Microbial biogeography and ecology of the mouth and implications for periodontal diseases

AbstractHuman-associated microbial communities differ in composition among body sites and between habitats within a site. Patterns of variation in the distribution of organisms across time and space is referred to as ‘biogeography’. The human oral cavity is a critical observatory for exploring microbial biogeography because it is spatially structured, easily accessible, and its microbiota has been linked to the promotion of both health and disease. The biogeographic features of microbial communities residing in spatially distinct but ecologically similar environments on the human body, including the subgingival crevice, have not yet been adequately explored. The purpose of this paper is twofold. First, we seek to provide the dental community with a primer on biogeographic theory, highlighting its relevance to the study of the human oral cavity. For this reason, we summarize what is known about the biogeographic variation of dental caries and periodontitis and postulate as to how this may be driven by spatial patterning in oral microbial community composition and structure. Second, we present a number of methods that investigators can use to test specific hypotheses using biogeographic theory.To anchor our discussion, we apply each method to a case study and examine the spatial variation of the human subgingival microbiota of 2 individuals. Our case study suggests that subgingival communities in the aggregate may conform to an anterior-to-posterior gradient in community composition. The gradient appears to be structured both by deterministic and non-deterministic processes, though additional work is needed to test and confirm specific hypotheses. A better understanding of biogeographic patterns and processes will advance our understanding of ways to optimize the efficacy of dental interventions targeting the oral microbiota.

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Antarctic Water Tracks: Microbial Community Responses to Variation in Soil Moisture, pH, and Salinity

Frontiers in Microbiology ◽

10.3389/fmicb.2021.616730 ◽

2021 ◽

Vol 12 ◽

Author(s):

Scott F. George ◽

Noah Fierer ◽

Joseph S. Levy ◽

Byron Adams

Keyword(s):

Microbial Community ◽

Microbial Communities ◽

Community Composition ◽

Environmental Conditions ◽

Microbial Community Composition ◽

Soil Microbial Communities ◽

Vapor Flow ◽

Arid Soils ◽

Opposite Pattern ◽

Dry Valley

Ice-free soils in the McMurdo Dry Valleys select for taxa able to cope with challenging environmental conditions, including extreme chemical water activity gradients, freeze-thaw cycling, desiccation, and solar radiation regimes. The low biotic complexity of Dry Valley soils makes them well suited to investigate environmental and spatial influences on bacterial community structure. Water tracks are annually wetted habitats in the cold-arid soils of Antarctica that form briefly each summer with moisture sourced from snow melt, ground ice thaw, and atmospheric deposition via deliquescence and vapor flow into brines. Compared to neighboring arid soils, water tracks are highly saline and relatively moist habitats. They represent a considerable area (∼5–10 km2) of the Dry Valley terrestrial ecosystem, an area that is expected to increase with ongoing climate change. The goal of this study was to determine how variation in the environmental conditions of water tracks influences the composition and diversity of microbial communities. We found significant differences in microbial community composition between on- and off-water track samples, and across two distinct locations. Of the tested environmental variables, soil salinity was the best predictor of community composition, with members of the Bacteroidetes phylum being relatively more abundant at higher salinities and the Actinobacteria phylum showing the opposite pattern. There was also a significant, inverse relationship between salinity and bacterial diversity. Our results suggest water track formation significantly alters dry soil microbial communities, likely influencing subsequent ecosystem functioning. We highlight how Dry Valley water tracks could be a useful model system for understanding the potential habitability of transiently wetted environments found on the surface of Mars.

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Temporal and spatial dynamics of peat microbiomes in drained and rewetted soils of three temperate peatlands

10.1101/2020.02.16.951285 ◽

2020 ◽

Author(s):

Haitao Wang ◽

Micha Weil ◽

Dominik Zak ◽

Diana Münch ◽

Anke Günther ◽

...

Keyword(s):

Microbial Communities ◽

Greenhouse Gas Emissions ◽

Greenhouse Gas ◽

Community Composition ◽

Structural Equation ◽

Structural Equation Models ◽

Temporal Dynamics ◽

Salt Water ◽

Microbial Community Composition ◽

Gas Emissions

AbstractBackgroundDrainage of high-organic peatlands for agricultural purposes has led to increased greenhouse gas emissions and loss of biodiversity. In the last decades, rewetting of peatlands is on the rise worldwide, to mitigate these negative impacts. However, it remains still questionable how rewetting would influence peat microbiota as important drivers of nutrient cycles and ecosystem restoration. Here, we investigate the spatial and temporal dynamics of the diversity, community composition and network interactions of prokaryotes and eukaryotes, and the influence of rewetting on these microbial features in formerly long-term drained and agriculturally used fens. Peat-soils were sampled seasonally from three drained and three rewetted sites representing the dominating fen peatland types of glacial landscapes in Northern Germany, namely alder forest, costal fen and percolation fen.ResultsCostal fens as salt-water impacted systems showed a lower microbial diversity and their microbial community composition showed the strongest distinction from the other two peatland types. Prokaryotic and eukaryotic community compositions showed a congruent pattern which was mostly driven by peatland type and rewetting. Rewetting decreased the abundances of fungi and prokaryotic decomposers, while the abundance of potential methanogens was significantly higher in the rewetted sites. Rewetting also influenced the abundance of ecological clusters in the microbial communities identified from the co-occurrence network. The microbial communities changed only slightly with depth and over time. According to structural equation models rewetted conditions affected the microbial communities through different mechanisms across the three studied peatland types.ConclusionsOur results suggest that rewetting strongly impacts the structure of microbial communities and, thus, important biogeochemical processes, which may explain the high variation in greenhouse gas emissions upon rewetting of peatlands. The improved understanding of functional mechanisms of rewetting in different peatland types lays the foundation for securing best practices to fulfil multiple restoration goals including those targeting on climate, water, and species protection.

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Soil microbial communities in microaggregates are less affected by top-down effects of collembolans than those in macroaggregates

10.5194/egusphere-egu21-10345 ◽

2021 ◽

Author(s):

Amandine Erktan ◽

MD Ekramul Haque ◽

Jérôme Cortet ◽

Paul Henning Krogh ◽

Stefan Scheu

Keyword(s):

Microbial Community ◽

Microbial Communities ◽

Community Composition ◽

Trophic Interactions ◽

Phospholipid Fatty Acid ◽

Microbial Community Composition ◽

Soil Microbial Communities ◽

Trophic Levels ◽

Soil Matrix ◽

Fungal Abundance

<p>Trophic regulation of microbial communities is receiving growing interest in soil ecology. Most studies investigated the effect of higher trophic levels on microbial communities at the bulk soil level. However, microbes are not equally accessible to consumers. They may be hidden in small pores and thus protected from consumers, suggesting that trophic regulation may depend on the localization of microbes within the soil matrix. As microaggregates (< 250 &#181;m) usually are more stable than macroaggregates (> 250 &#181;m) and embedded in the latter, we posit that they will be less affected by trophic regulations than larger aggregates. We quantified the effect of four contrasting species of collembolans (Ceratophysella denticulata, Protaphorura fimata, Folsomia candida, Sinella curviseta) on the microbial community composition in macro- (250 &#181;m &#8211; 2mm) and microaggregates (50 &#8211; 250 &#181;m). To do so, we re-built consumer-prey systems comprising remaining microbial background (post-autoclaving), fungal prey (Chaetomium globosum), and collembolan species (added as single species or combined). After three months, we quantified microbial community composition using phospholipid fatty acid markers (PLFAs). We found that the microbial communities in macroaggregates were more affected by the addition of collembolans than the communities in microaggregates. In particular, the fungal-to-bacterial (F:B) ratio significantly decreased in soil macroaggregates in the presence of collembolans. In the microaggregates, the F:B ratio remained lower and unaffected by collembolan inoculation. Presumably, fungal hyphae were more abundant in macroaggregates because they offered more habitat space for them, and the collembolans reduced fungal abundance because they consumed them. On the contrary, microaggregates presumably contained microbial communities protected from consumers. In addition, collembolans increased the formation of macroaggregates but did not influence their stability, despite their negative effect on fungal abundance, a well-known stabilizing agent. Overall, we show that trophic interactions between microbial communities and collembolans depend on the aggregate size class considered and, in return, soil macroaggregation is affected by these trophic interactions.</p>

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Changes in the Active, Dead, and Dormant Microbial Community Structure across a Pleistocene Permafrost Chronosequence

Applied and Environmental Microbiology ◽

10.1128/aem.02646-18 ◽

2019 ◽

Vol 85 (7) ◽

Cited By ~ 17

Author(s):

Alexander Burkert ◽

Thomas A. Douglas ◽

Mark P. Waldrop ◽

Rachel Mackelprang

Keyword(s):

Microbial Community ◽

16S Rrna ◽

16S Rrna Gene ◽

Microbial Communities ◽

Community Composition ◽

Environmental Conditions ◽

Microbial Community Composition ◽

Rrna Gene ◽

Subzero Temperatures ◽

Dormant Cells

ABSTRACTPermafrost hosts a community of microorganisms that survive and reproduce for millennia despite extreme environmental conditions, such as water stress, subzero temperatures, high salinity, and low nutrient availability. Many studies focused on permafrost microbial community composition use DNA-based methods, such as metagenomics and 16S rRNA gene sequencing. However, these methods do not distinguish among active, dead, and dormant cells. This is of particular concern in ancient permafrost, where constant subzero temperatures preserve DNA from dead organisms and dormancy may be a common survival strategy. To circumvent this, we applied (i) LIVE/DEAD differential staining coupled with microscopy, (ii) endospore enrichment, and (iii) selective depletion of DNA from dead cells to permafrost microbial communities across a Pleistocene permafrost chronosequence (19,000, 27,000, and 33,000 years old). Cell counts and analysis of 16S rRNA gene amplicons from live, dead, and dormant cells revealed how communities differ between these pools, how they are influenced by soil physicochemical properties, and whether they change over geologic time. We found evidence that cells capable of forming endospores are not necessarily dormant and that members of the classBacilliwere more likely to form endospores in response to long-term stressors associated with permafrost environmental conditions than members of theClostridia, which were more likely to persist as vegetative cells in our older samples. We also found that removing exogenous “relic” DNA preserved within permafrost did not significantly alter microbial community composition. These results link the live, dead, and dormant microbial communities to physicochemical characteristics and provide insights into the survival of microbial communities in ancient permafrost.IMPORTANCEPermafrost soils store more than half of Earth’s soil carbon despite covering ∼15% of the land area (C. Tarnocai et al., Global Biogeochem Cycles 23:GB2023, 2009, https://doi.org/10.1029/2008GB003327). This permafrost carbon is rapidly degraded following a thaw (E. A. G. Schuur et al., Nature 520:171–179, 2015, https://doi.org/10.1038/nature14338). Understanding microbial communities in permafrost will contribute to the knowledge base necessary to understand the rates and forms of permafrost C and N cycling postthaw. Permafrost is also an analog for frozen extraterrestrial environments, and evidence of viable organisms in ancient permafrost is of interest to those searching for potential life on distant worlds. If we can identify strategies microbial communities utilize to survive in permafrost, it may yield insights into how life (if it exists) survives in frozen environments outside of Earth. Our work is significant because it contributes to an understanding of how microbial life adapts and survives in the extreme environmental conditions in permafrost terrains.

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Oral Microbial Ecology and the Role of Salivary Immunoglobulin A

Microbiology and Molecular Biology Reviews ◽

10.1128/mmbr.62.1.71-109.1998 ◽

1998 ◽

Vol 62 (1) ◽

pp. 71-109 ◽

Cited By ~ 236

Author(s):

Harold Marcotte ◽

Marc C. Lavoie

Keyword(s):

Immune System ◽

Oral Cavity ◽

Microbial Ecology ◽

Periodontal Diseases ◽

Immunoglobulin A ◽

Basic Knowledge ◽

Oral Microbiota ◽

Indigenous Bacteria ◽

Indigenous Microbiota

SUMMARY In the oral cavity, indigenous bacteria are often associated with two major oral diseases, caries and periodontal diseases. These diseases seem to appear following an inbalance in the oral resident microbiota, leading to the emergence of potentially pathogenic bacteria. To define the process involved in caries and periodontal diseases, it is necessary to understand the ecology of the oral cavity and to identify the factors responsible for the transition of the oral microbiota from a commensal to a pathogenic relationship with the host. The regulatory forces influencing the oral ecosystem can be divided into three major categories: host related, microbe related, and external factors. Among host factors, secretory immunoglobulin A (SIgA) constitutes the main specific immune defense mechanism in saliva and may play an important role in the homeostasis of the oral microbiota. Naturally occurring SIgA antibodies that are reactive against a variety of indigenous bacteria are detectable in saliva. These antibodies may control the oral microbiota by reducing the adherence of bacteria to the oral mucosa and teeth. It is thought that protection against bacterial etiologic agents of caries and periodontal diseases could be conferred by the induction of SIgA antibodies via the stimulation of the mucosal immune system. However, elucidation of the role of the SIgA immune system in controlling the oral indigenous microbiota is a prerequisite for the development of effective vaccines against these diseases. The role of SIgA antibodies in the acquisition and the regulation of the indigenous microbiota is still controversial. Our review discusses the importance of SIgA among the multiple factors that control the oral microbiota. It describes the oral ecosystems, the principal factors that may control the oral microbiota, a basic knowledge of the secretory immune system, the biological functions of SIgA, and, finally, experiments related to the role of SIgA in oral microbial ecology.

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Impacts of Maize Domestication and Breeding on Rhizosphere Microbial Community Recruitment from a Nutrient Depleted Agricultural Soil

Scientific Reports ◽

10.1038/s41598-019-52148-y ◽

2019 ◽

Vol 9 (1) ◽

Cited By ~ 11

Author(s):

Vanessa L. Brisson ◽

Jennifer E. Schmidt ◽

Trent R. Northen ◽

John P. Vogel ◽

Amélie C. M. Gaudin

Keyword(s):

Microbial Community ◽

Microbial Communities ◽

Community Composition ◽

Microbial Community Composition ◽

Microbial Community Analysis ◽

Agricultural System ◽

Community Members ◽

Genetic Groups ◽

Maize Domestication ◽

Rhizosphere Microbial Community

Abstract Maize domestication and breeding have resulted in drastic and well documented changes in aboveground traits, but belowground effects on root system functioning and rhizosphere microbial communities remain poorly understood, despite their critical importance for nutrient and water acquisition. We investigated the rhizosphere microbial community composition and structure of ten Zea mays accessions along an evolutionary transect (two teosinte, three inbred maize lines, and five modern maize hybrids) grown in nutrient depleted soil from a low input agricultural system. Microbial community analysis revealed significant differences in community composition between soil compartments (proximal vs. distal rhizosphere) and between plant genetic groups (teosinte, inbred, and modern hybrid). Only a small portion of the microbial community was differentially selected across plant genetic groups: 3.7% of prokaryotic community members and 4.9% of fungal community members were significantly associated with a specific plant genetic group. Indicator species analysis showed the greatest differentiation between modern hybrids and the other two plant genetic groups. Co-occurrence network analysis revealed that microbial co-occurrence patterns of the inbred maize lines’ rhizosphere were significantly more similar to those of the teosintes than to the modern hybrids. Our results suggest that advances in hybrid development significantly impacted rhizosphere microbial communities and network assembly.

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Effects of Actinomycete Secondary Metabolites on Sediment Microbial Communities

Applied and Environmental Microbiology ◽

10.1128/aem.02676-16 ◽

2016 ◽

Vol 83 (4) ◽

Cited By ~ 18

Author(s):

Nastassia V. Patin ◽

Michelle Schorn ◽

Kristen Aguinaldo ◽

Tommie Lincecum ◽

Bradley S. Moore ◽

...

Keyword(s):

Microbial Community ◽

Secondary Metabolites ◽

Microbial Communities ◽

Community Composition ◽

Marine Sediments ◽

Microbial Community Composition ◽

Amplicon Sequencing ◽

Next Generation ◽

Content Type ◽

Predatory Bacteria

ABSTRACT Marine sediments harbor complex microbial communities that remain poorly studied relative to other biomes such as seawater. Moreover, bacteria in these communities produce antibiotics and other bioactive secondary metabolites, yet little is known about how these compounds affect microbial community structure. In this study, we used next-generation amplicon sequencing to assess native microbial community composition in shallow tropical marine sediments. The results revealed complex communities comprised of largely uncultured taxa, with considerable spatial heterogeneity and known antibiotic producers comprising only a small fraction of the total diversity. Organic extracts from cultured strains of the sediment-dwelling actinomycete genus Salinispora were then used in mesocosm studies to address how secondary metabolites shape sediment community composition. We identified predatory bacteria and other taxa that were consistently reduced in the extract-treated mesocosms, suggesting that they may be the targets of allelopathic interactions. We tested related taxa for extract sensitivity and found general agreement with the culture-independent results. Conversely, several taxa were enriched in the extract-treated mesocosms, suggesting that some bacteria benefited from the interactions. The results provide evidence that bacterial secondary metabolites can have complex and significant effects on sediment microbial communities. IMPORTANCE Ocean sediments represent one of Earth's largest and most poorly studied biomes. These habitats are characterized by complex microbial communities where competition for space and nutrients can be intense. This study addressed the hypothesis that secondary metabolites produced by the sediment-inhabiting actinomycete Salinispora arenicola affect community composition and thus mediate interactions among competing microbes. Next-generation amplicon sequencing of mesocosm experiments revealed complex communities that shifted following exposure to S. arenicola extracts. The results reveal that certain predatory bacteria were consistently less abundant following exposure to extracts, suggesting that microbial metabolites mediate competitive interactions. Other taxa increased in relative abundance, suggesting a benefit from the extracts themselves or the resulting changes in the community. This study takes a first step toward assessing the impacts of bacterial metabolites on sediment microbial communities. The results provide insight into how low-abundance organisms may help structure microbial communities in ocean sediments.

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Microbial Communities Show Parallels at Sites with Distinct Litter and Soil Characteristics

Applied and Environmental Microbiology ◽

10.1128/aem.00527-11 ◽

2011 ◽

Vol 77 (21) ◽

pp. 7560-7567 ◽

Cited By ~ 17

Author(s):

Marketa Sagova-Mareckova ◽

Marek Omelka ◽

Ladislav Cermak ◽

Zdenek Kamenik ◽

Jana Olsovska ◽

...

Keyword(s):

Microbial Community ◽

Microbial Communities ◽

Community Composition ◽

Soil Ph ◽

Soil Chemistry ◽

High Performance ◽

Bacterial Community Composition ◽

Microbial Community Composition ◽

Carbon Sources ◽

Soil Extracts

ABSTRACTPlant and microbial community composition in connection with soil chemistry determines soil nutrient cycling. The study aimed at demonstrating links between plant and microbial communities and soil chemistry occurring among and within four sites: two pine forests with contrasting soil pH and two grasslands of dissimilar soil chemistry and vegetation. Soil was characterized by C and N content, particle size, and profiles of low-molecular-weight compounds determined by high-performance liquid chromatography (HPLC) of soil extracts. Bacterial and actinobacterial community composition was assessed by terminal restriction fragment length polymorphism (T-RFLP) and cloning followed by sequencing. Abundances of bacteria, fungi, and actinobacteria were determined by quantitative PCR. In addition, a pool of secondary metabolites was estimated byermresistance genes coding for rRNA methyltransferases. The sites were characterized by a stable proportion of C/N within each site, while on a larger scale, the grasslands had a significantly lower C/N ratio than the forests. A Spearman's test showed that soil pH was correlated with bacterial community composition not only among sites but also within each site. Bacterial, actinobacterial, and fungal abundances were related to carbon sources while T-RFLP-assessed microbial community composition was correlated with the chemical environment represented by HPLC profiles. Actinobacteria community composition was the only studied microbial characteristic correlated to all measured factors. It was concluded that the microbial communities of our sites were influenced primarily not only by soil abiotic characteristics but also by dominant litter quality, particularly, by percentage of recalcitrant compounds.

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Application of Methods for Identifying Broiler Chicken Gut Bacterial Species Linked with Increased Energy Metabolism

Applied and Environmental Microbiology ◽

10.1128/aem.01384-07 ◽

2007 ◽

Vol 74 (3) ◽

pp. 783-791 ◽

Cited By ~ 105

Author(s):

Valeria A. Torok ◽

Kathy Ophel-Keller ◽

Maylene Loo ◽

Robert J. Hughes

Keyword(s):

Microbial Community ◽

Microbial Communities ◽

Community Composition ◽

Bacterial Species ◽

Bacterial Community Composition ◽

Microbial Community Composition ◽

Metabolizable Energy ◽

Principal Coordinates ◽

Improved Performance ◽

Gut Microbial Community

ABSTRACT A high-throughput microbial profiling tool based on terminal restriction fragment length polymorphism was developed to monitor the poultry gut microbiota in response to dietary manipulations. Gut microbial communities from the duodena, jejuna, ilea, and ceca of 48 birds fed either a barley control diet or barley diet supplemented with exogenous enzymes for degrading nonstarch polysaccharide were characterized by using multivariate statistical methods. Analysis of samples showed that gut microbial communities varied significantly among gut sections, except between the duodenum and jejunum. Significant diet-associated differences in gut microbial communities were detected within the ileum and cecum only. The dissimilarity in bacterial community composition between diets was 73 and 66% within the ileum and cecum, respectively. Operational taxonomic units, representing bacterial species or taxonomically related groups, contributing to diet-associated differences were identified. Several bacterial species contributed to differences between diet-related gut microbial community composition, with no individual bacterial species contributing more than 1 to 5% of the total. Using canonical analysis of principal coordinates biplots, we correlated differences in gut microbial community composition within the ileum and cecum to improved performance, as measured by apparent metabolizable energy. This is the first report that directly links differences in the composition of the gut microbial community with improved performance, which implies that the presence of specific beneficial and/or absence of specific detrimental bacterial species may contribute to the improved performance in these birds.

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Effects of Microbial Consortia, Applied as Fertilizer Coating, on Soil and Rhizosphere Microbial Communities and Potato Yield

Frontiers in Agronomy ◽

10.3389/fagro.2021.714700 ◽

2021 ◽

Vol 3 ◽

Author(s):

William Overbeek ◽

Thomas Jeanne ◽

Richard Hogue ◽

Donald L. Smith

Keyword(s):

Microbial Community ◽

Microbial Communities ◽

Community Composition ◽

Soil Microbial Community ◽

Microbial Community Composition ◽

Bulk Soil ◽

Microbial Inoculants ◽

Flowering Stage ◽

Soil Microbial ◽

Soil Microbial Community Composition

The use of biological inputs in crop production systems, as complements to synthetic inputs, is gaining popularity in the agricultural industry due to increasing consumer demand for more environmentally friendly agriculture. An approach to meeting this demand is the inoculation of field crops with beneficial microbes to promote plant growth and resistance to biotic and abiotic stresses. However, the scientific literature reports inconsistent results following applications of bio-inoculant to fields. The effects of inoculation with beneficial microbes on bulk soil and rhizospheric microbial communities is often overlooked as precise monitoring of soil microbial communities is difficult. The aim of this research was to use Illumina high throughput sequencing (HTS) to shed light on bulk soil and rhizospheric microbial community responses to two commercial microbial inoculants coated onto fertilizer granules, applied to potato fields. Bulk soil samples were collected 4 days before seeding (May 27th), 7 days after seeding (June 7th), at potato shoot emergence (June 21st) and at mid-flowering (July 26th). Rhizospheric soil was collected at the mid-flowering stage. The Illumina MiSeq HTS results indicated that the bulk soil microbial community composition, especially prokaryotes, changed significantly across potato growth stages. Microbial inoculation did not affect bulk soil or rhizospheric microbial communities sampled at the mid-flowering stage. However, a detailed analysis of the HTS results showed that bulk soil and rhizospheric microbial community richness and composition were different for the first treatment block compared to the other three blocks. The spatial heterogeneity of the soil microbial community between blocks of plots was associated with potato tuber yield changes, indicating links between crop productivity and soil microbial community composition. Understanding these links could help in production of high-quality microbial inoculants to promote potato productivity.

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