scholarly journals Locally Adapted Mimulus Ecotypes Differentially Impact Rhizosphere Bacterial and Archaeal Communities in an Environment-Dependent Manner

2020 ◽  
Vol 4 (1) ◽  
pp. 53-63 ◽  
Author(s):  
Alan W. Bowsher ◽  
Patrick J. Kearns ◽  
Damian Popovic ◽  
David B. Lowry ◽  
Ashley Shade
Keyword(s):  
Microbial Communities ◽  
Plant Root ◽  
Alpha Diversity ◽  
Local Environment ◽  
Rrna Gene ◽  
Transplant Experiment ◽  
Dependent Manner ◽  
Reciprocal Transplant Experiment ◽  
Soil Microbial Community Structure ◽  
Host Identity

Plant root−microbe interactions influence plant productivity, health, and resistance to stress. Although there is evidence that plant species and even genotypes can alter soil microbial community structure, environmental conditions can potentially outweigh plant genetic effects. Here, we used a reciprocal transplant experiment to understand the contributions of the environment and the host plant to rhizosphere microbiome composition in locally adapted ecotypes of Mimulus guttatus (syn. Erythranthe guttata). Two genotypes of a coastal ecotype and two genotypes of an inland ecotype were planted at coastal and inland sites. After 3 months, we collected rhizosphere and bulk soil and assessed microbial communities by 16S rRNA gene sequencing. We found that local environment (coastal versus inland site) strongly influenced rhizosphere communities, at least in part due to distinct local microbial species pools. Host identity played a smaller role: at each site, the ecotypes exhibited remarkably similar composition of microbial communities at the class level, indicating that divergent M. guttatus ecotypes recruit phylogenetically similar rhizosphere communities, even in environments to which they are maladapted. Nevertheless, the two ecotypes significantly differed in community composition at both sites due, in part, to an exclusive set of taxa associated with each ecotype. They also differed in alpha diversity at the inland site. Although this indicates that locally adapted M. guttatus ecotypes are genetically diverged in factors shaping rhizosphere communities, our findings highlight the context-specific interactions between host identity and local environment that shape those communities. [Formula: see text] Copyright © 2020 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license .

scholarly journals Locally-adapted Mimulus ecotypes differentially impact rhizosphere bacterial and archaeal communities in an environment-dependent manner

2019 ◽  
Author(s):  
Alan W. Bowsher ◽  
Patrick J. Kearns ◽  
Damian Popovic ◽  
David B. Lowry ◽  
Ashley Shade
Keyword(s):  
Microbial Community ◽  
Microbial Communities ◽  
Plant Root ◽  
16S Rrna Gene Sequencing ◽  
Wild Plants ◽  
Rrna Gene ◽  
Transplant Experiment ◽  
Dependent Manner ◽  
Reciprocal Transplant Experiment ◽  
Soil Microbial Community Structure

AbstractPlant root-microbe interactions influence plant productivity, health, and resistance to stress. Although there is evidence that plant species and even genotypes can alter soil microbial community structure, environmental conditions can potentially outweigh plant genetic effects. Here, we used a reciprocal transplant experiment to understand the contributions of the environment and the host plant to rhizosphere microbiome composition in locally-adapted ecotypes of Mimulus guttatus (syn. Erythranthe guttata (Fisch. ex DC.) G.L. Nesom). Two genotypes of a coastal ecotype and two genotypes of an inland ecotype were planted at coastal and inland sites. After three months, we collected rhizosphere and bulk soil and assessed microbial communities by 16S rRNA gene sequencing. We found that local environment (coastal versus inland site) strongly influenced rhizosphere communities, at least in part due to distinct local microbial species pools. Host identity played a smaller role: at each site, the ecotypes exhibited remarkably similar composition of microbial communities at the class level, indicating that divergent M. guttatus ecotypes recruit phylogenetically similar rhizosphere communities, even in environments to which they are maladapted. Nevertheless, the two ecotypes significantly differed in community composition at the inland site due to an exclusive set of rare taxa associated with each ecotype. Although our results indicate that locally-adapted M. guttatus ecotypes are genetically diverged in factors shaping rhizosphere communities, environmental factors can trump genetic factors in shaping the M. guttatus microbiome. Overall, our findings demonstrate that wild plants strongly impact root-associated microbial communities, but hierarchical drivers interact to shape microbial community assembly outcomes.

scholarly journals Diversity Indices of Plant Communities and Their Rhizosphere Microbiomes: An Attempt to Find the Connection

2021 ◽  
Vol 9 (11) ◽  
pp. 2339
Author(s):  
Aleksei O. Zverev ◽  
Arina A. Kichko ◽  
Aleksandr G. Pinaev ◽  
Nikolay A. Provorov ◽  
Evgeny E. Andronov
Keyword(s):  
Microbial Communities ◽  
Plant Communities ◽  
Plant Diversity ◽  
Beta Diversity ◽  
Mutual Influence ◽  
Plant Root ◽  
Alpha Diversity ◽  
Diversity Indices ◽  
Alpha And Beta Diversity ◽  
Highly Correlated

The rhizosphere community represents an “ecological interface” between plant and soil, providing the plant with a number of advantages. Despite close connection and mutual influence in this system, the knowledge about the connection of plant and rhizosphere diversity is still controversial. One of the most valuable factors of this uncertainty is a rough estimation of plant diversity. NGS sequencing can make the estimations of the plant community more precise than classical geobotanical methods. We investigate fallow and crop sites, which are similar in terms of environmental conditions and soil legacy, yet at the same time are significantly different in terms of plant diversity. We explored amplicons of both the plant root mass (ITS1 DNA) and the microbial communities (16S rDNA); determined alpha- and beta-diversity indices and their correlation, and performed differential abundance analysis. In the analysis, there is no correlation between the alpha-diversity indices of plants and the rhizosphere microbial communities. The beta-diversity between rhizosphere microbial communities and plant communities is highly correlated (R = 0.866, p = 0.01). ITS1 sequencing is effective for the description of plant root communities. There is a connection between rhizosphere communities and the composition of plants, but on the alpha-diversity level we found no correlation. In the future, the connection of alpha-diversities should be explored using ITS1 sequencing, even in more similar plant communities—for example, in different synusia.

Effect of ambient water conditions on microbial communities on the artificially produced aggregates: Evidence from experiments using two different seawater cultures

2021 ◽  
Author(s):  
Markus Weinbauer ◽  
Chiaki Motegi ◽  
Christophe Migon ◽  
Xavier Mari
Keyword(s):  
Microbial Communities ◽  
Water Flow ◽  
Bacterial Community Composition ◽  
Rrna Gene ◽  
Transplant Experiment ◽  
Ambient Water ◽  
Lagoon Water ◽  
Water Conditions ◽  
Flow Experiment ◽  
Water Treatments

<p>Microbial communities on marine aggregates could be influenced by ambient water conditions; however, empirical data are scarce. In this study, we used fingerprint analysis of PCR-amplified 16S rRNA gene fragment to examine how microbial communities on aggregates change in response to different conditions of ambient water. We conducted two experiments using seawater cultures from surface waters of the lagoon and the anthropogenically influenced bay of Nouméa, New Caledonia: a transplant experiment in which the artificially produced aggregates from one station was added to ultra-filtered seawater culture of another station, and a water-flow experiment in which the artificially produced aggregates placed in the ultra-filtered seawater culture with or without water-flow. In a transplant experiment, bacterial community composition (BCC) on the bay and lagoon water aggregates were significantly different (<em>p < 0.05</em>, ANOSIM) at the beginning of experiment. After 11 days of incubation, BCC on the lagoon water aggregates were significantly different (<em>p < 0.05</em>) from transplanted communities. Transplantation effect was also observed in the bay water treatments. In a water-flow experiment, BCC on the bay and lagoon water aggregates were significantly different (<em>p < 0.05</em>) at the beginning of the experiment. BCC on the lagoon and bay water aggregates with and without water-flow treatments were significantly different (<em>p </em>< 0.05) at the end of incubation, and effect of water-flow on BCC were observed in the bay and lagoon water treatments. Our experimental studies suggest that changes in ambient water conditions potentially influence microbial communities on aggregates in the Bay of Nouméa.</p>

scholarly journals Association between the microbiomes of tonsil and saliva samples isolated from pediatric patients subjected to tonsillectomy for the treatment of tonsillar hyperplasia

2020 ◽  
Vol 52 (9) ◽  
pp. 1564-1573
Author(s):  
Da Hyeon Choi ◽  
Jiwon Park ◽  
Ju Kwang Choi ◽  
Kyeong Eun Lee ◽  
Won Hee Lee ◽  
...  
Keyword(s):  
Oral Cavity ◽  
Microbial Communities ◽  
Alpha Diversity ◽  
16S Rrna Gene Sequencing ◽  
Diversity Indices ◽  
Rrna Gene ◽  
Strong Positive Correlation ◽  
Korean Children ◽  
Positive Correlation ◽  
Tonsillar Hyperplasia

Abstract Oral microbes have the capacity to spread throughout the gastrointestinal system and are strongly associated with multiple diseases. Given that tonsils are located between the oral cavity and the laryngopharynx at the gateway of the alimentary and respiratory tracts, tonsillar tissue may also be affected by microbiota from both the oral cavity (saliva) and the alimentary tract. Here, we analyzed the distribution and association of the microbial communities in the saliva and tonsils of Korean children subjected to tonsillectomy because of tonsil hyperplasia (n = 29). The microbiome profiles of saliva and tonsils were established via 16S rRNA gene sequencing. Based on the alpha diversity indices, the microbial communities of the two groups showed high similarities. According to Spearman’s ranking correlation analysis, the distribution of Treponema, the causative bacterium of periodontitis, in saliva and tonsils was found to have a significant positive correlation. Two representative microbes, Prevotella in saliva and Alloprevotella in tonsils, were negatively correlated, while Treponema 2 showed a strong positive correlation between saliva and tonsils. Taken together, strong similarities in the microbial communities of the tonsils and saliva are evident in terms of diversity and composition. The saliva microbiome is expected to significantly affect the tonsil microbiome. Furthermore, we suggest that our study creates an opportunity for tonsillar microbiome research to facilitate the development of novel microbiome-based therapeutic strategies.

scholarly journals Impact of Diabetes on the Gut and Salivary IgA Microbiomes

2020 ◽  
Vol 88 (12) ◽  
Author(s):  
Eric L. Brown ◽  
Heather T. Essigmann ◽  
Kristi L. Hoffman ◽  
Noah W. Palm ◽  
Sarah M. Gunter ◽  
...  
Keyword(s):  
Microbial Communities ◽  
Immunoglobulin A ◽  
Alpha Diversity ◽  
16S Rrna Gene Sequencing ◽  
Rrna Gene ◽  
Host Immune Responses ◽  
Mucosal Surfaces ◽  
Immune Mediated ◽  
Rrna Gene Sequencing ◽  
Immune Exclusion

ABSTRACT Mucosal surfaces like those present in the lung, gut, and mouth interface with distinct external environments. These mucosal gateways are not only portals of entry for potential pathogens but also homes to microbial communities that impact host health. Secretory immunoglobulin A (SIgA) is the single most abundant acquired immune component secreted onto mucosal surfaces and, via the process of immune exclusion, shapes the architecture of these microbiomes. Not all microorganisms at mucosal surfaces are targeted by SIgA; therefore, a better understanding of the SIgA-coated fraction may identify the microbial constituents that stimulate host immune responses in the context of health and disease. Chronic diseases like type 2 diabetes are associated with altered microbial communities (dysbiosis) that in turn affect immune-mediated homeostasis. 16S rRNA gene sequencing of SIgA-coated/uncoated bacteria (IgA-Biome) was conducted on stool and saliva samples of normoglycemic participants and individuals with prediabetes or diabetes (n = 8/group). These analyses demonstrated shifts in relative abundance in the IgA-Biome profiles between normoglycemic, prediabetic, or diabetic samples distinct from that of the overall microbiome. Differences in IgA-Biome alpha diversity were apparent for both stool and saliva, while overarching bacterial community differences (beta diversity) were also observed in saliva. These data suggest that IgA-Biome analyses can be used to identify novel microbial signatures associated with diabetes and support the need for further studies exploring these communities. Ultimately, an understanding of the IgA-Biome may promote the development of novel strategies to restructure the microbiome as a means of preventing or treating diseases associated with dysbiosis at mucosal surfaces.

scholarly journals Environmental exposure does not explain putative maladaptation in road-adjacent populations

2016 ◽  
Author(s):  
Steven P. Brady
Keyword(s):  
Natural Selection ◽  
Early Stage ◽  
Local Environment ◽  
Later Life ◽  
Pond Water ◽  
Transplant Experiment ◽  
Reciprocal Transplant Experiment ◽  
Embryonic Exposure ◽  
Reciprocal Transplants ◽  
Show Evidence

AbstractWhile the ecological consequences of roads are well described, little is known of their role as agents of natural selection, which can shape adaptive and maladaptive responses in populations influenced by roads. This is despite a growing appreciation for the influence of evolution in human-altered environments. There, insights indicate that natural selection typically results in local adaptation. Thus populations influenced by road-induced selection should evolve fitness advantages in their local environment. Contrary to this expectation, wood frog tadpoles from roadside populations show evidence of a fitness disadvantage, consistent with local maladaptation. Specifically, in reciprocal transplants, roadside populations survive at lower rates compared to populations away from roads. A key question remaining is whether roadside environmental conditions experienced by early-stage embryos induce this outcome. This represents an important missing piece in evaluating the evolutionary nature of this maladaptation pattern. Here, I address this gap using a reciprocal transplant experiment designed to test the hypothesis that embryonic exposure to roadside pond water induces a survival disadvantage. Contrary to this hypothesis, my results show that reduced survival persists when embryonic exposure is controlled. This indicates that the survival disadvantage is parentally mediated, either genetically and/or through inherited environmental effects. This result suggests that roadside populations are either truly maladapted or potentially locally adapted at later life stages. I discuss these interpretations, noting that regardless of mechanism, patterns consistent with maladaptation have important implications for conservation. In light of the pervasiveness of roads, further resolution explaining maladaptive responses remains a critical challenge in conservation.

scholarly journals Responses of Bacterial and Fungal Community Structure to Different Rates of 1,3-Dichloropropene Fumigation

2019 ◽  
Vol 3 (3) ◽  
pp. 212-223 ◽  
Author(s):  
Yuan Zeng ◽  
Zaid Abdo ◽  
Amy Charkowski ◽  
Jane E. Stewart ◽  
Kenneth Frost
Keyword(s):  
Community Structure ◽  
Microbial Communities ◽  
Management Practices ◽  
Soil Microbial Communities ◽  
Alpha Diversity ◽  
Potato Production ◽  
Crop Species ◽  
Soil Microbial Community Structure ◽  
Soil Microbial ◽  
Sample Depth

1,3-Dichloropropene (1,3-D) is a well-known nematicidal soil fumigant on many crop species. Currently, little is known about its impact on soil microbial communities using culture-free methods. In this study, we investigated changes in soil bacterial and fungal diversity and composition at two depths (30.5 and 61 cm) in response to management practices of applying 1,3-D at four different rates (103, 122, 140, and 187 liters/ha) relative to an untreated control in potato production fields using 16S rRNA and internal transcribed spacer (ITS) amplicon sequencing. A total of 12,783 operational taxonomic units (OTUs) for 16S and 1,706 OTUs for ITS were obtained. Sequencing revealed that Proteobacteria, Firmicutes, Actinobacteria, and Ascomycota were dominant phyla in soils. Comparing alpha diversity of microbial communities at the different chemical rates with untreated plots showed that bacterial communities in plots treated with 1,3-D fumigation at 140 liters/ha were richer, which was supported by higher richness indices. Other diversity indices and overall soil microbial community structure were not significantly influenced by any rates of 1,3-D fumigation, although higher bacterial and fungal richness and diversity were observed in posttreatment soils and/or at 30.5 cm. Of the identified microbial families, the differential abundance of 45 bacterial and 24 fungal families was affected by sample depth, 1,3-D rate, or the interaction of sample depth and 1,3-D. The bacterial family Enterobacteriaceae, which includes species that specialize in decay of complex carbohydrates, increased in abundance post-1,3-D fumigation, and the fungal family Ophiocordycipitaceae, which includes nematode and insect pathogens, decreased, suggesting that the nematode and soil insect death caused by fumigation may selectively impact specific fungal and bacterial families.

scholarly journals Urbanization promotes specific bacteria in freshwater microbiomes including potential pathogens

2020 ◽  
Author(s):  
Daniela Numberger ◽  
Luca Zoccarato ◽  
Jason Woodhouse ◽  
Lars Ganzert ◽  
Sascha Sauer ◽  
...  
Keyword(s):  
Microbial Communities ◽  
Treatment Plant ◽  
Environmental Parameters ◽  
Local Environment ◽  
Freshwater Ecosystems ◽  
Urban Environments ◽  
Rrna Gene ◽  
Global Increase ◽  
Bacterial Groups

ABSTRACTFreshwater ecosystems are not closed or sterile environments. They support complex and highly dynamic microbiological communities strongly structured by their local environment. Growing city populations and the process of urbanization is predicted to strongly alter freshwater environments. To determine the changes in freshwater microbial communities associated with urbanization, full-length 16S rRNA gene PacBio sequencing was performed on DNA from surface water and sediments from five lakes and a wastewater treatment plant in the Berlin-Brandenburg region of Germany. Water samples exhibited highly environment specific bacterial communities with multiple genera showing clear urban signatures. We identified potential harmful bacterial groups that were strongly associated with environmental parameters specific to urban environments such as Clostridium, Neisseria, Streptococcus, Yersinia and the toxic cyanobacterial genus Microcystis. We demonstrate that urbanization can alter natural microbial communities in lakes and promote specific bacterial genera which include potential pathogens. Urbanization, creates favourable conditions for pathogens that might be introduced by sporadic events or shift their proportions within the ecosystem. Our findings are of global relevance representing a long-term health risk in urbanized waterbodies at a time of global increase in urbanization.

scholarly journals Comparative analysis of 16S rRNA gene and metagenome sequencing in pediatric gut microbiomes

2021 ◽  
Author(s):  
Danielle Peterson ◽  
Kevin S. Bonham ◽  
Sophie Rowland ◽  
Cassandra W. Pattanayak ◽  
Vanja Klepac-Ceraj ◽  
...  
Keyword(s):  
16S Rrna ◽  
Microbial Communities ◽  
Gut Microbiome ◽  
Age Groups ◽  
Alpha Diversity ◽  
Sequencing Depth ◽  
Human Infant ◽  
Rrna Gene ◽  
Metagenomic Sequencing ◽  
Shotgun Metagenomic Sequencing

AbstractThe colonization of the human gut microbiome begins at birth, and, over time, these microbial communities become increasingly complex. Most of what we currently know about the human microbiome, especially in early stages of development, was described using culture-independent sequencing methods that allow us to identify the taxonomic composition of microbial communities using genomic techniques, such as amplicon or shotgun metagenomic sequencing. Each method has distinct tradeoffs, but there has not been a direct comparison of the utility of these methods in stool samples from very young children, which have different features than those of adults. We compared the effects of profiling the human infant gut microbiome with 16S rRNA amplicon versus shotgun metagenomic sequencing techniques in 130 fecal samples; younger than 15, 15-30, and older than 30 months of age. We demonstrate that observed changes in alpha-diversity and beta-diversity with age occur to similar extents using both profiling methods. We also show that 16S rRNA profiling identified a larger number of genera and we find several genera that are missed or underrepresented by each profiling method. We present the link between alpha diversity and shotgun metagenomic sequencing depth for children of different ages. These findings provide a guide for selecting an appropriate method and sequencing depth for the three studied age groups.

scholarly journals The Devils Hole pupfish gut microbiome and its potential role in paradoxical anaerobism

2019 ◽  
Author(s):  
Shrikant S Bhute ◽  
Brisa Escobedo ◽  
Mina Haider ◽  
Yididya Mekonen ◽  
Dafhner Ferrer ◽  
...  
Keyword(s):  
Gut Microbiota ◽  
Microbial Communities ◽  
Critical Role ◽  
16S Rrna Gene Sequencing ◽  
Wide Distribution ◽  
Control Group ◽  
Rrna Gene ◽  
Dependent Manner ◽  
Bacterial Phyla ◽  
Devils Hole

Abstract Background The Devils Hole Pupfish ( Cyprinodon diabolis ) frequently enters paradoxical anaerobism in response to endogenously produced or exogenously supplied ethanol in a dose-dependent manner. To decipher the role of the gut microbiota in ethanol-associated paradoxical anaerobism, gut microbial communities were depleted using a cocktail of antibiotics and profiled using 16S rRNA gene sequencing. Results Compared to the control group (n=12), microbiota-depleted fish (n=11) spent more time in paradoxical anaerobism. Our analysis indicated that the bacterial phyla Proteobacteria , Fusobacteria , Bacteroidetes , Firmicutes , Actinobacteria , Patescibacteria , and Dependentiae dominated the pupfish gut, which is consistent with other fish gut microbiota. Although the gut microbial communities with and without antibiotic treatment were similarly diverse, they were distinct and the greatest contribution to the dissimilarity (27.38%) was the common fish commensal Cetobacterium . We speculate that Cetobacterium , a primary fermenter, also consumes ethanol through secondary fermentation via an alcohol dehydrogenase and therefore regulates the transition from paradoxical anaerobism to aerobic respiration in fish. Conclusions This study reports the first characterization of gut microbial communities of critically endangered pupfish and suggests the microbiome may play a critical role in regulating metabolic strategies that are critical for survival in extremes of temperature and oxygen concentration. Given the wide distribution and abundance of Cetobacterium in warm-water fishes, this process may be of broad importance, and suggests that the microbiome be carefully considered for both conservation and aquaculture.

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