Change of rhizospheric bacterial community of the ancient wild tea along elevational gradients in Ailao mountain, China.

The rhizospheric microbial community is one of the major environmental factors affecting the distribution and fitness of plants. Ancient wild tea plants are rare genetic resource distributed in Southwest China. In this study, we investigated that rhizospheric bacterial communities of ancient wild tea plants along the elevational gradients (2050, 2200, 2350 and 2500 m) in QianJiaZhai Reserve of Ailao Mountains. According to the Illumina MiSeq sequencing of 16 S rRNA gene amplicons, Proteobacteria, Acidobacteria and Actinobacteria were the dominant phyla with the relative abundance 43.12%, 21.61% and 14.84%, respectively. The Variibacter was the most dominant genus in rhizosphere of ancient wild tea plant. Phylogenetic null modeling analysis suggested that rhizospheric bacterial communities of ancient wild tea plants were more phylogenetically clustered than expected by chance. The bacterial community at 2050 m was unique with the highest alpha diversity, tend to cluster the nearest taxon and simple co-occurrence network structure. The unique bacterial community was correlated to multiple soil factors, and the content soil ammonium nitrogen (NH4+-N) was the key factor affecting the diversity and distribution of bacterial community along the elevational gradients. This study provided the necessary basic information for the protection of ancient tea trees and cultivation of tea plants.

Isolation and Genomic Characterization of a Proteobacterial Methanotroph Requiring Lanthanides.

Although the bioavailability of rare earth elements (REEs, including scandium, yttrium, and 15 lanthanides) has not yet been examined in detail, methane-oxidizing bacteria (methanotrophs) were recently shown to harbor specific types of methanol dehydrogenases (XoxF-MDHs) that contain lanthanides in their active site, whereas their well-characterized counterparts (MxaF-MDHs) were Ca2+-dependent. However, lanthanide dependency in methanotrophs has not been demonstrated, except in acidic environments in which the solubility of lanthanides is high. We herein report the isolation of a lanthanide-dependent methanotroph from a circumneutral environment in which lanthanides only slightly dissolved. Methanotrophs were enriched and isolated from pond sediment using mineral medium supplemented with CaCl2 or REE chlorides. A methanotroph isolated from the cerium (Ce) chloride-supplemented culture, Methylosinus sp. strain Ce-a6, was clearly dependent on lanthanide. Strain Ce-a6 only required approximately 30 nM lanthanide chloride for its optimal growth and exhibited the ability to utilize insoluble lanthanide oxides, which may enable survival in circumneutral environments. Genome and gene expression analyses revealed that strain Ce-a6 lost the ability to produce functional MxaF-MDH, and this may have been due to a large-scale deletion around the mxa gene cluster. The present results provide evidence for lanthanide dependency as a novel survival strategy by methanotrophs in circumneutral environments.

The "pseudo-pathogenic" effect of plant growth-promoting Bacilli on starchy plant storage organs is due to their α-amylase activity which is stimulating endogenous opportunistic pathogens.

Many representatives of the Bacillus subtilis species complex are known as plant growth-promoting rhizobacteria (PGPR) and are widely used in agriculture as biofertilizers and biocontrol agents. Two bacterial strains, "Korea isolate" and ZL918, taxonomically classified as being Bacillus amyloliquefaciens, isolated from disease-damaged plant organs, were alleged to cause bacterial rot in starchy storage plant organs. The aim of this study was to elucidate whether these findings have consequences for the general use of beneficial Bacilli in agriculture. Whole genome sequencing revealed that the pathogenic ZL918 was a representative of Bacillus velezensis. B. velezensis FZB42 and other representatives of the B. subtilis species complex caused the same symptoms of bacterial rot only when injected inside of potato tubers and onion bulbs, but not when inoculated onto the surface of the storage organs. It seemed that the pathogenic effect was due to starch hydrolyzing activity that likely stimulates propagation of endophytic bacteria inside of starchy tissues. After removing the inherent microbiota via Co60 γ-ray irradiation, the storage organs inoculated by either FZB42 or purified α-amylase did not develop rot symptoms. Two opportunistic pathogens, Pantoea ananatis and Pantoea agglomerans, isolated from the rotted area, were shown to cause bacterial rot in x-ray treated potato tuber and onion starchy tissues when the proteobacteria were applied in high concentration. This suggests that opportunistic pathogenic bacteria residing inside of the starchy storage organ are the causal agents of bacterial soft rot disease in potato tubers and other starchy plant storage organs.

Study on the bacterial and archaeal community structure and diversity of activated sludge from three wastewater treatment plants.

In this study, the bacterial and archaeal communities along with their functions of activated sludge from three wastewater treatment plants were investigated by Illumina MiSeq Platform. The treatment processes were modified A/A/O, DE oxidation ditch and pre-anaerobic carrousel oxidation ditch, respectively. The taxonomic analyses showed that Proteobacteria was the predominant bacterial phylum, and Nitrosospira was the dominant nitrification genus. Candidatus Accumulibacter was abundant in DE oxidation ditch process, and the main archaea communities were methanosaeta-like species which had the capability to anaerobic ammonia oxidation. The results illustrated that anaerobic ammonium oxidation played an important role in the nitrogen metabolism and there might be other unknown phosphate-accumulating organisms (PAOs) performing phosphorus removal in activated sludge. The predicted function analyses indicated that both bacteria and archaea were involved in nitrification, denitrification, ammonification and phosphorus removal processes, and their relative abundance varied metabolic modules differed from each other.

Environmental Enrichment Induces Pericyte and IgA-Dependent Wound Repair and Lifespan Extension in a Colon Tumor Model.

Environmental enrichment (EE) replicates mind-body therapy by providing complex housing to laboratory animals to improve their activity levels, behavior, and social interactions. Using a Tcf4Het/+ApcMin/+-mediated model of colon tumorigenesis, we found that EE vastly improved the survival of tumor-bearing animals, with differential effect on tumor load in male compared to female animals. Analysis of Tcf4Het/+ApcMin/+ males showed drastically reduced expression of circulating inflammatory cytokines and induced nuclear hormone receptor (NHR) signaling, both of which are common in the wound repair process. Interestingly, EE provoked tumor wound repair resolution through revascularization, plasma cell recruitment and IgA secretion, replacement of glandular tumor structures with pericytes in a process reminiscent of scarring, and normalization of microbiota. These EE-dependent changes likely underlie the profound improvement in survival of colon-tumor-bearing Tcf4Het/+ApcMin/+ males. Our studies highlight the exciting promise of EE in the design of future therapeutic strategies for colon cancer patients.

Microbiota y enfermedades gastrointestinales / Microbiota and gastrointestinal diseases

La colonización bacteriana se establece inmediatamente después del nacimiento, por contacto directo con la microbiota materna, y puede modificarse durante la lactancia. Están apareciendo datos indicativos de que modificaciones cuantitativas y cualitativas de la microbiota intestinal son capaces de estimular cambios en la activación del sistema inmune que pueden conducir a la aparición de enfermedades gastrointestinales o extraintestinales. El equilibrio entre la microbiota patógena y beneficiosa durante la niñez y la adolescencia es importante para la salud gastrointestinal, incluyendo la protección frente a patógenos, la inhibición de patógenos, el procesamiento de nutrientes (síntesis de vitamina K), el estímulo de la angiogénesis y la regulación del almacenamiento de la grasa corporal. También los probióticos pueden modular la microbiota intestinal para favorecer la salud del huésped. Este artículo es una revisión sobre la acción moduladora de la microbiota intestinal en la prevención y el tratamiento coadyuvante de las enfermedades gastrointestinales pediátricas

The bacterial colonisation is established immediately after birth, through direct contact with maternal microbiota, and may be influenced during lactation. There is emerging evidence indicating that quantitative and qualitative changes on gut microbiota contribute to alterations in the mucosal activation of the immune system, leading to intra- or extra-intestinal diseases. A balance between pathogenic and beneficial microbiota throughout childhood and adolescence is important to gastrointestinal health, including protection against pathogens, inhibition of pathogens, nutrient processing (synthesis of vitamin K), stimulation of angiogenesis, and regulation of host fat storage. Probiotics can promote an intentional modulation of intestinal microbiota favouring the health of the host. A review is presented on the modulation of intestinal microbiota on prevention, and adjuvant treatment of some paediatric gastrointestinal diseases

Impacts of multiwalled carbon nanotubes on nutrient removal from wastewater and bacterial community structure in activated sludge.

BACKGROUND: The increasing use of multiwalled carbon nanotubes (MWCNTs) will inevitably lead to the exposure of wastewater treatment facilities. However, knowledge of the impacts of MWCNTs on wastewater nutrient removal and bacterial community structure in the activated sludge process is sparse. AIMS: To investigate the effects of MWCNTs on wastewater nutrient removal, and bacterial community structure in activated sludge. METHODS: Three triplicate sequencing batch reactors (SBR) were exposed to wastewater which contained 0, 1, and 20 mg/L MWCNTs. MiSeq sequencing was used to investigate the bacterial community structures in activated sludge samples which were exposed to different concentrations of MWCNTs. RESULTS: Exposure to 1 and 20 mg/L MWCNTs had no acute (1 day) impact on nutrient removal from wastewater. After long-term (180 days) exposure to 1 mg/L MWCNTs, the average total nitrogen (TN) removal efficiency was not significantly affected. TN removal efficiency decreased from 84.0% to 71.9% after long-term effects of 20 mg/L MWCNTs. After long-term exposure to 1 and 20 mg/L MWCNTs, the total phosphorus removal efficiencies decreased from 96.8% to 52.3% and from 98.2% to 34.0% respectively. Further study revealed that long-term exposure to 20 mg/L MWCNTs inhibited activities of ammonia monooxygenase and nitrite oxidoreductase. Long-term exposure to 1 and 20 mg/L MWCNTs both inhibited activities of exopolyphosphatase and polyphosphate kinase. MiSeq sequencing data indicated that 20 mg/L MWCNTs significantly decreased the diversity of bacterial community in activated sludge. Long-term exposure to 1 and 20 mg/L MWCNTs differentially decreased the abundance of nitrifying bacteria, especially ammonia-oxidizing bacteria. The abundance of PAOs was decreased after long-term exposure to 20 mg/L MWCNTs. The abundance of glycogen accumulating organisms (GAOs) was increased after long-term exposure to 1 mg/L MWCNTs. CONCLUSION: MWCNTs have adverse effects on biological wastewater nutrient removal, and altered the diversity and structure of bacterial community in activated sludge.

The potential role of 'Candidatus Microthrix parvicella' in phosphorus removal during sludge bulking in two full-scale enhanced biological phosphorus removal plants.

We investigated the bacterial community compositions and phosphorus removal performance under sludge bulking and non-bulking conditions in two biological wastewater treatment systems (conventional A²/O (anaerobic/anoxic/aerobic) and inverted A²/O (anoxic/anaerobic/aerobic) processes) receiving the same raw wastewater. Sludge bulking resulted in significant shift in bacterial compositions from Proteobacteria dominance to Actinobacteria dominance, characterized by the significant presence of filamentous 'Candidatus Microthrix parvicella'. Quantitative real-time polymerase chain reaction (PCR) analysis revealed that the relative abundance of 'Candidatus Accumulibacter phosphatis', a key polyphosphate-accumulating organism responsible for phosphorus removal, with respect to 16s rRNA genes of total bacteria was 0.8 and 0.7%, respectively, for the conventional and inverted A²/O systems when sludge bulking occurred, which increased to 8.2 and 12.3% during the non-bulking period. However, the total phosphorus removal performance during the bulking period (2-week average: 97 ± 1 and 96 ± 1%, respectively) was not adversely affected comparable to that during the non-bulking period (2-week average: 96 ± 1 and 96 ± 1%, respectively). Neisser staining revealed the presence of large polyphosphate granules in 'Candidatus Microthrix parvicella', suggesting that this microbial group might have been responsible for phosphorus removal during the sludge bulking period when 'Candidatus Accumulibacter phosphatis' was excluded from the systems.

[Effect of different treatment on endophytic bacterial communities in continuous cropping of Chrysanthemum morifoliu].

To reveal the effect of rotation cropping and bacterial manure on the growth of Chrysanthemum morifolium and screen the beneficial endophytic, the diversity of endophytic and dominant genera of different treatment groups were analyzed. Four different treatments were continuous cropping, rotation, self-made organic fertilizer and commercially available fertilizer, respectively. Endophytic bacterial diversity and dominant genera in different organs were examined using Terminal Restriction Fragment Length Polymorphism (T-RFLP). The results showed that enzyme Hae III was more appropriate than enzyme Hinfl because the number of TRFs digested by enzyme Hae III was more than that of enzyme Hinfl. In comparison of diversity, the endophytic bacterial communities' diversity index in group of cropping rotation and fertilizer was higher than that of continuous cropping which indicated that the addition of exogenous microorganism in soil could increase the diversity of plant endophyte. 18 dominant species were selected, including 3 kinds of Firmicutes, 4 kinds of Actinomycetes and 11 kinds of Proteobacteria. The results of dominant species comparison showed that the number of dominant species in continuous cropping of Ch. morifolium was significantly less than that of the rotation group. Some dominant bacteria in rotation group and fertilizer group such as Arthrobacter, Streptomyces, Streptomyces, Flavobacterium and Mycobacterium were not found in the continuous cropping of Ch. mortfolium group. Dominant species of fertilizer treatment group was similar with the rotation group, and the continuous cropping group's dominant species was more abundant. It indicates that these bacteria may be able to mitigate hindrance in continuous cropping, especially the Flavobacterium which can decompose the pathogenic fungi is worthy of further attention. Compared with leaves, there are more dominant species in roots and stems. The diversity of edophytic bacterial communities in continuous cropping of Ch. morifolium stays below than that in the rotation of Ch. morifolium, and fertilizer treatment can increase the diversity of continuous cropping so that it could mitigate hindrance in continuous cropping.

Deciphering the rhizosphere microbiome for disease-suppressive bacteria.

Disease-suppressive soils are exceptional ecosystems in which crop plants suffer less from specific soil-borne pathogens than expected owing to the activities of other soil microorganisms. For most disease-suppressive soils, the microbes and mechanisms involved in pathogen control are unknown. By coupling PhyloChip-based metagenomics of the rhizosphere microbiome with culture-dependent functional analyses, we identified key bacterial taxa and genes involved in suppression of a fungal root pathogen. More than 33,000 bacterial and archaeal species were detected, with Proteobacteria, Firmicutes, and Actinobacteria consistently associated with disease suppression. Members of the γ-Proteobacteria were shown to have disease-suppressive activity governed by nonribosomal peptide synthetases. Our data indicate that upon attack by a fungal root pathogen, plants can exploit microbial consortia from soil for protection against infections.

The complete genome sequence of 'Candidatus Liberibacter solanacearum', the bacterium associated with potato zebra chip disease.

Zebra Chip (ZC) is an emerging plant disease that causes aboveground decline of potato shoots and generally results in unusable tubers. This disease has led to multi-million dollar losses for growers in the central and western United States over the past decade and impacts the livelihood of potato farmers in Mexico and New Zealand. ZC is associated with 'Candidatus Liberibacter solanacearum', a fastidious alpha-proteobacterium that is transmitted by a phloem-feeding psyllid vector, Bactericera cockerelli Sulc. Research on this disease has been hampered by a lack of robust culture methods and paucity of genome sequence information for 'Ca. L. solanacearum'. Here we present the sequence of the 1.26 Mbp metagenome of 'Ca. L. solanacearum', based on DNA isolated from potato psyllids. The coding inventory of the 'Ca. L. solanacearum' genome was analyzed and compared to related Rhizobiaceae to better understand 'Ca. L. solanacearum' physiology and identify potential targets to develop improved treatment strategies. This analysis revealed a number of unique transporters and pathways, all potentially contributing to ZC pathogenesis. Some of these factors may have been acquired through horizontal gene transfer. Taxonomically, 'Ca. L. solanacearum' is related to 'Ca. L. asiaticus', a suspected causative agent of citrus huanglongbing, yet many genome rearrangements and several gene gains/losses are evident when comparing these two Liberibacter. species. Relative to 'Ca. L. asiaticus', 'Ca. L. solanacearum' probably has reduced capacity for nucleic acid modification, increased amino acid and vitamin biosynthesis functionalities, and gained a high-affinity iron transport system characteristic of several pathogenic microbes.

[Characterization of phosphate-accumulating organisms in starting-up EBPR by FISH analysis].

Enhanced biological phosphorus removal (EBPR) process was operated in a laboratory-scale sequencing batch reactor (SBR) for one-month fed with acetate as the carbon source. The characteristic and the microbial population structure and space distribution dynamics of phosphate-accumulating organisms (PAOs) of start-up period were analyzed by fluorescent in situ hybridization (FISH). The relationship between enrichment of PAOs and phosphorus removal was discussed. PAOs could be enriched by recirculation activated sludge containing heterotrophs through anaerobic aerobic conditions. Portion of PAOs in the sludge increase from 11.5% to 40.48%. Bacteria population competition lasted 34 days. It started from PAOs replacing heterotrophs which cost 5 days then followed by 19 days intra-specific competition of PAOs. The last step was re-increasing of PAOs predominance. Phosphorus uptake by the enriched microbial community was not observed immediately. An accumulating-phase was necessary for PHA and poly-P storage. A lag-stage of 4-8 days existed when taking the performance of the reactor into consideration. Phosphorus removal by the predominant PAOs through intra-specific competition was achieved after accumulating-phase too. The FISH picture indicated that in the quickly growing phase PAOs cells were small and community structure was loose. The latter "accumulating-phase" cells became larger and the community structure clustered densely. This stage presented by better reactor performance.

Presence of Rhodocyclus in a full-scale wastewater treatment plant and their participation in enhanced biological phosphorus removal.

The objective of this research was to assess the relevance of organisms related to Rhodocyclus in enhanced biological phosphorus removal in full-scale wastewater treatment plants. The presence of these organisms in full-scale plants was first confirmed by fluorescent in situ hybridization. To address which organisms were involved in phosphorus removal, a method was developed which selected polyphosphate-accumulating organisms from activated sludge samples by DAPI staining and flow cytometry. Sorted samples were characterized using fluorescent in situ hybridization. The results of these analyses confirmed the presence of organisms related to Rhodocyclus in full-scale wastewater treatment plants and supported the involvement of these organisms in enhanced biological phosphorus removal. However, a significant fraction of the polyphosphate-accumulating organisms were not related to Rhodocyclus.

Flow cytometric sorting and RFLP analysis of phosphate accumulating bacteria in an enhanced biological phosphorus removal system.

Phosphate accumulating organisms (PAOs) stained with 4',6-diamidino-2-phenylindol dihydrochloride (DAPI) at polyphosphate probing concentration were sorted from enhanced biological phosphorus removal (EBPR) sludge by flow cytometric sorting. All the genome DNA was extracted from the sorted bacteria and the 16S rDNA genes were cloned. Cloned 16S rDNA was PCR-amplified and analyzed by restriction fragment length polymorphism (RFLP) analysis. Eighty eight clones were analyzed and the RFLP patterns which appeared more than twice were classified into seven groups. The most dominant group (Group 1) contained four clones and accounted for 4.5% of the total clones. Four groups (from Group 2 to Group 5) contained three clones. Group 6 and 7 consisted of two clones. Sixty-eight clones gave unique RFLP patterns. By sequencing 16S rDNA in seven groups, Group 1, 2 and 5 were Rhodocyclus relatives (11%, 10/88). Rhodocyclus relatives were suggested to be one of the bacteria responsible for EBPR in this sludge. Groups 6 and 7 were related to b- or g-Proteobacteria. Group 4 belonged to e-Proteobacteria. Group 3 was related to green nonsulfur bacteria. Considering the complex RFLP pattern and the existence of the groups not related to Rhodocyclus by sequence analysis, in this EBPR system, together with Rhodocyclus relatives, some other bacteria might also play a role as PAOs.

Analysis of microbial community that performs enhanced biological phosphorus removal in activated sludge fed with acetate.

Enhanced biological phosphorus removal (EBPR) activated sludge was operated in a laboratory-scale sequencing batch reactor (SBR) fed with acetate as the sole carbon source. The microbial community of the sludge was analyzed using the polymerase chain reaction (PCR)-denaturing gradient gel electrophoresis (DGGE) method for about 2 months of start-up period. As a result, the number of major bands decreased during the enrichment, indicating that the microbial community structure was getting simpler. Since the phosphate removal activity was maintained at a high level, the bacteria which still remained at the end can be considered as the important bacteria playing key roles in the present EBPR sludge, maybe polyphosphate accumulating organisms (PAOs). The dominant band in the last sample on the DGGE gel was excised and the DNA recovered from it was sequenced. The sequence was closely related to one of the putative PAOs group which Crocetti et al. (2000) and Hesselmann et al. (1999) have proposed. This PAOs group is closely related to the Rhodocyclus group (b-Proteobacteria). The fluorescence in situ hybridization (FISH) method with the probe specific for this PAOs group and the DAPI staining at a phosphate-probing concentration indirectly showed that these Rhodocyclus related bacteria really accumulated polyphosphate.

Phylogenetic and physiological diversity of tetrad-forming organisms in deteriorated biological phosphorus removal systems.

Polyhydroxyalkanoate (PHA)- and polyphosphate-accumulating traits of different taxonomic tetrad-forming organisms (TFOs) in two anaerobic-aerobic sequential batch reactors (SBRs) were characterized by the simultaneous use of fluorescence in-situ hybridization, PHB stain and DAPI stain. The two SBRs with glucose as the main carbon source were operated under different P:total organic carbon feeding ratios for more than 300 days, but both exhibited no enhanced biological phosphorus removal (EBPR) activity. Microscopic observations on sludge samples taken at various times from those two SBRs revealed that TFOs consistently accounted for more than 50% of total cells, and were mostly affiliated with the beta- and gamma-subclasses of Proteobacteria and the high G+C phylum of gram-positive bacteria (HGC). Those TFOs from the beta-Proteobcateria exhibited PHB stain positive and DAPI stain negative, indicating that they could utilize compounds other than polyphosphate (i.e. glycogen) as reducing power for PHA synthesis from glucose. In contrast, two types of TFOs within the HGC group showed negative PHB stain and positive DAPI stain, indicating their capacity to accumulate polyphosphate without the synthesis and degradation of PHA. This metabolic trait was different from the widely accepted biochemical model of EBPR and non-EBPR metabolisms. Other TFOs within the HGC group and gamma-Proteobacteria showed negative responses to both PHA and DAPI stains, and their function in the deteriorated EBPR system need to be further clarified. Overall findings suggested that the phylogenic and physiological heterogeneity of TFOs in anaerobic-aerobic activated sludge systems were diverse and greatly exceeded the current understanding.

Density separation and molecular methods to characterize enhanced biological phosphorus removal system populations.

A novel approach to the identification of microorganisms that accumulate high density microbial storage products based on density separation, denaturing gradient gel electrophoresis (DGGE), and DNA sequencing was developed and applied to bench and pilot scale enhanced biological phosphorus removal (EBPR) systems. Polyphosphate (PP), glycogen, and polyhydroxyalkanoates (PHAs), are all of higher density than a typical bacterial cell. PP-accumulating organisms (PAOs), the organisms responsible for EBPR, accumulate all three of these storage products. Density separation in a homogenous solution of Percoll produced a high-density biomass fraction with a relatively high concentration of PAOs, as determined by Neisser staining. DNA was extracted from these fractions, amplified, and separated by DGGE. DGGE profiles demonstrated some bacterial strains were present at a greater concentration in the high density fractions than in low density fractions. These strains were considered PAO candidates. 5 of 12 PAO candidates from high density fractions were gamma Proteobacteria and only 1 was a beta Proteobacterium. 2 PAO candidates were most similar to recently identified gamma Proteobacteria sequences obtained by DGGE analysis of a deteriorated benchtop EBPR system.