Continental-Scale Microbiome Study Reveals Different Environmental Characteristics Determining Microbial Richness, Composition, and Quantity in Hotel Rooms

ABSTRACT Culture-independent microbiome surveys have been conducted in homes, hospitals, schools, kindergartens and vehicles for public transport, revealing diverse microbial distributions in built environments. However, microbiome composition and the associated environmental characteristics have not been characterized in hotel environments. We presented here the first continental-scale microbiome study of hotel rooms (n = 68) spanning Asia and Europe. Bacterial and fungal communities were described by amplicon sequencing of the 16S rRNA gene and internal transcribed spacer (ITS) region and quantitative PCR. Similar numbers of bacterial (4,344) and fungal (4,555) operational taxonomic units were identified in the same sequencing depth, but most fungal taxa showed a restricted distribution compared to bacterial taxa. Aerobic, ubiquitous bacteria dominated the hotel microbiome with compositional similarity to previous samples from building and human nasopharynx environments. The abundance of Aspergillus was negatively correlated with latitude and accounted for ∼80% of the total fungal load in seven low-latitude hotels. We calculated the association between hotel microbiome and 16 indoor and outdoor environmental characteristics. Fungal composition and absolute quantity showed concordant associations with the same environmental characteristics, including latitude, quality of the interior, proximity to the sea, and visible mold, while fungal richness was negatively associated with heavy traffic (95% confidence interval [CI] = −127.05 to −0.25) and wall-to-wall carpet (95% CI = −47.60 to −3.82). Bacterial compositional variation was associated with latitude, quality of the interior, and floor type, while bacterial richness was negatively associated with recent redecoration (95% CI −179.00 to −44.55) and mechanical ventilation (95% CI = −136.71 to −5.12). IMPORTANCE This is the first microbiome study to characterize the microbiome data and associated environmental characteristics in hotel environments. In this study, we found concordant variation between fungal compositional variation and absolute quantity and discordant variation between community variation/quantity and richness. Our study can be used to promote hotel hygiene standards and provide resource information for future microbiome and exposure studies associated with health effects in hotel rooms.

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Continental-scale microbiome study reveals different environmental characteristics determining microbial richness and composition/quantity in hotel rooms

10.1101/849430 ◽

2019 ◽

Author(s):

Xi Fu ◽

Yanling Li ◽

Qianqian Yuan ◽

Gui-hong Cai ◽

Yiqun Deng ◽

...

Keyword(s):

Heavy Traffic ◽

Its Region ◽

Amplicon Sequencing ◽

Rrna Gene ◽

Microbial Composition ◽

Environmental Characteristics ◽

Continental Scale ◽

Β Diversity ◽

Α Diversity

AbstractCulture-independent microbiome surveys have been conducted in homes, hospitals, schools, kindergartens and vehicles for public transport, revealing diverse microbial distributions in built environments. However, microbiome surveys have not been conducted in hotel environments; thus, the composition and associated environmental factors are not clear. We presented the first continental-scale microbiome study of hotel rooms (n = 68) spanning large geographic regions. Bacterial and fungal communities were described by amplicon sequencing of the 16S rRNA gene and internal transcribed spacer (ITS) region and quantitative PCR. Similar numbers of bacterial (4,344) and fungal (4,555) operational taxonomic units were identified, but fungal taxa showed a local distribution compared with bacterial taxa. Aerobic, ubiquitous bacteria dominated the hotel microbiome with high compositional similarity to previous samples from building and human nasopharynx environments. The abundance of Aspergillus was negatively correlated with latitude and accounted for ∼80% of the total fungal load in seven low-latitude hotels. We calculated the association between hotel microbial dynamics and 16 indoor and outdoor environmental characteristics. Fungal β-diversity and quantity showed concordant variation and were associated with the same environmental characteristics, including latitude, quality of the interior, proximity to the sea and visible mold, while α-diversity decreased with heavy traffic (95% CI: −127.05 to −0.25) and wall-to-wall carpet (95% CI: −47.60 to −3.82). Bacterial β-diversity was associated with latitude, quality of the interior and floor type, while α-diversity decreased with recent decoration (95% CI −179.00 to −44.55) and mechanical ventilation (95% CI: −136.71 to −5.12).ImportanceThis is the first microbiome study to characterize microbial composition and associated environmental characteristics. In this study, we found concordant variation between microbial β-diversity and absolute quantity and discordant variation between β-diversity/quantity and α-diversity. Our study can be used to promote hotel hygiene standards and provide resource information for future microbiome and exposure studies associated with health effects in hotel rooms.

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Relative and quantitative rhizosphere microbiome profiling result in distinct abundance patterns

10.1101/2021.02.19.431941 ◽

2021 ◽

Author(s):

Hamed Azarbad ◽

Julien Tremblay ◽

Luke D. Bainard ◽

Etienne Yergeau

Keyword(s):

Water Stress ◽

Relative Abundance ◽

Its Region ◽

Cost Effective ◽

Amplicon Sequencing ◽

Rrna Gene ◽

Real Time Quantitative Pcr ◽

Rhizosphere Microbiome ◽

History Of ◽

Almost All

AbstractNext-generation sequencing is recognized as one of the most popular and cost-effective way of characterizing microbiome in multiple samples. However, most of the currently available amplicon sequencing approaches are inherently limited, as they are often presented based on the relative abundance of microbial taxa, which may not fully represent actual microbiome profiles. Here, we combined amplicon sequencing (16S rRNA gene for bacteria and ITS region for fungi) with real-time quantitative PCR (qPCR) to characterize the rhizosphere microbiome of wheat. We show that the increase in relative abundance of major microbial phyla does not necessarily result in an increase in abundance. One striking observation when comparing relative and quantitative abundances was a substantial increase in the abundance of almost all phyla associated with the rhizosphere of plants grown in soil with no history of water stress as compared with the rhizosphere of plants growing in soil with a history of water stress, which was in contradiction with the trends observed in the relative abundance data. Our results suggest that the estimated absolute abundance approach gives a different perspective than the relative abundance approach, providing complementary information that helps to better understand the rhizosphere microbiome.

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Impact of Harvest on Switchgrass Leaf Microbial Communities

Genes ◽

10.3390/genes13010022 ◽

2021 ◽

Vol 13 (1) ◽

pp. 22

Author(s):

Esther Singer ◽

Elizabeth M. Carpenter ◽

Jason Bonnette ◽

Tanja Woyke ◽

Thomas E. Juenger

Keyword(s):

Microbial Community ◽

Panicum Virgatum ◽

Leaf Surface ◽

Its Region ◽

Amplicon Sequencing ◽

Biofuel Production ◽

Rrna Gene ◽

Community Studies ◽

Community Members ◽

Increase Productivity

Switchgrass is a promising feedstock for biofuel production, with potential for leveraging its native microbial community to increase productivity and resilience to environmental stress. Here, we characterized the bacterial, archaeal and fungal diversity of the leaf microbial community associated with four switchgrass (Panicum virgatum) genotypes, subjected to two harvest treatments (annual harvest and unharvested control), and two fertilization levels (fertilized and unfertilized control), based on 16S rRNA gene and internal transcribed spacer (ITS) region amplicon sequencing. Leaf surface and leaf endosphere bacterial communities were significantly different with Alphaproteobacteria enriched in the leaf surface and Gammaproteobacteria and Bacilli enriched in the leaf endosphere. Harvest treatment significantly shifted presence/absence and abundances of bacterial and fungal leaf surface community members: Gammaproteobacteria were significantly enriched in harvested and Alphaproteobacteria were significantly enriched in unharvested leaf surface communities. These shifts were most prominent in the upland genotype DAC where the leaf surface showed the highest enrichment of Gammaproteobacteria, including taxa with 100% identity to those previously shown to have phytopathogenic function. Fertilization did not have any significant impact on bacterial or fungal communities. We also identified bacterial and fungal taxa present in both the leaf surface and leaf endosphere across all genotypes and treatments. These core taxa were dominated by Methylobacterium, Enterobacteriaceae, and Curtobacterium, in addition to Aureobasidium, Cladosporium, Alternaria and Dothideales. Local core leaf bacterial and fungal taxa represent promising targets for plant microbe engineering and manipulation across various genotypes and harvest treatments. Our study showcases, for the first time, the significant impact that harvest treatment can have on bacterial and fungal taxa inhabiting switchgrass leaves and the need to include this factor in future plant microbial community studies.

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Microbial stowaways – waterbirds as dispersal vectors of aquatic pro- and microeukaryotic communities

10.1101/2021.10.21.465236 ◽

2021 ◽

Author(s):

Beáta Szabó ◽

Attila Szabó ◽

Csaba F Vad ◽

Emil Boros ◽

Dunja Lukić ◽

...

Keyword(s):

Microbial Communities ◽

Amplicon Sequencing ◽

Compositional Variation ◽

Rrna Gene ◽

Aquatic Habitats ◽

Aquatic Communities ◽

Anser Anser ◽

Filter Feeder ◽

Waterbird Species ◽

Dispersal Vectors

Aim: Waterbirds are important dispersal vectors of multicellular organisms such as macrophytes, aquatic macroinvertebrates, and zooplankton. However, no study to date has focused on their potential role in dispersing aquatic microbial communities. Here, we carried out the first explicit study on passive transport (endozoochory) of prokaryotes and unicellular microeukaryotes by waterbirds based on a metagenomic approach. By directly comparing the dispersed set of organisms to the source pool of a natural metacommunity, we aimed for a realistic estimate of the overall importance of waterbird zoochory for natural microbial communities. Location: Seewinkel region of Austria and Hungary. Taxon: Prokaryotes and unicellular microeukaryotes. Methods: In 2017 and 2018, water samples from natural aquatic habitats along with fresh droppings of the dominant greylag goose (Anser anser) and four other waterbird species were collected in a well-delineated habitat network of temporary saline ponds (soda pans). Their prokaryotic and microeukaryotic communities were identified via 16S and 18S rRNA gene amplicon sequencing and compared across years and waterbird species. Results: We found that up to 40% of the dominant aquatic microbial OTUs were transported by A. anser. OTU richness in A. anser droppings was lower, but compositional variation was higher compared to the aquatic communities, probably resulting from stochastic pick-up of microbes from multiple aquatic habitats. We furthermore found that prokaryote species composition of bird droppings followed the interannual turnover in the aquatic communities. Finally, we found species-specific differences among different waterbird species. Among them, the planktivore filter-feeder northern shovelers (Anas clypeata) collected and dispersed a more species-rich subset of microeukaryotes than shorebirds or geese. Main conclusions: Overall, our study provides the first quantitative empirical evidence of endozoochory in natural microorganism communities. These results imply that waterbirds may be crucial in maintaining ecological connectivity between discrete aquatic habitats at the level of microbial communities. Keywords: aquatic microorganisms, bacteria, connectivity, dispersal, endozoochory, phytoplankton, protists, waterbirds

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Comparing Community Measures in Lake Microbial Ecology: Metagenomes and Metatranscriptomes and Amplicons, oh my!

10.21203/rs.3.rs-29111/v1 ◽

2020 ◽

Author(s):

Julia Kristina Nuy ◽

Till Bornemann ◽

Daniela Beisser ◽

Alexander J. Probst ◽

Jens Boenigk

Keyword(s):

16S Rrna ◽

16S Rrna Gene ◽

Environmental Variables ◽

Physicochemical Parameters ◽

Redundancy Analysis ◽

Environmental Parameters ◽

Amplicon Sequencing ◽

Rrna Gene ◽

Lake Ecosystems

Abstract Lake ecosystems are hotspots on Earth for biogeochemical cycling yet linking their microbiome to physicochemical parameters remains a challenge. Here, we assess the quality of 16S rRNA gene-based metatranscriptomics, assembled metagenomics and 16S rRNA gene amplicon sequencing for 21 lake ecosystems across Europe. We identified method-dependent, massive differences between community composition and proportional activity for key taxa like Alphaproteobacteria suggesting different ecological conclusions for the same lake ecosystems. In redundancy analysis (RDA), environmental parameters explained the greatest amount of the variance in metatranscriptomes suggesting that the active community is heavily influenced by environmental parameters. While amplicon data recruited the least amount of environmental variables in RDA (pH and temperature), four additional parameters explained the sequenced metagenomes. These results suggest that metagenomes and metatranscriptomes are currently the best methods for linking lake microbiomes to physicochemical parameters and can be used as proxies for designing future ecological surveys.

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Competitive outcomes between native and invasive plants are linked to shifts in the bacterial rhizosphere microbiome

10.1101/2021.01.07.425800 ◽

2021 ◽

Author(s):

Marina L LaForgia ◽

Hannah Kang ◽

Cassandra L Ettinger

Keyword(s):

Bacterial Community ◽

Invasive Plant ◽

Plant Competition ◽

Its Region ◽

Amplicon Sequencing ◽

Rrna Gene ◽

Community Structures ◽

Competitive Response ◽

Species Dominance ◽

Competitive Outcomes

Background: Rhizosphere microbiomes have received growing attention in recent years for their role in plant health, stress tolerance, soil nutrition, and invasive species dominance. Still, relatively little is known about how these microbial communities are altered under plant competition, and even less about whether these shifts are tied to competitive outcomes between native and invasive plant species. We investigated the structure and diversity of rhizosphere bacterial and fungal microbiomes of native annual forbs and invasive annual grasses individually and in competition using high-throughput amplicon sequencing of the bacterial 16S rRNA gene and the fungal ITS region. We assessed how significant shifts in key microbial families correlate to plant competitive responses through changes in biomass (log competitive response ratios). Results: We find that bacterial diversity and structure differ between invasive grasses and native forbs, but fungal diversity and structure do not. Further, bacterial community structures under competition are distinct from both individual forb and grass bacterial community structures. We identified four bacterial families (Burkholderiaceae, Methylophilaceae, Clostridiaceae_1, and Fibrobacteraceae) that varied in relative abundance between treatments and that were significantly correlated with plant competitive responses. Conclusions: Invasive grass dominance may be partially due to effects on the rhizosphere community of native forbs, with changes in specific bacterial families potentially benefiting grasses at the expense of native forbs. Our study underscores the importance of considering plant-rhizosphere interactions for understanding outcomes of plant invasion on grassland ecosystems.

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Full-Length 16S rRNA and ITS Gene Sequencing Revealed Rich Microbial Flora in Roots of Cycas spp. in China

Evolutionary Bioinformatics ◽

10.1177/1176934321989713 ◽

2021 ◽

Vol 17 ◽

pp. 117693432198971

Author(s):

Melissa H Pecundo ◽

Aimee Caye G Chang ◽

Tao Chen ◽

Thomas Edison E dela Cruz ◽

Hai Ren ◽

...

Keyword(s):

Community Structure ◽

16S Rrna ◽

Current Knowledge ◽

Its Region ◽

Amplicon Sequencing ◽

Full Length ◽

Ex Situ ◽

Rrna Gene ◽

Coralloid Roots ◽

Different Strains

Cycads have developed a complex root system categorized either as normal or coralloid roots. Past literatures revealed that a great diversity of key microbes is associated with these roots. This recent study aims to comprehensively determine the diversity and community structure of bacteria and fungi associated with the roots of two Cycas spp. endemic to China, Cycas debaoensis Zhong & Chen and Cycas fairylakea D.Y. Wang using high-throughput amplicon sequencing of the full-length 16S rRNA (V1-V9 hypervariable) and short fragment ITS region. The total DNA from 12 root samples were extracted, amplified, sequenced, and analyzed. Resulting sequences were clustered into 61 bacteria and 2128 fungal OTUs. Analysis of community structure revealed that the coralloid roots were dominated mostly by the nitrogen-fixer Nostocaceae but also contain other non-diazotrophic bacteria. The sequencing of entire 16S rRNA gene identified four different strains of cyanobacteria under the heterocystous genera Nostoc and Desmonostoc. Meanwhile, the top bacterial families in normal roots were Xanthobacteraceae, Burkholderiaceae, and Bacillaceae. Moreover, a diverse fungal community was also found in the roots of cycads and the predominating families were Ophiocordycipitaceae, Nectriaceae, Bionectriaceae, and Trichocomaceae. Our results demonstrated that bacterial diversity in normal roots of C. fairylakea is higher in richness and abundance than C. debaoensis. On the other hand, a slight difference, albeit insignificant, was noted for the diversity of fungi among root types and host species as the number of shared taxa is relatively high (67%). Our results suggested that diverse microbes are present in roots of cycads which potentially interact together to support cycads survival. Our study provided additional knowledge on the microbial diversity and composition in cycads and thus expanding our current knowledge on cycad-microbe association. Our study also considered the possible impact of ex situ conservation on cyanobiont community of cycads.

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Invasive Grass Dominance over Native Forbs Is Linked to Shifts in the Bacterial Rhizosphere Microbiome

Microbial Ecology ◽

10.1007/s00248-021-01853-1 ◽

2021 ◽

Author(s):

Marina L. LaForgia ◽

Hannah Kang ◽

Cassandra L. Ettinger

Keyword(s):

Bacterial Community ◽

Plant Biomass ◽

Plant Competition ◽

Its Region ◽

Amplicon Sequencing ◽

Rrna Gene ◽

Community Structures ◽

Invasive Grass ◽

Soil Nutrition ◽

Annual Grasses

AbstractRhizosphere microbiomes have received growing attention in recent years for their role in plant health, stress tolerance, soil nutrition, and invasion. Still, relatively little is known about how these microbial communities are altered under plant competition, and even less about whether these shifts are tied to competitive outcomes between native and invasive plants. We investigated the structure and diversity of rhizosphere bacterial and fungal microbiomes of native annual forbs and invasive annual grasses grown in a shade-house both individually and in competition using high-throughput amplicon sequencing of the bacterial 16S rRNA gene and the fungal ITS region. We assessed how differentially abundant microbial families correlate to plant biomass under competition. We find that bacterial diversity and structure differ between native forbs and invasive grasses, but fungal diversity and structure do not. Furthermore, bacterial community structures under competition are distinct from individual bacterial community structures. We also identified five bacterial families that varied in normalized abundance between treatments and that were correlated with plant biomass under competition. We speculate that invasive grass dominance over these natives may be partially due to effects on the rhizosphere community, with changes in specific bacterial families potentially benefiting invaders at the expense of natives.

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The Determinants of Entrepreneurship Development in Spatial Systems

Przedsiębiorczość - Edukacja ◽

10.24917/20833296.13.1 ◽

2017 ◽

Vol 13 ◽

pp. 8-24

Author(s):

Zbigniew Zioło

Keyword(s):

Spatial Scales ◽

Institutional Barriers ◽

Entrepreneurship Development ◽

Continental Scale ◽

Spatial Systems ◽

Business Conditions ◽

Mutual Relations ◽

Growth Shape ◽

Strategic Goal

The processes of technological progress create new opportunities for economic, social and cultural growth, shape new relations between economic entities and their environment, and influence changes in the determinants of entrepreneurship development. These processes vary significantly in certain geographic locations, characterised by an enormous diversity of natural, social, economic and cultural structures. As a consequence, this creates different opportunities and different conditions for the development of entrepreneurship in certain spatial scales, from the continental scale, through national and regional to local scales. The article presents complex conditions for the development of entrepreneurship, highlights its limitations resulting from institutional barriers, and the importance of knowing the mechanisms of mutual relations between spatial systems and the influence of control instruments. The quality of central and local government authorities is of particular significance here, which do not always properly use the mechanisms of rational business support. A serious barrier to the development of entrepreneurship is the low quality of social capital, manifested in a lack of trust in institutional authorities and reluctance to engage in entrepreneurship and business development. The conclusions point out that further research should be developed that will take into account changing business conditions, with a defined strategic goal of raising the quality and standard of living, international competitiveness of the country and products in different market categories.

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Gut microbiome composition in the Hispanic Community Health Study/Study of Latinos is shaped by geographic relocation, environmental factors, and obesity

Genome Biology ◽

10.1186/s13059-019-1831-z ◽

2019 ◽

Vol 20 (1) ◽

Cited By ~ 14

Author(s):

Robert C. Kaplan ◽

Zheng Wang ◽

Mykhaylo Usyk ◽

Daniela Sotres-Alvarez ◽

Martha L. Daviglus ◽

...

Keyword(s):

Community Health ◽

Gut Microbiome ◽

Alpha Diversity ◽

Amplicon Sequencing ◽

Shannon Index ◽

Health Study ◽

Rrna Gene ◽

Cross Sectional ◽

Hispanic Community ◽

The Usa

Abstract Background Hispanics living in the USA may have unrecognized potential birthplace and lifestyle influences on the gut microbiome. We report a cross-sectional analysis of 1674 participants from four centers of the Hispanic Community Health Study/Study of Latinos (HCHS/SOL), aged 18 to 74 years old at recruitment. Results Amplicon sequencing of 16S rRNA gene V4 and fungal ITS1 fragments from self-collected stool samples indicate that the host microbiome is determined by sociodemographic and migration-related variables. Those who relocate from Latin America to the USA at an early age have reductions in Prevotella to Bacteroides ratios that persist across the life course. Shannon index of alpha diversity in fungi and bacteria is low in those who relocate to the USA in early life. In contrast, those who relocate to the USA during adulthood, over 45 years old, have high bacterial and fungal diversity and high Prevotella to Bacteroides ratios, compared to USA-born and childhood arrivals. Low bacterial diversity is associated in turn with obesity. Contrasting with prior studies, our study of the Latino population shows increasing Prevotella to Bacteroides ratio with greater obesity. Taxa within Acidaminococcus, Megasphaera, Ruminococcaceae, Coriobacteriaceae, Clostridiales, Christensenellaceae, YS2 (Cyanobacteria), and Victivallaceae are significantly associated with both obesity and earlier exposure to the USA, while Oscillospira and Anaerotruncus show paradoxical associations with both obesity and late-life introduction to the USA. Conclusions Our analysis of the gut microbiome of Latinos demonstrates unique features that might be responsible for health disparities affecting Hispanics living in the USA.

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