Number Of OTUs Research Articles

High Taxonomic and Functional Diversity of Bacterial Communities Associated with Melon Fly, Zeugodacus cucurbitae (Diptera: Tephritidae).

The next generation sequencing (NGS) approach has facilitated the investigations of gut microbiota with high throughput and resolution. The present study was focused on the taxonomic and functional characterization of bacterial community associated with different developmental stages of melon fly, Zeugodacus cucurbitae using 16S ribosomal RNA (rRNA) gene amplicons metagenomics. Z. cucurbitae is considered an invasive and most staid polyphagous pest of cucurbitaceous and other related crops. The taxonomic analysis of highly variable V3-V4 region of bacterial 16S rRNA gene sequencing indicated that the bacterial community associated with Z. cucurbitae consists of a total of 23 bacterial phyla (including unclassified and unassigned bacteria), comprising 32 classes, 69 orders, 99 families and 130 genera. Proteobacteria, Firmicutes, Actinobacteria and Tenericutes were dominant phyla of which family, Enterobacteriaceae was the most abundant in the larval and adult female stages, whereas Mycoplasmataceae was the dominant in the pupal stage. In larval stages of Z. cucurbitae, genus Providencia and Comamonas were the most abundant. However, genus Candidatus-Bacilloplasma and Klebsiella werethe most dominant in pupae and adult females of Z. cucurbitae, respectively. PICRUSt analysis conducted for prediction of metabolic activities revealed that associated microbiota were involved in membrane transport, carbohydrate metabolism, amino acid metabolism, energy metabolism, replication and repair processes as well as cellular processes and signalling. The higher number of OTUs was annotated for phosphoglycerate mutase and transketolase in adult females followed by larval stages, which may support the digestive function of the microbiota in larvae and adult females. Our findings provide insights about the high variation in microbiota across developmental stages and basis for microbiota-based management strategies of fruit flies.

Illumina-based identification of arbuscular mycorrhizal fungi from Karachay-Cherkessia soils for development of bio-fertilizers

The aim of the study was to investigate the species diversity of AM fungi in different parts of the North Caucasus, biodiversity hotspot, the center of the world’s biological diversity. Samples were taken from 5 locations (stationary trial plots, STPs) in different ecosystems and at various altitudes. Identification was performed using sequencing for ITS1 and ITS2 regions, amplified with universal primers, Illumina MiSeq was employed. 19 genera of AM fungi were found on all STPs. The work did not reveal a correlation between the altitude and the species composition of AM fungi. At the same time, it should be assumed that a correlation could be found between the biodiversity of AM fungi and the type of ecosystem, which should be done in the future. The study shows it is necessary to use an analysis for both ITS regions, since the data obtained for each ITS region differ and complement each other. Analysis for the ITS2 region revealed 1.3 times more virtual taxa than for the ITS1, while the number of OTUs identified per species was similar for both regions. The highest biodiversity of AM fungi was found in STP #3 (with meadow flora). Only 4 species (Rhizophagus irregularis, R. intraradices, Paraglomus laccatum, and Claroideoglomus claroideum) were found on all five analyzed STPs. We found unexpectedly that with such a high biodiversity among the identified fungi, no different species were found in the Paraglomus genus, all the sequences of Paraglomus belonged to Paraglomus laccatum, whereas at least 9 species are distinguished in the genus by morphology. Further research will allow us to identify new strains of AM fungi, the efficiency of which may be higher than already studied ones. In the future this will make it possible to create more effective microbial biofertilizers for agriculture.

Improved High-Throughput Sequencing of the Human Oral Microbiome: From Illumina to PacBio.

Background A comprehensive understanding of the commensal microflora and its relation to health is essential for preventing and combating diseases. The aim of this study was to examine the structure of the oral microbiome by using different sequencing technologies. Material and Methods. Five preschool children with no symptoms of oral and systemic diseases were recruited. Samples of saliva were collected. A 468 bp insert size library was constructed on the MiSeq platform and then subjected to 300 bp paired-end sequencing. Libraries with longer insert sizes, including a full-length 16S rDNA gene, were sequenced on the PacBio RS II platform. Results A total of 122.6 Mb of raw data, including 244,967 high-quality sequences, were generated by the MiSeq platform, while 134.6 Mb of raw data, including 70,030 high-quality reads, were generated by the PacBio RS II platform. Clustering of the unique sequences into OTUs at 3% dissimilarity resulted in an average of 225 OTUs on the MiSeq platform; however, the number of OTUs generated on the PacBio RS II platform was 449, far greater than the number of OTUs generated on the MiSeq platform. A total of 437 species belonging to 10 phyla and 60 genera were detected by the PacBio RS II platform, while 163 species belonging to 12 phyla and 72 genera were detected by the MiSeq platform. Conclusions The oral microflora of healthy Chinese children were analyzed. Compared with traditional 16S rRNA sequencing technology, the PacBio system, despite providing a lower amount of clean data, surpassed the resolution of the MiSeq platform by improving the read length and annotating the nucleotide sequences at the species or strain level. This trial is registered with NCT02341352.

The effect of different drinking water in culture medium on feces microbiota diversity.

The human gut harbors trillions of microbes, which are extremely important to the health of the host. However, the effect of drinking water on gut microbiota has been poorly understood. In this study, we explored the response of BALB/c mice gut bacterial community (feces) to the different types of drinking water, including commercial bottled mineral water (MW), natural water (NW), purified water (PW) and tap water (TW). Feces were cultured with brain heart infusion broth dissolved in four types of drinking water. 16S rRNA gene analysis was performed. Our results reveal that the microbiota composition is different among culturing with four types of drinking water. As the culture time increases, the number of OTUs significantly decreased, except under the aerobic condition of MW. Under aerobic conditions on the 5th day, the considerable differences of alpha diversity index are found between MW and three others, and these are the most unique taxa in the MW group. Importantly, the LEfSe analysis discovers that the Bacteroidetes taxa dominate the differences between MW and the other water types. Our findings demonstrate that the mineral water as a culture medium may lead to a progressive increase of the gut microbiota diversity by providing the growth convenience to Bacteroidetes.

Testing selectivity of bacterial and fungal culture media compared to original silage samples using next generation sequencing

Plate counts using selective culture media is still the most frequently used method for the enumeration of the different microbial groups that colonize silage, including lactic acid bacteria, yeasts and molds. Since different culture media have specific composition, they may allow the growth of specific populations. To date, no study has used next generation sequencing technology to compare the selective capacity of these different culture media although this approach could provide comprehensive insight into the relevance of using one culture medium over another. Sequencing of the 16S rDNA and ITS amplicon were performed to compare the selectivity of different culture media used in silage microbiology. Corn silage, grass-alfalfa silage and total mixed ration extracts were plated on five selective media for lactic acid bacteria, incubated under aerobic and anaerobic conditions, and on eight selective media for yeast and molds to compare their selectivity. Ensiling provided a pre-selection environment for specific microorganisms over forage and reduced the number of observed OTUs: only 12 OTUs of bacteria were observed in corn silage sampled in the center of a bunker silo, while the mean number of OTUs identified in samples taken closer to the side of the silo, influenced by higher oxygen and humidity level, increased to 79. Still, MRS and Rogosa plates had less than 12 different OTUs in the center and 24 at the side, mainly Lactobacillaceae, Acetobacteraceae, and Leuconostocaceae. Incubating the plates under anaerobic conditions was selective against Acetobacteraceae. MRS supplemented with acetic acid increased selectivity of lactic acid bacteria. When plated on culture media specific for yeast and molds, from 17 to 68 different OTUs were observed in corn silage. Mixed grass-alfalfa silage and total mixed ration samples usually had more observed OTUs and the diversity profile of the corresponding culture media was similar to that of the original samples. For yeasts and molds, Dichloran Rose Bengal Chloramphenicol Agar revealed a diversity profile close to the that of the corn silage.

Gut microbiota characteristics in mice with antibiotic-associated diarrhea

BackgroundAntibiotic-associated diarrhea (AAD), defined as diarrhea that occurs in association with the administration of antibiotics and without another clear etiology, is one of the most common adverse drug events of antibiotics therapy. We established a diarrhea model induced by gentamycin and cefradine to investigate the microbiota characteristics in the intestinal lumen of mice with AAD and provide insights into noteworthy bacteria related to gentamicin and cefradine-associated diarrhea.ResultsThe number of OTUs in the model group and the normal group was 983 and 2107, respectively, and 872 identical OTUs were shared between two groups. Species richness and species diversity of intestinal microbe were altered by antibiotics administration. PCoA showed a clear separation between AAD and health control. The dominant phyla of AAD mice were Firmicutes (52.63%) and Proteobacteria (46.37%). Among the genus with top 20 abundance, the relative abundance of 7 genera, Ruminococcus, Blautia, Enterococcus, Eubacterium, Clostridium, Coprococcus, and Aerococcus, were enriched in the model group. Based upon the LEfSe analysis, Enterococcus, Eubacterium, Ruminococcus, and Blautia were identified as potential biomarkers for AAD.ConclusionsThe bacterial diversity of the intestinal lumen was diminished after gentamicin and cefradine administration. The alterations in the abundance and composition of gut microbiota further led to the dysfunction of gut microbiota. More specifically, gentamicin and cefradine significantly increased the abundance of the opportunistic pathogens, of which Enterococcus and Clostridium were the most prominent and most worthy of attention.

Characteristics of Soil Nutrients and Fungal Community Composition in Crop Rhizosphere Under Different Rotation Patterns

To study the characteristics of soil nutrients and fungal community composition under different rotation patterns in the arid zone of central Ningxia, we used millet rotation soybean (MRG), rotation grain amaranth (MRA), rotation quinoa (MRQ), and continuous millet rotation (CK) as the objects. The soil nutrient content was determined, and the sequence of the ITS variation region of soil fungi was determined using the Illumina MiSeq high-throughput sequencing platform. The results showed that the effects of different rotation patterns on the soil nutrients were different. The soil pH and electrical conductivity decreased under three rotation patterns, and the soil total nitrogen, total potassium, total phosphorus, and organic matter contents increased. The number of OTUs and α diversity index was higher than those of continuous millet rotation. The results of the fungal community composition study showed that Ascomycota was the dominant flora in 4 patterns. The cluster analysis showed that the fungal genus composition of MRA and MRG was the most similar, followed by MRQ, and that of CK was significantly different with the other three rotation patterns. A correlation analysis showed that the soil nutrients were significantly correlated with several dominant fungal genera (P<0.05 or P<0.01). Further, the soil total nitrogen, total potassium, nitrate nitrogen, and organic matter contents were the most important factors influencing the soil fungal communities. Principal component analysis (PCA) showed that the MRG rotation patterns were better than those of the MRA and MRQ patterns. In summary, crop rotation improved the polytrophic index of the fungal community, changed the soil fungal community structure, and improved soil fertility. Among, the millet and soybean rotation were the best, and we have suggested to promote cereal rotation as one of the main rotation patterns in the cereal industry in the central dry zone.

Assessing the bacterial diversity and functional profiles of the River Yamuna using Illumina MiSeq sequencing.

A small percentage of the total freshwater on Earth is represented by river water. Microbes have an essential role to play in the biogeochemical cycles, mineralization of organic water, along with xenobiotics degradation. Microbial dynamics are susceptible to environmental stressors which includes pollutants such as antibiotics, metals, and other degradants. River Yamuna is polluted extensively by domestic and industrial wastes. Xenobiotics, when released into the environment, can lead to water pollution. The present study evaluates the microbial diversity in Yamuna River (28°40'5.53'' N, 77°15'0.35'' E) along with the prediction of the metagenome function. In this context, the metagenomic DNA was extracted and sequencing was done on Illumina@MiSeq platform. The total number of OTUs picked was 41,994, out of which 74% were classified within the kingdom Bacteria. 35% of the OTUs were assigned to phylum Proteobacteria, followed by Bacteriodetes (22%), whereas 26% of OTUs were unassigned. PICRUSt (Phylogenetic Investigation of Communities by Reconstruction of Unobserved States) was used to predict metagenomic functions using 16S rDNA as a marker. Metagenomic reads were assigned to the Kyoto Encyclopedia of Genes and Genomes (KEGG), Cluster of Orthologous (COG), and Gene Ontology (GO). Functional characterization reveals the presence of methyl-accepting chemotaxis protein which is an important adaptation for the microbes in the environment. The enzymes can be mapped for the bioremediation of xenobiotics. Information obtained from the amplicon sequencing of River Yamuna, collaborated with "omic" studies, may help in the design of bioremediation strategies and can be used for environmental clean-up of pollutants.

Effects of Climate Change Stressors on the Prokaryotic Communities of the Antarctic Sponge Isodictya kerguelenensis

Microbial symbionts of marine sponges play important roles for the hosts and also for the ecosystems. The unique tolerance of marine sponge to a wide diversity of microbial symbionts allows them to acquire a wide variety of “evolutionary solutions” to environmental challenges. Ice scour is one of the main forces structuring Antarctic benthic communities and its effect is expected to increase as further warming is projected for the Western Antarctic Peninsula (WAP). The interaction of these physical drivers may have a significant impact shaping the microbiome of Antarctic sponges under current and future scenarios of climate change. The aim of this research was to assess how stressors such as warming and injuries produced by ice scour, affect the microbiome of the marine Antarctic sponge Isodictya kerguelenensis. under current and predicted scenarios. Individuals of I. kerguelenensis were sampled in shallow waters (10 m) off the coast of Doumer Island, Palmer Archipelago, WAP. In order to mimic the effect of tissue damage produced by ice scour, tissue samples were taken at day 0 (T0d) and 15 (T15d) from individuals placed in control (0.5 °C) and two temperature treatments (3 and 6°C). Our analysis of 16S libraries from the V4-V5 region revealed two phyla of Archaea and 22 of Bacteria. Proteobacteria and Bacteroidetes were the most representative in terms of both number of OTUs and sequence abundances. The analysis at OTU level showed significant effect of injury and treatment. Principal Coordinates Analysis (PCoA) showed a clear group of uninjured sponges and three other groups of injured sponges according to temperature. Our results also showed a group of OTUs that were only present in injured sponges, being potential markers of sponge damage. Our study suggests that disturbance produced by icebergs may have direct impact on the sponge microbiome. Future climate change scenarios with warming and increases in iceberg impacts may lead to prokaryotic symbiont disruption on sponge species, having potential cascading effects for the host and the functional roles they play in the Antarctic ecosystem; however, the potential effects of this disruption are yet to be further studied.

Iterative taxonomic study of Pareiorhaphis hystrix (Siluriformes, Loricariidae) suggests a single, yet phenotypically variable, species in south Brazil.

Pareiorhaphis hystrix is a widely distributed species, occurring in the upper and middle Uruguay River and in the Taquari River basin, Patos Lagoon system, southern Brazil. Morphological variation has been detected throughout the distribution of P. hystrix, and this work seeks to test the conspecific nature of populations in several occurrence areas. Specimens from six areas in the Uruguay River basin and three in the Taquari River basin were compared. Variance analysis (ANOVA) was performed for the meristic data, and Principal Component Analysis (PCA) and Linear Discriminant Analysis (LDA) were conducted for morphometric data. Molecular analyses used coI, cytb, 12S and 16S mitochondrial genes, examining nucleotide diversity, haplotype diversity, genetic distance, and delimitation of possible multiple species through the Generalized Mixed Yule Coalescent (GMYC) method. Phylogenetic relationships of studied populations were also investigated through Bayesian inference. While PCA indicated a tendency of overlap between areas, ANOVA and LDA detected a subtle differentiation between populations from the two hydrographic basins. Yet, both latter analyses recovered the population from Pelotas River, a tributary to Uruguay River, as more similar to populations from Taquari River, which is congruent to morphological observations of anterior abdominal plates. The molecular data indicated a nucleotide diversity lower than the haplotypic diversity, suggestive of recent expansion. The concatenated haplotype network points to slight differentiation between areas, with each locality presenting unique and non-shared haplotypes, although with few mutational steps in general. The species delimitation by coalescence analysis suggested the presence of a variable number of OTUs depending on the inclusion or exclusion of an outgroup. In general, the morphological data suggest a subtle variation by river basin, while the genetic data indicates a weak population structuration by hydrographic areas, especially the Chapecó and Passo Fundo rivers. However, there is still not enough differentiation between the specimens to suggest multiple species. The iterative analyses indicate that Pareiorhaphis hystrix is composed of a single, although variable, species.

CDSnake: Snakemake pipeline for retrieval of annotated OTUs from paired-end reads using CD-HIT utilities

BackgroundIllumina paired-end reads are often used for 16S analysis in metagenomic studies. Since DNA fragment size is usually smaller than the sum of lengths of paired reads, reads can be merged for downstream analysis. In spite of development of several tools for merging of paired-end reads, poor quality at the 3′ ends within the overlapping region prevents the accurate combining of significant portion of read pairs. Recently CD-HIT-OTU-Miseq was presented as a new approach for 16S analysis using the paired-end reads, it completely avoids the reads merging process due to separate clustering of paired reads. CD-HIT-OTU-Miseq is a set of tools which are supposed to be successively launched by auxiliary shell scripts. This launch mode is not suitable for processing of big amounts of data generated in modern omics experiments. To solve this issue we created CDSnake – Snakemake pipeline utilizing CD-HIT tools for easier consecutive launch of CD-HIT-OTU-Miseq tools for complete processing of paired end reads in metagenomic studies. Usage of pipeline make 16S analysis easier due to one-command launch and helps to yield reproducible results.ResultsWe benchmarked our pipeline against two commonly used pipelines for OTU retrieval, incorporated into popular workflow for microbiome analysis, QIIME2 - DADA2 and deblur. Three mock datasets having highly overlapping paired-end 2 × 250 bp reads were used for benchmarking - Balanced, HMP, and Extreme. CDSnake outputted less OTUs than DADA2 and deblur. However, on Balanced and HMP datasets number of OTUs outputted by CDSnake was closer to real number of strains which were used for mock community generation, than those outputted by DADA2 and deblur. Though generally slower than other pipelines, CDSnake outputted higher total counts, preserving more information from raw data. Inheriting this properties from original CD-HIT-OTU-MiSeq utilities, CDSnake made their usage handier due to simple scalability, easier automated runs and other Snakemake benefits.ConclusionsWe developed Snakemake pipeline for OTU-MiSeq utilities, which simplified and automated data analysis. Benchmarking showed that this approach is capable to outperform popular tools in certain conditions.

Marine bacterial community analysis on 316L stainless steel coupons by Illumina MiSeq sequencing.

In order to evaluate the corrosive action of microorganisms on 316L metal exposed directly to a marine environment, a system was designed to immerse coupons in seawater. After periods of 30, 60 and 90days, the coupons were recovered, the corrosion rates evaluated and the biofilm samples on their surface were analyzed by 16S rRNA gene sequencing. The results of the corrosion rate showed an acceleration over the entire experimental period. Alpha diversity measurements showed higher rates after 60days of the experiment, while abundance measurements showed higher rates after 90days of exposure to the marine environment. The beta-diversity results showed a clear separation between the three conditions and proximity in the indices between replicates of the same experimental condition. The results of 16S rRNA gene sequencing showed that after 30days of exposure to seawater, there was massive representativeness of the pioneer bacteria, Gamma and Alphaproteobacteria, with emphasis on the genera Alcanivorax, Oceanospirillum and Shewanella. At the 60-day analysis, the Gammaproteobacteria class remained dominant, followed by Alphaproteobacteria and Flavobacteria, and the main representatives were Flexibacter and Pseudoalteromonas. In the last analysis, after 90days, a change in the described bacterial community profile was observed. The Gammaproteobacteria class was still the largest in diversity and OTUs. The most predominant genera in number of OTUs were Alteromonas, Bacteriovorax and, Nautella. Our results describe a change in the microbial community over coupons directly exposed to the marine environment, suggesting a redirection to the formation of a mature biofilm. The conditions created by the biofilm structure suggest said condition favor biocorrosion on the analyzed coupons.

The hidden layers of microbial community structure: extracting the concealed diversity dimensions from our sequencing data.

Microbial metabarcoding is the standard approach to assess communities' diversity. However reports are often limited to simple OTU abundances for each phylum, giving rather one-dimensional views of microbial assemblages, overlooking other accessible aspects. The first is masked by databases incompleteness; OTU picking involves clustering at 97% (near-species) sequence identity, but different OTUs regularly end up under a same taxon name. When expressing diversity as number of obtained taxonomical names, a large portion of the real diversity lying within the data remains underestimated. Using the 16S sequencing results of an environmental transect across a gradient of 17 coastal habitats we first extracted the number of OTUs hidden under the same name. Further, we observed which was the deepest rank yielded by annotation, revealing for which microbial groups are we missing most knowledge. Data were then used to infer an evolutionary aspect: what is, in each phylum the success of the present time individuals (abundances for each OTU) in relation to their prior evolutionary success in differentiation (number of OTUs). This information reveals whether the past speciation/diversification force is matched by the present competitiveness in reproduction/persistence. The final layer explored is functional diversity, i.e. abundances of groups involved in specific environmental processes.

Rapamycin and MCC950 modified gut microbiota in experimental autoimmune encephalomyelitis mouse by brain gut axis

AimsMultiple sclerosis (MS) whose pathogenesis is still unclear is a chronic progressive disease in the central nervous system. Gut microbiota can directly or indirectly affect the immune system through the brain gut axis to engage in the occurrence and development of the disease. Materials and methodsC57BL/6 mice which were immunized by MOG35–55 to prepare experimental autoimmune encephalomyelitis (EAE) animal models were treated with rapamycin and MCC950 (CP-456773) in combination or separately. After sequencing the 16S rRNA V4 region of gut microbiota, the species, abundance and composition of gut microbiota were analyzed by Alpha diversity, Bata diversity and LEfSe analysis. The pathological changes and the expression of CD4 and CD8 of brain, large intestine and spleen were detected. Key findingsThe results showed that rapamycin and MCC950 could alleviate the progression of the disease by inducing autophagy and inhibiting the immune response. The Alpha diversity of EAE model group was no significant difference compering to control group while the number of OTUs was decreased. After the treatment by rapamycin and MCC950, the abundance and composition of gut microbiota was relatively recovered, which was close to that of normal mice. SignificanceInhibiting immune cell-mediated inflammation and restoring the composition of gut microbiota may help to alleviate the clinical symptoms of multiple sclerosis. Furthermore, to research the regulatory effect between immune response and gut microbiota may be a new strategy for the prevention and treatment of multiple sclerosis.

Analysis of bacteria distribution characteristics in different layers of agarwood based on Hiseq sequencing

To explore the diversity of bacterial community structure between different layers of agarwood, Hiseq(high-throughput sequencing) was used to analyze the bacterial community structure of samples from different layers of agarwood. Our results showed that 1 150 096 optimized sequences and 9 690 OTUs were obtained from 15 samples of 5 layers of agarwood, which belonged to 28 bacterial phyla, 61 classes, 110 orders, 212 families and 384 genera. Further analysis revealed that the normal layer(NL) had the lowest bacterial species richness and the smallest number of OTUs. And the total number of OTUs of the agarwood layer(AL) and NL was zero, which was quite different.At the same time, there were significant differences in bacterial community structure and species diversity between NL and the other four layers. While there were some common dominant bacterial genera in both transition layer(TL) and NL. The similarity of bacterial distribution in 4 non-NL layers was relatively high, which had four common genera, such as Acidibacter, Bradyrhizobium, Acidothemus and Sphingomonas. While Acidibacter, Bradyrhizobium and Acidothemus were the dominant bacterial genus of DA and AL, and all of these layers contained volatile oil. In addition, the Bradyrhizobium was the most abundant in agarwood layer. Our results showed that bacterial community diversity and abundance were decreasing from DL to AL, and different layers showed significant differences in bacterial enrichment. It provided the clues to investigate how bacteria participate in the formation of agarwood.

Insights on comparative bacterial diversity between different arid zones of Cholistan Desert, Pakistan.

The present study was conducted to analyze bacterial diversity profile of Cholistan desert located in Pakistan. The study investigates the influence of physicochemical parameters of soil on distribution of different bacteria at all taxonomic levels and also study the distribution pattern between different desert environments, particularly rhizospheric and bulk desert sands. Species richness showed phyla Proteobacteria and Chloroflexi as the dominant OTUs in all the samples. Besides the two phyla, the rhizospheric soils with root remnants were dominated by Firmicutes, Deinococcus-Thermus, Actinobacteria and Acidobacteri, while phylum Thermotogae was present in significant quantity in rhizosheaths devoid of roots. In non-rhizospheric desert soils, a considerable number of OTUs belonged to phyla Proteobacteria, Chloroflexi, Bacteroidetes and Acidobacteria. An important finding from this study is that a bulk portion of the OTUs were assigned to unclassified taxa, indicating a large repertoire of unexplored taxa in the desert ecology of Pakistan. Distribution of taxonomic groups among various regions of the desert was collaborating well with the physicochemical parameters of the sites. The findings of this study establish the fundamental relationships between desert ecosystem, specific native plant and the total bacterial flora. This is the first study of microbial community analysis of any desert in Pakistan and thus, will serve as a future platform to explore further on desert ecosystem functioning by employing the ever-changing biotechnological tools.

Patterns in Microbial Assemblages Exported From the Meltwater of Arctic and Sub-Arctic Glaciers.

Meltwater streams connect the glacial cryosphere with downstream ecosystems. Dissolved and particulate matter exported from glacial ecosystems originates from contrasting supraglacial and subglacial environments, and exported microbial cells have the potential to serve as ecological and hydrological indicators for glacial ecosystem processes. Here, we compare exported microbial assemblages from the meltwater of 24 glaciers from six (sub)Arctic regions – the southwestern Greenland Ice Sheet, Qeqertarsuaq (Disko Island) in west Greenland, Iceland, Svalbard, western Norway, and southeast Alaska – differing in their lithology, catchment size, and climatic characteristics, to investigate spatial and environmental factors structuring exported meltwater assemblages. We found that 16S rRNA gene sequences of all samples were dominated by the phyla Proteobacteria, Bacteroidetes, and Actinobacteria, with Verrucomicrobia also common in Greenland localities. Clustered OTUs were largely composed of aerobic and anaerobic heterotrophs capable of degrading a wide variety of carbon substrates. A small number of OTUs dominated all assemblages, with the most abundant being from the genera Polaromonas, Methylophilus, and Nitrotoga. However, 16–32% of a region’s OTUs were unique to that region, and rare taxa revealed unique metabolic potentials and reflected differences between regions, such as the elevated relative abundances of sulfur oxidizers Sulfuricurvum sp. and Thiobacillus sp. at Svalbard sites. Meltwater alpha diversity showed a pronounced decrease with increasing latitude, and multivariate analyses of assemblages revealed significant regional clusters. Distance-based redundancy and correlation analyses further resolved associations between whole assemblages and individual OTUs with variables primarily corresponding with the sampled regions. Interestingly, some OTUs indicating specific metabolic processes were not strongly associated with corresponding meltwater characteristics (e.g., nitrification and inorganic nitrogen concentrations). Thus, while exported assemblage structure appears regionally specific, and probably reflects differences in dominant hydrological flowpaths, OTUs can also serve as indicators for more localized microbially mediated processes not captured by the traditional characterization of bulk meltwater hydrochemistry. These results collectively promote a better understanding of microbial distributions across the Arctic, as well as linkages between the terrestrial cryosphere habitats and downstream ecosystems.

Abstract B09: Unravelling the gastric microbiome in health and disease: Gastric cancer beyond Helicobacter pylori in a Brazilian cohort

Abstract Although numerous studies have shown the relevance of the gut microbiome in several diseases, underlying questions remain concerning the stomach microbiome and the establishment of a causal link between the microbiota and the development of gastric diseases, much beyond Helicobacter pylori and Epstein Barr virus. In this study, we aimed to characterize the bacterial composition of the stomach of subjects undergoing upper endoscopy, including gastric cancer (GC) individuals, aiming to identify fluctuations in bacterial populations that might be associated with stomach health. During endoscopic examination at A.C. Camargo Cancer Center (Sao Paulo, Brazil), gastric fluids (GF) were recovered from either GC patients (113) or individuals with gastric-related complaints, such as superficial gastritis (SG; 79), atrophic gastritis (AG; 12), and intestinal metaplasia (IM; 33). For eubacteria identification, the V3-V4 region of the 16S rRNA gene was amplified and paired-end sequenced (Illumina MiSeq). Analyses were carried out using Qiime2 and phyloseq packages. On average, we identified between 14 and 104 OTUs per subject, evidencing the potential of GFs for determining the stomach microbial composition and the interindividual variation. Testing of sample richness between GC and controls showed significant differences between the number of OTUs observed in each group (an average of 44 and 52 OTUs, respectively—Mann-Whitney test, p&amp;lt;0.05) and SG patients had a significantly increased alpha diversity (Shannon, p&amp;lt;0.05) as compared to AG, IM, and GC patients (both intestinal and diffuse subtypes), indicating dysbiosis already in early carcinogenesis steps. Additionally, the prolonged use of proton pump inhibitors or the presence of H. pylori (except for SG) did not seem to interfere with bacterial diversity. Specific genera are enriched in the sample subsets, including a lower presence of Corynebacterium and increased Streptococcus (Linear discriminant analysis Effect Size, LDA score &amp;gt;2) in AG samples as compared to SG patients, which are also increased in the IM, and GC. These results indicate these bacteria to be potentially associated with the stomach dysbiosis that may lead to the carcinogenesis cascade. Besides the regular turnover of the gastric epithelial tissue and pouring of cells onto the gastric cavity, GF certainly contains a high proportion of transient oral-derived bacteria, while stomach-resident microbiota is expected to be in close contact with the gastric epithelia. Preliminary data analyzing the bacterial content of the saliva x GF in a subset of patients showed no significant beta-diversity differences, but both fluids differ significantly from their biopsies’ composition. We are currently performing culturomics and transcriptomics to identify bacteria that are alive in the stomach. As GC is a complex malignancy with limited treatment options, these results may contribute to developing new interventions to treat and to better understand this disease. Citation Format: Thais F. Bartelli, Gabriela E. Albuquerque, Alexandre Defelicibus, Marianna S. Serpa, Lais L.S. Abrantes, Rodrigo Borges, Felipe Coimbra, Adriane G. Pelosof, Israel T. Silva, Diana N. Nunes, Emmanuel Dias-Neto. Unravelling the gastric microbiome in health and disease: Gastric cancer beyond Helicobacter pylori in a Brazilian cohort [abstract]. In: Proceedings of the AACR Special Conference on the Microbiome, Viruses, and Cancer; 2020 Feb 21-24; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2020;80(8 Suppl):Abstract nr B09.

Effects of re-vegetation restoration on soil bacterial community structure in degraded land in subtropical China

Ecosystem degradation is one of the most pressing environmental problems in the world. Re-vegetation is the major method in land restoration, playing an important role in improving soil quality and biodiversity. Bacteria constitute a vital part of terrestrial ecosystems; however, the relationship between bacteria and restoration of degraded land is not well understood. In this study, we investigated how restoration of degraded land impacts soil physicochemical properties and soil bacterial communities 7, 17, 23 and 35 years after re-vegetation, along with an adjacent control of degraded land. Results showed increases in OTUs, Chao1 and Shannon indices by 54.7%–69.7%, 55.6%–66.0% and 13.5%–17.8% after restoration, with Proteobacteria, Acidobacteria, Chloroflexi and Actinobacteria being the dominant phyla in the study area. Bacterial diversity increased, more strongly during the initial 7 years, but continuous until 35 years. There were positive correlation between the number of OTUs, the Chao1 and Shannon indices and soil nutrients, indicating that improved nutrient contents after restoration was an important driver of bacterial richness and diversity. Vegetation restoration increased the relative abundance of Alphaproteobacteria by 55.9%–118%, especially the genus Bradyrhizobium, which doubled. The relative abundance of Nitrospira (a nitrite-oxidizing bacterial group) was very low (<0.1%), corresponding well with the low NO3−-N content (less than 1.4 mg kg−1soil) in all soil samples, despite increasing soil organic carbon and total nitrogen levels with vegetation restoration age. The results indicated that vegetation restorations have positive effects on the richness and diversity of soil bacteria, and that these effects are the most pronounced during the first 7 years after restoration.

The soil fungal communities in nurseries producing Abies alba

Silver fir is an important forest-forming species in the mountain and upland parts of Poland. It was determined that fir lost the possibility of spontaneous return to the forests of the region. That is why the Polish State Forests has launched a programme to restore its resources in the Sudetes. Until now, fungi and their relationship with fir have not been fully addressed in the Sudetes Restitution Programme, therefore this study was undertaken. The aim of this study was to determine the species composition of soil fungi from quarters producing silver fir seedlings. The research material was rhizosphere soil collected from 3-year-old saplings produced in forest nurseries of the Międzylesie Forest District. Fungal composition was determined by Next-Generation sequencing (Illumina NextSeq 500). The total number of OTUs obtained (638 435) included sequences of cultivated horcultured fungi (433 412 OTUs = 52.7%), non-cultivable fungi, that is which cannot be cultured (97 108 OTUs = 22.41 %) and potential fungi with no reference sequence in UNITE (73 419 OTUs = 16.93%) and non-fungal organisms (34 496 = 7.96%). The following taxa as Mortierella sp. (8.23%). Tylospora sp. (6.68%) and Russula sp. (3.76%) had the largest share in the soil fungal communities. The results of the study indicate the dominance of saprotrophic and mycorrhizal fungi in the communities of fir roots, which proves that saplings are of good quality. Small share of pathogens sequences suggests that soil-born fungal pathogens are not a major threat to fir seedlings in nurseries.&#x0D; Key words: mycorrhizal fungi, nursery, Abies alba, seedlings, Międzylesie Forest District.