Pyrosequencing Data Research Articles

Microbial Community of Saline, Alkaline Lakes in the Nebraska Sandhills Based on 16S rRNA Gene Amplicon Sequence Data.

The Nebraska Sandhills region contains over 1,500 geochemically diverse interdunal lakes, some of which are potassium rich, alkaline, and hypersaline. Here, we report 16S rRNA amplicon pyrosequencing data on the water and sediment microbial communities of eight alkaline lakes in the Sandhills of western Nebraska.

Impact of ultrasonic pre-treatment on domestic sludge digestion performance and microbial community dynamics

ABSTRACTUltrasonication-assisted sludge digestion technology is a lately used alternative sludge treatment method in wastewater treatment plants (WWTPs). This study focused on determining the influence of ultrasonication on aerobic and anaerobic sludge digestion, two most commonly used sludge handling processes, as well as on the investigation of microbial community structure after digestion. The effect of ultrasonication as a pre-treatment technique prior to sludge digestion on microbial population dynamics was not yet investigated comprehensively. Sludge sample taken from the primary and secondary settling tanks of a domestic wastewater treatment plant was used during the experiments. Based on the relevant data, while applied ultrasonication did not improve the anaerobic digestion efficiency, progress was achieved in the sludge dewaterability characteristics at the end of aerobic digestion. According to the results of both denaturant gradient gel electrophoresis and pyrosequencing data, ultrasonic pre-treatment decreased the richness of the microbial population in aerobic digestion, whereas increased the biocomplexity of the population in anaerobic digestion. We revealed that sludge pre-treatment with ultrasonication does not always improve the digestion performance. Composition of the sludge was the main factor defining the digestion performance.

Pyrosequencing and culturing of Hawaiian corticolous biofilms demonstrate high diversity and confirm phylogenetic placement of the green alga Spongiochrysis hawaiiensis in Cladophorales (Ulvophyceae)

:Spongiochrysis hawaiiensis, a terrestrial green alga found in subaerial biofilms along the windward coast of O'ahu, was originally described as a member of the Cladophorales, a primarily marine and freshwater order, based on DNA sequence data. However, a subsequent report allied this taxon with the entirely terrestrial order Trentepohliales. Yet biofilm communities may contain multiple species of green algae, and sequences from both studies were generated from uncultured environmental samples using Sanger sequencing, rendering these results uncertain. In the current study, pyrosequencing of the SSU rDNA gene was used to determinate the algal species composition of these communities, and Sanger sequences of unialgal cultures were generated to unambiguously determine the phylogenetic placement of S. hawaiiensis. Results of the current study indicated that communities were composed primarily of ‘cladophoralean S. hawaiiensis’; numerous trentepohlialean taxa, including one that formed a clade with the previously published ‘trentepohlialean S. hawaiiensis’; and members of the Trebouxiophyceae. Abundances of the ‘cladophoralean S. hawaiiensis’ and the most abundant trentepohlialean taxon were too similar to determine which was the dominant member of the community based on pyrosequencing data alone. Phylogenetic analysis of Spongiochrysis SSU sequences from unialgal culture clearly allied the taxon within the Cladophorales, thus refuting the hypothesis that Spongiochrysis is a member of the Trentepohliales.

Taxonomic and Functional Changes of Bacterial Communities in the Rhizosphere of Kimchi Cabbage After Seed Bacterization with Proteus vulgaris JBLS202.

Maintenance of a beneficial microbial community, especially in the rhizosphere, is indispensable for plant growth and agricultural sustainability. In this sense, plant growth-promoting rhizobacteria (PGPR) have been extensively studied for their role in plant growth promotion and disease resistance. However, the impact of introducing PGPR strains into rhizosphere microbial communities is still underexplored. We previously found that the Proteus vulgaris JBLS202 strain (JBLS202) promoted growth of Kimchi cabbage and altered the relative abundance of total bacteria and Pseudomonas spp. in the treated rhizosphere. To extend these findings, we used pyrosequencing to analyze the changes in bacterial communities in the rhizosphere of Kimchi cabbage after introduction of JBLS202. The alterations were also evaluated by taxon-specific real-time PCR (qPCR). The pyrosequencing data revealed an increase in total bacteria abundance, including specific groups such as Proteobacteria, Acidobacteria, and Actinobacteria, in the treated rhizosphere. Time-course qPCR analysis confirmed the increase in the abundance of Acidobacteria, Actinobacteria, Alphaproteobacteria, and Betaproteobacteria. Furthermore, genes involved in nitrogen cycling were upregulated by JBLS202 treatment indicating changes in ecological function of the rhizosphere soil. Overall, these results indicate that introduction of JBLS202 alters both the composition and function of the rhizosphere bacterial community, which can have direct and indirect effects on plant growth. Therefore, we propose that long-term changes in bacterial composition and community-level function need to be considered for practical use of PGPRs.

Soil amendment alters soil physicochemical properties and bacterial community structure of a replanted apple orchard

Compost amendment reportedly improved apple tree growth in replant soils. However, its effects should be evaluated at different soil depths and locations. This study investigated the impact of soil improvement with compost on soil physicochemical properties and bacterial community structure of a replanted apple orchard in comparison with the original orchard without compost improvement. The V1–V3 region of the bacterial 16S rRNA gene was subjected to high-throughput 454 pyrosequencing, and data were analyzed using the Mothur pipeline. The results showed that the soil improvement benefited tree growth and fruit quality during the study period. The compost amendment markedly increased tree height and stem diameter by a range of 6.1%–21.0% and 4.0%–14.0%, respectively. Fruit yield (9.5%), average weight (9.6%), and soluble solid content (5.6%) were also increased by compost amendment compared to those of the unimproved treatment. The pH, organic matter, and available N, P, and K contents were significantly increased by 5.7%–21.9%, 0.2%–62.9%, 9.3%–29.3%, 36.7%–64.5%, and 17.2%–100.3% in the compost improved soil. The pyrosequencing data showed that the soil improvement changed the bacterial community structure at all soil depths (0–20 cm and 20–40 cm) and locations (in-row and inter-row) considered; e.g., the relative abundance of Proteobacteria (20.2%), Bacteroidetes (2.5%), and Cyanobacteria (1.0%) was increased while that of Chloroflexi (5.5%), Acidobacteria (5.2%), Nitrospirae (4.5%), Gemmatimonadetes (3.8%), and Actinobacteria (1.8%) was decreased. The relative abundance of some dominant genera Burkholderia (2.3%), Pseudomonas (1.0%), and Paenibacillus (0.5%) were enhanced in the compost improved soil. Moreover, other dominant genera such as Nitrospira (6.4%), Gemmatimonas (2.2%), and Phenylobacterium (0.3%) were reduced by the application of compost. Our results indicate that soil improvement benefits the growth of tree and fruit quality, and is likely mediated by increased soil pH, organic matter, and available nutrient contents and beneficial bacterial community composition.

Viral Communities of Shark Bay Modern Stromatolites.

Single stranded DNA viruses have been previously shown to populate the oceans on a global scale, and are endemic in microbialites of both marine and freshwater systems. We undertook for the first time direct viral metagenomic shotgun sequencing to explore the diversity of viruses in the modern stromatolites of Shark Bay Australia. The data indicate that Shark Bay marine stromatolites have similar diversity of ssDNA viruses to that of Highbourne Cay, Bahamas. ssDNA viruses in cluster uniquely in Shark Bay and Highbourne Cay, potentially due to enrichment by phi29-mediated amplification bias. Further, pyrosequencing data was assembled from the Shark Bay systems into two putative viral genomes that are related to Genomoviridae family of ssDNA viruses. In addition, the cellular fraction was shown to be enriched for antiviral defense genes including CRISPR-Cas, BREX (bacteriophage exclusion), and DISARM (defense island system associated with restriction-modification), a potentially novel finding for these systems. This is the first evidence for viruses in the Shark Bay stromatolites, and these viruses may play key roles in modulating microbial diversity as well as potentially impacting ecosystem function through infection and the recycling of key nutrients.

Promoter DNA methylation contributes to human β-defensin-1 deficiency in atopic dermatitis

ABSTRACTAtopic dermatitis (AD) is a chronic inflammatory skin disease caused by epidermal barrier dysfunction and dysregulation of innate and adaptive immunity. Epigenetic regulation of human β-defensin-1 (HBD-1) might be associated with a variety of defects in the innate immune system during AD pathogenesis. We investigated the possible mechanism of decreased HBD-1 gene expression in AD and demonstrated the restoration of HBD-1 transcription in undifferentiated normal human epidermal keratinocyte cells after treatment with a DNA methyltransferase inhibitor. We also conducted an in vitro methylated reporter assay using a reporter containing 14 CpG sites. Methylation of the 14 CpG sites within the HBD-1 5′ region resulted in an approximately 86% reduction in promoter activity and affected HBD-1 transcriptional regulation. We then compared methylation frequencies at CpG 3 and CpG 4 between non-lesional and lesional epidermis samples of patients with severe AD and between these paired tissues and healthy control epidermis from normal volunteers without AD history. Bisulfite pyrosequencing data showed significantly higher methylation frequencies at the CpG 3 and 4 sites in AD lesional samples than in non-lesional AD skin and normal skin samples (P < 0.05). These results suggest that the DNA methylation signature of HBD-1 is a novel diagnostic/prognostic marker and a promising therapeutic target for the compromised stratum corneum barrier attributed to HBD-1 deficiency.

Bioavailability of weathered hydrocarbons in engine oil-contaminated soil: Impact of bioaugmentation mediated by Pseudomonas spp. on bioremediation

Heavier fraction hydrocarbons (C15-C36) formed in soil after biotic and abiotic weatherings of engine oil are the continuing constraints in the bioremediation strategy, and their bioavailability remains a poorly quantified regulatory factor. In a microcosm study, we used two strains of Pseudomonas, P. putida TPHK-1 and P. aeruginosa TPHK-4, in strategies of bioremediation, viz., natural attenuation, biostimulation and bioaugmentation, for removal of weathered total petroleum hydrocarbons (TPHs) in soil contaminated long-term with high concentrations of engine oil (39,000–41,000 mg TPHs kg−1 soil). Both the bacterial strains exhibited a great potential in remediating weathered hydrocarbons of engine oil. Addition of inorganic fertilizers (NPK), at recommended levels for bioremediation, resulted in significant inhibition in biostimulation/enhanced natural attenuation as well as bioaugmentation. The data on dehydrogenase activity clearly confirmed those of bioremediation strategies used, indicating that this enzyme assay could serve as an indicator of bioremediation potential of oil-contaminated soil. Extraction of TPHs from engine oil-contaminated soil with hydroxypropyl-β-cyclodextrin (HPCD), but not 1-butanol, was found reliable in predicting the bioavailability of weathered hydrocarbons. Also, 454 pyrosequencing data were in accordance with those of bioremediation strategies used in the present microcosm study, suggesting the possible use of pyrosequencing in designing approaches for bioremediation.

Response of soil microbes to a reduction in phosphorus fertilizer in rice-wheat rotation paddy soils with varying soil P levels

Reducing chemical fertilization is one of the best management practices in agro-ecosystems where soil phosphorus (P) has accumulated to excessive levels. However, few studies have focused on the response of soil microbes to decreases in P input in a rice-wheat rotation. To determine the feasibility of a P reduction regime and its impacts on soil microbes, we modified P fertilizer inputs in a four-year pot experiment. Our treatments contained P fertilization during both rice and wheat seasons (PR + W), P fertilization during wheat-growing season only (PW), P fertilization during the rice season only (PR), and no P fertilization during either rice or wheat season (Pzero) as the control. We used ten paddy soils with varied P levels, including P-rich, P-moderate, and P-low. After four years of rice-wheat cropping, the PW treatment maintained crop yields but reduced soil Olsen-P accumulation by 20.8–88.7% (p < 0.05) compared to current farming practices (PR + W); however, the PR and Pzero treatments significantly decreased wheat yield (p < 0.05). The critical levels of soil Olsen-P were 4.19–5.24 and 7.00–16.8 mg kg−1 for optimal rice and wheat yield, respectively. Analysis of 454 pyrosequencing data from fresh samples revealed that the fertilizer regime was the main factor impacting the soil microbiome, followed by soil properties and available P. Subsequent stepwise regression analysis further indicated that soil pH was a major driver of bacterial community composition. Furthermore, the relative abundances of Alphaproteobacteria and Gammaproteobacteria were higher in P-fertilized soils. There were no significant changes in the taxonomic composition of the nine dominant bacteria phyla between the PW and PR + W treatments in soils form Yixing city, suggesting that this P fertilization reduction regime did not alter the bacterial community composition in this region. The results could help to understand the effects of P fertilizer reduction on the soil microbial community in rice-wheat rotation paddy soils.

Efficiency of surfactant-enhanced bioremediation of aged polycyclic aromatic hydrocarbon-contaminated soil: Link with bioavailability and the dynamics of the bacterial community

Shifts in the bacterial-community dynamics, bioavailability, and biodegradation of polycyclic aromatic hydrocarbons (PAHs) of chronically contaminated soil were analyzed in Triton X-100–treated microcosms at the critical micelle concentration (T-CMC) and at two sub-CMC doses. Only the sub-CMC-dose microcosms reached sorbed-PAH concentrations significantly lower than the control: 166±32 and 135±4mgkg−1 dry soil versus 266±51mgkg−1; consequently an increase in high- and low-molecular-weight PAHs biodegradation was observed. After 63days of incubation pyrosequencing data evidenced differences in diversity and composition between the surfactant-modified microcosms and the control, with those with sub-CMC doses containing a predominance of the orders Sphingomonadales, Acidobacteriales, and Gemmatimonadales (groups of known PAHs-degrading capability). The T-CMC microcosm exhibited a lower richness and diversity index with a marked predominance of the order Xanthomonadales, mainly represented by the Stenotrophomonas genus, a PAHs- and Triton X-100–degrading bacterium. In the T-CMC microcosm, whereas the initial surface tension was 35mNm−1, after 63days of incubation an increase up to 40mNm−1 was registered. The previous observation and the gas-chromatography data indicated that the surfactant may have been degraded at the CMC by a highly selective bacterial community with a consequent negative impact on PAHs biodegradation. This work obtained strong evidence for the involvement of physicochemical and biologic influences determining the different behaviors of the studied microcosms. The results reported here contribute significantly to an optimization of, surfactant-enhanced bioremediation strategies for chronically contaminated soil since the application of doses below the CMC would reduce the overall costs.

Spent coffee ground as a new bulking agent for accelerated biodrying of dewatered sludge

The feasibility of using spent coffee ground (SCG) as a new bulking agent for biodrying of dewatered sludge (DS) was investigated in comparison with two other frequently-used bulking agents, air-dried sludge (AS) and sawdust (SD). Results showed that the moisture contents (MC) of 16-day DS biodrying with AS (Trial A), SCG (Trial B) and SD (Trial C) decreased from 70.14 wt%, 68.25 wt% and 71.63 wt% to 59.12 wt%, 41.35 wt% and 57.69 wt%, respectively. In case of Trial B, the MC rapidly decreased to 46.16 wt% with the highest water removal (70.87%) within 8 days because of the longest high-temperature period (5.8 days). Further studies indicated that the abundant biodegradable volatile solids (BVS) and high dissolved organic matter (DOM) contents in SCG were the main driving forces for water removal. According to pyrosequencing data, Firmicutes, most of which were recognized as thermophiles, was rapidly enriched on Day 8 and became the dominant phylum in Trial B. Four thermophilic genera, Bacillus, Ureibacillus, Geobacillus and Thermobifida, which can produce thermostable hydrolytic extracellular enzymes, were the most abundant in Trial B, indicating that these thermophilic bacteria evolved during the long high-temperature period enhanced the biodegradation of BVS in SCG. The 8-day biodried product of Trial B was demonstrated to be an excellent solid fuel with low heating value (LHV) of 9284 kJ kg−1, which was 2.1 and 1.8 times those of biodried products with AS and SD, respectively. Thus SCG was found to be an excellent bulking agent accelerating DS biodrying and producing a solid fuel with a high calorific value.

Combined chemical and microbiological degradation of tetrachloroethene during the application of Carbo-Iron at a contaminated field site

After the injection of Carbo-Iron® into an aquifer contaminated with tetrachloroethene (PCE), combined chemical and microbiological contaminant degradation processes were found in a long-term study of the field site in Lower Saxony (Germany). The applied composite material Carbo-Iron, which consists of colloidal activated carbon and embedded nanoscale zero-valent iron (ZVI) structures, functioned as intended: accumulating the pollutants and promoting their reductive dechlorination. Furthermore, the particles decreased the redox potential of the groundwater due to their reaction with oxygen and to the ZVI-corrosion-induced formation of molecular hydrogen up to 190 days after the injection, the latter promoting sulphate-reducing conditions. The emergence of cis-dichloroethene (cis-DCE), which was only found in trace quantities before the injection of Carbo-Iron, together with the presence of organisms related to Sulfospirillum multivorans, Desulfitobacterium spp. and Dehalococcoides mccartyi, indicate that Carbo-Iron is also able to support microbial degradation of PCE. However, cis-DCE did not accumulate in the present case study, although it is often observed at sites with active microbial dechlorination. The results of compound-specific isotope analysis in combination with pyrosequencing data suggested the oxidative degradation of cis-DCE by an organism related to Polaromonas sp. strain JS666. Consequently, the formation of the carcinogenic degradation intermediate vinyl chloride was circumvented. Overall, the moderate and slow change of environmental conditions mediated by Carbo-Iron not only supported organohalide-respiring bacteria, but also created the basis for a subsequent microbial oxidation step.

Acclimation of Culturable Bacterial Communities under the Stresses of Different Organic Compounds.

The phylogenetic diversity of bacterial communities in response to environmental disturbances such as organic pollution has been well studied, but little is known about the way in which organic contaminants influence the acclimation of functional bacteria. In the present study, tolerance assays for bacterial communities from the sediment in the Pearl River Estuary were conducted with the isolation of functional bacteria using pyrene and different estrogens as environmental stressors. Molecular ecological networks and phylogenetic trees were constructed using both 16S rRNA gene sequences of cultured bacterial strains and 16S rRNA gene-based pyrosequencing data to illustrate the successions of bacterial communities and their acclimations to the different organic compounds. A total of 111 bacterial strains exhibiting degradation and endurance capabilities in response to the pyrene estrogen-induced stress were successfully isolated and were mainly affiliated with three orders, Pseudomonadales, Vibrionales, and Rhodobacterales. Molecular ecological networks and phylogenetic trees showed various adaptive abilities of bacteria to the different organic compounds. For instance, some bacterial OTUs could be found only in particular organic compound-treated groups while some other OTUs could tolerate stresses from different organic compounds. Furthermore, the results indicated that some new phylotypes were emerged under stresses of different organic pollutions and these new phylotypes could adapt to the contaminated environments and contribute significantly to the microbial community shifts. Overall, this study demonstrated a crucial role of the community succession and the acclimation of functional bacteria in the adaptive responses to various environmental disturbances.

IDH1 and IDH2 mutations in postoperative diffuse glioma-associated epilepsy

ObjectiveIsocitrate dehydrogenase 1 and 2 mutations (IDH1/2) have an established association with preoperative seizures in patients with grades II–IV diffuse gliomas. Here, we examined if IDH1/2 mutations are a biomarker of postoperative seizure frequency. MethodsThis was a retrospective study. Patients with grades II–IV supratentorial diffuse glioma, immunohistochemistry results of IDH1-R132H, and antiepileptic drug (AED) prescribed postoperatively were included. The primary outcome was seizure frequency over the first 12 postoperative months: Group A — postoperative seizure freedom; Group B — 1–11 seizures over 12months (less than one seizure per month); and Group C — greater than one seizure per month. Rates of IDH1-R132H mutation were compared between the three outcome groups in univariate and multivariate analyses. Subgroup analysis was performed in 64 patients with IDH1/2 pyrosequencing data. ResultsOne hundred cases were included in the analysis: 30.0% grade II, 20.0% grade III, and 50.0% grade IV gliomas. Group B patients averaged 1 seizure over 12months, compared with 2 seizures per month in Group C. Isocitrate dehydrogense 1-R132H mutation was present in 29.3% (17/58) of Group A, 18.2% (14/22) of Group B, and 70.0% (14/20) of Group C patients (p=0.001). On multivariate analysis, after controlling for preoperative seizure, grade, and temporal tumor location, IDH1-R132H was associated with Group C when compared with both Group A (RR 4.75, p=0.032) and Group B (RR 9.70, p=0.012). In the subgroup with IDH1/2 molecular data, an IDH1/2 mutation was present in 64.7% (22/34) of Group A, 28.6% (4/14) of Group C, and 87.5% (14/16) of Group C patients (p=0.004). SignificanceIn patients with supratentorial diffuse gliomas, IDH1-R132H mutations are associated with a more severe phenotype of postoperative epilepsy. These findings support further research into IDH mutations, and the potential for an antiepileptic therapeutic effect of their inhibitors, in patients with glioma-associated epilepsy.

Composition and variation of respiratory microbiota in healthy military personnel.

Certain occupational and geographical exposures have been associated with an increased risk of lung disease. As a baseline for future studies, we sought to characterize the upper respiratory microbiomes of healthy military personnel in a garrison environment. Nasal, oropharyngeal, and nasopharyngeal swabs were collected from 50 healthy active duty volunteers eight times over the course of one year (1107 swabs, completion rate = 92.25%) and subjected to pyrosequencing of the V1–V3 region of 16S rDNA. Respiratory bacterial taxa were characterized at the genus level, using QIIME 1.8 and the Ribosomal Database Project classifier. High levels of Staphylococcus, Corynebacterium, and Propionibacterium were observed among both nasal and nasopharyngeal microbiota, comprising more than 75% of all operational taxonomical units (OTUs). In contrast, Streptococcus was the sole dominant bacterial genus (approximately 50% of all OTUs) in the oropharynx. The average bacterial diversity was greater in the oropharynx than in the nasal or nasopharyngeal region at all time points. Diversity analysis indicated a significant overlap between nasal and nasopharyngeal samples, whereas oropharyngeal samples formed a cluster distinct from these two regions. The study produced a large set of pyrosequencing data on the V1–V3 region of bacterial 16S rDNA for the respiratory microbiomes of healthy active duty Service Members. Pre-processing of sequencing reads showed good data quality. The derived microbiome profiles were consistent both internally and with previous reports, suggesting their utility for further analyses and association studies based on sequence and demographic data.

Clinical Implications of Quantitative JAK2 V617F Analysis using Droplet Digital PCR in Myeloproliferative Neoplasms.

BackgroundJAK2 V617F is the most common mutation in myeloproliferative neoplasms (MPNs) and is a major diagnostic criterion. Mutation quantification is useful for classifying patients with MPN into subgroups and for prognostic prediction. Droplet digital PCR (ddPCR) can provide accurate and reproducible quantitative analysis of DNA. This study was designed to verify the correlation of ddPCR with pyrosequencing results in the diagnosis of MPN and to investigate clinical implications of the mutational burden.MethodsPeripheral blood or bone marrow samples were obtained from 56 patients newly diagnosed with MPN or previously diagnosed with MPN but not yet indicated for JAK2 inhibitor treatment between 2012 and 2016. The JAK2 V617F mutation was detected by pyrosequencing as a diagnostic work-up. The same samples were used for ddPCR to determine the correlation between assays and establish a detection sensitivity cut-off. Clinical and hematologic aspects were reviewed.ResultsForty-two (75%) and 46 (82.1%) patients were positive for JAK2 V617F by pyrosequencing and ddPCR, respectively. The mean mutated allele frequency at diagnosis was 37.5±30.1% and was 40.7±31.2% with ddPCR, representing a strong correlation (r=0.9712, P<0.001). Follow-up samples were available for 12 patients, including eight that were JAK2 V617F-positive. Of these, mutational burden reduction after treatment was observed in six patients (75%), consistent with trends of hematologic improvement.ConclusionsQuantitative analysis of the JAK2 V617F mutation using ddPCR was highly correlated with pyrosequencing data and may reflect the clinical response to treatment.

Differences in planktonic microbial communities associated with three types of macrophyte stands in a shallow lake.

Little is known about how various substances from living and decomposing aquatic macrophytes affect the horizontal patterns of planktonic bacterial communities. Study sites were located within Lake Kolon, which is a freshwater marsh and can be characterised by open-water sites and small ponds with different macrovegetation (Phragmites australis, Nymphea alba and Utricularia vulgaris). Our aim was to reveal the impact of these macrophytes on the composition of the planktonic microbial communities using comparative analysis of environmental parameters, microscopy and pyrosequencing data. Bacterial 16S rRNA gene sequences were dominated by members of phyla Proteobacteria (36%-72%), Bacteroidetes (12%-33%) and Actinobacteria (5%-26%), but in the anoxic sample the ratio of Chlorobi (54%) was also remarkable. In the phytoplankton community, Cryptomonas sp., Dinobryon divergens, Euglena acus and chrysoflagellates had the highest proportion. Despite the similarities in most of the measured environmental parameters, the inner ponds had different bacterial and algal communities, suggesting that the presence and quality of macrophytes directly and indirectly controlled the composition of microbial plankton.

Alteration of soil bacterial interaction networks driven by different long-term fertilization management practices in the red soil of South China

Interactions among soil bacteria occur widely and play important roles in the maintenance of soil functions. Long-term fertilization management practices have distinct effects on soil fertility and the soil microbial activity and community, which are closely associated with soil microbial interactions. Red soil is typically low-productivity soil in South China. Chemical nitrogen fertilization caused serious soil acidification and low-productivity (defined as the acidified soil group, Ac), whereas the application of lime to the acidified soil increased the soil pH (defined as the quicklime improvement soil group, Qlime). Long-term manure or fallow treatment maintained the soil pH and increased the soil fertility (defined as the high-productivity potential soil group, HPP). A molecular ecological network analysis method was used to analyze 454 pyrosequencing data of bacterial communities from the HPP, Ac and Qlime soils. Several major differences were observed among the three constructed networks. First, the HPP network contained the largest ratio of positive to negative correlations, whereas the Ac network contained the smallest. Second, the HPP and Ac networks shared only 8.67% of their operational taxonomic units (OTUs), whereas Ac and Qlime shared 27.04%. Third, the HPP network contained the most “module hubs” (A set of OTUs that have strong interactions or common functions are grouped as a “module” in network analysis. These OTUs are called “nodes”. And the nodes with high connectivity to many other nodes within the same module are “module hubs”.), whereas Ac contained the fewest. These results demonstrated that the bacterial community of HPP was a better organized or a better operated community than Ac and that quicklime application helped to order the bacterial community. By comparing the topological roles of nodes in different networks, we proposed that there should be more module hubs in the networks of higher-productivity soils and hypothesized that these OTUs could be indicators of high-productivity.

Two novel Alphaflexiviridae members revealed by deep sequencing of the Vanilla (Orchidaceae) virome.

The genomes of two novel viruses were assembled from 454 pyrosequencing data obtained from vanilla leaves from La Réunion. Based on genome organization and homologies, one agent was unambiguously classified as a member of the genus Potexvirus and named vanilla virus X (VVX). The second one, vanilla latent virus (VLV), is phylogenetically close to three unclassified members of the family Alphaflexiviridae with similarity to allexiviruses, and despite the presence of an additional 8-kDa open reading frame, we propose to include VLV as a new member of the genus Allexivirus. Both VVX and VLV were mechanically transmitted to vanilla plants, resulting in asymptomatic infections.

Fungal communities in a Korean red pine stand, Gwangneung Forest, Korea

For the seasonal changes of fungi (Ascomycota and Basidiomycota) diversity, we performed a biweekly survey of macrofungi on defined plot in a Korean red pine (Pinus densiflora) stand (Gwangneung Forest, Pochen-si, Korea) from April 2014 to December 2014. The plot was surveyed 18 times. We also investigated the diversity of the soil fungi community during four seasons using pyrosequencing method. The collected macrofungi (25 specimens) were classified into one phylum, one class, four orders, 10 families, 13 genera, and 17 species; the soil fungal communities were classified into two phyla, 15 classes, 43 orders, 91 families, and 124 genera (49,937 sequence reads), designated as 124 genus-level operational taxonomic units. Using macrofungal collection data, environmental factor data (n = 10), and pyrosequencing data, we evaluated changes in fungal diversity with seasons and soil layers. Nonmetric multidimensional scaling ordination revealed distinct clusters of genus-level operational taxonomic units assemblage with season. Two environmental factors (exchangeable K and C/N ratio) were found to be significantly associated with soil fungi communities in the Korean red pine stand. This study will lead to a better understanding of relationships between Korean red pine stand stands and soil fungal communities.