16S rDNA Gene Sequence Research Articles

TOLUENE DEGRADATION BY FREE STAPHYLOCOCCUS GALLINARUM AND IMMOBILIZED ON MULTI-WALLED CARBON NANOTUBES

Hydrocarbons pollution is a most important environmental and healthanxiety . Using free and immobilized bacteria could be a suitable attitude to find a proper bioaugmentation agent. A toluene degrading bacterium was isolated from oil-contaminated environs (located in Bandar-Anzali, Guilan, Iran). The strain was molecularly identified as Staphylococcus gallinarum ATHH41 (Accession number: KX344723) by partial sequencing of 16SrDNA gene. The response surface methodology (RSM) was expended for biodegradation of the toluene by ATHH41. The central composite design (CCD) was utilized to optimize pH, temperature, and toluene concentration by ATHH41. In accordance with the optimization purpose of the Design-Expert software, the optimum circumstances of toluene degradation were obtained when pH, temperature and toluene concentration were adjusted to 7.68, 31.73°C and 630.04 mg.l-1, respectively. Multi-walled carbon nanotubes (MWCNTs) were used to immobilize the strain. Infrared spectroscopy and scanning electron microscopy showed that the cells adhered to the MWCNT surface and developed a biofilm. Results reveal that free cells were able to degrade 68.01% of the toluene as the sole carbon and energy source within 24 h under optimized conditions. The immobilized cells reached 95.68%.

Nutrient availability is a dominant predictor of soil bacterial and fungal community composition after nitrogen addition in subtropical acidic forests.

Nutrient addition to forest ecosystems significantly influences belowground microbial diversity, community structure, and ecosystem functioning. Nitrogen (N) addition in forests is common in China, especially in the southeast region. However, the influence of N addition on belowground soil microbial community diversity in subtropical forests remains unclear. In May 2018, we randomly selected 12 experimental plots in a Pinus taiwanensis forest within the Daiyun Mountain Nature Reserve, Fujian Province, China, and subjected them to N addition treatments for one year. We investigated the responses of the soil microbial communities and identified the major elements that influenced microbial community composition in the experimental plots. The present study included three N treatments, i.e., the control (CT), low N addition (LN, 40 kg N ha-1 yr-1), and high N addition (HN, 80 kg N ha-1 yr-1), and two depths, 0-10 cm (topsoil) and 10-20 cm (subsoil), which were all sampled in the growing season (May) of 2019. Soil microbial diversity and community composition in the topsoil and subsoil were investigated using high-throughput sequencing of bacterial 16S rDNA genes and fungal internal transcribed spacer sequences. According to our results, 1) soil dissolved organic carbon (DOC) significantly decreased after HN addition, and available nitrogen (AN) significantly declined after LN addition, 2) bacterial α-diversity in the subsoil significantly decreased with HN addition, which was affected significantly by the interaction between N addition and soil layer, and 3) soil DOC, rather than pH, was the dominant environmental factor influencing soil bacterial community composition, while AN and MBN were the best predictors of soil fungal community structure dynamics. Moreover, N addition influence both diversity and community composition of soil bacteria more than those of fungi in the subtropical forests. The results of the present study provide further evidence to support shifts in soil microbial community structure in acidic subtropical forests in response to increasing N deposition.

Isolation and Identification of Biosurfactant Producing Bacterial Strain from Saline Soil Samples in Iran; Evaluation of Factors on Biosurfactant Production

Background: Biosurfactants are a group of valuable amphiphilic molecules that have been widely used in different industries such as pharmaceuticals and cosmetics. Objectives: The current study aimed to screen and identify a bacterial strain able to produce biosurfactant from environmental soil samples, followed by evaluating factors that contribute to biosurfactant production. Methods: The biosurfactants production was evaluated every 24 hours by emulsification index (EI), oil spreading ability, and surface tension measurement. Thereafter, the sequences of 16S rDNA genes and biochemical tests were performed to identify the isolated bacterial. Furthermore, the effect of different factors, including nitrogen, vegetable oil, and cations on biosurfactant productivity of the selected bacterial strain, was also evaluated. Results: In primary screening, out of the six bacterial strains, only one isolate was found to produce a hemolytic zone on the blood agar plate. The EI index was increased in a time-dependent manner with a maximum EI of 10% after 12h. Surface tension measurement revealed decreased surface tension (51 mN/m) after 12 hours' incubation compared to that of the blank sample. The selected isolate was recognized as Bacillus atrophaeus by 16S rDNA gene sequencing and biochemical test. All applied factors in culture media could decrease the surface tension of culture broth compared to that of the blank sample. Conclusions: This study demonstrated a Bacillus strain able to produce biosurfactants. Such biosurfactant producers would have great potentials in bioremediation activities and microbial enhanced oil recovery.

Isolation, identification and evaluation of Lactic acid synthesis of bacteria in traditional fermented products in Vietnam

Nowadays, many food products are promoted as being particularly healthy due to the characteristics of certain strains of lactic acid bacteria. Lactic acid bacteria (LAB) play a vital role in different fields, including food, pharmacy due to their benefit for young children, pregnant women and the elderly. LAB is one of the most significant groups of microorganisms used in food fermentations. They improve the flavour and texture of fermented foods. Moreover, LAB kills food spoilage bacteria by developing growth-inhibiting compounds. In this study, seven strains of LAB were isolated from traditional fermented products in VietNamm including fermented rice, kimchi, and yoghurt. Moreover, LAB isolated was identified by amplification and sequencing of 16s rDNA gene. The isolated strains were Lactobacillus plantarum (M2 and M7), Lactobacillus paracasei (M4), Lactobacillus sakei (M10), Leuconostoc mesenteroides (M15), Lactobacillus curvatus (M17), Lactobacillus delbruekii sub sp. (M19). Cultural characteristics of M1 and M7 surface colony are 2mm wide, raised, smooth and white on MRS agar. The morphology of the colonies M4 and M10 is rounded, smooth, light yellow. Nevertheless, M4 and M10 are quite different in colour, white and light yellow, respectively. Moreover, M15 colonies are convex, with flat edges, smooth, semitransparent. M17 and M19 are small, normally rough and non-pigment. Acid lactic content produced by the isolated strains determined by spectral absorbance at 390 nm with FeCl3 (0.2%), was highest in M2 strain (37.814g/l), followed by M17 (32.357g/l), M19 (27.336g/l), M4 (20.853g/l), M10 (9.408g/l), M7 (8.864g/l), and M15 (6.645g/l). In this study, the highest lactic acid content produced was M2 stain (Lactobacillus plantarum) and the lowest was M15 (Leuconostoc mesenteroides).

Changes in heterotrophic microbial communities induced by biocidal treatments in the Monastery of San Martiño Pinario (Santiago de Compostela, NW Spain)

Previous studies have provided evidence that chemical biocides can condition the behaviour of microbial populations, thereby promoting recolonization by some groups of microorganisms. We conducted a year-long study to evaluate the extent to which fungal and bacterial communities are affected by the biocidal treatments Biotin R®, Biotin T®, Preventol RI80®, New Des 50®, benzalkonium chloride and an ethanol-water (1:1) mixture, used to remove Apatococcus lobatus from the granite walls of the San Martiño Pinario Monastery in Santiago de Compostela (NW Spain). Bacterial, fungal, algal and cyanobacterial concentrations were enumerated via microscopic counts of colony-forming units on agar plates, one, six and twelve months after application of the biocidal treatments. Cultivable species were further characterized by morphological taxonomic analysis (algae and fungi) and DNA analysis by sequencing of 16S rDNA gene (bacteria) and the ITS region plus the D1/D2 region of the 28S rDNA gene (fungi) before and after one-year treatment. None of the treatments led to overgrowth of bacteria or fungi, while benzalkonium chloride and water (used as control) treatments were the most effective in preventing bacterial recolonization and Biotin T® was the most effective in preventing fungal recolonization. Although the bacterial population did not increase in numbers after any of the treatments, the diversity was altered, with Bacillus halotolerans disappearing and Bacillus pumilus and Brachybacterium paraconglomeratum appearing in the areas treated with biocides. In fungi, Eutypa sp. was eliminated with all biocides except with Preventol RI80® and no species was promoted.

A case report of wrist synovial infection due to Mycobacterium jacuzzii, Iran

BackgroundMycobacterium jacuzzii (M. jacuzzii) was first isolated in 2003 by insertion of breast implants in Tel Aviv, Israel. In this case report, we describe our experience in detection of M. jacuzzii using phenotypic and genotypic test of wrist synovial sample.Case presentationA 73-year-old woman complained of pain and swelling in the right wrist for 4 months. Her body temperature was 37–38 °C, and symptoms, such as pain, swelling, and some movement limitation, were reported. Clinical laboratory parameters showed an elevated C-reactive protein (CRP) level, erythrocyte sedimentation rate (ESR), and white blood cells (WBC) count. The sequences of hsp65, rpoB, 16S rDNA, and sodA genes indicated very high homology to M. jacuzzii.ConclusionWe report a case of synovial infection caused by M. jacuzzii in a patient with severe wrist pain in Iran, who was treated with amikacin, levofloxacin, and ethambutol. The outcomes of treatment after 8 months were positive, and no recurrence of infection was reported in the patient.

Phylogenetic Analysis of Streptomyces spp. Isolated from Soil Samples in Sulaimani Governorate

Streptomyces species have been an important source of bioactive secondary metabolites and clinically useful for antibiotic production, including fosfomycin, daptomycin, oxytetracycline, streptomycin, and chloramphenicol. The main objective of this study was to isolate actinomycetes, especially Streptomyces from 8 soil samples that collected from two different places, which are districts in Sulaimani governorate, Kurdistan Region of Iraq. Totally, 30 diagnostic tests were carried out for representative of isolated Streptomyces depending on the color groups. The 16Sr DNA gene was sequenced, for ten isolated test strains were amplified with 2 universal primers after extraction of genomic DNA, only 8 of them were successfully sequenced. Phylogenetic analysis of 8 test strains carried out using base sequences of 16Sr DNA genes in the core genome. Four of isolated test strains were identified as a Streptomyces fulvissimus, and others were nominated as a Streptomyces anulatus. The obtained sequence data were compared with the sequence data of the closest related species in the international databases using EzTaxon Server program and (%) similarities were determined. Finally, phylogenetic analysis indicated that isolated test strains were nominated as (H001, H002, H003, and H004), which recognized members of the S. anulatus and the similarity with their type strain is 99.93%. Whereas, other four isolated test strains, including D001, D002, D003, and D004 recognized as members of the S. fulvissimus and similarity with their type strain is 100%.

Amblyomma nodosum Neumann, 1889 on collared anteaters (Tamandua tetradactyla) from the Andean region of Colombia.

Amblyomma nodosum is a Neotropical tick species distributed from Mexico to Argentina, with adult individuals infesting different mammal species, including anteaters (Pilosa: Myrmecophagidae). Few reports in Colombia have recorded this species in departments such as Meta, Tolima and Valle del Cauca. In this paper we describe this species using taxonomic, morphometric and molecular methods after collecting individuals parasitizing collared anteaters (Tamandua tetradactyla) in the departments of Cundinamarca and Tolima. Adult specimens were identified based on current taxonomic keys and different morphometric variables were documented in nonengorged individuals. Also, DNA was extracted for PCR amplification and sequencing of 16S rDNA, COI and ITS2 genes. Phylogenetic trees were built. One hundred and thirty-four adult ticks were collected and identified as Amblyomma nodosum, based on morphological, morphometric, molecular and phylogenetic analyses. This is the first study to report the presence of this tick species in the department of Cundinamarca, using multiple identification approaches, thus expanding its geographical records in Colombia.

A new species of Petrolisthes (Crustacea, Anomura, Porcellanidae) inhabiting vermetid formations (Mollusca, Gastropoda, Vermetidae) in the southern Caribbean Sea.

Petrolisthes virgiliussp. nov. from the Caribbean Sea of Colombia is described. The new species resembles P. tonsorius morphologically but differs from it principally by its color and habitat. Petrolisthes tonsorius is brown or blueish brown and occurs under intertidal boulders strongly exposed to water movement. Petrolisthes virgiliussp. nov. is pale brown to beige and lives exclusively in intertidal areas dominated by vermetid snails, exposed to heavy wave action. The entangled tubular shells of vermetids are cemented to each other and to a hard substrate like beach rock, forming a microhabitat for the new crab species and other porcellanids of the genera Neopisosoma and Clastotoechus. Large genetic distances between DNA sequences of the mitochondrial 16S rDNA gene from P. virgiliussp. nov. and P. tonsorius confirmed that they comprise different species. Petrolisthes virgiliussp. nov. is the 53rd member of the West Atlantic porcellanid fauna.

Exploring the diversity and dynamic of bacterial community vertically distributed in Tongguling National Nature Reserve in Hainan Island, China.

National nature reserves are important for preserving ecological resources and constructing national ecological security barriers. Tongguling National Nature Reserve (TNNR) is known for its unique tropical island ecosystem and abundant biological resources. This study was conducted to characterize and compare its bacterial community diversity and composition in soils from 10, 20, and 30cm in depth using high-throughput sequencing of 16S rDNA genes. We found that soils from 20cm had the highest diversity and might serve as a "middle bridge" to the dynamic distribution between the 10- and 30-cm soil samples. The diversity pattern indicated that the main abundant groups varied distinctly and significantly among soils of different depths. Moreover, Chloroflexi was the most dynamic group in TNNR soils, together with another abundant but rarely reported group, Verrucomicrobia, which greatly enhanced the microbial diversity of TNNR soils. Overall, the results of this study emphasize the urgent need for greater understanding of bacterial community variations in response to human activities and climate change.

Wolbachia of phylogenetic supergroup E identified in oribatid mite Gustavia microcephala (Acari: Oribatida)

Heritable endosymbionts have been observed in arthropod and nematode hosts. The most-known among them is Wolbachia. Although the bacterium was previously identified in oribatid mites (Acari: Oribatida), it was not assigned to any phylogenetic group. Endosymbionts have a profound influence on their hosts, playing various functions that affect invertebrate’s biology such as changing the way of reproduction. Oribatida provide the very unique examples of groups in which even whole families appear to be thelytokous, so we considered that it is worth to investigate the occurrence of endosymbiotic microorganisms in oribatid mites, especially that the knowledge on the symbionts occurrence in this invertebrate group is negligible. We report for the first time Wolbachia in oribatid mite Gustavia microcephala. The sequences of 16S rDNA, gltA, and ftsZ genes of the endosymbiont from the mite showed the highest similarity to Wolbachia found in Collembola. Phylogenetic analysis based on single gene and concatenated alignments of three genes revealed that the bacteria from G. microcephala and Collembola were related and clustered together with supergroup E. Relatively close relationship of Wolbachia from oribatid and collembolan hosts might mean at the evolutionary scale that horizontal transfer of bacteria between these two groups of invertebrates may take place.

ISOLATION AND MOLECULAR IDENTIFICATION OF INDIGENOUS BACTERIAL ISOLATES ABLE TO DEGRADE ORGANOPHOSPHATES

The wide and indiscriminate use of pesticides for pest control in agriculture has inflicted serious harm and problems to humans as well as to the biodiversity. Microbial degradation of pesticides in contaminated soils has been considered advantageous to decontaminate areas that have been polluted by pesticides. Chlorpyrifos and diazinon were the most persistent residues in Egyptian soils. Four bacterial isolates were isolated from organophosphorus insecticides contaminated soils and genetically identified based on DNA sequence of 16s rDNA gene, Cronobacter muytjensii GH10, Achromobacter xylosoxidans GH9OP, Pseudomonas aeruginosa GH2NO8 and Pseudomonas putida GH4SNO/P were able to degrade 92.59%, 97.75%, 91.82%, and 90.78% of diazinon (600mg/l) as compared with 16.99% in control and 93.43%, 78.51%, 93.18% and 95.36% of chlorpyrifos (480mg/l) as compared with 4.28%, in control, respectively after 20 days of incubation.

Dissemination of resistance genes in duck/fish polyculture ponds in Guangdong Province: correlations between Cu and Zn and antibiotic resistance genes.

Duck/fish polyculture farming is a typical farming model in the Pearl River delta in southern China. We examined soil, water, and sediment samples from three duck-fish farms in Guangdong Province in September and December 2014. We determined the abundance of three metal resistance genes, 16S rDNA, and 23 antibiotic resistance genes encoding resistance to tetracycline, sulfonamides, quinolones, chloramphenicol, and β-lactamases. Microbial community structure was quantified by Illumina high-throughput sequencing of 16S rDNA genes. We found a prevalence of antibiotic resistance genes and the sul1, sul2, tetA, tetM, aac(6')-Ib, and floR genes were the most abundant. Levels of Cu and Zn were significantly correlated with numerous ARG types and sul2, floR, and tetM were identified as potential antibiotic resistance gene indicators. Cu levels were significantly and positively correlated with the relative abundance of sul3, tetT, tetW, qnrB, qnrS, fexB, sul1, sul2, tetM, and qnrA. Zn was significantly correlated to relative abundance of sul2, sul3, tetM, tetA, tetT, tetW, qnrA, qnrB, qnrS, aac(6')-Ib, qepA, blaSHV, cmlA, floR, fexA, cfr, and fexB. The levels of Acinetobacter, Brevibacillus, and Wautersiella showed significant positive correlations with metal resistance genes as well as qnrB, oqxA, oqxB, and blaSHV (p > 0.8). Sphingobacterium, Flavobacterium, Acidothermus, and Corynebacterium had significant correlations with abundance of tetracycline resistance genes, sulfonamide resistance genes, blaTEM, blaCTX, and cfr (p > 0.8). Sphingobacterium, Flavobacterium, Acidothermus, and Corynebacterium were most abundant in soil samples while Acinetobacter, Brevibacillus, and Wautersiella were most abundant in water samples. Dissemination of antibiotic resistance genes in aquaculture environments is extensive and tracing their origins is necessary to establish risk assessment methods required for aquatic environmental protection.

The influence of land use on nitrogen and sulfur turnover: a microbial approach

Saline lakes are subject to numerous environmental impacts related to human activities. Pollution is one of the major threats to water bodies, since it produces the increase of nitrogen and sulfur contents, changing the chemical and biological conditions of the ecosystem. Microbially mediated redox processes exert a fundamental control on nutrient and contaminant turnover. Therefore, the aim of this study was to determine the influence of land use on the microbial communities responsible for N and S turnover in the lacustrine sediments from Pétrola Lake (SE Spain) disturbed by anthropogenic activities (agriculture, farming, mining, and wastewaters). To reach this goal, chemical and molecular tools (sequencing of 16S rDNA gene) were applied. The results showed the influence of land use on the chemistry and microbial community structure of the sediments from the saline lake. Compared to natural conditions, wastewater and mining showed the largest differences in terms of microbial structure as a result of salinity. These findings provide better understanding of how land use affects the water chemistry and the abundance of organisms responsible for nutrient turnover.

A new species of Pheronematidae (Porifera: Hexactinellida: Amphidiscosida) from the Northwest Pacific Ocean

A new species of the family Pheronematidae is described in this study. Specimens were collected at Yap seamount and Caroline seamount in the Northwest Pacific Ocean. Poliopogon distortus sp. nov. contains oval macramphidiscs, three categories of amphidiscs, clavate monaxons and sceptres, making it distinguished from the eight known congeners easily. This is the fourth record of genus Poliopogon from the Northwest Pacific Ocean. We also used a partial sequence of 16S rDNA gene to confirm the family assignment of the new specimen.

Bacteriological sampling of peritoneal dialysis fluids. How to limit negative-culture peritonitis rate?

Peritonitis is a major and serious complication in terms of morbi-mortality for patients treated with peritoneal dialysis. Their microbiological diagnosis is challenging for both the detection of the etiological agents and in interpreting positive cultures.
 Many microorganisms can cause this infection; usual micro-organisms such as coagulase-negative staphylococci or Enterobacteriaceae, but also ‘atypical’ bacteria, which culture or detection, is more tedious can be found.
 To identify the responsible bacteria, molecular biology and culture techniques can be set up. Molecular biology (particularly the sequencing of the universal 16s rDNA gene) makes it possible to identify atypical agents, but antimicrobial susceptibility testing cannot be performed following these technics.
 The culture of peritoneal dialysis fluids remains the ‘gold-standard’ for the diagnosis of these infections. Nevertheless this must be optimized to enhance its sensitivity.
 The etiological diagnosis of peritonitis in patients treated with peritoneal dialysis may be difficult, but modern microbiology combined with a bacterioclinical discussion allow the identification of the microorganism responsible for the infection in the great majority of the cases.

Exploring Monacha cantiana (Montagu, 1803) phylogeography: cryptic lineages and new insights into the origin of the English populations (Eupulmonata, Stylommatophora, Hygromiidae).

Molecular analysis of nucleotide sequences of mitochondrial cytochrome oxidase subunit 1 (COI) and 16S ribosomal DNA (16SrDNA) as well as nuclear histone 3 (H3) and internal transcribed spacer 2 of rDNA (ITS2) gene fragments together with morphological analysis of shell and genitalia features showed that English, French and Italian populations usually assigned to Monacha cantiana consist of four distinct lineages (CAN-1, CAN-2, CAN-3, CAN-4). One of these lineages (CAN-1) included most of the UK (five sites) and Italian (five sites) populations examined. Three other lineages represented populations from two sites in northern Italy (CAN-2), three sites in northern Italy and Austria (CAN-3), and two sites in south-eastern France (CAN-4). The taxonomic and nomenclatural setting is only currently available for lineages CAN-1 and CAN-4; a definitive frame for the other two requires much more research. The lineage CAN-1 corresponds to the true M. cantiana (Montagu, 1803) because it is the only one that includes topotypical English populations. The relationships and genetic distances support the hypothesis of the Italian origin of this lineage which was probably introduced to England by the Romans. The lineage CAN-4 is attributed to M. cemenelea (Risso, 1826), for which a neotype has been designated and deposited. Its diagnostic sequences of COI, 16SrDNA, H3 and ITS2 genes have also been deposited in GenBank. Molecular and morphological (shell and genitalia) features showed that M. parumcincta (Rossmässler, 1834) is a distinct taxon from the M. cantiana lineages.

Endophytic bacteria isolated from Angleton pasture (Dichantium aristatum, Benth) in Sucre Department, Colombia

Objective: This study evaluated in vitro the growth promotion activity of endophytic bacteria extracted from different tissues of Dichantium aristatum from livestock farms localized in the zone of Santiago de Tolu, Sucre Department, Colombia. Methods/Statistical Analysis: Endophytic bacteria from different tissues were isolated, and the population was determined in CFU/g of tissue. Each isolated morphotype was used to quantitatively and qualitatively evaluate the BNF, PS, siderophore and indole acetic acid production in vitro. The bacteria that showed this activity were sequenced for identification for sequencing of the 16S rDNA gene for eubacteria. 62 morphotypes of endophyte bacteria from different Angleton pasture tissues were isolated, of which 28 had siderophore production, five ammonium ion production, 12 soluble phosphates and six indole acetic acid in mg/L. The population of these bacteria varied, from 3.210 × 106 ± 1.2 × 108 CFU/g of tissue, with higher quantity found in the Angleton pasture roots. Findings: The results of the sequencing showed the presence of a high percentage of similarity with the bacterial species Serratia marcescens, Enterobacter cloacae and Bacillus cereus, presenting phosphate solubilization, reduction of N2 to ammonium, and production of indole acetic acid and siderophores. Application: The findings of this study constitute important alternatives to mitigate the impact of the continuous use of pesticides in the production agricultural; the use of endophytic bacteria associated with vegetable species with the ability to produce multiple benefits has gained attention. Studies have shown the goodnesses of plant growth promoting-bacteria as an alternative for obtaining biofertilizers, with the ability to stimulate the growth and productivity of plants, making it are possible to improve the yield of crops. Keywords: Biological Nitrogen Fixation, Indole Acetic Acid, Pasture, Phosphate Solubilization, Siderophore

Comparative analysis of Sanger and next generation sequencing methods for 16S rDNA analysis of post-mortem specimens

Forensic microbiology is widely applied to identify people at crime scenes and determine the cause and time of deaths by examination of trace evidence. In particular, identification of bacteria from post-mortem specimens is important because the cause of death could be an infection with clinically significant bacteria that results in a fatal outcome, such as sepsis. The MicroSEQ 500 16S rDNA Bacteria Identification system (MicroSeq ID) from Applied Biosystems is a molecular technique for profiling of bacteria isolated by cultures, based on Sanger sequencing of the bacterial 16S rDNA gene. The MiSeq Illumina platform uses next-generation sequencing (NGS) for metagenomic analysis of 16S rDNA and culture-independent identification of bacteria. In this study, we analysed 65 post-mortem specimens by both methods and compared the workflows involved with regard to methodology, time-efficiency, cost-efficiency, and performance to determine the limitations and benefits of these techniques for forensic application. We found that MiSeq is more time-efficient, and exhibits superior cost-efficiency when more than 30 samples are analysed. In addition, MiSeq has a number of other advantages over MicroSeq ID, including a simpler identification of bacteria that are difficult to culture and use of a larger library of 16S rDNA, allowing more precise identification of bacterial species.

Fate of potential indicator antimicrobial resistance genes (ARGs) and bacterial community diversity in simulated manure-soil microcosms

The aim of this study was to investigate the fate of nine potential indicator antimicrobial resistance genes (ARGs) (sul1, sul2, tetB, tetM, ermB, ermF, fexA, cfr, intI1) and the diversity of bacterial communities in response to poultry manure applications to arable soil over a 90 day period. Quantitative real time PCR and Illumina high-throughput sequencing of 16S rDNA gene were used to quantify and trace ARG fate. The levels of all genes dramatically decreased over time and intI1, sul1, sul2 and tetM always had the greatest abundance and lowest dissipation rates. This indicated that more effort should be focused on the ARG elimination from manure rather than waiting for subsequent attenuation in the environment. Our sequencing results documented dramatic changes in the microbial community structure and diversity during these experiments. In poultry manure groups, Bacteroidetes and Actinobacteria were the two dominant phyla while Acidobacteria dominated the control groups. Moreover, the relative abundance of genera Corynebacterium, Pseudomonas, Ochrobactrum, Actinomadura and Bacillus, which contained potential opportunistic pathogens, changed over time suggesting that poultry manure not only strongly influenced bacterial community composition, but also selected specific bacterial communities. This study provides a glimpse of ARG fates and bacterial community diversity in soil after the application of poultry manure.