scholarly journals Bacterial communities of herbivores and pollinators that have co-evolved Cucurbita spp

2019 ◽  
Author(s):  
Lori R. Shapiro ◽  
Madison Youngblom ◽  
Erin D. Scully ◽  
Jorge Rocha ◽  
Joseph Nathaniel Paulson ◽  
...  
Keyword(s):  
Microbial Communities ◽  
Bacterial Communities ◽  
Host Plants ◽  
Rrna Gene ◽  
Erwinia Tracheiphila ◽  
Plant Feeding ◽  
Cucumber Beetle ◽  
Striped Cucumber Beetle ◽  
Peponapis Pruinosa ◽  
Environmental Microbes

AbstractInsects, like all animals, are exposed to diverse environmental microbes throughout their life cycle. Yet, we know little about variation in the microbial communities associated with the majority of wild, unmanaged insect species. Here, we use a 16S rRNA gene metabarcoding approach to characterize temporal and geographic variation in the gut bacterial communities of herbivores (Acalymma vittatum and A. trivittatum) and pollinators (Eucera (Peponapis) pruinosa) that have co-evolved with the plant genus Cucurbita (pumpkin, squash, zucchini and gourds). Overall, we find high variability in the composition of bacterial communities in squash bees and beetles collected from different geographic locations and different time points throughout a growing season. Still, many of the most common OTUs are shared in E. (P.) pruinosa, A. vittatum and A. trivittatum. This suggests these insects may be exposed to similar environmental microbial sources while foraging on the same genus of host plants, and that similar microbial taxa may aid in digestion of Cucurbita plant material. The striped cucumber beetle A. vittatum can also transmit Erwinia tracheiphila, the causal agent of bacterial wilt of cucurbits. We find that few field-collected A. vittatum individuals have detectable E. tracheiphila, and when this plant pathogen is detected, it comprises less than 1% of the gut bacterial community. Together, these results are consistent with previous studies showing that plant feeding insects have highly variable gut bacterial communities, and provides a first step towards understanding the spatiotemporal variation in the microbial communities associated with herbivores and pollinators that depend on Cucurbita host plants.

scholarly journals The female urinary microbiota in relation to the reproductive tract microbiota

2019 ◽  
Author(s):  
Chen Chen ◽  
Lilan Hao ◽  
Weixia Wei ◽  
Fei Li ◽  
Liju Song ◽  
...  
Keyword(s):  
Microbial Communities ◽  
Bacterial Communities ◽  
Reproductive Tract ◽  
Chinese Women ◽  
Uterine Cavity ◽  
Detailed Comparison ◽  
Reproductive Age ◽  
Rrna Gene ◽  
Urogenital System ◽  
Urinary Microbiota

AbstractHuman urine is traditionally considered to be sterile, and whether the urine harbours distinct microbial communities has been a matter of debate. The potential link between female urine and reproductive tract microbial communities is currently not clear.Here we collected the urine samples from 147 Chinese women of reproductive age, and explored the nature of colonization by 16S rRNA gene amplicon sequencing, real-time qPCR and live bacteria culture. To demonstrate utility intra-individual Spearman’s correlation was used to explore the relationship between urine and multi-sites of the reproductive tract. PERMANOVA was also performed to explore potential correlations between the lifestyle and various clinical factors and urinary bacterial communities. Our data demonstrated distinct bacterial communities in urine, indicative of a non-sterile environment. Types of diverse, Streptococcus-dominated, and Lactobacillus-dominated were the three most common types in the cohort. Detailed comparison of the urinary microbiota to the multi-sites of reproductive tract microbiota demonstrated the urinary microbiota was more similar to the microbiota in the cervix and uterine cavity instead of vagina in the same women.Our data demonstrates the potential connectivity of the microbiota in the female urogenital system and provided insight into the exploration of urethra and genital tract diseases.

scholarly journals Variation in Sodic Soil Bacterial Communities Associated with Different Alkali Vegetation Types

2021 ◽  
Vol 9 (8) ◽  
pp. 1673
Author(s):  
Andrea K. Borsodi ◽  
Márton Mucsi ◽  
Gergely Krett ◽  
Attila Szabó ◽  
Tamás Felföldi ◽  
...  
Keyword(s):  
Microbial Communities ◽  
Relative Abundance ◽  
Bacterial Communities ◽  
Soil Microbial Communities ◽  
Rrna Gene ◽  
Vegetation Types ◽  
Metabolic Potential ◽  
Sodic Soils ◽  
Sodic Soil ◽  
Strain Collection

In this study, we examined the effect of salinity and alkalinity on the metabolic potential and taxonomic composition of microbiota inhabiting the sodic soils in different plant communities. The soil samples were collected in the Pannonian steppe (Hungary, Central Europe) under extreme dry and wet weather conditions. The metabolic profiles of microorganisms were analyzed using the MicroResp method, the bacterial diversity was assessed by cultivation and next-generation amplicon sequencing based on the 16S rRNA gene. Catabolic profiles of microbial communities varied primarily according to the alkali vegetation types. Most members of the strain collection were identified as plant associated and halophilic/alkaliphilic species of Micrococcus, Nesterenkonia, Nocardiopsis, Streptomyces (Actinobacteria) and Bacillus, Paenibacillus (Firmicutes) genera. Based on the pyrosequencing data, the relative abundance of the phyla Proteobacteria, Actinobacteria, Acidobacteria, Gemmatimonadetes and Bacteroidetes also changed mainly with the sample types, indicating distinctions within the compositions of bacterial communities according to the sodic soil alkalinity-salinity gradient. The effect of weather extremes was the most pronounced in the relative abundance of the phyla Actinobacteria and Acidobacteria. The type of alkali vegetation caused greater shifts in both the diversity and activity of sodic soil microbial communities than the extreme aridity and moisture.

scholarly journals Individual variation of natural D. melanogaster associated bacterial communities

2017 ◽  
Author(s):  
Yun Wang ◽  
Fabian Staubach
Keyword(s):  
Microbial Communities ◽  
Individual Variation ◽  
Bacterial Communities ◽  
Evolutionary Biology ◽  
Model Organism ◽  
Rrna Gene ◽  
Single Population ◽  
Data Set ◽  
Natural Microbiota ◽  
Bacterial 16S Rrna Gene

AbstractD. melanogaster has become an important model organism to study host-microbe interaction. However, we still know little about the natural microbial communities that are associated with D. melanogaster. Especially, information on inter-individual variation is still lacking because most studies so far have used pooled material from several flies. Here, we collected bacterial 16S rRNA gene community profiles from a set of 32 individuals from a single population and compare the variation to that of samples collected from different substrates and locations. While community differences were on average larger between samples collected from different substrates, there was still a surprising amount of variation of microbial communities between individual flies. The samples clustered into two groups suggesting that there are yet unknown factors that affect the composition of natural fly associated microbial communities and need research.ImportanceD. melanogaster is an important model organism in evolutionary biology and also for the study of host-microbe interaction. In order to connect these to aspects of D. melanogaster biology, it is crucial to better understand the natural D. melanogaster microbiota because only the natural microbiota can affect the evolution of the host. We present, to our knowledge, the first data set that captures inter-individual variation of D. melanogaster associated bacterial communities. Clustering of communities into two larger groups suggests that there are important drivers of these communities that we do not understand yet suggesting in return that more research on the natural microbiota of D. melanogaster is needed.

scholarly journals Diversity and Structural Variability of Bacterial Microbial Communities in Rhizocompartments of Desert Leguminous Plants

2020 ◽  
Author(s):  
Ziyuan Zhou ◽  
Guodong Ding ◽  
Minghan Yu ◽  
Guanglei Gao ◽  
Genzhu Wang
Keyword(s):  
Microbial Communities ◽  
Bacterial Communities ◽  
Host Plants ◽  
Soil Microbial Communities ◽  
Niche Differentiation ◽  
Leguminous Plant ◽  
Leguminous Plants ◽  
Soil Microbial ◽  
The Core ◽  
Structural Variability

ABSTRACTBy assessing diversity variations of bacterial communities under different rhizocompartment types (i.e., roots, rhizosphere soil, root zone soil, and inter-shrub bulk soil), we explore the structural variability of bacterial communities in different root microenvironments under desert leguminous plant shrubs. Results will enable the influence of niche differentiation of plant roots and root soil on the structural stability of bacterial communities under three desert leguminous plant shrubs to be examined. High-throughput 16S rRNA genome sequencing was used to characterize diversity and structural differences of bacterial microbes in the rhizocompartments of three xeric leguminous plants. Results from this study confirm previous findings relating to niche differentiation in rhizocompartments under related shrubs, and they demonstrate that diversity and structural composition of bacterial communities have significant hierarchical differences across four rhizocompartment types under leguminous plant shrubs. Desert leguminous plants had significant effects on the enrichment and filtration of specific bacterial microbiomes across different rhizocompartments (P<0.05). The core bacterial microbiomes causing structure and composition variability of bacterial communities across different niches of desert leguminous plants are also identified. By investigating the influence of niches on the structural variability of soil bacterial communities with the differentiation of rhizocompartments under desert leguminous plant shrubs, we provide data support for the identification of dominant bacteria and future preparation of inocula, and provide a foundation for further study of the host plants-microbial interactions.IMPORTANCEColonization by plant communities make valued contribution to sand-fixing in poor ecological desert environments, thereby reducing the effects of wind erosion in these areas. Our study revealed that specific core bacterial microbiomes in under-shrub soil microbial communities had a significant hierarchical enrichment effect among rhizocompartments, and were filtered into roots. The root endophyte microbiomes thus formed had low abundance and diversity, but their structural variability was the highest. In addition, our data also verified that the rhizocompartments of under desert leguminous plant shrubs had a significant differentiation effect for the core bacterial microbiomes enriched and filtered by host plants, and that each rhizocompartment represented a unique niche of bacterial communities. Understanding the interactions between xeric shrubs and soil microbial communities is a fundamental step for describing desert soil ecosystems, which in turn can offer a microbe-associated reference for evaluating the restoration of desert vegetation.

scholarly journals Trait-based life-history strategies explain succession scenario for complex bacterial communities under varying disturbance

2019 ◽  
Author(s):  
Ezequiel Santillan ◽  
Hari Seshan ◽  
Florentin Constancias ◽  
Stefan Wuertz
Keyword(s):  
Life History ◽  
Network Analysis ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Microbial Communities ◽  
Bacterial Communities ◽  
Life History Strategies ◽  
System Response ◽  
Rrna Gene ◽  
Shotgun Metagenomics

SummaryTrait-based approaches are increasingly gaining importance in community ecology, as a way of finding general rules for the mechanisms driving changes in community structure and function under the influence of perturbations. Frameworks for life-history strategies have been successfully applied to describe changes in plant and animal communities upon disturbance. To evaluate their applicability to complex bacterial communities, we operated replicated wastewater treatment bioreactors for 35 days and subjected them to eight different disturbance frequencies of a toxic pollutant (3-chloroaniline), starting with a mixed inoculum from a full-scale treatment plant. Relevant ecosystem functions were tracked and microbial communities assessed through metagenomics and 16S rRNA gene sequencing. Combining a series of ordination, statistical and network analysis methods, we associated different life-history strategies with microbial communities across the disturbance range. These strategies were evaluated using tradeoffs in community function and genotypic potential, and changes in bacterial genus composition. We further compared our findings with other ecological studies and adopted a semi-quantitative CSR (competitors, ruderals, stress-tolerants) classification. The framework reduces complex datasets of microbial traits, functions, and taxa into ecologically meaningful components to help understand the system response to disturbance, and hence represents a promising tool for managing microbial communities.Originality-Significance StatementThis study establishes, for the first time, CSR life-history strategies in the context of bacterial communities. This framework is explained using community aggregated traits in an environment other than soil, also a first, using a combination of ordination methods, network analysis, and genotypic information from shotgun metagenomics and 16S rRNA gene amplicon sequencing.

scholarly journals Postmortem succession of gut microbial communities in deceased human subjects

PeerJ ◽  
2017 ◽  
Vol 5 ◽  
pp. e3437 ◽  
Author(s):  
Jennifer M. DeBruyn ◽  
Kathleen A. Hauther
Keyword(s):  
Microbial Communities ◽  
Bacterial Communities ◽  
Human Subjects ◽  
Human Microbiome ◽  
Amplicon Sequencing ◽  
Postmortem Changes ◽  
Rrna Gene ◽  
Human Gut ◽  
Decomposition Processes ◽  
Over Time

The human microbiome has demonstrated an importance for the health and functioning in living individuals. However, the fate of the microbiome after death is less understood. In addition to a better understanding of microbe-mediated decomposition processes, postmortem succession of human-associated microbial communities has been suggested as a possible forensic tool for estimating time since death, or postmortem interval (PMI). The objective of our study was to document postmortem changes in human gut bacterial communities. Gut microflora were repeatedly sampled from the caeca of cadavers as they decayed under natural environmental conditions. 16S rRNA gene amplicon sequencing revealed that over time, bacterial richness significantly increased (rs = 0.449) while diversity decreased (rs =  − 0.701). The composition of gut bacterial communities changed in a similar manner over time towards a common decay community. OTUs belonging to Bacteroidales (Bacteroides, Parabacteroides) significantly declined while Clostridiales (Clostridium, Anaerosphaera) and the fly-associated Gammaproteobacteria Ignatzschineria and Wohlfahrtiimonas increased. Our examination of human caeca microflora in decomposing cadavers adds to the growing literature on postmortem microbial communities, which will ultimately contribute to a better understanding of decomposition processes.

scholarly journals The Microbiome of the Reef Macroalga Sargassum ilicifolium in Singapore

2021 ◽  
Vol 9 (5) ◽  
pp. 898
Author(s):  
Ren Min Oh ◽  
Elena Bollati ◽  
Prasha Maithani ◽  
Danwei Huang ◽  
Benjamin J. Wainwright
Keyword(s):  
Coral Reef ◽  
Microbial Communities ◽  
Bacterial Communities ◽  
Microbial Community Composition ◽  
Pcr Amplification ◽  
Rrna Gene ◽  
Benthic Organisms ◽  
Polymerase Chain ◽  
Microbial Change ◽  
The 16S Rrna Gene

The large canopy-forming macroalga, Sargassum ilicifolium, provides shelter and food for numerous coral reef species, but it can also be detrimental at high abundances where it outcompetes other benthic organisms for light and space. Here, we investigate the microbial communities associated with S. ilicifolium in Singapore, where it is an abundant and important member of coral reef communities. We collected eight complete S. ilicifolium thalli from eight island locations along an approximate 14 km east-to-west transect. Each thallus was dissected into three separate parts: holdfast, vesicles, and leaves. We then characterized the bacterial communities associated with each part via polymerase chain reaction (PCR) amplification of the 16S rRNA gene V4 region. We then inferred predicted metagenome functions using METAGENassist. Despite the comparatively short distances between sample sites, we show significant differences in microbial community composition, with communities further differentiated by part sampled. Holdfast, vesicles and leaves all harbor distinct microbial communities. Functional predictions reveal some separation between holdfast and leaf communities, with higher representation of sulphur cycling taxa in the holdfast and higher representation of nitrogen cycling taxa in the leaves. This study provides valuable baseline data that can be used to monitor microbial change, and helps lay the foundation upon which we can begin to understand the complexities of reef-associated microbial communities and the roles they play in the functioning and diversity of marine ecosystems.

scholarly journals Characterization of External Mucosal Microbiomes of Nile Tilapia and Grey Mullet Co-cultured in Semi-Intensive Pond Systems

2021 ◽  
Vol 12 ◽  
Author(s):  
Ahmed Elsheshtawy ◽  
Benjamin Gregory James Clokie ◽  
Amaya Albalat ◽  
Allan Beveridge ◽  
Ahmad Hamza ◽  
...  
Keyword(s):  
Microbial Communities ◽  
Bacterial Communities ◽  
Nile Tilapia ◽  
Pond Water ◽  
Rrna Gene ◽  
Grey Mullet ◽  
Core Microbiome ◽  
Bacterial Phyla ◽  
Organ Specific

The external mucosal surfaces of the fish harbor complex microbial communities, which may play pivotal roles in the physiological, metabolic, and immunological status of the host. Currently, little is known about the composition and role of these communities, whether they are species and/or tissue specific and whether they reflect their surrounding environment. Co-culture of fish, a common practice in semi-intensive aquaculture, where different fish species cohabit in the same contained environment, is an easily accessible and informative model toward understanding such interactions. This study provides the first in-depth characterization of gill and skin microbiomes in co-cultured Nile tilapia (Oreochromis niloticus) and grey mullet (Mugil capito) in semi-intensive pond systems in Egypt using 16S rRNA gene-based amplicon sequencing. Results showed that the microbiome composition of the external surfaces of both species and pond water was dominated by the following bacterial phyla: Proteobacteria, Fusobacteriota, Firmicutes, Planctomycetota, Verrucomicrobiota, Bacteroidota, and Actinobacteriota. However, water microbial communities had the highest abundance and richness and significantly diverged from the external microbiome of both species; thus, the external autochthonous communities are not a passive reflection of their allochthonous communities. The autochthonous bacterial communities of the skin were distinct from those of the gill in both species, indicating that the external microbiome is likely organ specific. However, gill autochthonous communities were clearly species specific, whereas skin communities showed higher commonalities between both species. Core microbiome analysis identified the presence of shared core taxa between both species and pond water in addition to organ-specific taxa within and between the core community of each species. These core taxa included possibly beneficial genera such as Uncultured Pirellulaceae, Exiguobacterium, and Cetobacterium and opportunistic potential pathogens such as Aeromonas, Plesiomonas, and Vibrio. This study provides the first in-depth mapping of bacterial communities in this semi-intensive system that in turn provides a foundation for further studies toward enhancing the health and welfare of these cultured fish and ensuring sustainability.

scholarly journals Viable bacterial communities on hospital window components in patient rooms

PeerJ ◽  
2020 ◽  
Vol 8 ◽  
pp. e9580
Author(s):  
Patrick F. Horve ◽  
Leslie G. Dietz ◽  
Suzanne L. Ishaq ◽  
Jeff Kline ◽  
Mark Fretz ◽  
...  
Keyword(s):  
Microbial Communities ◽  
Bacterial Communities ◽  
Light Exposure ◽  
Window Glass ◽  
Hospital Setting ◽  
Sunlight Exposure ◽  
Bacterial Attachment ◽  
Rrna Gene ◽  
Nutrient Density ◽  
Viable Bacteria

Previous studies demonstrate an exchange of bacteria between hospital room surfaces and patients, and a reduction in survival of microorganisms in dust inside buildings from sunlight exposure. While the transmission of microorganisms between humans and their local environment is a continuous exchange which generally does not raise cause for alarm, in a hospital setting with immunocompromised patients, these building-source microbial reservoirs may pose a risk. Window glass is often neglected during hospital disinfection protocols, and the microbial communities found there have not previously been examined. This pilot study examined whether living bacterial communities, and specifically the pathogens Methicillin-resistant Staphylococcus aureus (MRSA) and Clostridioides difficile (C. difficile), were present on window components of exterior-facing windows inside patient rooms, and whether relative light exposure (direct or indirect) was associated with changes in bacterial communities on those hospital surfaces. Environmental samples were collected from 30 patient rooms in a single ward at Oregon Health & Science University (OHSU) in Portland, Oregon, USA. Sampling locations within each room included the window glass surface, both sides of the window curtain, two surfaces of the window frame, and the air return grille. Viable bacterial abundances were quantified using qPCR, and community composition was assessed using Illumina MiSeq sequencing of the 16S rRNA gene V3/V4 region. Viable bacteria occupied all sampled locations, but was not associated with a specific hospital surface or relative sunlight exposure. Bacterial communities were similar between window glass and the rest of the room, but had significantly lower Shannon Diversity, theorized to be related to low nutrient density and resistance to bacterial attachment of glass compared to other surface materials. Rooms with windows that were facing west demonstrated a higher abundance of viable bacteria than those facing other directions, potentially because at the time of sampling (morning) west-facing rooms had not yet been exposed to sunlight that day. Viable C. difficile was not detected and viable MRSA was detected at very low abundance. Bacterial abundance was negatively correlated with distance from the central staff area containing the break room and nursing station. In the present study, it can be assumed that there is more human traffic in the center of the ward, and is likely responsible for the observed gradient of total abundance in rooms along the ward, as healthcare staff both deposit more bacteria during activities and affect microbial transit indoors. Overall, hospital window components possess similar microbial communities to other previously identified room locations known to act as reservoirs for microbial agents of hospital-associated infections.

scholarly journals Postmortem succession of gut microbial communities in human cadavers

2017 ◽  
Author(s):  
Jennifer M DeBruyn ◽  
Kathleen A Hauther
Keyword(s):  
Microbial Communities ◽  
Bacterial Communities ◽  
Human Microbiome ◽  
Amplicon Sequencing ◽  
Multiple Regression Model ◽  
Postmortem Changes ◽  
Rrna Gene ◽  
Decomposition Processes ◽  
Human Cadavers ◽  
Over Time

The human microbiome has demonstrated importance for health and functioning in living individuals. However the fate of the microbiome after death is poorly understood. In addition to a better understanding of microbe-mediated decomposition processes, postmortem succession of human-associated microbial communities has been suggested as a possible forensic tool for estimating time since death, or postmortem interval (PMI). The objective of our study was to document postmortem changes in human gut bacterial communities. Gut microflora were repeatedly sampled from the caeca of cadavers as they decayed under natural environmental conditions. 16S rRNA gene amplicon sequencing revealed that over time, bacterial richness significantly increased (rs = 0.449) while diversity decreased (rs = -0.701). The composition of gut bacterial communities changed in a similar manner over time towards a common decay community. OTUs belonging to Bacteroidales (Bacteroides, Parabacteroides) significantly declined while Clostridiales (Clostridium, Anaerosphaera) and the fly-associated Gammaproteobacteria Ignatzschineria and Wohlfahrtiimonas increased. A best fit multiple regression model, which included five OTUs, improved the ability to predict PMI (R2 = 0.824; p < 0.001). Our examination of human caeca microflora in decomposing cadavers adds to the growing literature on postmortem microbial communities, which will ultimately contribute to a better understanding of decomposition processes.

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