genera such as Arcobacter, Pseudomonas, Sulfurospirillum and Cloacibacterium has an inverse relationship with BOD and COD. Our observations based on the bacterial community structure and deteriorated water quality indicate the ineffective functioning and poor management of this man-made constructed wetland.

The impact of the addition of natural materials on the composting of animal manure

Article Details: Received: 2020-10-14 | Accepted: 2020-11-27 | Available online: 2021-01-31 https://doi.org/10.15414/afz.2021.24.mi-prap.93-97 In this study we investigated the microbiological and chemical parameters during the composting of different substrates. Composting of two types of substrates amended with natural materials, manure mixed with zeolite (S1) and manure mixed with zeolite and lime (S2), was investigated and compared with that in the amendment-free substrate (C). During the composting the counts of coliform and faecal coliform bacteria in S2 and C differred significantly (P ˂ 0.001). There were also significant differences in coliform and faecal coliform bacterial counts between substrates S1 and S2 (P &gt; 0.01 and P &gt; 0.05, resp.). The total bacterial counts in C, S1 and S2 showed no significant differences throughout the composting (P &gt; 0.05). Degradation of organic matter was significantly increased in S2 compared to C (P ˂ 0.001) due to relatively rapid decomposition of organic matter by microorganisms in this substrate. Determination of chemical parameters also showed significant differences between individual substrates. The pH level in S2 was higher and varied from 9.16 to 7.99. Release of N-NH 4 + from S2 substrate was significantly reduced. The total nitrogen (N t ) content in S2 substrate was increased by 45.01% compared to the other two substrates and resulted in a decreased C/N ratio towards the end of composting. Our results indicated that composting of manure amended with natural material provided promising results and has a potential for implementation in practice.  Keywords: composting,chemical parameters, microorganism, zeolite, lime References Alavi, N. et al. (2017). Investigating the efficiency of co-composting and vermicomposting of vinasse with the mixture of cow manure wastes, bagasse, and natural zeolite. Waste Management , 69, 117–126. doi:10.1016/j.wasman.2017.07.039 Awasthi, M. K. et al. (2016). Role of biochar amendment in mitigation of nitrogen loss and greenhouse gas emission during sewage sludge composting. Bioresource Technology , 219, 270–280.doi:10.1016/j.biortech.2016.07.128 Bougnom, B. P. et al. (2020). Evaluation of wood ash as additive for cow manure composting. International Annals of Science , 9(1), 100–110. DOI: https://doi.org/10.21467/ias.9.1.100-110 Chan, M. T. et al. (2016). Reducing nitrogen loss and salinity during “struvite” food waste composting by zeolite amendment. Bioresource Technology , 200, 838–844. doi:10.1016/j.biortech.2015.10.093 Chandna, P. (2013). Assessment of bacterial diversity during composting of agricultural byproducts. BMC Microbiol ., 13, 99. https://doi.org/10.1186/1471-2180-13-99 Chang, R. et al. (2019). Comparing the effects of three in situ methods on nitrogen loss control, temperature dynamics and maturity during composting of agricultural wastes with a stage of temperatures over 70 °C. Journal of Environmental Management , 230, 119–127. doi:10.1016/j.jenvman.2018.09.076 Li, R. et al. (2012). Nutrient transformations during composting of pig manure with bentonite. Bioresource Technology , 121, 362–368. https://doi.org/10.1016/j.biortech.2012.06.065 Lim, S. S. et al. (2017). Nitrogen, carbon, and dry matter losses during composting of livestock manure with two bulking agents as affected by co-amendments of phosphogypsum and zeolite. Ecological Engineering .102, 280–290. doi:10.1016/j.ecoleng.2017.02.031 Meng, Q. et al. (2019). Microbial Community Succession and Response to Environmental Variables During Cow Manure and Corn Straw Composting. Frontiers in Microbilogy , 10. doi:10.3389/fmicb.2019.00529 Ren, G. (2016).Evaluation of microbial population dynamics in the co–composting of cow manure and rice straw using high throughput sequencing analysis. World J. Microbiol. Biotechnol ., 32, 1–11. doi: 10.1007/s11274-016-2059-7 Sasáková, N. (2015). Environmental and environmental risks associated with the treatment and utilization of animal excrements and sewage sludge and their environmental impact. Habilitation thesis. p.3-11. University of veterinary medicine and pharmacy in Košice. Szogi, A. A. et al. (2015). Methods for treatment of animal manures to reduce nutrient pollution prior to soil application. Curr. Pollut. Rep ., 1(1), 47-56. https://doi.org/10.1007/s40726-015-0005-1 Villaseñor, J. et al. (2011). Composting domestic sewage sludge with natural zeolites in a rotary drum reactor. Bioresource Technology , 102(2), 1447–1454. doi:10.1016/j.biortech.2010.09.085 Wagas, M. et al. (2019). Untapped potential of zeolites in optimization of food waste composting. Journal of Environmental Management , 241, 99–112. doi:10.1016/j.jenvman.2019.04.014

Metabarcoding for bacterial diversity assessment: looking inside Didymosphenia geminata mats in Patagonian aquatic ecosystems

Metabarcoding for bacterial diversity assessment: looking inside Didymosphenia geminata mats in Patagonian aquatic ecosystems

Assessment of bacterial diversity and their antibiotic resistance profiles in wastewater treatment plants and their receiving Ganges River in Prayagraj (Allahabad), India

The wastewater treatment plant is the silent reservoir of the broad spectrum of microbial populations, including pathogenic ones, which have the potential to cause contamination and pose risks to public and environmental health. In this work, we estimated the actual bacterial load present in the pre and post-treated wastewater samples from WWTPs of Prayagraj region of India. Furthermore, we also studied the distribution of antibiotic-resistant bacteria (ARB) from WWTPs to Ganges river samples. Data indicated that the majority of the isolates were identified as Bacillus spp. (42.4%) followed by Gammaproteobacteria (27%) which included members of the genera Aeromonas, Acinetobacter, Pseudomonas and Enterobacter. Most bacterial isolates regardless of the site of sampling resulted resistance to cefotaxime and ampicillin (50% and 41.6%) respectively. This study concluded that the municipal wastewater offers an atmosphere conducive to bacteria with antibiotic resistance that can harbor resistant bacteria and their resistant genes to receiving water sections with potential public health danger.

Taxonomic Diversity of Bacteria and Their Filterable Forms in the Soils of Eastern Antarctica (Larsemann Hills and Bunger Hills)

Increasing interest in microbial communities of Arctic and Antarctic extreme environments, their taxonomic diversity, and forms and mechanisms of adaptation of inhabitants of Antarctic biotopes to extreme conditions determined the goal of the present work. Next generation sequencing of the 16S rRNA gene fragments was used to determine the taxonomic structure of microbial communities in soil samples from the Larsemann Hills and Bunger Hills. Revealed differences in the composition of predominant bacterial phyla and genera indicate that the type of the biotope developing on the soil surface and a combination of various physicochemical factors play a major role in formation of Antarctic microbial communities. High number of filterable forms of prokaryotes (FFP) was found in the communities. Analysis of the libraries of the 16S rRNA gene clones revealed that the FFP from three Larsemann Hills samples belonged to the phylum Proteobacteria. In all three samples, the dominant FFP group exhibited the highest similarity (99%) to an uncultured bacterial clone of the class Deltaproteobacteria revealed by assessment of bacterial diversity of rocks and groundwater of the Donghai County, China. The FFP capable of growth of standard nutrient media belonged to the phyla Actinobacteria, Bacteroidetes, Deinococcus-Thermus, Firmicutes, and Proteobacteria. Taking into account the data of high FFP number in the samples and their taxonomic composition, their significant contribution to stability of the bacterial composition of Antarctic soils may be suggested. The FFP fraction was mainly represented by bacterial dormant forms able to revert to active growth under favorable conditions. Rapid transition of a vegetative part of the population to small dormant forms under unfavorable conditions is probably one of the strategies enabling their survival in extreme environments. The FFP fraction also contained the cells belonging to novel bacterial species, probably ultramicrobacteria.

Assessment of bacterial diversity of Rhipicephalus microplus ticks from two livestock agroecosystems in Antioquia, Colombia.

Rhipicephalus microplus is recognized as a tick species highly prevalent in cattle, with a wide pantropical distribution that seems to continue spreading geographically. However, its role as a biological vector has been scarcely studied in the livestock context. In this study, a 16S rRNA next-generation sequencing analysis was used to determine bacterial diversity in salivary glands and gut of R. microplus from two contrasting livestock agroecosystems in Antioquia, Colombia. Both the culture-independent approach (CI) and the culture-dependent (CD) approach were complementarily adopted in this study. A total of 341 unique OTUs were assigned, the richness showed to be higher in the Northern than in the Middle Magdalena region, and a high diversity was found at the phylum and genus levels in the samples obtained. With the CI approach, Proteobacteria, Bacteroidetes, Firmicutes, and Actinobacteria were the most common phylum of bacteria regardless of the organ, or geographic origin of the specimens analyzed. While the relative abundance of bacteria at a phylum level with the CD approach varied between analyzed samples, the data obtained suggest that a high diversity of species of bacteria occurs in R. microplus from both livestock agroecosystems. Bacterial genera such as Anaplasma, Coxiella, and Ehrlichia, recognized for their implications in tick-borne diseases, were also detected, together with endosymbionts such as Lysinibacillus, previously reported as a potential tool for biological control. This information is useful to deepen the knowledge about microbial diversity regarding the relations between endosymbionts and pathogens and could facilitate the future development of epidemiological surveillance in livestock systems.

Assessment of Bacterial Diversity of Sandy-Loam Soil Polluted by Hydrocarbons Using 454 Pyrosequencing

The study was conducted on polluted soil from a refitting oil station at Pointe-Noire in Congo. The aim of the work was to study the composition of the soil microbial community. Microbial diversity was assessed using the 454 pyrosequencing. The results showed that microbial diversity was represented by 1986 OTUs assigned to the Bacteria domain with 97% of similarity. However, only 246 OTUs were affiliated with 12 Phyla, 24 Classes, 56 Orders and 85 Families. The Proteobacteria (73%), Chloroflexi (16.85%), Bacteroidetes (2.68%) and Actinobacteria (2.65%) were the most representative bacterial phyla. The dominant classes were Alphaproteobacteria, Betaproteobacteria, Gammaproteobacteria, Actinobacteria, Sphingobacteria. The most abundant orders are represented by Rhizobiales (22.94%), Sphingomodales (7.07%), Caulobacterales (6.68%) and three unknown orders corresponding to 28.96%. Bradyrhizobiaceae (14.10%), Sphingomonadaceae (7.05%) and Caulobacteraceae (6.68%) were the best distributed families in the microbial community. This soil could serve for isolation of microorganism consortia for bioremediation.

Study of Symbiont Bacteria of &lt;i&gt;Acropora digitifera&lt;/i&gt; Coral From Ciletuh Bay, Sukabumi by Using Culture and Molecular Approach

Bacteria are one of the prokaryotic microorganisms that are symbiotic with coral reefs. These microorganisms help corals in secreting mucus layers which are used as a place to live for bacteria and control the presence of pathogenic bacteria in corals. The purpose of this study was to determine the diversity of bacterial communities associated with Acropora digitifera corals in Ciletuh bay, West Java, by culture approach. Sampling was carried out at a depth of 4 meters. Morphology-based identification and molecular approach based on sequence of the small ribosomal unit (16S) rRNA gene were used to determine the bacterial species in the samples. A total of six pure isolates were identified based on morphological observation and the molecular DNA characteristics from three of them were identified with 16S rRNA gene sequences. The identification using 16S rRNA gene showed that the isolate ACD.P4.PH7.P had a close relationship with the BF strain and zb strain of Bacillus flexus (acc number MH569560.1) with a similarity of 85.44 %. While ACD.P4.PH9.P isolate has a close relationship with Bacillus sp. c234 (acc number FJ950647.1) with a similarity of 98.50 %. Additionally, ACD.P4.PH9.K isolates closely related to Bacillus sp. of strain 6RM1 (acc number MK134607.1) with a similarity of 94.78 %. This study also revealed that both microscopic identifications by morphological traits and molecular approach using 16S rRNA gene can be used in bacterial diversity assessment.

CO2 management using carbonic anhydrase producing microbes from western Indian Himalaya

Microbial diversity was investigated in the soil samples from Himachal Pradesh and Kumaun Himalaya. Phylogenetic analysis of all bacterial strains confirms the presence of Proteobacteria (55%), Firmicutes (27%), Actinobacteria (18%) and Bacteroidetes (6%) like mesophilic microbial communities in the study area. Shannon Index was used as a tool for bacterial diversity assessment. Isolated bacterial strains were further screened for extracellular crude carbonic anhydrase (CA) production. Pseudomonas spp. is able to produce extracellular CA, while other bacterial strains showed intracellular activity. 16s rRNA sequencing and FT-IR was used to identify the isolates and CA application in CO2 mineralization.