Illumina MiSeq Sequencing Research Articles

Determination of Community Structure and Diversity of Seed-Vectored Endophytic Fungi in Alpinia zerumbet.

Endophytic fungi act as seed endosymbiont, thereby playing a very crucial role in the growth and development of seeds. Seed-vectored endophytic fungi establish an everlasting association with seeds and travel from generation to generation. To explore the composition and diversity of endophytic fungi in Alpinia zerumbet seeds, high-throughput Illumina MiSeq sequencing was employed for the following stages: fruit formation period (YSJ1), young fruit period (YSJ2), early mature period (YSJ3), middle mature period (YSJ4), and late mature period (YSJ5). A total of 906,694 sequence reads and 745 operational taxonomic units (OTUs) were obtained and further classified into 8 phyla, 30 classes, 73 orders, 163 families, 302 genera, and 449 species. The highest endophytic fungal diversity was observed at YSJ5. The genera with the highest abundance were Cladosporium, Kodamaea, Hannaella, Mycothermus, Gibberella, Sarocladium, and Neopestalotiopsis. Functional Guild (FUNGuild) analysis revealed that endophytic fungi were undefined saprotroph, plant pathogens, animal pathogen–endophyte–lichen parasite–plant pathogen–wood saprotroph, and soil saprotrophs. Alternaria, Fusarium, Cladosporium, and Sarocladium, which are potential probiotics and can be used as biocontrol agents, were also abundant. This study is part of the Sustainable Development Goals of United Nations Organization (UNO) to “Establish Good Health and Well-Being.”

An enhanced excess sludge fermentation process by anthraquinone-2-sulfonate as electron shuttles for the biorefinery of zero-carbon hydrogen

Excess sludge (ES) largely produced in municipal wastewater treatment plants is known as a waste biomass and the traditional treatment processes such as landfill and incineration are considered as unsustainable due to the negative environmental impact. Fermentation process of ES for the biorefinery of zero-carbon hydrogen has attracted an increasing interesting and was extensively researched in the last decades. However, the technology is far from commercial application due to the insufficient effectivity. In the present study, anthraquinone-2-sulfonate (AQS) as electron shuttles was introduced into the fermentation process of ES for mediating the composition and activity of bacterial community to get an enhanced biohydrogen production. Inoculated with the same anaerobic activated sludge of 1.12 gVSS/L, a series of batch anaerobic fermentation systems with various dosage of AQS were conducted at the same ES load of 2.75 gVSS/L, initial pH 6.5 and 35 °C. The results showed that the fermentation process was remarkably enhanced by the introduction of 100 mg/L AQS, accompanying the lag phase was shortened to 1.35 h from 7.62. The obtained biohydrogen yield and the specific biohydrogen production rate were also remarkably enhanced to 24.9 mL/gVSS and 0.3 mL/(gVSS·h), respectively. Illumina Miseq sequencing showed that Longilinea and Guggenheimella as the dominant genera had been enriched from 9.2% to 0–12.0% and 4.7%, respectively, in the presence of 100 mg/L AQS. Function predicted analysis suggested that the presence of AQS had increased the abundance of genes involved in the transport and metabolism of carbohydrate, amino acid and energy production. Further redundancy analysis (RDA) revealed that the enhanced hydrogen production was highly positively correlated with the enrichment of genera such as Longilinea and Guggenheimella. The research work presents a novel potential biorefinery of ES for the effective production of zero-carbon hydrogen.

Interspecies transfer of biosynthetic cobalamin for complete dechlorination of trichloroethene by Dehalococcoides mccartyi.

Complete dechlorination of trichloroethene (TCE) by Dehalococcoides mccartyi is catalyzed by reductive dehalogenases (RDases), which possess cobalamin as the crucial cofactor. However, virtually all D. mccartyi isolated thus far are corrinoid auxotrophs. The exogenous addition of commercially available cobalamin for TCE-contaminated site decontamination is costly. In this study, TCE reduction by a D. mccartyi-containing microbial consortium utilizing biosynthetic cobalamin generated by interior corrinoid-producing organisms within this microbial consortium was studied. The results confirmed that subcultures without exogenous cobalamin in the medium were apparently unaffected and were able to successively metabolize TCE to nonchlorinated ethene. The 2-bromoethanesulfonate and ampicillin resistance tests results suggested that ampicillin-sensitive bacteria rather than methanogenic archaea within this microbial consortium were responsible for biosynthesizing cobalamin. Moreover, relatively stable carbon isotopic enrichment factor (ɛ-carbon) values of TCE were obtained regardless of whether exogenous cobalamin or selective inhibitors existed in the medium, indicating that the cobalamin biosynthesized by these organisms was absorbed and utilized by D. mccartyi for RDase synthesis and eventually participated in TCE reduction. Finally, the Illumina MiSeq sequencing analysis indicated that Desulfitobacterium and Acetobacterium in this microbial consortium were responsible for the de novo cobalamin biosynthesis to fulfill the requirements of D. mccartyi for TCE metabolism.

Shifts in microbial communities in shallow lakes depending on trophic states: Feasibility as an evaluation index for eutrophication

Microbial communities are an important component of aquatic ecosystems. They play active roles in the biogeochemical cycles of organic matter and nutrients to maintain the health and stability of aquatic ecosystems. In the present study, the shifts in microbial communities in overlying water of 15 shallow lakes with different trophic states in Hubei Province (China) were assessed using Illumina MiSeq sequencing technology. The results revealed that the proteobacteria to be the most abundant phylum in lakes with different trophic states. Mesotrophic lakes were found to be similar to moderately eutrophic lakes in terms of the microbial community composition, the interrelation between microbial communities, and expression level of metabolic pathways. In mesotrophic and moderately eutrophic lakes, Bacillus and Pseudomonas were the dominant genera in overlying water. In lakes with less eutrophication, the microbial diversity tended to be higher. Lightly eutrophic lakes had the most microbial species; however, the interaction between microorganisms was the weakest in these lakes and the internal steady-state balance of the lakes was most susceptible to being broken. These results indicate that lightly eutrophication may be one of the most unstable transition states in the eutrophication process. Particulate organic matter, chlorophyll-a, and ammonium nitrogen were the main drivers affecting the distribution of microbial communities in the overlying water of lakes with different trophic states. In addition, the correlation between microbial communities and lake trophic states was analyzed based on the bacterial eutrophic index (BEI). An obvious positive correlation was noted between BEI and the trophic level index (TLI), indicating that microbial communities could play a role as biological factors in the evaluation of lake trophic states along with other known physicochemical indicators.

Long-Term Application of Bio-Compost Increased Soil Microbial Community Diversity and Altered Its Composition and Network.

The influence of bio-compost on the diversity, composition and structure of soil microbial communities is less understood. Here, Illumina MiSeq sequencing and a network analysis were used to comprehensively characterize the effects of 25 years of bio-compost application on the microbial diversity of soil and community composition. High dosages of bio-compost significantly increased the bacterial and fungal richness. The compositions of bacterial and fungal communities were significantly altered by bio-compost addition. Bio-compost addition enriched the relative abundance of beneficial microorganisms (such as Sphingomonas, Acidibacter, Nocardioides, etc.) and reduced the relative abundance of harmful microorganisms (such as Stachybotrys and Aspergillus). Electrical conductivity, soil organic matter and total phosphorus were the key factors in shaping soil microbial community composition. The bacterial network was more complex than fungal network, and bacteria were more sensitive to changes in environmental factors than fungi. Positive interactions dominated both the bacterial and fungal networks, with stronger positive interactions found in the bacterial network. Functional prediction suggested that bio-composts altered the soil bacterial-community metabolic function with respect to carbon, nitrogen and phosphorus cycles and fungal community trophic modes. In conclusion, suitable bio-compost addition is beneficial to the improvement of soil health and crop quality and therefore the sustainability of agriculture.

Combination of gut microbiota and plasma amyloid-\u03b2 as a potential index for identifying preclinical Alzheimer\u2019s disease: a cross-sectional analysis from the SILCODE study

BackgroundPlasma amyloid-β (Aβ) may facilitate identification of individuals with brain amyloidosis. Gut microbial dysbiosis in Alzheimer’s disease (AD) is increasingly being recognized. However, knowledge about alterations of gut microbiota in preclinical AD, as well as whether the combination of plasma Aβ and gut microbiota could identify preclinical AD, remains largely unknown.MethodsThis study recruited 34 Aβ-negative cognitively normal (CN−) participants, 32 Aβ-positive cognitively normal (CN+) participants, and 22 patients with cognitive impairment (CI), including 11 patients with mild cognitive impairment (MCI) and 11 AD dementia patients. All participants underwent neuropsychological assessments and fecal microbiota analysis through 16S ribosomal RNA (rRNA) Illumina Miseq sequencing technique. Meso Scale Discovery (MSD) kits were used to quantify the plasma Aβ40, Aβ42, and Aβ42/Aβ40 in CN− and CN+ participants. Using Spearman’s correlation analysis, the associations of global standard uptake value rate (SUVR) with altered gut microbiota and plasma Aβ markers were separately evaluated. Furthermore, the discriminative power of the combination of gut microbiota and plasma Aβ markers for identifying CN+ individuals was investigated.ResultsCompared with the CN− group, the CN+ group showed significantly reduced plasma Aβ42 (p = 0.011) and Aβ42/Aβ40 (p = 0.003). The relative abundance of phylum Bacteroidetes was significantly enriched, whereas phylum Firmicutes and class Deltaproteobacteria were significantly decreased in CN+ individuals in comparison with that in CN− individuals. Particularly, the relative abundance of phylum Firmicutes and its corresponding SCFA-producing bacteria exhibited a progressive decline tendency from CN− to CN+ and CI. Besides, the global brain Aβ burden was negatively associated with the plasma Aβ42/Aβ40 (r = −0.298, p = 0.015), family Desulfovibrionaceae (r = −0.331, p = 0.007), genus Bilophila (r = −0.247, p = 0.046), and genus Faecalibacterium (r = −0.291, p = 0.018) for all CN participants. Finally, the combination of plasma Aβ markers, altered gut microbiota, and cognitive performance reached a relatively good discriminative power in identifying individuals with CN+ from CN− (AUC = 0.869, 95% CI 0.782 ~ 0.955).ConclusionsThis study provided the evidence that the gut microbial composition was altered in preclinical AD. The combination of plasma Aβ and gut microbiota may serve as a non-invasive, cost-effective diagnostic tool for early AD screening. Targeting the gut microbiota may be a novel therapeutic strategy for AD.Trial registrationThis study has been registered in ClinicalTrials.gov (NCT03370744, https://www.clinicaltrials.gov) in November 15, 2017.

A 16S Next Generation Sequencing Based Molecular and Bioinformatics Pipeline to Identify Processed Meat Products Contamination and Mislabelling.

Simple SummaryMeat adulteration and fraud encompasses the deliberate fraudulent addition or substitution of proteins of animal or plant origin in edible products primarily for economic gain. The mitochondrial 16S ribosomal (rRNA) gene was used to identify species that are present in pure and processed meat samples. The meat samples were sequenced using an Illumina sequencing platform, and bioinformatics analysis was carried out for species identification. The results indicated that pork was the major contaminant in most of the meat samples. The bioinformatics pipeline demonstrated its specificity through identification of species specific and quantification of the contamination levels across all samples. Food business operators and regulatory sectors can validate this method for food fraud checks and manage any form of mislabeling in the animal or plant protein food ecosystem.Processed meat is a target in meat adulteration for economic gain. This study demonstrates a molecular and bioinformatics diagnostic pipeline, utilizing the mitochondrial 16S ribosomal RNA (rRNA) gene, to determine processed meat product mislabeling through Next-Generation Sequencing. Nine pure meat samples were collected and artificially mixed at different ratios to verify the specificity and sensitivity of the pipeline. Processed meat products (n = 155), namely, minced meat, biltong, burger patties, and sausages, were collected across South Africa. Sequencing was performed using the Illumina MiSeq sequencing platform. Each sample had paired-end reads with a length of ±300 bp. Quality control and filtering was performed using BBDuk (version 37.90a). Each sample had an average of 134,000 reads aligned to the mitochondrial genomes using BBMap v37.90. All species in the artificial DNA mixtures were detected. Processed meat samples had reads that mapped to the Bos (90% and above) genus, with traces of reads mapping to Sus and Ovis (2–5%) genus. Sausage samples showed the highest level of contamination with 46% of the samples having mixtures of beef, pork, or mutton in one sample. This method can be used to authenticate meat products, investigate, and manage any form of mislabeling.

Phage Genome Diversity in a Biogas-Producing Microbiome Analyzed by Illumina and Nanopore GridION Sequencing.

The microbial biogas network is complex and intertwined, and therefore relatively stable in its overall functionality. However, if key functional groups of microorganisms are affected by biotic or abiotic factors, the entire efficacy may be impaired. Bacteriophages are hypothesized to alter the steering process of the microbial network. In this study, an enriched fraction of virus-like particles was extracted from a mesophilic biogas reactor and sequenced on the Illumina MiSeq and Nanopore GridION sequencing platforms. Metagenome data analysis resulted in identifying 375 metagenome-assembled viral genomes (MAVGs). Two-thirds of the classified sequences were only assigned to the superkingdom Viruses and the remaining third to the family Siphoviridae, followed by Myoviridae, Podoviridae, Tectiviridae, and Inoviridae. The metavirome showed a close relationship to the phage genomes that infect members of the classes Clostridia and Bacilli. Using publicly available biogas metagenomic data, a fragment recruitment approach showed the widespread distribution of the MAVGs studied in other biogas microbiomes. In particular, phage sequences from mesophilic microbiomes were highly similar to the phage sequences of this study. Accordingly, the virus particle enrichment approach and metavirome sequencing provided additional genome sequence information for novel virome members, thus expanding the current knowledge of viral genetic diversity in biogas reactors.

Effects of cultivation soils and ages on microbiome in the rhizosphere soil of Panax ginseng

To protect the limited forest resources, forestry soils for Panax ginseng cultivation is gradually replaced by farmland, but the extent to which soil type and cultivation age affects soil microbiome in the ginseng rhizosphere is not well known. By using Illumina MiSeq sequencing of the 16S and ITS2 rRNA genes, we tested the effects of two soil types (forest, and farmland) and three cultivation ages (four, five, and six years) on soil microbiome in the ginseng rhizosphere from nine locations in Jilin Province, China. Relative abundance and diversity of rhizosphere microbes differed among soil samples, and Ascomycota, Acidobacteria, Proteobacteria, Actinobacteria and Chloroflexi were the dominant phyla. Soil type positively influenced fungal community, while cultivation age had more positive effect on bacterial than on fungal community. Richness and diversity of fungal community was greater in forest than in farmland soils, while these parameters for bacterial communities were lower in forest than in farmland soils. A deterioration of soil fertility and continuous cultivation increased the proportion of pathogens such as Fusarium, Cylindrocarpon, but reduced the proportion of beneficial and neutral fungi and bacteria. The observed changes in soil properties (pH, organic matter, total nitrogen, total phosphorus, and total potassium) caused by soil type and cultivation age could be explained by the variations in the microbiome. A network analysis indicated that farmland and increasing cultivation age augmented the proportion of pathogens but diminished the proportion of beneficial and neutral fungi and bacteria. The present study showed that the rhizosphere microbiome differed between forest and farmland soils. Cultivation age had a stronger influence on bacterial than on fungal community. These findings suggested that soil microbiome dynamics may be a bioindicator of soil quality, and defining the microbial players involved in various cultivation ages will promote the selection and adoption of favorable ginseng cultivation lands.

NirS-type denitrifying bacteria in aerobic water layers of two drinking water reservoirs: Insights into the abundance, community diversity and co-existence model

The nirS-type denitrifying bacterial community is the main drivers of the nitrogen loss process in drinking water reservoir ecosystems. The temporal patterns in nirS gene abundance and nirS-type denitrifying bacterial community harbored in aerobic water layers of drinking water reservoirs have not been studied well. In this study, quantitative polymerase chain reaction (qPCR) and Illumina Miseq sequencing were employed to explore the nirS gene abundance and denitrifying bacterial community structure in two drinking water reservoirs. The overall results showed that the water quality parameters in two reservoirs had obvious differences. The qPCR results suggested that nirS gene abundance ranged from (2.61 ± 0.12) × 105 to (3.68 ± 0.16) × 105 copies/mL and (3.01 ± 0.12) × 105 to (5.36 ± 0.31) × 105 copies/mL in Jinpen and Lijiahe reservoirs, respectively. The sequencing results revealed that Paracoccus sp., Azoarcus sp., Dechloromonas sp. and Thauera sp. were the dominant genera observed. At species level, Cupriavidus necator, Dechloromonas sp. R-28400, Paracoccus denitrificans and Pseudomonas stutzeri accounted for more proportions in two reservoirs. More importantly, the co-occurrence network analysis demonstrated that Paracoccus sp. R-24615 and Staphylococcus sp. N23 were the keystone species observed in Jinpen and Lijiahe reservoirs, respectively. Redundancy analysis indicated that water quality (particularly turbidity, water temperature, pH and Chlorophyll a) and sampling time had significant influence on the nirS-type denitrifying bacterial community in both reservoirs. These results will shed new lights on exploring the dynamics of nirS-type denitrifying bacteria in aerobic water layers of drinking water reservoirs.

Clinical and genomic data of sars-cov-2 detected in maternal–fetal interface during the first wave of infection in Brazil

Brazil has the highest SARS-CoV-2 case-fatality rate in pregnant women in the Americas. In this study, clinical and virological findings of five mildly symptomatic pregnant women and their infected fetuses/newborns treated at a referral hospital for COVID19-pregnant women in Midwestern Brazil are reported. Mother and fetal samples were tested by RT-qPCR, ECLIA and Illumina MiSeq sequencing. From the five cases, one resulted in spontaneous abortion, one was stillborn, two were preterm births and one full-term birth. Maternal and fetal placenta, newborn and stillborn secretions were SARS-CoV-2+; one neonate developed ground-glass opacities in his lungs. One neonate's umbilical cord was IgG+ and all were IgM negative upon hospital discharge. Genomes recovered from two placentas belong to the B.1.1.28 and B.1.1.33 lineages and present nonsynonymous mutations associated with virus fitness and infectivity; other not frequently reported mutations (B.1.1.33: NSP3 V2090G, M A2S and ORF3ab S253P and Y264N; B.1.1.28: NSP3 E995D, NSP12 R240K, NSP14H1897Y and in ORF7b V21F) were found in proteins involved in viral replication, viral induction of apoptosis, viral interference on interferon and on NF-Κβ pathways. Phylogeny indicates the south of Brazil as the possible origin of these lineages circulating in Mato Grosso State. These findings contribute to describe SARS-CoV-2 infection and outcomes in pregnant women and their fetuses, at any stage of gestation and even in mild symptomatic cases.

Distribution characteristics of bacterial communities in photovoltaic industrial parks in Northwest China

Despite the rapid development of the green energy industry represented by solar photovoltaic, its ecological and environmental effects cannot be ignored. There were few reports on the impact of photovoltaic power station construction on soil bacterial community variation. In this study, the community abundance, diversity, structure, and distribution characteristics of soil bacterial in Gonghe photovoltaic power station, Qinghai Province were analyzed using quantitative Polymerase Chain Reaction techniques and Illumina MiSeq sequencing of the 16S ribosomal RNA gene. Quantitative PCR assay showed that the average16S rRNA gene copy numbers of bacteria in the soil were 8.04×109 copies per gram dry soil, which was significantly affected by the physicochemical properties of the soil. Illumina MiSeq sequencing illustrated that Actinobacteria (30.04%), Proteobacteria (29.38%), Firmicutes (2.69%), Bacteroidetes (1.51%), and Chloroflexi (1.07%) were the major phylum of soil bacterial communities, while Rubrobacter (2.51%) and Streptomyces (2.38%) was the main genera. The beta diversity indices of samples assessed via non-metric multidimensional scaling and cluster analysis indicated that the construction of a photovoltaic power station had no significant impact on the soil bacterial community structure. In addition, statistical product and service solutions and redundancy analysis demonstrated that the bacterial abundance and diversity were mainly regulated by soil water content, electrical conductivity, and other environmental factors. This study was the first time to analyze the spatial change of soil bacterial community in the desert under a photovoltaic field, which was of positive significance for the future assessment of how human disturbance affects the plant-bacteria-soil relationship in the desert ecosystem.

Effects of Lactobacillus paracasei N1115 on dyslipidaemia: A randomized controlled study

• This is a randomized, single-blind, controlled intervention study to explore the effects of Lactobacillus paracasei N1115 on dyslipidaemia. • Lactobacillus paracasei N1115 might have the potential to regulate metabolic disorders such as TC, LDL-C and FPG. • Lactobacillus paracasei N1115 might increase some of the abundance and diversity index of gut microbiota in dyslipidemias population. Probiotics could improve our health by balancing the gut microbiota or interacting with intestinal mucosa directly. This randomized, single-blind, controlled intervention study purposed to explore the effects of Lactobacillus paracasei N1115 (LP N1115) on dyslipidaemia. A total of 109 dyslipidaemia subjects were recruited and divided randomly into two groups: 52 subjects in probiotics group and 57 subjects in placebo group. Blood samples were collected to test serum lipid parameters. Fecal samples were collected to analyze the gut microbiota by Illumina Miseq sequence machine. Administration of 4 × 10 10 CFU/day LP N1115 for 12 weeks was found to improve dyslipidaemia profiles by lowering serum total cholesterol (TC) ( P = 0.028) and apolipoprotein B (Apo-B) ( P = 0.028). A significant decrease in FPG was also found in probiotic group ( P = 0.001). The Chao1 index increased significantly in probiotic group after intervention ( P < 0.01), which did not happen in placebo group. Shannon Index increased and Simpson index decreased significantly between groups at week 12 ( P < 0.001). The relative abundance of Alistipes spp. and Fusobacterium spp. decreased significantly, and the relative abundance of Faecalibacterium spp. and Lactobacillus spp. increased significantly in placebo group. The relative abundance of Megamonas spp. Faecalibacterium spp. and Lactobacillus spp. increased significantly, the relative abundance of Bacteroides spp. and Phascolarctobacterium spp. decreased significantly in probiotic group. However, the overall gut microbial structure did not change significantly from the view of Principal coordinates analysis (PCoA) of Bray-Curtis distance in probiotic group. The above results showed that LP N1115 might have the potential to regulate metabolic disorders such as TC, LDL-C and FPG, and also increased some of the abundance and diversity index of gut microbiota in dyslipidemias population. However, the evidence is not strong enough. Larger sample size and longer intervention period are needed to verify the efficacy of LP N1115. The mechanism is still vague and will need further well-designed studies to clarify.

A Correlation Study of the Microbiota Between Oral Cavity and Tonsils in Children With Tonsillar Hypertrophy.

Tonsillar hypertrophy is a common disease in 3-to-6-year-old children, which may cause serve symptoms like airway obstruction. Microbiological factors play an important role in the etiology of tonsillar hypertrophy. As the starting point of digestive and respiratory tracts, the microbial composition of the oral cavity is not only unique but also closely related to the resident microbiota in other body sites. Here we reported a correlation study of the microbiota between oral cavity and tonsils in children with tonsillar hypertrophy. Saliva, supragingival plaque, and wiped samples from the tonsil surface were collected from both tonsillar hypertrophy patients and participants with healthy tonsils and were then analyzed using Illumina Miseq Sequencing of the 16S rRNA gene. In the tonsillar hypertrophic state, more genera were detected on the tonsil surface than in the tonsil parenchyma, with more intra-microbiota correlations. When tonsillar hypertrophy occurred, both the oral cavity and tonsil surface endured microbiome shift with increased genera category and more active bacterial interactions. Over half of the newly detected genera from the tonsillar hypertrophic state were associated with infection and inflammation process or exhibited antibiotic-resistant characters. Of each individual, the microbial composition and structure of saliva seemed more similar to that of the tonsil surface, compared with the supragingival plaque. In salivary microbiota, genus Johnsonella might be relative with the healthy state of tonsils, while Pseudoxanthomonas might be relative with tonsillar hypertrophy. Our study supported the link between oral microbiota with the healthy and hypertrophic states of tonsils and may provide new directions for future researches in the specific role of oral microbiota in the etiology of tonsil diseases.

Snowstorm Enhanced the Deterministic Processes of the Microbial Community in Cryoconite at Laohugou Glacier, Tibetan Plateau.

Cryoconites harbor diverse microbial communities and are the metabolic hotspot in the glacial ecosystem. Glacial ecosystems are subjected to frequent climate disturbances such as precipitation (snowing), but little is known about whether microbial communities in cryoconite can maintain stability under such disturbance. Here, we investigated the bacterial community in supraglacial cryoconite before and after a snowfall event on the Laohugou Glacier (Tibetan Plateau), based on Illumina MiSeq sequencing of the 16S rRNA gene. Our results showed that the diversity of the microbial community significantly decreased, and the structure of the microbial community changed significantly after the disturbance of snowfall. This was partly due to the relative abundance increased of cold-tolerant bacterial taxa, which turned from rare into abundant sub-communities. After snowfall disturbance, the contribution of the deterministic process increased from 38 to 67%, which is likely due to the enhancement of environmental filtering caused by nitrogen limitation. These findings enhanced our understanding of the distribution patterns and assembly mechanisms of cryoconite bacterial communities on mountain glaciers.

Application of a Partial Nitrogen Lab-Scale Sequencing Batch Reactor for the Treatment of Organic Wastewater and Its N2O Production Pathways, and the Microbial Mechanism

Partial nitrification (PN) is a widely used wastewater treatment process. Here a lab-scale sequencing batch reactor for PN (PN-SBR) was constructed and run with artificial organic wastewater for 225 days. Results showed that the SBR reached a stable PN state after 174 days of operation and &gt;98% of NH4+-N was removed and &gt;60% was converted to NO2−-N with low effluent NO3−-N content. In a PN-SBR cycle at stage IV, the release of N2O was accompanied by the production of hydroxylamine, occurring mainly in the conversion from anaerobic to aerobic phases, and the amount of N2O produced was about 6.3% of the total nitrogen. The N2O isotopic signature results suggested that hydroxylamine oxidation was the main pathway for N2O production. Illumina MiSeq sequencing results showed that Proteobacteria and Bacteroidetes were the dominant phyla throughout the operation period. Many heterotrophic nitrifiers were significantly enriched, leading to ammonia removal and nitrite accumulation, including Acidovorax, Paracoccus, Propionibacteriaceae_unclassified, Shinella, Comamonas and Brevundimonas. Representative strains were isolated from the reactor and they were capable of efficiently producing nitrite from ammonia. These results provide a guide for the direct running of PN reactors for treating organic wastewater and help to understand the microbial processes and N2O release pathways and the microbial mechanism of partial nitrification.

High variation of fungal communities and associated potential plant pathogens induced by long-term addition of N fertilizers rather than P, K fertilizers: A case study in a Mollisol field

Nitrogen (N), phosphate (P), and potassium (K) are the three most important nutrients applied into agricultural soils, but the impacts of their single or combined application on soil fungal community structure and stability are still open questions. Using qPCR and Illumina Miseq sequencing, the variation of soil fungal communities in response to long-term addition of N, P, or K fertilization alone and their combinations in a Mollisol field was investigated in this study. In addition, the fungal community resistance indices and network structure were studied. Results showed that N fertilizations (N, NK, NP and NPK treatments) rather than P, K fertilizations (P, K and PK treatments) significantly increased fungal abundance, but decreased fungal diversity and shifted fungal community structures when compared to non-fertilization (NoF). Additionally, N fertilization treatments presented lower resistance of fungal communities to environment disturbances than those of P, K fertilization treatments. More numbers and higher abundances of changed fungal taxa at the genus and OTU levels were induced by N fertilizations rather than by addition of P, K fertilizers. In addition, N fertilizations induced a more changeable fungal network and complex pathogenic subnetwork with many positive interactions among responding plant pathogens (RP, the changeable plant pathogens induced by fertilizers addition compared to NoF) when compared to P, K fertilizations. These RP directly and negatively influenced fungal community resistance examined by structural equation modeling (SEM), which were indirectly detrimental to soybean yields. Our findings revealed that addition of N fertilizers significantly disturbed fungal communities and promoted pathogenic interactions, and provided insights into the optimization of fertilization strategies toward agricultural sustainability.

P712 Fungal microbiota composition in Inflammatory Bowel Disease patients in a Norwegian cohort: characterization of disease phenotypes and correlation with clinical activity and disease course

Abstract Background There is growing evidence of the role of the fungal microbiota in the pathogenesis of IBD, but a definite pattern defining the mycobiome in IBD is currently lacking. In addition, the variations within the different phenotypes as well as the correlation between fungal composition and disease outcomes has been poorly characterized. Our aim is to evaluate the fungal composition within the different IBD phenotypes, the changes with disease activity and the association with disease outcomes. Methods This prospective study presents sequencing of the faecal fungi of 111 individuals: 89 IBD (52 UC/37 CD) and 22 HC. Demographics,medication,Montreal Classification and disease history was collected. A fCalpro&amp;gt;100 was considered active disease. A subset of IBD patients was followed clinically (6±2 y) and classified as either “Complicated” or “Uncomplicated” based on the need of intensified medication and/or surgery. Sequencing was done on amplicons targeting the ITS1 region of fungal DNA on a Illumina MiSeq sequencer. Chosen OTUs were compiled taxonomically.Data analysis was performed in R(phyloseq and deSeq2-packages). Results We found significant variations in the fungal microbiota composition in the different IBD phenotypes(Fig1) In UC, Saccharomyces was predominant in pancolitis (E3), while Penicillium was more abundant in proctitis(E1) and Galactomyces in left-side UC (E2)(Pan.A). At species level, Rhodotorula mucilaginosa was significantly depleted in E3 (p≤0.05)(Pan.B) In CD, Aspergillus was predominant in ileal affection(L1) while Candida and Rhodotorula genus were more abundant in L2-L3.Patients with structuring phenotype(B2) were depleted of Apergillus and Rodhotorula (Pan.A). At species level, ileal (L1) patients were depleted of Candida tropicalis and Penicillium kudriavzevii. B1 patients had a marked predominance of Candida albicans vs B2(p≤0.01)(Pan.B) The mycobiome correlation with disease activity is depicted (Pan.C). Candida dublinensis was overrepresented in activity, while Saccharomyces pastorianus was depleted(p≤0.01) The correlation of the mycobiome with disease outcomes is represented in Pan.D. Penicillium glabrum was significantly overrepresented in patients with a complicated course. The abundance of Candida tropicalis and D. nepalensis was correlated with the need for surgery. Conclusion This study shows important differences in the fungal microbiota composition in the different IBD phenotypes. Some species are clearly correlated with the activity of the disease and worse clinical outcomes suggesting a potential deleterious role.Candida tropicalis was associated with the need of surgery in CD. This in-depth characterization of the mycobiome serves as a significant addition to the understanding of the role of fungi in IBD.

P718 Characterization of microbiota and metabolomic profile in human colonic surgical resections of UC patients

Abstract Background Ulcerative colitis (UC) is characterized by a diffuse, continuous, and chronic inflammation of mucosa and submucosa layers in the colon whose etiology is still unknown. Intestinal microbiota dysbiosis and alterations in the metabolomic profile have been reported in mucosal biopsies from Inflammatory Bowel Disease (IBD) patients. We aim to characterize the microbiota composition and metabolomic profile in colonic resections of UC patients. Methods Colonic resections from UC (n=18) and non-IBD (n=20) patients were obtained. Microbiota identification, composition and classification was performed by 16S rRNA gene Illumina Miseq sequencing. The bioinformatic analysis of sequencing data was performed using constrained correspondence analysis (CCA) and non-parametric Wilcoxon test to compare species and genera proportions. Bacterial load was estimated by qPCR. Metabolomic analysis was performed using Nuclear Magnetic Resonance (NMR) to study polar metabolites and Gas-Chromatography or Liquid-Chromatography Mass-Spectrometry to study non-polar metabolites. Results Microbiota analysis revealed differences at genus and species level between UC and non-IBD patients. Cellulosimicrobium was found at 10-fold higher levels in UC samples while Escherichia genus was 3.88 times more abundant in controls. A reduction in bacterial load was seen in UC samples. Levels of short-chain fatty acids (FA), medium-chain FA, long-chain FA, carboxylic acids and amino acids were obtained from the metabolomics analysis and a positive correlation between propionic, aspartic and hydroxybutyric acids and Cellulosimicrobium and Pseudomonas was found (Fig1B). Gut commensals such as unclassified Agathobacter, Blautia faecis, Oscillospiraceae or Faecalibacterium prausnitzii positively correlated with the abundance of butyric acid, acetic acid and succinic acid; meanwhile Subdoligranulum, Lachnospireace or unclassified Blautia negatively correlated with some medium or long chain fatty acids (Fig1B). Fig1. Correlations between bacterial species and metabolites in (A) controls and (B) UC patients. Performed with mixOmics library in R. Conclusion Significant differences in microbiota composition and abundance are found in UC patients, which undergo a clear gut dysbiosis in colonic tissue. Correlation analysis suggests Cellulosimicrobium and Pseudomonas as sources of propionic, aspartic and hydroxybutyric acid. These results point at Cellulosimicrobium as a potential candidate in UC pathology.

Inducing banana Fusarium wilt disease suppression through soil microbiome reshaping by pineapple–banana rotation combined with biofertilizer application

Abstract. Crop rotation and biofertilizer application have historically been employed as efficient management strategies for soil-borne disease suppression through soil microbiome manipulation. However, how this occurs and to what extent the combination of methods affects the microbiota reconstruction of diseased soil is unknown. In this study, pineapple–banana rotation combined with biofertilizer application was used to suppress banana Fusarium wilt disease, and the effects on both bacterial and fungal communities were investigated using the MiSeq Illumina sequencing platform. Our results showed that pineapple–banana rotation significantly reduced Fusarium wilt disease incidence and the application of biofertilizer caused additional suppression. Bacterial and fungal communities thrived using rotation combined with biofertilizer application: taxonomic and phylogenetic α diversity of both bacteria and fungi increased along with disease suppression. Between the two strategies, biofertilizer application predominantly affected both bacterial and fungal community composition compared to rotation. Burkholderia genus may have been attributed to the general wilt suppression for its change in network structure and high relative importance in linear models. Our results indicated that pineapple–banana rotation combined with biofertilizer application has strong potential for the sustainable management of banana Fusarium wilt disease.