scholarly journals Dietary Fiber Hierarchical Specificity: the Missing Link for Predictable and Strong Shifts in Gut Bacterial Communities

mBio ◽  
2021 ◽  
Author(s):  
Thaisa M. Cantu-Jungles ◽  
Nuseybe Bulut ◽  
Eponine Chambry ◽  
Andrea Ruthes ◽  
Marcello Iacomini ◽  
...  
Keyword(s):  
Microbial Communities ◽  
Dietary Fiber ◽  
Bacterial Communities ◽  
Interindividual Variability ◽  
High Specificity ◽  
Competitive Interactions ◽  
Missing Link ◽  
The Face

In the face of interindividual variability and complexity of gut microbial communities, prediction of outcomes from a given fiber utilized by many microbes would require a sophisticated comprehension of all competitive interactions that occur in the gut. Results presented here suggest that high-specificity fibers potentially circumvent the competitive scope in the gut for fiber utilization, providing a promising path to targeted and predictable microbial shifts in different individuals.

scholarly journals Diversity and Dynamics of Seaweed Associated Microbial Communities Inhabiting the Lagoon of Venice

2020 ◽  
Vol 8 (11) ◽  
pp. 1657
Author(s):  
Abdul-Salam Juhmani ◽  
Alessandro Vezzi ◽  
Mohammad Wahsha ◽  
Alessandro Buosi ◽  
Fabio De Pascale ◽  
...  
Keyword(s):  
Microbial Communities ◽  
Bacterial Communities ◽  
Host Response ◽  
Environmental Parameters ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Nutrient Concentrations ◽  
Lagoon Of Venice ◽  
Anthropogenic Stressors ◽  
Rich Diversity

Seaweeds are a group of essential photosynthetic organisms that harbor a rich diversity of associated microbial communities with substantial functions related to host health and defense. Environmental and anthropogenic stressors may disrupt the microbial communities and their metabolic activity, leading to host physiological alterations that negatively affect seaweeds’ performance and survival. Here, the bacterial communities associated with one of the most common seaweed, Ulva laetevirens Areshough, were sampled over a year at three sites of the lagoon of Venice affected by different environmental and anthropogenic stressors. Bacterial communities were characterized through Illumina sequencing of the V4 hypervariable region of 16S rRNA genes. The study demonstrated that the seaweed associated bacterial communities at sites impacted by environmental stressors were host-specific and differed significantly from the less affected site. Furthermore, these communities were significantly distinct from those of the surrounding seawater. The bacterial communities’ composition was significantly correlated with environmental parameters (nutrient concentrations, dissolved oxygen saturation, and pH) across sites. This study showed that several more abundant bacteria on U. laetevirens at stressed sites belonged to taxa related to the host response to the stressors. Overall, environmental parameters and anthropogenic stressors were shown to substantially affect seaweed associated bacterial communities, which reflect the host response to environmental variations.

scholarly journals Competitive interactions among zoanthids (cnidaria: zoanthidae) in an intertidal zone of northeastern Brazil

2013 ◽  
Vol 61 (1) ◽  
pp. 35-42 ◽  
Author(s):  
Emanuelle Fontenele Rabelo ◽  
Marcelo de Oliveira Soares ◽  
Helena Matthews-Cascon
Keyword(s):  
Intertidal Zone ◽  
Northeastern Brazil ◽  
Competitive Interactions ◽  
Aggressive Interaction ◽  
Reef Environment ◽  
Palythoa Caribaeorum ◽  
The Face ◽  
Similar Growth ◽  
Sessile Organisms ◽  
Intertidal Environments

Sessile organisms that live in consolidated substrates frequently compete for space. Coral species have many strategies to face this competition, including harming their opponents or hindering their growth. In the present study, the competitive interactions between three species of zoanthids were investigated in the intertidal zone of a sandstone reef environment in northeastern Brazil. The competitive abilities of the three species were evaluated by periodic observation of the natural fringes of contact and experimental evaluation of their growth rate through removal of 100 cm² of colonies of each species. Palythoa caribaeorum and Zoanthus sociatus had similar growth rates, and both species grew faster than Protopalythoa variabilis. The recolonization strategy seems to differ among species. The contact fringes between P. caribaeorum and Z. sociatus remained unchanged over time, without any type of aggressive interaction between them, suggesting that stand-off was the strategy used by these organisms. Palythoa caribaeorum and Z. sociatus grew among the polyps of P. variabilis, often killing its colonies. The coexistence of zoanthids reveals a capacity for survival in the face of competition for limited resources such as free substrate, which led to the colonization and establishment of zoanthids in intertidal environments.

scholarly journals Do soil bacterial communities respond differently to abrupt or gradual additions of copper?

2018 ◽  
Vol 95 (1) ◽  
Author(s):  
Michael McTee ◽  
Lorinda Bullington ◽  
Matthias C Rillig ◽  
Philip W Ramsey
Keyword(s):  
Heavy Metals ◽  
Soil Respiration ◽  
Microbial Communities ◽  
Bacterial Communities ◽  
Diversity Indices ◽  
Microbial Populations ◽  
Metal Concentrations ◽  
Soil Bacterial Communities ◽  
Bacterial Richness

ABSTRACTMany experiments that measure the response of microbial communities to heavy metals increase metal concentrations abruptly in the soil. However, it is unclear whether abrupt additions mimic the gradual and often long-term accumulation of these metals in the environment where microbial populations may adapt. In a greenhouse experiment that lasted 26 months, we tested whether bacterial communities and soil respiration differed between soils that received an abrupt or a gradual addition of copper or no copper at all. Bacterial richness and other diversity indices were consistently lower in the abrupt treatment compared to the ambient treatment that received no copper. The abrupt addition of copper yielded different initial bacterial communities than the gradual addition; however, these communities appeared to converge once copper concentrations were approximately equal. Soil respiration in the abrupt treatment was initially suppressed but recovered after four months. Afterwards, respiration in both the gradual and abrupt treatments wavered between being below or equal to the ambient treatment. Overall, our study indicates that gradual and abrupt additions of copper can yield similar bacterial communities and respiration, but these responses may drastically vary until copper concentrations are equal.

scholarly journals Lack of evidence for microbiota in the placental and fetal tissues of rhesus macaques

2020 ◽  
Author(s):  
Kevin R. Theis ◽  
Roberto Romero ◽  
Andrew D. Winters ◽  
Alan H. Jobe ◽  
Nardhy Gomez-Lopez
Keyword(s):  
Dna Sequencing ◽  
Microbial Communities ◽  
Bacterial Communities ◽  
Rhesus Macaques ◽  
Uterine Wall ◽  
Bacterial Burden ◽  
Multiple Modes ◽  
Fetal Tissues ◽  
Microbial Invasion ◽  
Cutibacterium Acnes

ABSTRACTThe prevailing paradigm in obstetrics has been the sterile womb hypothesis. However, some are asserting that the placenta, intra-amniotic environment, and fetus harbor microbial communities. The objective of this study was to determine if the fetal and placental tissues of rhesus macaques harbor viable bacterial communities. Fetal, placental, and uterine wall samples were obtained from cesarean deliveries without labor (∼130/166 days gestation). The presence of viable bacteria in the fetal intestine and placenta was investigated through culture. The bacterial burden and profile of the placenta, umbilical cord, and fetal brain, heart, liver, and colon were determined through quantitative real-time PCR and DNA sequencing. These data were compared with those of the uterine wall, as well as to negative and positive technical controls. Bacterial cultures of fetal and placental tissues yielded only a single colony of Cutibacterium acnes. This bacterium was detected at a low relative abundance (0.02%) in the 16S rRNA gene profile of the villous tree sample from which it was cultured, yet it was also identified in 12/29 background technical controls. The bacterial burden and profile of fetal and placental tissues did not exceed or differ from those of background technical controls. In contrast, the bacterial burden and profiles of positive controls exceeded and differed from those of background controls. Among the macaque samples, distinct microbial signals were limited to the uterine wall. Therefore, using multiple modes of microbiologic inquiry, there was not consistent evidence of viable bacterial communities in the fetal and placental tissues of rhesus macaques.IMPORTANCEMicrobial invasion of the amniotic cavity (i.e. intra-amniotic infection) has been causally linked to pregnancy complications, especially preterm birth. Therefore, if the placenta and the fetus are typically populated by low biomass yet viable microbial communities, current understanding of the role of microbes in reproduction and pregnancy outcomes will need to be fundamentally reconsidered. Could these communities be of benefit by competitively excluding potential pathogens or priming the fetal immune system for the microbial bombardment it will experience upon delivery? If so, what properties (e.g. microbial load, community membership) of these microbial communities preclude versus promote intra-amniotic infection? Given the ramifications of the in utero colonization hypothesis, critical evaluation is required. In this study, using multiple modes of microbiologic inquiry (i.e. culture, qPCR, DNA sequencing) and controlling for potential background DNA contamination, we did not find consistent evidence for microbial communities in the placenta and fetal tissues of rhesus macaques.

scholarly journals Ecological succession of fungal and bacterial communities in Antarctic mosses affected by a fairy ring disease

2021 ◽  
Author(s):  
Luiz Henrique Rosa ◽  
Otávio Henrique Bezerra Pinto ◽  
Lívia Costa Coelho ◽  
Peter Convey ◽  
Micheline Carvalho-Silva ◽  
...  
Keyword(s):  
Microbial Communities ◽  
Bacterial Diversity ◽  
Fungal Community ◽  
Bacterial Communities ◽  
Pathogenic Fungi ◽  
Plant Pathogenic Fungi ◽  
King George Island ◽  
Fairy Rings ◽  
Fungal Assemblages ◽  
Antarctic Mosses

Abstract We evaluated fungal and bacterial diversity in an established moss carpet on King George Island, Antarctica, affected by ‘fairy ring’ disease using metabarcoding. These microbial communities were assessed through the main stages of the disease. A total of 127 fungal and 706 bacterial taxa were assigned. The phylum Ascomycota dominated the fungal assemblages, followed by Basidiomycota, Rozellomycota, Chytridiomycota, Mortierellomycota and Monoblepharomycota. The fungal community displayed high indices of diversity, richness and dominance, which increased from healthy through infected to dead moss samples. Bacterial diversity and richness were greatest in healthy moss and least within the infected fairy ring. Chalara sp. 1, Alpinaria sp., Helotiaceae sp. 2, Chaetothyriales sp. 1, Ascomycota sp. 1, Rozellomycota sp. and Fungi sp. were most abundant within the fairy ring samples. A range of fungal taxa were more abundant in dead rather than healthy or fairy ring moss samples. The dominant prokaryotic phyla were Actinobacteriota, Proteobacteria, Bacteroidota and Cyanobacteria. The taxon Cyanobacteriia sp., whilst consistently dominant, were less abundant in fairy ring samples. Microbacteriaceae sp. and Chloroflexi sp. were the most abundant taxa within the fairy rings. Our data confirmed the presence and abundance of a range of plant pathogenic fungi, supporting the hypothesis that the disease is linked with multiple fungal taxas. Further studies are required to characterise the interactions between plant pathogenic fungi and their host Antarctic mosses. Monitoring the dynamics of mutualist, phytopathogenic and decomposer microorganisms associated with moss carpets may provide bioindicators of moss health.

scholarly journals Time-series genome-centric analysis unveils bacterial response to operational disturbance in activated sludge

2019 ◽  
Author(s):  
María Victoria Pérez ◽  
Leandro D. Guerrero ◽  
Esteban Orellana ◽  
Eva L. Figuerola ◽  
Leonardo Erijman
Keyword(s):  
Growth Rate ◽  
Time Series ◽  
Wastewater Treatment ◽  
Activated Sludge ◽  
Microbial Communities ◽  
Wastewater Treatment Plant ◽  
Treatment Plant ◽  
Operating Conditions ◽  
The Face

ABSTRACTUnderstanding ecosystem response to disturbances and identifying the most critical traits for the maintenance of ecosystem functioning are important goals for microbial community ecology. In this study, we used 16S rRNA amplicon sequencing and metagenomics to investigate the assembly of bacterial populations in a full-scale municipal activated sludge wastewater treatment plant over a period of three years, including a period of nine month of disturbance, characterized by short-term plant shutdowns. Following the reconstruction of 173 metagenome-assembled genomes, we assessed the functional potential, the number of rRNA gene operons and thein situgrowth rate of microorganisms present throughout the time series. Operational disturbances caused a significant decrease in bacteria with a single copy of the ribosomal RNA (rrn) operon. Despite only moderate differences in resource availability, replication rates were distributed uniformly throughout time, with no differences between disturbed and stable periods. We suggest that the length of the growth lag phase, rather than the growth rate, as the primary driver of selection under disturbed conditions. Thus, the system could maintain its function in the face of disturbance by recruiting bacteria with the capacity to rapidly resume growth under unsteady operating conditions.IMPORTANCEIn this work we investigated the response of microbial communities to disturbances in a full-scale activated sludge wastewater treatment plant over a time-scale that included periods of stability and disturbance. We performed a genome-wide analysis, which allowed us the direct estimation of specific cellular traits, including the rRNA operon copy number and the in situ growth rate of bacteria. This work builds upon recent efforts to incorporate growth efficiency for the understanding of the physiological and ecological processes shaping microbial communities in nature. We found evidence that would suggest that activated sludge could maintain its function in the face of disturbance by recruiting bacteria with the capacity to rapidly resume growth under unsteady operating conditions. This paper provides relevant insights into wastewater treatment process, and may also reveal a key role for growth traits in the adaptive response of bacteria to unsteady environmental conditions.

scholarly journals Ecological networks reveal contrasting patterns of bacterial and fungal communities in glacier-fed streams in Central Asia

2019 ◽  
Author(s):  
Ze Ren ◽  
Hongkai Gao
Keyword(s):  
Bacterial Community ◽  
Microbial Communities ◽  
Central Asia ◽  
Fungal Community ◽  
Bacterial Communities ◽  
Beta Diversity ◽  
Hydrological Modeling ◽  
Alpha Diversity ◽  
Environmental Variation ◽  
Fungal Communities

Bacterial and fungal communities in biofilms are important components in driving biogeochemical processes in stream ecosystems. Previous studies have well documented the patterns of bacterial alpha diversity in stream biofilms in glacier-fed streams, where, however, beta diversity of the microbial communities has received much less attention especially considering both bacterial and fungal communities. A focus on beta diversity can provide insights into the mechanisms driving community changes associated to large environmental fluctuations and disturbances, such as in glacier-fed streams. Moreover, modularity of co-occurrence networks can reveal more ecological and evolutionary properties of microbial communities beyond taxonomic groups. Here, integrating beta diversity and co-occurrence approach, we explored the network topology and modularity of the bacterial and fungal communities with consideration of environmental variation in glacier-fed streams in Central Asia. Combining results from hydrological modeling and normalized difference of vegetation index, this study highlighted that hydrological variables and vegetation status are major variables determining the environmental heterogeneity of glacier-fed streams. Bacterial communities formed a more complex and connected network, while the fungal communities formed a more clustered network. Moreover, the strong interrelations among the taxonomic dissimilarities of bacterial community and modules suggest they had common processes in driving diversity and taxonomic compositions across the heterogeneous environment. In contrast, fungal community and modules generally showed distinct driving processes to each other. Moreover, bacterial and fungal communities also had different driving processes. Furthermore, the variation of bacterial community and modules were strongly correlated with hydrological properties and vegetation status but not with nutrients, while fungal community and modules (except one module) were not associated with environmental variation. Our results suggest that bacterial and fungal communities had distinct mechanisms in structuring microbial networks, and environmental variation had strong influences on bacterial communities but not on fungal communities. The fungal communities have unique assembly mechanisms and physiological properties which might lead to their insensitive responses to environmental variations compared to bacterial communities. Overall, beyond alpha diversity in previous studies, these results add our knowledge that bacterial and fungal communities have contrasting assembly mechanisms and respond differently to environmental variation in glacier-fed streams.

scholarly journals Ecological networks reveal contrasting patterns of bacterial and fungal communities in glacier-fed streams in Central Asia

2019 ◽  
Author(s):  
Ze Ren ◽  
Hongkai Gao
Keyword(s):  
Bacterial Community ◽  
Microbial Communities ◽  
Central Asia ◽  
Fungal Community ◽  
Bacterial Communities ◽  
Beta Diversity ◽  
Hydrological Modeling ◽  
Alpha Diversity ◽  
Environmental Variation ◽  
Fungal Communities

Bacterial and fungal communities in biofilms are important components in driving biogeochemical processes in stream ecosystems. Previous studies have well documented the patterns of bacterial alpha diversity in stream biofilms in glacier-fed streams, where, however, beta diversity of the microbial communities has received much less attention especially considering both bacterial and fungal communities. A focus on beta diversity can provide insights into the mechanisms driving community changes associated to large environmental fluctuations and disturbances, such as in glacier-fed streams. Moreover, modularity of co-occurrence networks can reveal more ecological and evolutionary properties of microbial communities beyond taxonomic groups. Here, integrating beta diversity and co-occurrence approach, we explored the network topology and modularity of the bacterial and fungal communities with consideration of environmental variation in glacier-fed streams in Central Asia. Combining results from hydrological modeling and normalized difference of vegetation index, this study highlighted that hydrological variables and vegetation status are major variables determining the environmental heterogeneity of glacier-fed streams. Bacterial communities formed a more complex and connected network, while the fungal communities formed a more clustered network. Moreover, the strong interrelations among the taxonomic dissimilarities of bacterial community and modules suggest they had common processes in driving diversity and taxonomic compositions across the heterogeneous environment. In contrast, fungal community and modules generally showed distinct driving processes to each other. Moreover, bacterial and fungal communities also had different driving processes. Furthermore, the variation of bacterial community and modules were strongly correlated with hydrological properties and vegetation status but not with nutrients, while fungal community and modules (except one module) were not associated with environmental variation. Our results suggest that bacterial and fungal communities had distinct mechanisms in structuring microbial networks, and environmental variation had strong influences on bacterial communities but not on fungal communities. The fungal communities have unique assembly mechanisms and physiological properties which might lead to their insensitive responses to environmental variations compared to bacterial communities. Overall, beyond alpha diversity in previous studies, these results add our knowledge that bacterial and fungal communities have contrasting assembly mechanisms and respond differently to environmental variation in glacier-fed streams.

scholarly journals Neutral processes and high inter-annual turnover shape the assembly of soil bacterial communities in a Mediterranean watershed

2019 ◽  
Author(s):  
Myrto Tsiknia ◽  
Stilianos Fodelianakis ◽  
Nikolaos P. Nikolaidis ◽  
Nikolaos V. Paranychianakis
Keyword(s):  
Stochastic Processes ◽  
Microbial Communities ◽  
Bacterial Communities ◽  
Ecosystem Functioning ◽  
Soil Microbial Communities ◽  
Soil Bacterial Communities ◽  
Environmental Selection ◽  
Mediterranean Landscapes ◽  
Soil Bacterial ◽  
Annual Turnover

AbstractThere is a renewed interest in recent years on the ecological processes (stochastic vs selective) driving the assembly of microbial communities. Such information could potentially improve our understanding on ecosystem functioning and resilience to disturbances, ecosystem response to environmental shifts, and adoption of sustainable soil management practices. Herein, employing a suite of existing methodologies, we show that stochastic processes have an important role on the assembly of soil bacterial communities at a Mediterranean watershed. Moreover, we document that the relative contribution of assembly processes varies over the years. The observed intensification of stochastic processes was accompanied by a decrease in the contribution of variable selection in favor of homogeneous selection and dispersal and this trend was only marginally affected by land use (natural vs agricultural lands) or soil depth. Our study also revealed a high inter-annual turnover of soil microbial communities that was likely stimulated by the weak environmental selection and the prevailing environmental conditions (drying-wetting cycles) in Mediterranean landscapes, implying potential impacts on ecosystem functioning and our ability to predict soil response to environmental shifts. Using nitrogen mineralization rate (NMR) as a representative function we document highly variable NMR over the sampling years, land uses and soil depths and lack of significant associations with the monitored environmental variables and individual taxa. In summary, our study provides novel insights on the organization and functioning of microbial communities at Mediterranean ecosystems and sets directions towards a more advanced understanding of the relationships among environmental factors, microbial community structure, and ecosystem functioning that could contribute to sustainable management of these severely degraded ecosystems.

scholarly journals Composition and predictive functional analysis of bacterial communities in the surface seawater of the Changjiang Estuary

2017 ◽  
Author(s):  
Dong-Mei Wu ◽  
Jian-Xin Wang ◽  
Xiao-Hui Liu ◽  
Ying-Ping Fan ◽  
Ran Jiang ◽  
...  
Keyword(s):  
Dissolved Oxygen ◽  
Microbial Communities ◽  
Bacterial Communities ◽  
High Throughput Sequencing ◽  
Carbon Fixation ◽  
Oxygen Demand ◽  
Environmental Parameters ◽  
Changjiang Estuary ◽  
Surface Seawater ◽  
The Changjiang Estuary

The objective of this study was to characterize the structure and function of microbial communities in surface seawater from the Changjiang Estuary and adjacent areas, China. Sample water was collected at 12 sites and environmental parameters were measured. Community structure was analyzed using high-throughput sequencing of 16S rDNA genes. Predictive metagenomic approach was used to predict the function of bacterial communities. Result showed that sample site A0102 had the highest bacterial abundance and diversity. The heatmap indicated that different samples could be clustered into six groups. Phylogenetic analysis showed that Proteobacteria was the predominant phylum in all samples, followed by Bacteroidetes and Actinobacteria. Alphaproteobacteria and Gammaproteobacteria were the dominant classes. The analysis of predictive metagenomic showed carbon fixation pathways in prokaryotes, nitrogen metabolism, carbon fixation in photosynthetic organisms, photosynthesis and polycyclic aromatic hydrocarbon degradation were enriched in all samples. Redundancy analysis (RDA) identified that dissolved oxygen (DO) and PO43– concentration had positive correlations with the bacterial communities while chemical oxygen demand (COD), dissolved oxygen (DO) and PO43– concentration were significantly associated with microbial functional diversity. This study adds to our knowledge of functional and taxonomic composition of microbial communities.

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