Presence Of Actinobacteria Research Articles

Ignored microbial-induced taste and odor in drinking water reservoirs: Novel insight into actinobacterial community structure, assembly, and odor-producing potential

The presence of actinobacteria in reservoirs can lead to taste and odor issues, posing potential risks to the safety of drinking water supply. However, the response of actinobacterial communities to environmental factors in drinking water reservoirs remains largely unexplored. To address this gap, this study investigated the community structure and metabolic characteristics of odor-producing actinobacteria in water reservoirs across northern and southern China. The findings revealed differences in the actinobacterial composition across the reservoirs, with Mycobacterium sp. and Candidatus Nanopelagicus being the most prevalent genera. Notably, water temperature, nutrient levels, and metal concentrations were associated with differences in actinobacterial communities, with stochastic processes playing a major role in shaping the community assembly. In addition, three strains of odor-producing actinobacteria were cultured in raw reservoir water, namely Streptomyces antibioticus LJH21, Streptomyces sp. ZEU13, and Streptomyces sp. PQK19, with peak ATP concentrations of 51 nmol/L, 66 nmol/L, and 70 nmol/L, respectively, indicating that odor-producing actinobacteria could remain metabolically active under poor nutrient pressure. Additionally, Streptomyces antibioticus LJH21 produced the highest concentration of geosmin at 24.4 ng/L. These findings enhance our understanding of regional variances and reproductive metabolic mechanisms of actinobacteria in drinking water reservoirs, providing a solid foundation for improving drinking water quality control, especially for taste and odor.

Effects of Four-Year Oilseed Flax Rotations on the Soil Bacterial Community in a Semi-Arid Agroecosystem

Crop rotation aims to improve the sustainability and production efficiency of agricultural ecosystems, especially as demands for food and energy continue to increase. However, the regulation of soil microbial communities using crop rotation with oilseed flax and its relationship with key soil physicochemical driving factors are still not clear. In order to investigate this matter, we carried out a field study lasting four years involving various crop rotation sequences including FWPF, FPFW, PFWF, FWFP, ContF, and ContF1. In addition to evaluating soil physicochemical parameters, we employed Illumina high-throughput sequencing technology to explore the structure and variety of soil microbial communities. The findings indicated a notable rise in pH value with the FPFW treatment in contrast to other treatments, along with significant increases in AP, MBC, MBN, and qSMBC compared to ContF. The number of OTUs in the FPFW, WFPF, FPFW, and PFWF treatments was significantly increased by 4.10–11.11% compared to ContF (p < 0.05). The presence of Actinobacteria and Acidobacteria was greatly impacted by the FPFW treatment, whereas the presence of Actinobacteria and Chloroflexi was notably influenced by the ContF treatment. The soil bacterial community was primarily influenced by TC, pH, and NO3−-N according to correlation analysis. Specifically, the FPFW therapy notably raised the soil pH level while lowering the TC level. Furthermore, the FPFW therapy led to a notable rise in the proportion of Acidobacteria and a significant decline in the proportion of Actinobacteria. These findings provide important theoretical support for using FPFW rotation to regulate soil microbial communities and solve the problems of continuous cropping.

Exploring microbial diversity responses in agricultural fields: a comparative analysis under pesticide stress and non-stress conditions

Exposure to pesticides changes the microbial community structure in contaminated agricultural fields. To analyze the changes in the native microbial composition qRT-PCR, a metagenomic study was conducted. The qRT-PCR results exhibited that the uncontaminated soil has a higher copy number of 16S rDNA relative to the soil contaminated with pesticide. Metagenome analysis interprets that uncontaminated soil is enriched with proteobacteria in comparison with pesticide-contaminated soil. However, the presence of Actinobacteria, Firmicutes, and Bacteroides was found to be dominant in the pesticide-spiked soil. Additionally, the presence of new phyla such as Chloroflexi, Planctomycetes, and Verrucomicrobia was noted in the pesticide-spiked soil, while Acidobacteria and Crenarchaeota were observed to be extinct. These findings highlight that exposure to pesticides on soil significantly impacts the biological composition of the soil. The abundance of microbial composition under pesticide stress could be of better use for the treatment of biodegradation and bioremediation of pesticides in contaminated environments.

Survival of Extremotolerant Bacteria from the Mukundpura Meteorite Impact Crater.

Carbonaceous meteorites provide clues with regard to prebiotic chemistry and the origin of life. Geological Survey of India recorded a carbonaceous chondrite meteorite fall in Mukundpura, India, on June 6, 2017. We conducted a study to investigate the microbial community that survived the meteorite impact. 16S rRNA metagenomic sequencing indicates the presence of Actinobacteria, Proteobacteria, and Acidobacteria in meteorite impact soil. Comparative phylogenetic analysis revealed an intriguing abundance of class Bacilli in the impact soil. Bacillus thermocopriae IR-1, a moderately thermotolerant organism, was isolated from a rock, impacted by the Mukundpura meteorite. We investigated the resilience of B. thermocopriae IR-1 to environmental stresses and impact shock in a Reddy shock tube. Bacillus thermocopriae IR-1 survived (28.82% survival) the effect of shock waves at a peak shock pressure of 300 kPa, temperature 400 K, and Mach number of 1.47. This investigation presents the first report on the effect of impact shock on B. thermocopriae IR-1. The study is also the first report on studying the microbial diversity and isolation of bacteria from impact crater soil immediately after meteorite impact event.

Abstract 1533: 16S rRNA saliva analysis unveils differences in the head and neck squamous cell carcinoma microbiome before and after surgical resection

Abstract Systemic inflammatory events and localized disease, mediated by the microbiome, may be measured in saliva as head and neck squamous cell carcinoma (HNSCC) diagnostic and prognostic biomonitors. We compared the saliva microbiome in DNA isolated from 38 patients and 25 normal oral cavity epithelium controls to characterize the HNSCC microbiota before and after surgical resection. PCR amplification of the 16S rRNA V3-V5 gene region was performed using the 357F/926R primer set prior to multiplexing on the Roche/454 GS Junior sequencing platform. Data were screened for chimeric sequences and contaminant chloroplast DNA after pre-processing. Passing sequences were characterized for diversity and taxonomic composition using QIIME and R before cross-tabulation analyses were performed. After preprocessing 142,887 reads were obtained with an average length of 491 bp. The number of sequences per sample was rarefied at 3,487 to guarantee equal depth. Bacteroidetes, Firmicutes, and Proteobacteria dominated the microbiome in our sample set with less frequent presence of Actinobacteria and Fusobacteria members. At lower taxonomic levels, the most abundant genera observed were Streptococcus, Prevotella, Haemophilus and Veillonella with lower numbers of Citrobacter and Neisseraceae genus Kingella. We found that 46 OTUs changed significantly in HNSCC patients (p<0.05) when compared to the controls mainly due to the loss of Neisseria and Aggregatibacter (Proteobacteria), Leptotrichia (Fusobacteria) and Veilonella (Firmicutes) with an increase in some Lactobacillus (Firmicutes). Within bacteroidetes, Prevotella OTUs were found more abundant in control samples. HNSCC patients had a significant loss in richness and diversity (p<0.05) compared to the controls. HPV positive samples were more diverse (higher Shannon values and richness) than HPV negative samples. Longitudinal analyses (3 time periods) of samples taken before and after surgery revealed a reduction in the alpha diversity measure after surgery, together with an increase of this measure in patients that recurred. We also observed statistically significant differences (p<0.05) at the phyla (Actinobacteria and Fusobacteria), and genus (Veillonella and Prevotella) levels. Interestingly, in one patient whose HPV status shifted from HPV positive to HPV negative after surgery, the abundance of Lactobacillus OTUs decreased, and Streptococcus (OTU 1009) increased significantly, being also associated with an HPV negative status in another patient. We are the first to observe that OTUs and several microbial communities at different taxonomic levels discriminate HNSCC from control samples; HPV positive and HPV negative samples; and pre- vs postsurgical treatment samples. Future work will determine the correlation of microbial communities in paired tissue and saliva HNSCC samples, as well as their link to treatment response and survival. Citation Format: Rafael E. Guerrero-Preston, Filipa Godoy-Vitorino, Herminio González, Christina Michailidi, Anne Jedlicka, Amanda Dziedzic, Rajagowthamee Thangavel, Tal Hadar, Maartje G. Noordhuis, William Westra, Wayne Koch, David Sidransky. 16S rRNA saliva analysis unveils differences in the head and neck squamous cell carcinoma microbiome before and after surgical resection. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 1533. doi:10.1158/1538-7445.AM2015-1533

Bacterial community composition in three freshwater reservoirs of different alkalinity and trophic status.

In order to investigate the factors controlling the bacterial community composition (BCC) in reservoirs, we sampled three freshwater reservoirs with contrasted physical and chemical characteristics and trophic status. The BCC was analysed by 16S rRNA gene amplicon 454 pyrosequencing. In parallel, a complete dataset of environmental parameters and phytoplankton community composition was also collected. BCC in the analysed reservoirs resembled that of epilimnetic waters of natural freshwater lakes with presence of Actinobacteria, Alpha- and Betaproteobacteria, Cytophaga–Flavobacteria–Bacteroidetes (CFB) and Verrucomicrobia groups. Our results evidenced that the retrieved BCC in the analysed reservoirs was strongly influenced by pH, alkalinity and organic carbon content, whereas comparatively little change was observed among layers in stratified conditions.

Abstract 870: 16S rRNA saliva analysis unveils microbiome biomonitors linked to human papilloma virus and oropharyngeal squamous cell carcinoma

Abstract Microbiota markers in saliva able to distinguish HPV positive from HPV negative Head and Neck Squamous Cell Carcinoma (HNSCC) patients, as well as HNSCC patients from controls, will enable increases in treatment options, reductions in treatment costs and improvements in survival rates. In the present study we compared the microbiota present in saliva DNA from HPV positive and HPV negative oropharyngeal cancer (OPSCC) patients to saliva DNA from uvulopalatopharyngoplasty (UPPP) patients, used as normal oral mucosa controls. PCR amplification of the 16S rRNA V3-V5 gene region was performed using the 357F/926R primer set. Amplified fragments were multiplexed on the Roche/454 GS Junior sequencing platform. Data were screened for chimeric sequences and contaminant chloroplast DNA after pre-processing. Passing sequences were characterized for diversity and taxonomic composition using QIIME and R before cross-tabulation analyses were performed. Bacteroidetes, Firmicutes, and Proteobacteria dominated the microbiome in our sample set with less frequent presence of Actinobacteria and Fusobacteria members. At lower taxonomic levels, the most abundant genera observed were Streptococcus, Prevotella and Veillonella. We found statistically significant associations in the alpha-diversity estimators of UPPP and OPSCC patients. Specifically, the microbiota communities present in UPPP are significantly enriched in the observed_species category (P<0.001). The raw number of operational taxonomic units (OTUs) was also significantly higher in UPPP when compared to OPSCC patients (p=0.02). Specifically, a threshold of 80 OTUs was enough to discriminate UPPP from OPSCC patients. At the phylum level, we did not detect a significant difference in taxa of UPPP and OPSCC patients. Yet at the family level, the taxon Fusobacteriales_Leptotrichiaceae is dramatically enriched in UPPP samples when compared to OPSCC (p=0.02) and is present in very high numbers in all UPPP samples. A threshold of 10 sequences assigned to Fusobacteriales_Leptotrichiaceae discriminated UPPP from OPSCC patients. At the genera level we found that the genus Tannerella is exclusively observed in UPPP patients (p=0.03). At the class level, Bacteroidetes_Flavobacteria appears significantly enriched in HPV- when compared to HPV+ OPSCC patients (p=0.02). A threshold of 5 sequences assigned to Flavobacteria discriminated HPV+ from HPV- OPSCC patients. At the class level, we also observed enrichment of the taxon Bacteroidetes_Flavobacteria in UPPP relative to OPSCC HPV+ patients (p=0.03). And at the genus level, the low-level presence of Aerococcaceae_Abiotrophia discriminated UPPP from OPSCC HPV+ patients (p=0.02). Our preliminary results suggest that the microbial diversity and taxonomic composition of the microbiota in saliva may be useful diagnostic and early detection biomonitors for OPSCC. Citation Format: Rafael E. Guerrero-Preston, Christina Michailidi, Anne Jedlicka, Rajagowthamee Thangavel, Tal Hadar, Maartje G. Nordhuis, William Westra, Wayne Koch, Joseph Califano, David Sidransky. 16S rRNA saliva analysis unveils microbiome biomonitors linked to human papilloma virus and oropharyngeal squamous cell carcinoma. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 870. doi:10.1158/1538-7445.AM2014-870

A molecular study on bacterial resistance to arsenic-toxicity in surface and underground waters of Latium (Italy)

Latium, a region in central Italy, is known for its extensive volcanic areas that make a significant contribution to the arsenic (As) contamination of freshwater environments, even though some degree of As water pollution may be caused by human activities. The information available on indigenous As-resistant prokaryotes in aquatic environments of Latium is, however, still limited. In this study, we describe new bacteria that are resistant to arsenic toxicity and were isolated from the surface waters of Lake Vico and the Sacco River, two groundwater systems in Latium, as well as from bottled natural mineral water from the same region. The 16S rRNA gene sequence analysis for the As-resistant strains in lake and river waters points to a prevalence of β- and γ-Proteobacteria, while α-Proteobacteria, Firmicutes and Bacteroidetes are represented to a lesser extent. By contrast, solely γ-Proteobacteria were isolated from groundwater samples. The presence of Actinobacteria was documented exclusively in bottled mineral water. In addition, we conducted a DNA sequence-based study on the gene codifying arsB, an As(III) efflux membrane protein pump related to arsenic resistance, for all the As-resistant bacterial isolates. A phylogenetic analysis was carried out on the newly sequenced 16S rRNA genes and arsB in the present study as well as on an additional 16S rRNA/arsB dataset we obtained previously from Lake Albano, from the Tiber and from a well in Bassano Romano located in Latium (Davolos and Pietrangeli, 2011). Overall, the phylogenetic diversity of As-resistant bacteria in underground water was very limited if compared with lentic and lotic waters. Lastly, our molecular data support the hypothesis that the horizontal gene transfer of ars in As-containing freshwater environments is not limited to closely-related genomes, but also occurs between bacteria that are distant from an evolutionary viewpoint, thereby indicating that such genetic events may be considered a source of microbial resistance to arsenic-toxicity.

Characterisation of the first actinobacterial group isolated from a Mexican extremophile environment

The "Cave of Crystals" (aka 'Naica') in Chihuahua Mexico is a natural unique subterranean ecosystem which mainly consists of crystals made of calcium sulfate. The main system of caves are found at a depth of 300meters (m) below sea level with crystals that range in size from a few centimeters to 15m. The crystals date from nearly 400,000years old and are thought to be formed when the cave was fully covered by water. At present time, this place shows a nearly constant temperature of 55°C over the year and a humidity of 100% which makes this place incomparable and unbearable to animal and/or human life. In the present study, two actinobacterial groups were isolated from within this system of caves and subjected to a systematic study to establish their phylogenetic relationship to microorganisms belonging to this vast group of Gram positive bacteria. Phenotypic properties, chemotaxonomic and 16S rRNA gene sequencing show that the microorganisms are members of the family Pseudonocardiaceae and are most closely related to the genus Prauserella. The present study is the first to report the isolation and presence of Actinobacteria or any other microbial form of life in this exceptional place. Moreover, this unexpected biodiversity can also provide an insight of the antibiotic resistome present in the isolates reported in this study.

Analysis of Bacterial Community Associated with Aaptos sp. from Rote and Seribu Islands

Aaptos sp. is a marine sponge that could produce bioactive compounds such as aaptamin, aaptosin, and isoaaptamin which have activities as antitumor, antimicrobial, and antiviral. Community of bacteria associated with the sponge might correlate with production of those bioactive compounds and be affected by water environment where the sponge grow. The presence of anthropogenic stressor such as pollutans might become a burden to the waters where the biota grown and could affect the microbial biodiversity in the sponge and its active metabolite produced. The objective of this research was to analyze bacterial community associated with Aaptos sp. from Rote Island and Seribu Islands, using T-RFLP method. The results showed that bacterial community associated with Aaptos sp. from both sampling sites shared 40.81% similarity in which they were dominated by the same bacteria class of Actinobacteria, Flavobacteria, α-proteobacteria, δ-proteobacteria, and γ–proteobacteria. The bacteria collected from Rote island were more highly distributed and diverse than those from Seribu Islands. A total of 23 classes of microorganism were identified in Rote Island waters, while in Seribu Islands was 14 classes of microorganism. The presence of Actinobacteria and Proteobacteria in Aaptos sp., is allegedly involved in the production of secondary metabolites.

Ecophysiology of mycolic acid-containing Actinobacteria (Mycolata) in activated sludge foams

Increasing incidences of activated sludge foaming have been reported in the last decade in Danish plants treating both municipal and industrial wastewaters. In most cases, foaming is caused by the presence of Actinobacteria; branched mycolic acid-containing filaments (the Mycolata) and the unbranched Candidatus'Microthix parvicella'. Surveys from wastewater treatment plants revealed that the Mycolata were the dominant filamentous bacteria in the foam. Gordonia amarae-like organisms and those with the morphology of Skermania piniformis were frequently observed, and they often coexisted. Their identity was confirmed by FISH, using a new permeabilization procedure. It was not possible to identify all abundant Mycolata using existing FISH probes, which suggests the presence of currently undetectable and potentially undescribed populations. Furthermore, some Mycolata failed to give any FISH signal, although substrate uptake experiments with microautoradiography revealed that they were physiologically active. Ecophysiological studies were performed on the Mycolata identified by their morphology or FISH in both foams and mixed liquors. Large differences were seen among the Mycolata in levels of substrate assimilation and substrate uptake abilities in the presence of different electron acceptors. These differences were ascribed mainly to the presence of currently undescribed Mycolata species and/or differences in foam age.

Microbial Diversity in Sediments of Saline Qinghai Lake, China: Linking Geochemical Controls to Microbial Ecology

Saline lakes at high altitudes represent an important and extreme microbial ecosystem, yet little is known about microbial diversity in such environments. The objective of this study was to examine the change of microbial diversity from the bottom of the lake to sediments of 40 cm in depth in a core from Qinghai Lake. The lake is saline (12.5 g/L salinity) and alkaline (pH 9.4) and is located on the Qinghai-Tibetan Plateau at an altitude of 3196 m above sea level. Pore water chemistry of the core revealed low concentrations of sulfate and iron (<1 mM), but high concentrations of acetate (40-70 mM) and dissolved organic carbon (1596-5443 mg/L). Total organic carbon and total nitrogen contents in the sediments were approximately 2 and <0.5%, respectively. Acridine orange direct count data indicated that cell numbers decreased from 4 x 10(9) cells/g at the water-sediment interface to 6 x 10(7) cells/g wet sediment at the 40-cm depth. This change in biomass was positively correlated with acetate concentration in pore water. Phospholipid fatty acid (PLFA) community structure analyses determined decrease in the proportion of the Proteobacteria and increase in the Firmicutes with increased depth. Characterization of small subunit (SSU) rRNA genes amplified from the sediments indicated a shift in the bacterial community with depth. Whereas the alpha-, beta-, and gamma-Proteobacteria and the Cytophaga/Flavobacterium/Bacteroides (CFB) were dominant at the water-sediment interface, low G + C gram-positive bacteria (a subgroup of Firmicutes) became the predominant group in the anoxic sediments. Both PLFA and the sequence data showed similar trend. The Proteobacteria, CFB, and gram-positive bacteria are present in other saline lakes, but the presence of Actinobacteria and Acidobacteria/Holophaga in significant proportions in the Qinghai Lake sediments appears to be unique. The archaeal diversity was much lower, and clone sequences could be grouped in the Euryarchaeota and Crenarchaeota domains. The archaeal clones were not related to any known cultures but to sequences previously found in methane-rich sediments. Acetate-utilizing methanogens were isolated from sediment incubations, and alpha- and gamma-proteobacterial isolates were obtained from a water sample from the lake-bottom (23 m). Our data collectively showed that the observed diversity and shift in the community structure with depth was correlated with geochemical parameters (the redox state and availability of electron acceptor and donor). Heterotrophic methanogenesis is possibly adominant metabolic process in the Qinghai Lake sediments. These results reinforce the importance of geochemical controls on microbial ecology in saline and alkaline lake environments.

Diversity of cyanobacteria and heterotrophic bacteria in cyanobacterial blooms in Lake Joutikas, Finland

3 Present address: National Product Control Agency for Welfare and Health, PO Box 210, 00531 Helsinki, Finland ABSTRACT: Water samples were collected in August 2001 and 2002 from the eutrophic Lake Joutikas during cyanobacterial blooms. DNA and RNA were isolated from size fractionated samples and the diversity of the bacteria present in each fraction was studied by PCR amplification of partial 16S rRNA and denaturing gradient gel electrophoresis (DGGE) fingerprinting. Major bands from the gels were sequenced for further identification. Cyanobacteria were also identified and counted under the microscope. Anabaena/Aphanizomenon were the most abundant cyanobacteria in both years, although the dominant species was different each year. When comparing the 2 techniques, equal numbers of abundant Anabaena/Aphanizomenon morphotypes were detected by microscopy and phylotypes by DGGE. The genera Microcystis and Synechococcus appeared more abundant in the DGGE analysis than under the microscope. In the heterotrophic bacterial community variation was observed between the bloom samples from the 2 years. Verrucomicrobia was the most abundant group in both years in both DNA- and RNA-derived profiles. Otherwise the patterns based on DNA- and RNA-derived DGGE-profiles differed, especially in 2002. The presence of Actinobacteria and Chloroflexi was less pronounced in RNA-based than in DNA-based analysis. This indicates that their relative biomass was smaller than estimated by DNA-analysis. It might also indicate that they were metabolically inactive. In contrast, in 2002, the CFB group (Cytophaga-Flavobacterium-Bacteroides) and δ-Proteobacteria were more prominent in the RNA-based than in the DNA-based profiles. Thus they probably formed a substantial fraction of biomass and/or were active members in the blooms.