Characterization Of Bacterial Diversity Research Articles

Characterization of bacterial diversity and screening of cellulose-degrading bacteria in the gut system of Glenea cantor (Fabricius) larvae.

The intestinal bacteria of longhorn beetles would be ideal targets for pest control and lignocellulosic resources by destroying or exploiting their cellulose-degrading function. This article aims to investigate the diversity and community structure of intestinal bacteria the oligophagous longhorn beetle Glenea cantor. Additionally, it seeks to identify the presence of lignocellulose-degrading bacteria in the gut, and explore their role in consuming host kapok trees Bombax malabaricum. In this study, the bacterial community from G. cantor was examined by Illumina sequencing of 16S ribosomal RNA (rRNA) targeting the V3 and V4 regions. A total of 563,201 valid sequences and 814 OTUs were obtained. The dominant phyla were Proteobacteria, and the dominant genera were Acinetobacter and Lactococcus. The analysis of microbial diversity revealed a high bacterial diversity in the samples, with the gut bacteria playing a crucial role in the physiological activities of the host, particularly, 9 genera of intestinal bacteria with cellulose degradation function were found, highlighting their vital role in cellulose degradation. Five strains of cellulose-degrading bacteria, belonging to the genus Pseudomonas, were obtained from the intestinal tract of G. cantor larvae using traditional isolation and culture techniques as well as 16S rDNA sequencing. Among these strains, A4 exhibited a cellulase activity of 94.42 ± 0.42U/mL, while A5 displayed the highest filter paper enzyme activity of 127.46 ± 3.54U/mL. These results offered valuable insights into potential targets for pest control through internal attack digestion and cellulose-degrading bacteria in longhorn beetles.

Characterization of Bacterial Diversity in Aguamiel and Two Types of Pulque from the Zacatlán Region, México

Pulque is a traditional Mexican fermented beverage associated with numerous health benefits. Over time, there has been considerable interest in studying the bacterial diversity of pulque, and microbial characterization has been carried out using traditional microbiological and molecular methods. Therefore, the objective of this research was to characterize the microbiota of artisanal pulque obtained from the Zacatlán region in Puebla, México, by the means of Illumina sequencing, and to compare it with the microbial diversity of aguamiel (sap before fermentation), commercial pulque (supplemented with additives to increase its yield), and its seed (batch of pulque previously fermented). An analysis of the Shannon index showed medium diversity for both aguamiel and pulque samples (score > 2), while the Chao 1 index exhibited a non-significant difference between them. On the other hand, a principal components analysis confirmed the role of the seed as an essential inoculum to define the microbial diversity of pulque, emphasizing the importance of its preservation as a quality standard during the elaboration process. In addition, results showed that the dominant phyla in artisanal and commercial pulque were Firmicutes and Bacteroidetes. As the fermentation process progressed, it was possible to observe an increase in the population of lactic acid bacteria (LAB) in both types of pulque compared to those detected in aguamiel. Of these, the species Lactobacillus, Leuconostoc, and Lactococcus represented almost 95% of the total LAB. Finally, even though the safety of pulque has been in question due to its non-aseptic manufacturing process, the present study confirmed that less than 1% of its microbiota corresponds to the genera with a pathogenic potential such as γ-proteobacteria (Enterobacter and Hafnia), which decreases as the fermentation process advances.

Consumer feces impact coral health in guild-specific ways

Animal waste products are an important component of nutrient cycles and result in the trophic transmission of diverse microorganisms. There is growing recognition that the feces of consumers, such as predators, may impact resource species, their prey, via physical effects and/or microbial activity. We tested the effect of feces from distinct fish trophic groups on coral health and used heat-killed fecal controls to tease apart physical versus microbial effects of contact with fecal material. Fresh grazer/detritivore fish feces caused lesions more frequently on corals, and lesions were 4.2-fold larger than those from sterilized grazer/detritivore feces; in contrast, fresh corallivore feces did not cause more frequent or larger lesions than sterilized corallivore feces. Thus, microbial activity in grazer/detritivore feces, but not corallivore feces, was harmful to corals. Characterization of bacterial diversity in feces of 10 reef fish species, ranging from obligate corallivores to grazer/detritivores, indicated that our experimental findings may be broadly generalizable to consumer guild, since feces of some obligate corallivores contained ~2-fold higher relative abundances of coral mutualist bacteria (e.g., Endozoicomonadaceae), and lower abundances of the coral pathogen, Vibrio coralliilyticus, than feces of some grazer/detritivores. These findings recontextualize the ecological roles of consumers on coral reefs: although grazer/detritivores support coral reef health in various ways (e.g., promoting coral settlement and herbivory through the removal of detritus and sediments from the algal matrix), they also disperse coral pathogens. Corallivore predation can wound corals, yet their feces contain potentially beneficial coral-associated bacteria, supporting the hypothesized role of consumers, and corallivores in particular, in coral symbiont dispersal. Such consumer-mediated microbial dispersal as demonstrated here has broad implications for environmental management.

Occurrence of antibiotic resistance genes and potentially pathogenic bacteria in the Yangtze River tributary (Nanjing section) and their correlation with environmental factors

Freshwater environments are vulnerable to emerging contaminants such as Antibiotic resistance genes (ARGs), and their occurrence is gaining more attention. However, the occurrence of ARGs along with potential pathogens is less explored. The current study aimed to evaluate the abundance of ARGs and explore bacterial communities for the presence of potential bacterial pathogens in water samples collected from a tributary to the Yangtze River in Nanjing. Twelve physico-chemical parameters were analyzed, followed by quantifying 10 ARGs targeting sulfonamide (sul1, sul2), tetracycline (tetG, tetM, tetQ), erythromycin (ermB), vancomycin (vanA, vanR), and streptomycin (strA, strB) using real-time PCR and bacterial diversity characterization using high-throughput 16 S rRNA sequencing. The results indicated poor water quality and high-level eutrophication in most sampling locations. sul1, sul2, and strB were dominant in the study area with average concentrations of 6.8, 7.1, and 6.5 Log10 gene copies/100 ml, respectively. Proteobacteria, Cyanobacteria, Bacteroidetes, and Actinobacteria were the main phyla detected in the study area, and genus-level analysis revealed the presence of eight potential pathogenic and ten fecal-associated bacterial genera at several locations in the study area. The distance-based Redundancy analysis indicated that total phosphorus, electrical conductivity, dissolved oxygen, total dissolved solids, ammonium-N (NH4 +-N), and chlorophyll a had significantly influenced the bacterial community composition in the monitored locations. Correlation analysis demonstrated that water temperature, pH, NH4 +-N, and total organic carbon were positively correlated with sul2, tetG, and vanR genes, indicating that these environmental parameters significantly affected the ARGs distribution pattern. Overall, our results provide valuable information regarding the occurrence of ARGs and potential bacterial pathogens in the study area; however, their co-existence highlights increased human health risks.

Characterization of bacterial diversity and capacity to remove lead of a consortium from mining soil.

At present, the presence of lead (Pb2+) continues to be a problem in water bodies due to its continuous use and high toxicity. The aim of this study was to investigate the bacterial diversity of a potential consortium used as a biosorbent for the removal of lead in an aqueous solution. The minimum inhibitory concentration and the mean lethal dose of the consortium were determined, and then the optimal variables of pH and temperature for the removal process were obtained. With the optimal conditions, the kinetic behavior was evaluated, and adjustments were made to different mathematical models. A Fourier transform infrared spectroscopy analysis was performed to determine the functional groups of the biomass participating in the removal process, and the diversity of the bacterial consortium was evaluated during Pb2+ removal by an Ion Torrent Personal Genome Machine System. It was found that the intraparticle diffusion model was the one that described the adsorption kinetics showing a higher rate constant with a higher concentration of Pb2+, while the Langmuir model was that explained the isotherm at 35°C, defining a maximum adsorption load for the consortium of 54mg/g. In addition, it was found that Pb2+ modified the diversity and abundance of the bacterial consortium, detecting genera such as Pseudomonas, Enterobacter, Citrobacter, among others. Thus, it can be concluded that the bacterial consortium from mining soil was a biosorbent with the ability to tolerate high concentrations of Pb2+ exposure. The population dynamics during adsorption showed enrichment of Proteobacteria phyla, with a wide range of bacterial families and genera capable of resisting and removing Pb2+ in solution.

Characterization of bacterial diversity between two coastal regions with heterogeneous soil texture

Studying microbial diversity and the effects of external factors on the microbiome could expand our understanding of environmental alterations. Silt and sand are mineral particles that form soil texture and even though most of the soils on earth contain a fraction of them and some other soils form almost by them, their effects on the microbiome remained to elucidate. In this study, the bacterial biodiversity of sand and silt clay soils was investigated. Furthermore, their effects on plant growth have been determined. Our data showed that biodiversity and biomass of microbiome are higher in silt-based soil. It is interesting that the pseudomonas genera only exist in silt-based soil while it is in the absence of sand-based soil. In contrast, B. thuringiensis could be found in sand-based soil while it is not found in silt texture. Our data also demonstrated that there are no significant changes in stress response between the two groups however, differential physiological changes in plants inoculated with silt and sand based bacterial isolates have been observed. This data could indicate that smaller size particles could contain more bacteria with higher biodiversity due to providing more surfaces for bacteria to grow.

Coupling of metataxonomics and culturing improves bacterial diversity characterization and identifies a novel Rhizorhapis sp. with metal resistance potential in a multi-contaminated waste sediment

Long-term contaminated environments have been recognized as potential hotspots for bacterial discovery in taxonomic and functional terms for bioremediation purposes. Here, bacterial diversity in waste sediment collected from a former industrial dumpsite and contaminated with petroleum hydrocarbon and heavy metals was investigated through the parallel application of culture-independent (16S rRNA gene amplicon sequencing) and -dependent (plate culturing followed by colony picking and identification of isolates by 16S rRNA gene Sanger sequencing) approaches. The bacterial diversities retrieved by both approaches greatly differed. Bacteroidetes and Proteobacteria were dominant in the culture-independent community, while Firmicutes and Actinobacteria were the main culturable groups. Only 2.7% of OTUs (operational taxonomic units) in the culture-independent dataset were cultured. Most of the culturable OTUs were absent or in very low abundances in the culture-independent dataset, revealing that culturing is a useful tool to study the rare bacterial biosphere. One culturable OTUs (comprising only the isolate SPR117) was identified as a potential new species in the genus Rhizorhapis (class Alphaproteobacteria) and was selected for further characterization. Phytopathogenicity tests showed that Rhizorhapis sp. strain SPR117 (ATCC TSD-228) is not pathogenic to lettuce, despite the only described species in this genus, Rhizorhapis suberifaciens, is causal agent of the lettuce corky root disease. The genome of the strain SPR117 was sequenced, assembled in 256 contigs, with a length of 4,419,522 bp and a GC content of 59.9%, and its further annotation revealed the presence of genes related to the resistance to arsenic, copper, iron, and mercury, among other metals. Therefore, the coupling of metataxonomics and culturing is a useful tool to obtain not only an improved description of bacterial communities in contaminated environments, but also to isolate microorganisms with bioremediation potential.

Characterization of bacterial diversity in wastewater of Indian paper industries with special reference to water quality

The bacterial diversity in terms of structure and community profile, with special reference to water quality in the wastewater treatment plant of Indian paper industries, is poorly understood. In the present work, characterization of bacterial diversity using 16S (V3-V4 region) rRNA gene amplicon sequencing data with reference to physicochemical parameters in the wastewater treatment plant of two paper industries has been carried out. Amplicon data analysis revealed the presence of bacterial taxa belonging to the phylum such as Bacteroidetes, Proteobacteria, Patescibacteria, Firmicutes, Actinobacteria, etc. Further, taxonomic classification upto genus level and functional analysis data indicated that genera such as Cloacibacterium, Aerococcus, Chryseobacterium, Microbacterium, Acinetobacter, Sphingobium, etc., were involved in the predicted metabolic pathways like carbohydrate metabolism, fatty acid and aromatic compounds biosynthesis as well as degradation. Canonical correspondence analysis confirmed a significant correlation between the microbial pollutions loads and physicochemical parameters. Further, the chemical oxygen demand, biochemical oxygen demand and total suspended solids exceeded the acceptable limits prescribed by Central Pollution Control Board New Delhi, Government of India, for discharge of wastewater. This study finds the correlation between the bacterial community residing in the polluted water of wastewater treatment plant and their environmental preferences. The presence of these bacterial diversity in the wastewater treatment plant of paper industries may affect the maintenance as well as paper quality. In future, it will provide a benchmark for the better understanding and management of wastewater treatment plant in paper industries across the globe.

Characterization of bacterial diversity and assessing the cyanide biodegradation potential of bacterial isolates from gold processing plants

Cyanide is the basic component of many industrial processes, among which is gold processing, being very toxic or even lethal. Treatment, with the help of microorganisms, can be used effectively to reduce the load of harmful chemicals into the environment. The combination of microbiological methods and molecular tools allowed inferring the presence of a dominant population and the composition varied both in the places of origin and in the method used. The dominant phylogenetic affiliations of the bacteria were determined by sequencing the 16S rRNA gene. The isolates identified, as Bacillus and Enterococcus were capable to degrade 41.9 and 27.5 mg CN- L-1 respectively. This study provides information about the presence of a diverse bacterial community associated with residual effluents from cyanidation processes in Colombia and suggests that their presence could play a role in the biological degradation of cyanide compounds, offering an alternative for mining wastewater treatment.

A Metagenomic-Based Approach for the Characterization of Bacterial Diversity Associated with Spontaneous Malolactic Fermentations in Wine.

This study reports the first application of a next generation sequencing (NGS) analysis. The analysis was designed to monitor the effect of the management of microbial resources associated with alcoholic fermentation on spontaneous malolactic consortium. Together with the analysis of 16S rRNA genes from the metagenome, we monitored the principal parameters linked to MLF (e.g., malic and lactic acid concentration, pH). We encompass seven dissimilar concrete practices to manage microorganisms associated with alcoholic fermentation: Un-inoculated must (UM), pied-de-cuve (PdC), Saccharomyces cerevisiae (SC), S. cerevisiae and Torulaspora delbrueckii co-inoculated and sequentially inoculated, as well as S. cerevisiae and Metschnikowia pulcherrima co-inoculated and sequentially inoculated. Surprisingly, each experimental modes led to different taxonomic composition of the bacterial communities of the malolactic consortia, in terms of prokaryotic phyla and genera. Our findings indicated that, uncontrolled AF (UM, PdC) led to heterogeneous consortia associated with MLF (with a relevant presence of the genera Acetobacter and Gluconobacter), when compared with controlled AF (SC) (showing a clear dominance of the genus Oenococcus). Effectively, the SC trial malic acid was completely degraded in about two weeks after the end of AF, while, on the contrary, malic acid decarboxylation remained uncomplete after 7 weeks in the case of UM and PdC. In addition, for the first time, we demonstrated that both (i) the inoculation of different non-Saccharomyces (T. delbrueckii and M. pulcherrima) and, (ii) the inoculation time of the non-Saccharomyces with respect to S. cerevisiae resources (co-inoculated and sequentially inoculated) influence the composition of the connected MLF consortia, modulating MLF performance. Finally, we demonstrated the first findings of delayed and inhibited MLF when M. pulcherrima, and T. delbrueckii were inoculated, respectively. In addition, as a further control test, we also assessed the effect of the inoculation with Oenococcus oeni and Lactobacillus plantarum at the end of alcoholic fermentation, as MLF starter cultures. Our study suggests the potential interest in the application of NGS analysis, to monitor the effect of alcoholic fermentation on the spontaneous malolactic consortium, in relation to wine.

Inhibition of Microbial Methylation via arsM in the Rhizosphere: Arsenic Speciation in the Soil to Plant Continuum.

The interplay between rice roots and manuring with respect to arsenic speciation, subsequent assimilation into roots, and translocation to shoots in paddy soil was investigated, alongside bacterial diversity characterization. Planting increased soil Eh and decreased soil solution arsenic species: inorganic arsenic, monomethylarsonic acid, trimethylarsenic oxide, and dimethylarsinic acid. Presence of plant roots increased the copy number of Clostridium and Tumebacillus 16S rRNA as well as Streptomyces arsenic methylating gene ( arsM), but decreased Acidobacteria_GP1 16S rRNA and Rhodopseudomonas. palustris BisB5 arsM. Sum of arsenic species decreased under root influence due to the interplay of inorganic arsenic mobilization in bulk soil under anaerobic and immobilization under oxygenated rhizospheric conditions. Manuring increased all soil solution arsenic species (>90%), shoot total arsenic (60%), copy number of Geobacter 16S rRNA, and R. palustris TIE-1 arsM, indicative of a shift towards microbes with iron reduction and oxidation as well as arsenic methylation capabilities.

Characterization of bacterial diversity and ice-nucleating ability during different monsoon seasons over a southern tropical Indian region

Bioaerosols abundantly found in the atmosphere can potentially influence the climate by acting as ice nuclei and thus profoundly influencing the hydrological cycle. As the first attempt over India, we report the diversity, abundance, and ice nucleating ability of bacteria present in the rainwater collected at Chennai, during summer and two contrasting monsoon seasons. Diverse bacterial communities were present in all the twenty rainwater samples and predominantly belonged to Actinobacteria (6%), Alpha proteobacter (9%), Bacilli (29%), Betaproterobacteria (14%), Flavobacteria (3%), and Gammaproteobacteria (39%). The most efficient ice nucleating bacteria such as Pseudomonas sp. and Pantoea sp. were present in our precipitation samples and they contributed to 8.4% and 9.4% of the total cultivable bacterial species obtained. The relative abundance of Pseudomonas was highest during the south-west monsoon (75%) whereas Pantoea was abundant in the north-east monsoon (51.8%). The dominant bacteria belonging to the known ice nucleating genera Pseudomonas, Pantoea, and Bacillus were chosen for the determination of their freezing temperatures using tube freeze assay technique. The onset freezing temperature of species belonging to Pseudomonas and Pantoea was recorded as −12 °C and for those species belonging to Bacillus it was found to be −14 °C. Further, the number of bacterial cells making up an ice nucleus was estimated at the temperatures ranging from −18 °C to −12 °C for all the ice nucleating bacteria and it was found to vary from 106 to 109 (cells/nucleus).

Multilayer approach for characterization of bacterial diversity in a marginal sea: From surface to seabed

Bacteria are the most important microorganisms in the world oceans, accounting for up to 75% of the total biomass. They are responsible for fundamental biogeochemical processes and therefore often used as ecological indicators. In this study, bacteria were quantified by flow cytometry and their diversity assessed by High Throughput Sequencing (HTS) in the southern Adriatic Sea. The most abundant bacterial groups were also quantified by qPCR. The samples were collected from the surface to the seabed over a total of 16 different depths at four stations during the late winter BIOTA (BIO-Tracing Adriatic water masses) cruise conducted in March 2016. The investigated area showed unusual water mass properties and was characterized by a shallow mixed layer, which differed from the usual winter convection conditions, typical of middle-altitude ecosystems and important for the seasonal picoplankton dynamics of this area. Heterotrophic bacteria were separated into HNA (relative High Nucleic Acid content) and LNA (Low Nucleic Acid content) subpopulations with abundances up to 1.8 × 105 and 8.8 × 105 cells mL−1, respectively. HNA dominated at offshore stations reaching their maximum at depths below the euphotic zone. The bacterial community was dominated by Alphaproteobacteria, accounting for >40% of the total sequence reads and were mainly represented by the SAR11 clade (90.84%), followed by Marinimicrobia (18% of the total sequence reads), mainly represented by clade SAR406 (8.44%). Distinctive bacterial groups were found in the euphotic layer (Bacteroidetes and Actinobacteria) and aphotic layer samples (Deltaproteobacteria, Marinimicrobia, Chloroflexi, Acidobacteria and Planctomycetes). Results of the qPCR analyses further confirmed HTS results with highest abundances obtained for Alphaproteobacteria, followed by Gammaproteobacteria and Bacteroidetes. The adopted multiple approach, combining different molecular tools, critically supported by optics and flow cytometry, reveal changes in the bacterial assemblages during the unusual thermohaline conditions observed in 2016 in the southern Adriatic Sea.

Characterization of bacterial diversity in soil contaminated with the macrolide antibiotic erythromycin and/or inoculated with a multidrug-resistant Raoultella sp. strain using the PCR-DGGE approach

Antibiotics and microorganisms that are resistant to these drugs enter the soil via the use of sewage sludge, effluents and manure from antibiotic-treated animals and may cause significant changes in the diversity of microorganisms. The goal of this research was to evaluate the changes in the genetic diversity of a bacterial community in the soil after the addition of two different doses of erythromycin (EM) (1 and 10 mg/kg soil) and/or a multidrug-resistant Raoultella sp. strain (1.6 × 107 cells/g soil). The Raoultella sp. strain was isolated from raw sewage and expressed a resistance to erythromycin, clindamycin, tetracycline and vancomycin. A denaturing gradient gel electrophoresis (DGGE) analysis revealed that the pattern for the EM10-treated soil was significantly different from the one that was obtained for the control soil, which was also shown by a significant decrease in the values of the DGGE indices (diversity and richness) on days 15, 30 and 60. In turn, a lower dose of EM and/or the introduced bacterial strain had no effect on the diversity and richness of the dominant member of the soil bacterial community. A multivariate analysis demonstrated that the DGGE indices were significantly influenced by the dose of EM and the duration of the incubation. A principal component analysis (PCA) also revealed that EM and/or the bacterial strain significantly changed the microbial community structure on days 15, 30 and 60, which was also demonstrated by analyses of the PC scores using the MANOVA analysis for all of the sampling days and each day. Although the negative effect of a higher dose of EM on the biodiversity of soil bacteria (less number of genus) was transient, the application of EM into soil may temporarily pose a potential risk for soil functioning.

Characterization of bacterial diversity in contaminated groundwater using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry

Groundwater is a major source for drinking water in the United States, and therefore, its quality and quantity is of extreme importance. One major concern that has emerged is the possible contamination of groundwater due to the unconventional oil and gas extraction activities. As such, the impacts of exogenous contaminants on microbial ecology is an area to be explored to understand what are the chemical and physical conditions that allow the proliferation of pathogenic bacteria and to find alternatives for water treatment by identifying organic-degrading bacteria. In this work, we assess the interplay between groundwater quality and the microbiome in contaminated groundwaters rich in hydrocarbon gases, volatile organic and inorganic compounds, and various metals. Opportunistic pathogenic bacteria, such as Aeromonas hydrophila, Bacillus cereus, Pseudomonas aeruginosa, and Stenotrophomonas maltophilia, were identified, increasing the risk for consumption of and exposure to these contaminated groundwaters. Additionally, antimicrobial tests revealed that many of the identified bacteria were resistant to different antibiotics. The MALDI-TOF MS results were successfully confirmed with 16S rRNA gene sequencing, proving the accuracy of this high-throughput method. Collectively, these data provide a seminal understanding of the microbial populations in contaminated groundwater overlying anthropogenic activities like unconventional oil and gas development.

Characterization of bacterial diversity in an atrazine degrading enrichment culture and degradation of atrazine, cyanuric acid and biuret in industrial wastewater

abstractAn enrichment culture was used to study atrazine degradation in mineral salt medium (MSM) (T1), MSM+soil extract (1:1, v/v) (T2) and soil extract (T3). Results suggested that enrichment culture required soil extract to degrade atrazine, as after second sequential transfer only partial atrazine degradation was observed in T1 treatment while atrazine was completely degraded in T2 and T3 treatments even after fourth transfer. Culture independent polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE) technique confirmed selective enrichment of genus Bacillus along with Pseudomonas and Burkholderia. Degradation of atrazine/metabolites in the industrial wastewater was studied at different initial concentrations of the contaminants [wastewater-water (v/v) ratio: T1, 1:9; T2, 2:8; T3, 3:7; T4, 5:5 and T5, undiluted effluent]. The initial concentrations of atrazine, cyanuric acid and biuret ranged between 5.32 and 53.92 µg mL−1, 265.6 and 1805.2 µg mL−1 and 1.85 and 16.12 µg mL−1, respectively. The enrichment culture was able to completely degrade atrazine, cyanuric acid and biuret up to T4 treatment, while no appreciable degradation of contaminants was observed in the undiluted effluent (T5). Inability of enrichment culture to degrade atrazine/metabolites might be due to high concentrations of cyanuric acid. Therefore, a separate study on cyanuric acid degradation suggested: (i) no appreciable cyanuric acid degradation with accumulation of an unidentified metabolite in the medium where cyanuric acid was supplemented as the sole source of carbon and nitrogen; (ii) partial cyanuric acid degradation with accumulation of unidentified metabolite in the medium containing additional nitrogen source; and (iii) complete cyanuric acid degradation in the medium supplemented with an additional carbon source. This unidentified metabolite observed during cyanuric acid degradation and also detected in the enrichment culture inoculated wastewater samples, however, was degraded up to T4 treatments and was persistent in the T5 treatment. Probably, accumulation of this metabolite inhibited atrazine/cyanuric acid degradation by the enrichment culture in undiluted wastewater.

Characterization of bacterial diversity associated with calcareous deposits and drip-waters, and isolation of calcifying bacteria from two Colombian mines

Bacterial carbonate precipitation has implications in geological processes and important biotechnological applications. Bacteria capable of precipitating carbonates have been isolated from different calcium carbonate deposits (speleothems) in caves, soil, freshwater and seawater around the world. However, the diversity of bacteria from calcareous deposits in Colombia, and their ability to precipitate carbonates, remains unknown. In this study, conventional microbiological methods and molecular tools, such as temporal temperature gradient electrophoresis (TTGE), were used to assess the composition of bacterial communities associated with carbonate deposits and drip-waters from two Colombian mines. A genetic analysis of these bacterial communities revealed a similar level of diversity, based on the number of bands detected using TTGE. The dominant phylogenetic affiliations of the bacteria, determined using 16S rRNA gene sequencing, were grouped into two phyla: Proteobacteria and Firmicutes. Within these phyla, seven genera were capable of precipitating calcium carbonates: Lysinibacillus, Bacillus, Strenotophomonas, Brevibacillus, Methylobacterium, Aeromicrobium and Acinetobacter. FTIR and SEM/EDX were used to analyze calcium carbonate crystals produced by isolated Acinetobacter gyllenbergii. The results showed that rhombohedral and angular calcite crystals with sizes of 90μm were precipitated. This research provides information regarding the presence of complex bacterial communities in secondary carbonate deposits from mines and their ability to precipitate calcium carbonate from calcareous deposits of Colombian mines.

Characterization of bacterial diversity associated with deep sea ferromanganese nodules from the South China Sea.

Deep sea ferromanganese (FeMn) nodules contain metallic mineral resources and have great economic potential. In this study, a combination of culture-dependent and culture-independent (16S rRNA genes clone library and pyrosequencing) methods was used to investigate the bacterial diversity in FeMn nodules from Jiaolong Seamount, the South China Sea. Eleven bacterial strains including some moderate thermophiles were isolated. The majority of strains belonged to the phylum Proteobacteria; one isolate belonged to the phylum Firmicutes. A total of 259 near full-length bacterial 16S rRNA gene sequences in a clone library and 67,079 valid reads obtained using pyrosequencing indicated that members of the Gammaproteobacteria dominated, with the most abundant bacterial genera being Pseudomonas and Alteromonas. Sequence analysis indicated the presence of many organisms whose closest relatives are known manganese oxidizers, iron reducers, hydrogen-oxidizing bacteria and methylotrophs. This is the first reported investigation of bacterial diversity associated with deep sea FeMn nodules from the South China Sea.

Erratum to: Deodorization of pig slurry and characterization of bacterial diversity using 16S rDNA sequence analysis

Erratum to: Deodorization of pig slurry and characterization of bacterial diversity using 16S rDNA sequence analysis

Deodorization of pig slurry and characterization of bacterial diversity using 16S rDNA sequence analysis.

The concentration of major odor-causing compounds including phenols, indoles, short-chain fatty acids (SCFAs) and branched chain fatty acids (BCFAs) in response to the addition of powdered horse radish (PHR) and spent mushroom compost (SMC) was compared with control non-treated slurry (CNS) samples. A total of 97,465 rDNAs sequence reads were generated from three different samples (CNS, n = 2; PHR, n = 3; SMC, n = 3) using bar-coded pyrosequencing. The number of operational taxonomic units (OTUs) was lower in the PHR slurry compared with the other samples. A total of 11 phyla were observed in the slurry samples, while the phylogenetic analysis revealed that the slurry microbiome predominantly comprised members of the Bacteroidetes, Firmicutes, and Proteobacteria phyla. The rarefaction analysis showed the bacterial species richness varied among the treated samples. Overall, at the OTU level, 2,558 individual genera were classified, 276 genera were found among the three samples, and 1,832 additional genera were identified in the individual samples. A principal component analysis revealed the differences in microbial communities among the CNS, PHR, and SMC pig slurries. Correlation of the bacterial community structure with the Kyoto Encyclopedia of Genes and Genomes (KEGG) predicted pathways showed that the treatments altered the metabolic capabilities of the slurry microbiota. Overall, these results demonstrated that the PHR and S MC treatments significantly reduced the malodor compounds in pig slurry (P < 0.05).