Host species shapes the co-occurrence patterns rather than diversity of stomach bacterial communities in pikas

2017 ◽  
Vol 101 (13) ◽  
pp. 5519-5529 ◽  
Author(s):  
Huan Li ◽  
Tongtong Li ◽  
Bo Tu ◽  
Yongping Kou ◽  
Xiangzhen Li
Keyword(s):  
Host Species ◽  
Bacterial Communities ◽  
Occurrence Patterns

scholarly journals The dilution effect limits plasmid horizontal transmission in multispecies bacterial communities

Microbiology ◽  
2021 ◽  
Vol 167 (9) ◽  
Author(s):  
Anastasia Kottara ◽  
Laura Carrilero ◽  
Ellie Harrison ◽  
James P. J. Hall ◽  
Michael A. Brockhurst
Keyword(s):  
Host Species ◽  
Bacterial Communities ◽  
Horizontal Transmission ◽  
Dilution Effect ◽  
Infection Risk ◽  
Host Cells ◽  
Evolutionary Innovation ◽  
Genomic Divergence ◽  
Plasmid Diversity ◽  
Plasmid Conjugation

By transferring ecologically important traits between species, plasmids drive genomic divergence and evolutionary innovation in their bacterial hosts. Bacterial communities are often diverse and contain multiple coexisting plasmids, but the dynamics of plasmids in multi-species communities are poorly understood. Here, we show, using experimental multi-species communities containing two plasmids, that bacterial diversity limits the horizontal transmission of plasmids due to the ‘dilution effect’; this is an epidemiological phenomenon whereby living alongside less proficient host species reduces the expected infection risk for a focal host species. In addition, plasmid horizontal transmission was also affected by plasmid diversity, such that the rate of plasmid conjugation was reduced from co-infected host cells carrying both plasmids. In diverse microbial communities, plasmid spread may be limited by the dilution effect and plasmid–plasmid interactions, reducing the rate of horizontal transmission.

scholarly journals Host species, pathogens and disease associated with divergent nasal microbial communities in tortoises

2018 ◽  
Vol 5 (10) ◽  
pp. 181068
Author(s):  
Chava L. Weitzman ◽  
Franziska C. Sandmeier ◽  
C. Richard Tracy
Keyword(s):  
Host Species ◽  
Bacterial Communities ◽  
Sonoran Desert ◽  
Bacterial Community Composition ◽  
Operational Taxonomic Unit ◽  
Nasal Discharge ◽  
Microbiome Composition ◽  
Technological Advances ◽  
Repeated Sampling ◽  
Pathogen Colonization

Diverse bacterial communities are found on every surface of macro-organisms, and they play important roles in maintaining normal physiological functions in their hosts. While the study of microbiomes has expanded with the influx of data enabled by recent technological advances, microbiome research in reptiles lags behind other organisms. We sequenced the nasal microbiomes in a sample of four North American tortoise species, and we found differing community compositions among tortoise species and sampling sites, with higher richness and diversity in Texas and Sonoran desert tortoises. Using these data, we investigated the prevalence and operational taxonomic unit (OTU) diversity of the potential pathogen Pasteurella testudinis and found it to be common, abundant and highly diverse. However, the presence of this bacterium was not associated with differences in bacterial community composition within host species. We also found that the presence of nasal discharge from tortoises at the time of sampling was associated with a decline in diversity and a change in microbiome composition, which we posit is due to the harsh epithelial environment associated with immune responses. Repeated sampling across seasons, and at different points of pathogen colonization, should contribute to our understanding of the causes and consequences of different bacterial communities in these long-lived hosts.

scholarly journals Co-occurrence patterns in aquatic bacterial communities across changing permafrost landscapes

2015 ◽  
Vol 12 (13) ◽  
pp. 10233-10269 ◽  
Author(s):  
J. Comte ◽  
C. Lovejoy ◽  
S. Crevecoeur ◽  
W. F. Vincent
Keyword(s):  
Bacterial Communities ◽  
High Throughput Sequencing ◽  
Habitat Preferences ◽  
Keystone Species ◽  
Small World ◽  
Rrna Gene ◽  
Permafrost Degradation ◽  
Bacterial Phyla ◽  
Organic Carbon Concentration ◽  
Occurrence Patterns

Abstract. Permafrost thaw ponds and lakes are widespread across the northern landscape and may play a central role in global biogeochemical cycles, yet knowledge about their microbial ecology is limited. We sampled a set of thaw ponds and lakes as well as shallow rock-basin lakes that are located in distinct valleys along a North–South permafrost degradation gradient. We applied high-throughput sequencing of the 16S rRNA gene to determine co-occurrence patterns among bacterial taxa, and then analyzed these results relative to environmental variables to identify factors controlling bacterial community structure. Network analysis was applied to identify possible ecological linkages among the bacterial taxa and with abiotic and biotic variables. The results showed an overall high level of shared taxa among bacterial communities within each valley, however the bacterial co-occurrence patterns were non-random, with evidence of habitat preferences. There were taxonomic differences in bacterial assemblages among the different valleys that were statistically related to dissolved organic carbon concentration, conductivity and phytoplankton biomass. Co-occurrence networks revealed complex interdependencies within the bacterioplankton communities and showed contrasting linkages to environmental conditions among the main bacterial phyla. The thaw pond networks were composed of a limited number of highly connected taxa. This "small world network" property would render the communities more robust to environmental change but vulnerable to the loss of microbial keystone species.

scholarly journals Tree phyllosphere bacterial communities: exploring the magnitude of intra- and inter-individual variation among host species

PeerJ ◽  
2016 ◽  
Vol 4 ◽  
pp. e2367 ◽  
Author(s):  
Isabelle Laforest-Lapointe ◽  
Christian Messier ◽  
Steven W. Kembel
Keyword(s):  
Community Structure ◽  
Bacterial Community ◽  
Individual Variation ◽  
Host Species ◽  
Bacterial Communities ◽  
Bacterial Community Structure ◽  
Temperate Forest ◽  
Abies Balsamea ◽  
Tree Canopy ◽  
Individual Tree

BackgroundThe diversity and composition of the microbial community of tree leaves (the phyllosphere) varies among trees and host species and along spatial, temporal, and environmental gradients. Phyllosphere community variation within the canopy of an individual tree exists but the importance of this variation relative to among-tree and among-species variation is poorly understood. Sampling techniques employed for phyllosphere studies include picking leaves from one canopy location to mixing randomly selected leaves from throughout the canopy. In this context, our goal was to characterize the relative importance of intra-individual variation in phyllosphere communities across multiple species, and compare this variation to inter-individual and interspecific variation of phyllosphere epiphytic bacterial communities in a natural temperate forest in Quebec, Canada.MethodsWe targeted five dominant temperate forest tree species including angiosperms and gymnosperms:Acer saccharum,Acer rubrum,Betula papyrifera,Abies balsameaandPicea glauca. For one randomly selected tree of each species, we sampled microbial communities at six distinct canopy locations: bottom-canopy (1–2 m height), the four cardinal points of mid-canopy (2–4 m height), and the top-canopy (4–6 m height). We also collected bottom-canopy leaves from five additional trees from each species.ResultsBased on an analysis of bacterial community structure measured via Illumina sequencing of the bacterial 16S gene, we demonstrate that 65% of the intra-individual variation in leaf bacterial community structure could be attributed to the effect of inter-individual and inter-specific differences while the effect of canopy location was not significant. In comparison, host species identity explains 47% of inter-individual and inter-specific variation in leaf bacterial community structure followed by individual identity (32%) and canopy location (6%).DiscussionOur results suggest that individual samples from consistent positions within the tree canopy from multiple individuals per species can be used to accurately quantify variation in phyllosphere bacterial community structure. However, the considerable amount of intra-individual variation within a tree canopy ask for a better understanding of how changes in leaf characteristics and local abiotic conditions drive spatial variation in the phyllosphere microbiome.

scholarly journals Yeast Communities of Diverse Drosophila Species: Comparison of Two Symbiont Groups in the Same Hosts

2012 ◽  
Vol 78 (20) ◽  
pp. 7327-7336 ◽  
Author(s):  
James Angus Chandler ◽  
Jonathan A. Eisen ◽  
Artyom Kopp
Keyword(s):  
Host Species ◽  
Bacterial Communities ◽  
Sampling Strategy ◽  
Holistic Approach ◽  
Content Type ◽  
Yeast Community ◽  
Comprehensive Picture ◽  
Host Diet ◽  
Host Microbe Interactions ◽  
Future Work

ABSTRACTThe combination of ecological diversity with genetic and experimental tractability makesDrosophilaa powerful model for the study of animal-associated microbial communities. Despite the known importance of yeasts inDrosophilaphysiology, behavior, and fitness, most recent work has focused onDrosophila-bacterial interactions. In order to get a more complete understanding of theDrosophilamicrobiome, we characterized the yeast communities associated with differentDrosophilaspecies collected around the world. We focused on the phylum Ascomycota because it constitutes the vast majority of theDrosophila-associated yeasts. Our sampling strategy allowed us to compare the distribution and structure of the yeast and bacterial communities in the same host populations. We show that yeast communities are dominated by a small number of abundant taxa, that the same yeast lineages are associated with different host species and populations, and that host diet has a greater effect than host species on yeast community composition. These patterns closely parallel those observed inDrosophilabacterial communities. However, we do not detect a significant correlation between the yeast and bacterial communities of the same host populations. Comparative analysis of different symbiont groups provides a more comprehensive picture of host-microbe interactions. Future work on the role of symbiont communities in animal physiology, ecological adaptation, and evolution would benefit from a similarly holistic approach.

scholarly journals Compositions and Co-occurrence Patterns of Bacterial Communities Associated With Polymer- and ASP-Flooded Petroleum Reservoir Blocks

2020 ◽  
Vol 11 ◽  
Author(s):  
Guoling Ren ◽  
Jinlong Wang ◽  
Lina Qu ◽  
Wei Li ◽  
Min Hu ◽  
...  
Keyword(s):  
Oil Recovery ◽  
Bacterial Communities ◽  
Chemical Properties ◽  
Oil Production ◽  
Chemical Flooding ◽  
Petroleum Reservoir ◽  
Promising Alternative ◽  
Asp Flooding ◽  
Production Wells ◽  
Occurrence Patterns

Polymer flooding technology and alkaline-surfactant-polymer (ASP) flooding technology have been widely used in some oil reservoirs. About 50% of remaining oil is trapped, however, in polymer-flooded and ASP-flooded reservoirs. How to further improve oil recovery of these reservoirs after chemical flooding is technically challenging. Microbial enhanced oil recovery (MEOR) technology is a promising alternative technology. However, the bacterial communities in the polymer-flooded and ASP-flooded reservoirs have rarely been investigated. We investigated the distribution and co-occurrence patterns of bacterial communities in ASP-flooded and polymer-flooded oil production wells. We found that Arcobacter and Pseudomonas were dominant both in the polymer-flooded and ASP-flooded production wells. Halomonas accounted for a large amount of the bacterial communities inhabiting in the ASP-flooded blocks, whereas they were hardly detected in the polymer-flooded blocks, and the trends for Acetomicrobium were the opposite. RDA analysis indicated that bacterial communities in ASP-flooded and polymer-flooded oil production wells are closely related to the physical and chemical properties, such as high salinity and strong alkaline, which together accounted for 56.91% of total variance. Co-occurrence network analysis revealed non-random combination patterns of bacterial composition from production wells of ASP-flooded and polymer-flooded blocks, and the ASP-flooded treatment decreased bacterial network complexity, suggesting that the application of ASP flooding technology reduced the tightness of bacterial interactions.

scholarly journals Co-occurrence patterns in aquatic bacterial communities across changing permafrost landscapes

2016 ◽  
Vol 13 (1) ◽  
pp. 175-190 ◽  
Author(s):  
J. Comte ◽  
C. Lovejoy ◽  
S. Crevecoeur ◽  
W. F. Vincent
Keyword(s):  
Bacterial Communities ◽  
High Throughput Sequencing ◽  
Habitat Preferences ◽  
Microbial Consortia ◽  
Rrna Gene ◽  
Permafrost Degradation ◽  
Food Web Structure ◽  
Bacterial Phyla ◽  
Organic Carbon Concentration ◽  
Occurrence Patterns

Abstract. Permafrost thaw ponds and lakes are widespread across the northern landscape and may play a central role in global biogeochemical cycles, yet knowledge about their microbial ecology is limited. We sampled a set of thaw ponds and lakes as well as shallow rock-basin lakes that are located in distinct valleys along a north–south permafrost degradation gradient. We applied high-throughput sequencing of the 16S rRNA gene to determine co-occurrence patterns among bacterial taxa (operational taxonomic units, OTUs), and then analyzed these results relative to environmental variables to identify variables controlling bacterial community structure. Network analysis was applied to identify possible ecological linkages among the bacterial taxa and with abiotic and biotic variables. The results showed an overall high level of shared taxa among bacterial communities within each valley; however, the bacterial co-occurrence patterns were non-random, with evidence of habitat preferences. There were taxonomic differences in bacterial assemblages among the different valleys that were statistically related to dissolved organic carbon concentration, conductivity and phytoplankton biomass. Co-occurrence networks revealed complex interdependencies within the bacterioplankton communities and showed contrasting linkages to environmental conditions among the main bacterial phyla. The thaw pond networks were composed of a limited number of highly connected taxa. This “small world network” property would render the communities more robust to environmental change but vulnerable to the loss of microbial “keystone species”. These highly connected nodes (OTUs) in the network were not merely the numerically dominant taxa, and their loss would alter the organization of microbial consortia and ultimately the food web structure and functioning of these aquatic ecosystems.

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