Species Composition Of Bacterial Communities Research Articles

Long-term application of nitrogen and phosphorus fertilizers changes the process of community construction by affecting keystone species of crop rhizosphere microorganisms

Keystone species of microbial communities play a very important role in community structure and ecosystem function; however, the effect of long-term nitrogen (N) and phosphorus (P) fertilizers on key taxa and the mechanisms of community construction of rhizosphere microbial communities remain unclear. In this study, the effect of nine fertilization treatments (N0P0, N0P1, N0P2, N1P0, N1P1, N1P2, N2P0, N2P1, and N2P2) on soil microbial community diversity, keystone species, and construction methods in the crop rhizosphere were studied in a loess hilly area after 26 years of fertilization. The results showed that fertilization significantly increased the nutrient contents of the rhizospheric soil and root system and significantly affected microbial community composition (based on the Bray-Curtis distance) and community construction process (β-nearest taxon index: βNTI). The decrease in the abundance of oligotrophic bacteria (from phyla Acidobacteriota and Chloroflexi) in the keystone species of bacterial communities shifted the community construction process from homogenizing dispersal to variable selection process and was significantly regulated by soil factors (total P and carbon-N ratio). However, the decrease in the abundance of keystone species (from phylum Basidiomycota) in the fungal communities did not have a significant effect on community construction, which was mainly affected by root characteristics (root N content and soluble sugar). This study found that long-term N and P fertilization changed the keystone species composition of bacterial communities by affecting the nutrient content of the rhizospheric soil, such as total P, so that the construction mode of communities changed from a stochastic to a deterministic process, and the N2 fertilization, especially the N1P2 treatment was better for increasing network stability (modularity and clustering coefficient).

Taxonomic diversity of sputum microbiome in lung cancer patients and its relationship with chromosomal aberrations in blood lymphocytes

Here we report a pilot-sized study to compare the taxonomic composition of sputum microbiome in 17 newly-diagnosed lung cancer (LC) patients and 17 controls. Another object was to compare the representation of individual bacterial genera and species in sputum with the frequency of chromosomal aberrations in the blood lymphocytes of LC patients and in controls. Both groups were male; average age 56.1 ± 11.5 in patients and 55.7 ± 4.1 in controls. Differences in the species composition of bacterial communities in LC patients and controls were significant (pseudo-F = 1.94; p = 0.005). Increased prevalence in LC patients was detected for the genera Haemophilus and Bergeyella; whereas a decrease was observed for the genera Atopobium, Stomatobaculum, Treponema and Porphyromonas. Donors with high frequencies of chromosomal aberrations had a significant reduction in the microbiome of representatives of the genus Atopobium in the microbiome and a simultaneous increase in representatives of the species Alloprevotella compared to donors with a low level of chromosomal aberrations in lymphocytes. Thus, a comparison of the bacterial composition in the sputum of donors with cytogenetic damages in theirs lymphocytes, warrants further investigations on the potential role of microorganisms in the process of mutagenesis in somatic cells of the host body.

Bacterial microbiome of the chigger mite Leptotrombidium imphalum varies by life stage and infection with the scrub typhus pathogen Orientia tsutsugamushi.

Scrub typhus is a mites-borne rickettsiosis caused by the obligate intracellular Gram-negative bacterium Orientia tsutsugamushi. The disease is potentially life threatening and is prevalent in tropical Asia, islands of the western Pacific Ocean and northern Australia where an estimated one million cases occur annually. Orientia tsutsugamushi is transmitted by the bite of larval mites in the genus Leptotrombidium. In the present study, the composition of the microbiome in larvae, deutonymphs and adult males and females from laboratory colonies of L. imphalum that were infected as well as uninfected with O. tsutsugamushi were investigated by high-throughput sequencing of the bacterial 16S rRNA gene. Notably, the bacterial microbiomes of infected adult females were dominated by sequences of O. tsutsugamushi and an unidentified species of Amoebophilaceae, which together comprised 98.2% of bacterial sequences. To improve the taxonomic resolution of the Amoebophilaceae OTU a nearly full length sequence of the 16S rRNA gene was amplified, cloned, and Sanger sequenced. Infected female mites had 89 to 92% nucleotide identity with the Amoebophilaceae family, indicating that the bacterium was likely to be a species of a novel genus. The species composition of bacterial communities varied between mite life stages regardless of their infection status. Uninfected adults exhibited greater species diversity than adults infected with O. tsutsugamushi. In the infected colony, the rate of filial infection with Orientia was less than 100%. Larval and male mites that were PCR-negative for Orientia contained low numbers of sequences of Amoebophilaceae (0.01 and 0.06%, respectively) in their taxonomic profiles, suggesting that a mutualistic relationship exists between the novel species of Amoebophilaceae and O. tsutsugamushi. Our study findings provide the basis for further research to determine the influence of the novel Amoebophilaceae species on the bacterial microbiome and on vector susceptibility to and transovarial transmission of O. tsutsugamushi.

科尔沁沙地草甸草地开垦农田对土壤细菌群落结构的影响

选择天然草甸草地及开垦农田后7年和50年样地，采用IlluminaMiSeq高通量测序的方法研究了草甸草地利用方式改变后，土壤细菌群落结构的变化特征及与土壤理化性质的关系。结果表明，天然草地开垦农田对土壤理化性质有显著影响，有机质和全N含量迅速下降，电导率提高。Proteobacteria，Acidobacteria，Actinobacteria，Bacteroidetes，Chloroflexi，Gemmatimonadetes，Firmicutes，Planctomycetes，Verrucomicrobia，Thaumarchaeota和Nitrospirae是本地区的优势菌群。草地利用方式改变对土壤细菌群落结构有显著影响，引起优势菌群相对优势度改变，但对物种组成没有显著影响。土壤理化性质对细菌群落结构的形成有重要作用。 To investigate how soil bacterial communities respond to the change during conversion from natural meadow grassland to farmland, and the relationship between bacterial community and soil properties, we detected the shifts in diversities and compositions of soil bacterial communities as well as the relative abundance of dominant bacterial taxa with the high throughput IlluminaMiSeq sequencing technique from natural grassland, 7-yr farmland, and 50-yr farmland in Horqin Sandy Land. We found that land-use change resulted in the significant changes in soil physical and chemical properties with the distinct decreases in soil organic matter and total N contents and the increase in soil conductivity. Soil bacterial community structure was affected by land-use change, with the significant change in relative abundance of dominant bacterial populations. However, species composition of bacterial community remained unchanged. Soil properties had important effects on the structure of soil bacterial community. Proteobacteria, Acidobacteria, Actinobacteria, Bacteroidetes, Chloroflexi, Gemmatimonadetes, Firmicutes, Planctomycetes, Verrucomicrobia, Thau- marchaeota, and Nitrospirae were the dominant taxa in the Horqin area.

Marine bacteria from the French Atlantic coast displaying high forming-biofilm abilities anddifferent biofilm 3D architectures.

BackgroundFew studies have reported the species composition of bacterial communities in marine biofilms formed on natural or on man-made existing structures. In particular, the roles and surface specificities of primary colonizers are largely unknown for most surface types. The aim of this study was to obtain potentially pioneering bacterial strains with high forming-biofilm abilities from two kinds of marine biofilms, collected from two different surfaces of the French Atlantic coast: an intertidal mudflat which plays a central role in aquaculture and a carbon steel structure of a harbour, where biofilms may cause important damages.ResultsA collection of 156 marine heterotrophic aerobic bacteria isolated from both biofilms was screened for their ability to form biofilms on polystyrene 96-well microtiter plates. Out of 25 strains able to build a biofilm in these conditions, only four bacteria also formed a thick and stable biofilm on glass surfaces under dynamic conditions. These strains developed biofilms with four different three - dimensional architectures when observed by confocal laser scanning microscopy: Flavobacterium sp. II2003 biofilms harboured mushroom-like structures, Roseobacter sp. IV3009 biofilms were quite homogeneous, Shewanella sp. IV3014 displayed hairy biofilms with horizontal fibres, whereas Roseovarius sp. VA014 developed heterogeneous and tousled biofilms.ConclusionsThis work led for the first time to the obtaining of four marine bacterial strains, potentially pioneering bacteria in marine biofilms, able to adhere to at least two different surfaces (polystyrene and glass) and to build specific 3D biofilms. The four selected strains are appropriate models for a better understanding of the colonization of a surface as well as the interactions that can occur between bacteria in a marine biofilm, which are crucial events for the initiation of biofouling.

Phylogenetic diversity of aqueous microorganisms separated after the advanced tertiary of tap water

The species composition of bacterial community of the drinking tap water and water samples taken at different purification stages of the water conditioning plant at an enterprise producing special drinks has been analyzed. This study involves the analysis of 16S rRNA gene sequences and the use of molecular biology methods based on the phylogenetic analysis. The following bacterial species were identified: Bacillus nanhaiensis, Brevibacterium frigoritolerans, and Lysinibacillus fusiformis. All the studied strains belong to phylum Firmicutes, class Bacilli representing Gram-positive microorganisms that are not pathogenic to human. The presence of the bacteria investigated in different habitats such as the drinking chlorinated water, in the presence of stress factors (arid climate, high or low temperatures, depleted soil, and the occurrence of disinfectants) indicates their ability to easily adapt to new living conditions expanding their habitat.

Characterization of Culturable PAH and BTEX Degrading Bacteria from Heavy Oil of the Rancho La Brea Tarpits

Novel petroleum degrading bacteria have been identified in heavy oil from natural asphalt seeps using DNA-based methods, but there is little knowledge of the extent to which these bacteria can be cultured by selective enrichments on different aromatic hydrocarbons. Here we report the species composition of bacterial communities from a 40,000 yr-old asphalt deposit that could be grown on selected petroleum compounds. Species compositions of the degrader communities determined by PCR-DGGE and 16S rDNA sequencing showed that selective enrichment using (PAHs) and BTEX (benzene, toluene, ethyl benzene, and xylene) as growth substrates produced relatively simple degrader communities, and included a predominant species, Pseudomonas stutzeri, which grew on multiple compounds. PCR-based techniques further identified genes encoding naphthalene dioxygenase and catechol 2,3-dioxygenase from P. stutzeri in the enrichment cultures. The results suggest that only a small portion of the asphalt-inhabiting community can be cultured under aerobic conditions on individual substrates. Within these communities were several new species that merit further characterization as consortia, as well as new isolates of the cosmopolitan degrader, P. stutzeri.

P4-S4.04 Temporal dynamics of vaginal bacterial communities

BackgroundDysbiosis of vaginal bacterial communities have been associated with increased risk for sexually transmitted infections and bacterial vaginosis. This is the first observational study to model temporal dynamics of vaginal microbiota using frequently collected samples, behavioural data and culture-independent methods.MethodsThirty-three asymptomatic, reproductive-age women self-collected mid-vaginal swabs every 3rd day for 16 weeks (998 samples). Participants reported behaviours and menstrual data on daily diaries. Bacterial communities were determined by pyrosequencing of barcoded 16S rRNA genes (V1–V2 region). Participants were clustered into five community classes based on temporal patterns of vaginal bacterial community composition using transition probabilities. A linear mixed effect model for the log of Jensen-Shannon rate of community change was utilised. The model accounted for correlations between samples from the same participant and was adjusted for time-varying confounders and normalised menstrual cycle time.ResultsThree of the community classes were most often dominated byLactobacillus iners,L crispatus, orL gasseri, respectively, while two lacked significant numbers ofLactobacillusspp. The latter classes were split into subtype A typified by Corynebacterium, Anaerococcus, Peptinophilus, Prevotella, and Finegoldia, while those of subtype B showed a higher abundance of the genus Atopobium. The rank abundance and species composition of bacterial communities in some women changed markedly over short periods of time while others were relatively stable. Classes dominated byL crispatusandL gasseriexperienced the fewest fluctuations in community composition, and communities that lacked significant number ofLactobacillus spp. also demonstrated some stability. Vaginal communities dominated byL inersdemonstrated either a lack of constancy or notable stability. The menstrual cycle was associated with temporal dynamics, but these effects were influenced by bacterial community class. Sexual activity the day prior to sampling was of borderline statistical significance (p=0.065) and is a variable of interest in supplementary modelling.ConclusionsVaginal microbiota can fluctuate rapidly. Future studies should investigate the role of temporal changes in vaginal microbiota on sexually transmitted infection risk. Longitudinal studies of the vaginal microbiome may allow for the future development of targeted individualised therapeutic approaches.

Species Composition of Bacterial Communities Influences Attraction of Mosquitoes to Experimental Plant Infusions

In the container habitats of immature mosquitoes, catabolism of plant matter and other organic detritus by microbial organisms produces metabolites that mediate the oviposition behavior of Aedes aegypti and Aedes albopictus. Public health agencies commonly use oviposition traps containing plant infusions for monitoring populations of these mosquito species, which are global vectors of dengue viruses. In laboratory experiments, gravid females exhibited significantly diminished responses to experimental infusions made with sterilized white oak leaves, showing that attractive odorants were produced through microbial metabolic activity. We evaluated effects of infusion concentration and fermentation time on attraction of gravid females to infusions made from senescent bamboo or white oak leaves. We used plate counts of heterotrophic bacteria, total counts of 4',6-diamidino-2-phenylindole-stained bacterial cells, and 16S ribosomal DNA (rDNA) polymerase chain reaction-denaturing gradient gel electrophoresis (DGGE) to show that changes in the relative abundance of bacteria and the species composition of bacterial communities influenced attraction of gravid A. aegypti and A. albopictus mosquitoes to infusions. DGGE profiles showed that bacterial species composition in infusions changed over time. Principal components analysis indicated that oviposition responses to plant infusions were in general most affected by bacterial diversity and abundance. Analysis of bacterial 16S rDNA sequences derived from DGGE bands revealed that Proteobacteria (Alpha-, Beta-, Delta-, and Gamma-) were the predominant bacteria detected in both types of plant infusions. Gravid A. aegypti were significantly attracted to a mix of 14 bacterial species cultured from bamboo leaf infusion. The oviposition response of gravid mosquitoes to plant infusions is strongly influenced by abundance and diversity of bacterial species, which in turn is affected by plant species, leaf biomass, and fermentation time.

Molecular insight into activated sludge producing polyhydroxyalkanoates under aerobic–anaerobic conditions

One of the options enabling more economic production of polyhydroxyalkanoates compared to pure cultures is the application of mixed cultures. The use of a microbial community in a sequencing batch reactor has a few advantages: a simple process control, no necessity for sterile processing, and possibilities of using cheap substrates as a source of carbon. Nevertheless, while cultivation methods to achieve high PHAs biomass concentration and high productivity in wild and recombinant strains are defined, knowledge about the cultivation strategy for PHAs production by mixed culture and species composition of bacterial communities is still very limited. The main object of this study was to characterize on the molecular level the composition and activity of PHAs producing microorganism in activated sludge cultivated under oxygen limitation conditions. PHAs producers were detected using a PCR technique and the created PHA synthase gene library was analyzed by DNA sequencing. The obtained results indicate that PHAs-producers belonged to Pseudomonas sp., and possessed genes coding for mcl-PHA synthase. The kinetics of mcl-PHA synthase expression was relatively estimated using real-time PCR technology at several timepoints. Performed quantitative and qualitative analysis of total bacterial activity showed that there were differences in total activity during the process but differential expression of various groups of microorganisms examined by using DGGE was not observed.

Analysis of rhizosphere bacteria of rice cultivated in Andosol lowland and upland fields using molecular biological methods

Bacteria in the rhizosphere influence plant growth and interact with plant roots. Microscopy and culture method have been used for studies of microorganisms of the rhizosphere, but these methods are insufficient for evaluation because most rhizosphere bacteria are viable but non-culturable (VBNC). Bacteria in the rhizosphere of rice cultivated in Andosol lowland and upland fields were analyzed in this study using PCR-DGGE and FISH, in combination with modified pretreatments. Results show that the two methods with the pretreatments, more than conventional methods, provided a rapid and simple analysis of rhizosphere bacteria. The 16S rDNA band pattern of bacteria in the rhizosphere obtained using PCR-DGGE indicated different species composition of bacterial community in the two ecosystems and greater diversity of bacteria in the rhizosphere in upland field. Sequencing of major 16S rDNA bands identified Bacterium A35 and Clostridium bifermentans as dominant bacteria in the rhizosphere of rice in lowland fields and Klebsiella planticola and Bacillus fusiformis in upland fields. Furthermore, FISH observation indicated the predominance of gram-positive low GC bacteria in both rhizospheres and a higher proportion of Clostridium spp. in lowland fields, which is consistent with results of PCR-DGGE analysis. The results suggest that the bacteria in the rice rhizosphere can be changed depending on aerobic and anaerobic conditions of fields. It is expected to apply the PCR-DGGE and FISH to agricultural field experiments as reliable methods to evaluate the rhizosphere bacteria.