Size-Resolved Community Structure of Bacteria and Fungi Transported by Dust in the Middle East

The atmosphere plays an important role in transporting microorganisms on a global scale, yet the processes affecting the composition of the airborne microbiome, the aerobiome, are not fully outlined. Here we present the community compositions of bacteria and fungi obtained by DNA amplicon-sequencing of aerosol samples collected in a size-resolved manner during nine consecutive days in central Israel. The campaign captured dust events originating from the Sahara and the Arabian deserts, as well as days without dust (“clear days”). We found that the source of the aerosol was the main variable contributing to the composition of both fungal and bacterial communities. Significant differences were also observed between communities representing particles of different sizes. We show evidence for the significant transport of bacteria as cell-aggregates and/or via bacterial attachment to particles during dust events. Our findings further point to the mixing of local and transported bacterial communities, observed mostly in particles smaller than 0.6 μm in diameter, representing bacterial single cells. Fungal communities showed the highest dependence on the source of the aerosols, along with significant daily variability, and without significant mixing between sources, possibly due to their larger aerodynamic size and shorter atmospheric residence times. These results, obtained under highly varied atmospheric conditions, provide significant assurances to previously raised hypotheses and could set the course for future studies on aerobiome composition.

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Metagenome-validated Parallel Amplicon Sequencing and Text Mining-based Annotations for Simultaneous Profiling of Bacteria and Fungi: Vaginal Microbiome and Mycobiota in Healthy Women

10.21203/rs.3.rs-321778/v1 ◽

2021 ◽

Author(s):

Seppo Virtanen ◽

Schahzad Saqib ◽

Tinja Kanerva ◽

Pekka Nieminen ◽

Ilkka Kalliala ◽

...

Keyword(s):

16S Rrna ◽

16S Rrna Gene ◽

Cost Effective ◽

Amplicon Sequencing ◽

Rrna Gene ◽

Extensive Literature ◽

Metagenomic Sequencing ◽

Text Extraction ◽

Healthy Women ◽

Bacteria And Fungi

Abstract Background: Amplicon sequencing of kingdom-specific tags such as 16S rRNA gene for bacteria and internal transcribed spacer (ITS) region for fungi are widely used for investigating microbial populations. So far most human studies have focused on bacteria while studies on host-associated fungi in health and disease have only recently started to accumulate. To enable cost-effective parallel analysis of bacterial and fungal communities in human and environmental samples, we developed a method where 16S rRNA gene and ITS-1 amplicons were pooled together for a single Illumina MiSeq or HiSeq run and analysed after primer-based segregation. Taxonomic assignments were performed with Blast in combination with an iterative text-extraction based filtration approach, which uses extensive literature records from public databases to select the most probable hits that were further validated by shotgun metagenomic sequencing. Results: Using 50 vaginal samples, we show that the combined run provides comparable results on bacterial composition and diversity to conventional 16S rRNA gene amplicon sequencing. The text-extraction-based taxonomic assignment guided tool provided ecosystem specific annotations that were confirmed by Metagenomic Phylogenetic Analysis (MetaPhlAn). The metagenome analysis revealed distinct functional differences between the bacterial community types while fungi were undetected, despite being identified in all samples based on ITS amplicons. Co-abundance analysis of bacteria and fungi did not show strong between-kingdom correlations within the vaginal ecosystem of healthy women.Conclusion: Combined amplicon sequencing for bacteria and fungi provides a simple and cost-effective method for simultaneous analysis of microbiota and mycobiota within the same samples. Text extraction-based annotation tool facilitates the characterization and interpretation of defined microbial communities from rapidly accumulating sequencing and metadata readily available through public databases.

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From the Andes to the desert: First overview of the bacterial community in the Rimac river, the main source of water for Lima, Peru

10.1101/2020.08.16.252965 ◽

2020 ◽

Author(s):

Pedro E. Romero ◽

Erika Calla-Quispe ◽

Camila Castillo-Vilcahuaman ◽

Mateo Yokoo ◽

Hammerly Lino Fuentes-Rivera ◽

...

Keyword(s):

Metropolitan Area ◽

Bacterial Communities ◽

Geographical Location ◽

Microbiological Quality ◽

Amplicon Sequencing ◽

Urban Sewage ◽

16S Rrna Amplicon Sequencing ◽

The Andes ◽

Metabolic Functions ◽

Quality Assessments

AbstractBackgroundThe Rimac river is the main source of water for Lima, Peru’s capital megacity. The river is constantly affected by different types of contamination including mine tailings in the Andes and urban sewage in the metropolitan area. We aim to produce the first characterization of bacterial communities in the Rimac river using a 16S rRNA amplicon sequencing approach which would be useful to identify bacterial diversity and potential understudied pathogens.ResultsWe report a higher diversity in bacterial communities from the Upper and, especially, Middle Rimac compared to the Lower Rimac (Metropolitan zone). Samples were generally grouped according to their geographical location. Bacterial classes Alphaproteobacteria, Bacteroidia, Campylobacteria, Fusobacteriia, and Gammaproteobacteria were the most frequent along the river. Arcobacter cryaerophilus (Campylobacteria) was the most frequent species in the Lower Rimac while Flavobacterium succinicans (Bacteroidia) and Hypnocyclicus (Fusobacteriia) were the most predominant in the Upper Rimac. Predicted metabolic functions in the microbiota include bacterial motility, quorum sensing and xenobiotics metabolism. Additional metabolomic analyses showed the presence natural flavonoids and antibiotics in the Upper Rimac, and herbicides in the Lower Rimac.ConclusionsThe dominance in the Metropolitan area of Arcobacter cryaerophilus, an emergent pathogen associated with fecal contamination and antibiotic multiresistance, but that is not usually reported in traditional microbiological quality assessments, highlights the necessity to apply next-generation sequencing tools to improve pathogen surveillance. We believe that our study will encourage the integration of omics sciences in Peru and its application on current environmental and public health issues.

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Optics from the Single Cell to the Mesoscale

Ocean Optics ◽

10.1093/oso/9780195068436.003.0009 ◽

1994 ◽

Author(s):

Andre Morél

Keyword(s):

Optical Properties ◽

Single Cells ◽

Radiant Energy ◽

Global Scale ◽

Natural Environments ◽

Photosynthetic Performances ◽

The Individual ◽

Optical Oceanography ◽

Optical Behavior

The inherent optical properties of a water body (mesoscale), namely, the absorption coefficient, the scattering coefficient, and the volume scattering function combine with the radiant distribution above the sea to yield the apparent optical properties (Preisendorfer, 1961). The radiative transfer equation is the link between these two classes of optical properties. Locally, the inherent properties of seawater are governed by, and strictly result from, the sum of the contributions of the various components, namely, the water itself, the various particles in suspension able to scatter and absorb the radiant energy, and finally the dissolved absorbing compounds. Analyzing these contributions is an important goal of optical oceanography. Among these particles, the phytoplanktonic cells, with their photosynthetic pigments, are of prime importance, in particular in oceanic waters far from terrestrial influence. They also are at the origin of other kinds of particles, such as their own debris, as well as other living “particles” grazing on them (bacteria, flagellates and other heterotrophs). Studying optics at the level of single cells and particles is therefore a requirement for a better understanding of bulk optical properties of oceanic waters. Independently of this goal, the study of the individual cell optics per se is fundamental when analyzing the pathways of radiant energy, in particular the light harvesting capabilities and the photosynthetic performances of various algae or their fluorescence responses. The following presentation is a guidline for readers who will find detailed studies in the classic books Light Scattering by Small Particles by van de Hulst (1957) and Light and Photosynthesis in Aquatic Ecosystems by Kirk (1983), as well as in a paper dealing specifically with the optics of phytoplankton by Morel and Bricaud (1986). This chapter is organized according to the title, with first a summary of the relevant theories to be applied when studying the interaction of an electromagnetic field with a particle, and then, as a transition between this scale and that of in vitro experiments, some results concerning the optical behavior of pure algal suspensions; finally the more complicated situations encountered in natural environments are briefly described to introduce the “nonlinear biological” effect (Smith and Baker, 1978a) upon the optical coefficients for oceanic waters, and to examine some of the empirical relationships, as presently available, between the pigment concentration and the optical properties of the upper ocean at mesoscale and global scale.

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Community dynamics of duckweed-associated bacteria upon inoculation of plant growth-promoting bacteria

FEMS Microbiology Ecology ◽

10.1093/femsec/fiaa101 ◽

2020 ◽

Vol 96 (7) ◽

Author(s):

Hidehiro Ishizawa ◽

Masashi Kuroda ◽

Daisuke Inoue ◽

Masaaki Morikawa ◽

Michihiko Ike

Keyword(s):

Plant Growth ◽

Bacterial Communities ◽

Production Efficiency ◽

Community Dynamics ◽

Amplicon Sequencing ◽

Plant Colonization ◽

Plant Growth Promoting Bacteria ◽

Short Period ◽

Plant Growth Promoting ◽

Growth Promoting

ABSTRACT Plant growth-promoting bacteria (PGPB) have recently been demonstrated as a promising agent to improve wastewater treatment and biomass production efficiency of duckweed hydrocultures. With a view to their reliable use in aqueous environments, this study analysed the plant colonization dynamics of PGPB and the ecological consequences for the entire duckweed-associated bacterial community. A PGPB strain, Aquitalea magnusonii H3, was inoculated to duckweed at different cell densities or timings in the presence of three environmental bacterial communities. The results showed that strain H3 improved duckweed growth by 11.7–32.1% in five out of nine experiments. Quantitative-PCR and amplicon sequencing analyses showed that strain H3 successfully colonized duckweed after 1 and 3 d of inoculation in all cultivation tests. However, it significantly decreased in number after 7 d, and similar bacterial communities were observed on duckweed regardless of H3 inoculation. Predicted metagenome analysis suggested that genes related to bacterial chemotactic motility and surface attachment systems are consistently enriched through community assembly on duckweed. Taken together, strain H3 dominantly colonized duckweed for a short period and improved duckweed growth. However, the inoculation of the PGPB did not have a lasting impact due to the strong resilience of the natural duckweed microbiome.

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Influences of Ingredients and Bakers on the Bacteria and Fungi in Sourdough Starters and Bread

mSphere ◽

10.1128/msphere.00950-19 ◽

2020 ◽

Vol 5 (1) ◽

Cited By ~ 4

Author(s):

Aspen T. Reese ◽

Anne A. Madden ◽

Marie Joossens ◽

Guylaine Lacaze ◽

Robert R. Dunn

Keyword(s):

Microbial Community ◽

Internal Transcribed Spacer ◽

Amplicon Sequencing ◽

Rrna Gene ◽

Skin Microbiome ◽

Relative Importance ◽

Naturally Occurring ◽

Sourdough Bread ◽

Bacteria And Fungi ◽

Bidirectional Exchange

ABSTRACT Sourdough starters are naturally occurring microbial communities in which the environment, ingredients, and bakers are potential sources of microorganisms. The relative importance of these pools remains unknown. Here, bakers from two continents used a standardized recipe and ingredients to make starters that were then baked into breads. We characterized the fungi and bacteria associated with the starters, bakers’ hands, and ingredients using 16S and internal transcribed spacer (ITS) rRNA gene amplicon sequencing and then measured dough acidity and bread flavor. Starter communities were much less uniform than expected, and this variation manifested in the flavor of the bread. Starter communities were most similar to those found in flour but shared some species with the bakers’ skin. While humans likely contribute microorganisms to the starters, the reverse also appears to be true. This bidirectional exchange of microorganisms between starters and bakers highlights the importance of microbial diversity on bodies and in our environments as it relates to foods. IMPORTANCE Sourdough starters are complex communities of yeast and bacteria which confer characteristic flavor and texture to sourdough bread. The microbes present in starters can be sourced from ingredients or the baking environment and are typically consistent over time. Herein, we show that even when the recipe and ingredients for starter and bread are identical, different bakers around the globe produce highly diverse starters which then alter bread acidity and flavor. Much of the starter microbial community comes from bread flour, but the diversity is also associated with differences in the microbial community on the hands of bakers. These results indicate that bakers may be a source for yeast and bacteria in their breads and/or that bakers’ jobs are reflected in their skin microbiome.

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Application of a High-Throughput Amplicon Sequencing Method to Chart the Bacterial Communities that Are Associated with European Fermented Meats from Different Origins

Foods ◽

10.3390/foods9091247 ◽

2020 ◽

Vol 9 (9) ◽

pp. 1247

Author(s):

Emiel Van Reckem ◽

Christina Charmpi ◽

David Van der Veken ◽

Wim Borremans ◽

Luc De Vuyst ◽

...

Keyword(s):

Microbial Communities ◽

High Throughput ◽

Bacterial Communities ◽

Geographical Origin ◽

Salt Content ◽

Amplicon Sequencing ◽

Taxonomic Resolution ◽

Future Application ◽

Processing Conditions ◽

The Impact

Insight into the microbial species diversity of fermented meats is not only paramount to gain control over quality development, but also to better understand the link with processing technology and geographical origin. To study the composition of the microbial communities, the use of culture-independent methods is increasingly popular but often still suffers from drawbacks, such as a limited taxonomic resolution. This study aimed to apply a previously developed high-throughput amplicon sequencing (HTS) method targeting the 16S rRNA and tuf genes to characterize the bacterial communities in European fermented meats in greater detail. The data obtained broadened the view on the microbial communities that were associated with the various products examined, revealing the presence of previously underreported subdominant species. Moreover, the composition of these communities could be linked to the specificities of individual products, in particular pH, salt content, and geographical origin. In contrast, no clear links were found between the volatile organic compound profiles of the different products and the country of origin, distinct processing conditions, or microbial communities. Future application of the HTS method offers the potential to further unravel complex microbial communities in fermented meats, as well as to assess the impact of different processing conditions on microbial consortia.

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Gut microbiota composition is associated with narcolepsy type 1

Neurology Neuroimmunology & Neuroinflammation ◽

10.1212/nxi.0000000000000896 ◽

2020 ◽

Vol 7 (6) ◽

pp. e896

Author(s):

Alexandre Lecomte ◽

Lucie Barateau ◽

Pedro Pereira ◽

Lars Paulin ◽

Petri Auvinen ◽

...

Keyword(s):

Community Structure ◽

Gut Microbiota ◽

Bacterial Communities ◽

Beta Diversity ◽

Alpha Diversity ◽

Amplicon Sequencing ◽

Rrna Gene ◽

Differential Abundance ◽

Alpha And Beta Diversity

ObjectiveTo test the hypothesis that narcolepsy type 1 (NT1) is related to the gut microbiota, we compared the microbiota bacterial communities of patients with NT1 and control subjects.MethodsThirty-five patients with NT1 (51.43% women, mean age 38.29 ± 19.98 years) and 41 controls (57.14% women, mean age 36.14 ± 12.68 years) were included. Stool samples were collected, and the fecal microbiota bacterial communities were compared between patients and controls using the well-standardized 16S rRNA gene amplicon sequencing approach. We studied alpha and beta diversity and differential abundance analysis between patients and controls, and between subgroups of patients with NT1.ResultsWe found no between-group differences for alpha diversity, but we discovered in NT1 a link with NT1 disease duration. We highlighted differences in the global bacterial community structure as assessed by beta diversity metrics even after adjustments for potential confounders as body mass index (BMI), often increased in NT1. Our results revealed differential abundance of several operational taxonomic units within Bacteroidetes, Bacteroides, and Flavonifractor between patients and controls, but not after adjusting for BMI.ConclusionWe provide evidence of gut microbial community structure alterations in NT1. However, further larger and longitudinal multiomics studies are required to replicate and elucidate the relationship between the gut microbiota, immunity dysregulation and NT1.

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The Wheat Microbiome Under Four Management Strategies, and Potential for Endophytes in Disease Protection

Phytobiomes Journal ◽

10.1094/pbiomes-05-17-0023-r ◽

2017 ◽

Vol 1 (3) ◽

pp. 158-168 ◽

Cited By ~ 51

Author(s):

Kristi Gdanetz ◽

Frances Trail

Keyword(s):

Bacterial Communities ◽

Management Strategy ◽

Crop Yields ◽

Management Strategies ◽

Growing Season ◽

Amplicon Sequencing ◽

Antagonistic Activity ◽

Rrna Gene ◽

Operational Taxonomic Units ◽

Plant Organ

Manipulating plant-associated microbes to reduce disease or improve crop yields requires a thorough understanding of interactions within the phytobiome. Plants were sampled from a wheat/maize/soybean crop rotation site that implements four different crop management strategies. We analyzed the fungal and bacterial communities of leaves, stems, and roots of wheat throughout the growing season using 16S and fungal internal transcribed spacer 2 rRNA gene amplicon sequencing. The most prevalent operational taxonomic units (OTUs) were shared across all samples, although levels of the low-abundance OTUs varied. Endophytes were isolated from plants, and tested for antagonistic activity toward the wheat pathogen Fusarium graminearum. Antagonistic strains were assessed for plant protective activity in seedling assays. Our results suggest that microbial communities were strongly affected by plant organ and plant age, and may be influenced by management strategy.

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Amplicon sequencing and imputed metagenomic analysis of waste soil and sediment microbiome reveals unique bacterial communities and their functional attributes

Environmental Monitoring and Assessment ◽

10.1007/s10661-019-7879-0 ◽

2019 ◽

Vol 191 (12) ◽

Cited By ~ 4

Author(s):

Surajit De Mandal ◽

Vabeiryureilai Mathipi ◽

Rajendra Bose Muthukumaran ◽

Guruswami Gurusubramanian ◽

Esther Lalnunmawii ◽

...

Keyword(s):

Bacterial Communities ◽

Amplicon Sequencing ◽

Metagenomic Analysis ◽

Functional Attributes ◽

Waste Soil ◽

Soil And Sediment

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Temporal variation in soil bacterial communities can be confounded with spatial variation

FEMS Microbiology Ecology ◽

10.1093/femsec/fiaa192 ◽

2020 ◽

Vol 96 (12) ◽

Author(s):

Syrie M Hermans ◽

Hannah L Buckley ◽

Fiona Curran-Cournane ◽

Matthew Taylor ◽

Gavin Lear

Keyword(s):

Temporal Variation ◽

Bacterial Communities ◽

Amplicon Sequencing ◽

Spatial Distance ◽

Rrna Gene ◽

Soil Bacterial Communities ◽

Causal Processes ◽

Fundamental Understanding ◽

Soil Bacterial ◽

Indigenous Forest

ABSTRACT Investigating temporal variation in soil bacterial communities advances our fundamental understanding of the causal processes driving biological variation, and how the composition of these important ecosystem members may change into the future. Despite this, temporal variation in soil bacteria remains understudied, and the effects of spatial heterogeneity in bacterial communities on the detection of temporal changes is largely unknown. Using 16S rRNA gene amplicon sequencing, we evaluated temporal patterns in soil bacterial communities from indigenous forest and human-impacted sites sampled repeatedly over a 5-year period. Temporal variation appeared to be greater when fewer spatial samples per site were analysed, as well as in human-impacted compared to indigenous sites (P < 0.01 for both). The biggest portion of variation in bacterial community richness and composition was explained by soil physicochemical variables (13–24%) rather than spatial distance or sampling time (<1%). These results highlight the importance of adequate spatiotemporal replication when sampling soil communities for environmental monitoring, and the importance of conducting temporal research across a wide variety of land uses. This will ensure we have a true understanding of how bacterial communities change over space and time; the work presented here provides important considerations for how such research should be designed.

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