scholarly journals Salt marsh sediment bacterial communities maintain original population structure after transplantation across a latitudinal gradient

PeerJ ◽  
2018 ◽  
Vol 6 ◽  
pp. e4735 ◽  
Author(s):  
Angus Angermeyer ◽  
Sarah C. Crosby ◽  
Julie A. Huber
Keyword(s):  
Salt Marsh ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Microbial Communities ◽  
Community Composition ◽  
Bacterial Communities ◽  
Latitudinal Gradient ◽  
Rrna Gene ◽  
Transplant Experiment ◽  
Environmental Selection

Dispersal and environmental selection are two of the most important factors that govern the distributions of microbial communities in nature. While dispersal rates are often inferred by measuring the degree to which community similarity diminishes with increasing geographic distance, determining the extent to which environmental selection impacts the distribution of microbes is more complex. To address this knowledge gap, we performed a large reciprocal transplant experiment to simulate the dispersal of US East Coast salt marsh Spartina alterniflora rhizome-associated microbial sediment communities across a latitudinal gradient and determined if any shifts in microbial community composition occurred as a result of the transplantation. Using bacterial 16S rRNA gene sequencing, we did not observe large-scale changes in community composition over a five-month S. alterniflora summer growing season and found that transplanted communities more closely resembled their origin sites than their destination sites. Furthermore, transplanted communities grouped predominantly by region, with two sites from the north and three sites to the south hosting distinct bacterial taxa, suggesting that sediment communities transplanted from north to south tended to retain their northern microbial distributions, and south to north maintained a southern distribution. A small number of potential indicator 16S rRNA gene sequences had distributions that were strongly correlated to both temperature and nitrogen, indicating that some organisms are more sensitive to environmental factors than others. These results provide new insight into the microbial biogeography of salt marsh sediments and suggest that established bacterial communities in frequently-inundated environments may be both highly resistant to invasion and resilient to some environmental shifts. However, the extent to which environmental selection impacts these communities is taxon specific and variable, highlighting the complex interplay between dispersal and environmental selection for microbial communities in nature.

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

2019 ◽  
Vol 85 (7) ◽  
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.

scholarly journals The impact of persistent bacterial bronchitis on the pulmonary microbiome of children

2017 ◽  
Author(s):  
Leah Cuthbertson ◽  
Vanessa Craven ◽  
Lynne Bingle ◽  
William O.C.M. Cookson ◽  
Mark L. Everard ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Bacterial Diversity ◽  
Community Composition ◽  
Bacterial Communities ◽  
Microbial Community Analysis ◽  
Rrna Gene ◽  
Healthy Children ◽  
Significant Difference ◽  
The Impact

AbstractPersistent bacterial bronchitis is a leading cause of chronic wet cough in young children. This study aimed to characterise the respiratory bacterial microbiota of healthy children and to assess the impact of the changes associated with the development of persistent bacterial bronchitis.Blind, protected brushings were obtained from 20 healthy controls and 24 children with persistent bacterial bronchitis, with an additional directed sample obtained from persistent bacterial bronchitis patients. DNA was extracted, quantified using a 16S rRNA gene quantitative PCR assay prior to microbial community analysis by 16S rRNA gene sequencing.No significant difference in bacterial diversity or community composition (R2 = 0.01, P = 0.36) was observed between paired blind and non-blind brushes, showing that blind brushings are a valid means of accessing the airway microbiota. This has important implications for collecting lower respiratory samples from healthy children. A significant decrease in bacterial diversity (P < 0.001) and change in community composition (R2 = 0.08, P = 0.004) was observed between controls and patients. Bacterial communities within patients with PBB were dominated by Proteobacteria, and indicator species analysis showed that Haemophilus and Neisseria were significantly associated with the patient group. In 15 (52.9%) cases the dominant organism by sequencing was not identified by standard routine clinical culture.The bacteria present in the lungs of patients with persistent bacterial bronchitis were less diverse in terms of richness and evenness. The results validate the clinical diagnosis, and suggest that more attention to bacterial communities in children with chronic cough may lead to more rapid recognition of this condition with earlier treatment and reduction in disease burden.

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

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

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

Effects of geographic location and water quality on bacterial communities in full-scale biofilters across North America

2020 ◽  
Vol 96 (2) ◽  
Author(s):  
Ben Ma ◽  
Timothy M LaPara ◽  
Ashley N. Evans ◽  
Raymond M Hozalski
Keyword(s):  
Water Quality ◽  
North America ◽  
Bacterial Community ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Community Composition ◽  
Bacterial Communities ◽  
Bacterial Community Composition ◽  
Geographic Location ◽  
Rrna Gene

ABSTRACT Spatial patterns of bacterial community composition often follow a distance–decay relationship in which community dissimilarity increases with geographic distance. Such a relationship has been commonly observed in natural environments, but less so in engineered environments. In this study, bacterial abundance and community composition in filter media samples (n = 57) from full-scale rapid biofilters at 14 water treatment facilities across North America were determined using quantitative polymerase chain reaction and Illumina HiSeq high-throughput sequencing targeting the 16S rRNA gene, respectively. Bacteria were abundant on the filter media (108.8±0.3 to 1010.7±0.2 16S rRNA gene copies/cm3 bed volume) and the bacterial communities were highly diverse (Shannon index: 5.3 ± 0.1 to 8.4 ± 0.0). Significant inter-filter variations in bacterial community composition were observed, with weighted UniFrac dissimilarity values following a weak but highly significant distance–decay relationship (z = 0.0057 ± 0.0006; P = 1.8 × 10−22). Approximately 50% of the variance in bacterial community composition was explained by the water quality parameters measured at the time of media sample collection (i.e. pH, temperature and dissolved organic carbon concentration). Overall, this study suggested that the microbiomes of biofilters are primarily shaped by geographic location and local water quality conditions but the influence of these factors on the microbiomes is tempered by filter design and operating conditions.

scholarly journals The microbiomes of seven lichen genera reveal host specificity, a reduced core community and potential as source of antimicrobials

2019 ◽  
Author(s):  
Maria A Sierra ◽  
David C Danko ◽  
Tito A Sandoval ◽  
Gleb Pishchany ◽  
Bibiana Moncada ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Microbial Communities ◽  
Host Specificity ◽  
Bacterial Communities ◽  
Soil Formation ◽  
Rrna Gene ◽  
Diverse Group

AbstractThe High Andean Paramo ecosystem is a unique neotropical mountain biome considered a diversity and evolutionary hotspot. Lichens, which are complex symbiotic structures that contain diverse commensal microbial communities, are prevalent in Paramos. There they play vital roles in soil formation and mineral fixation. In this study we analyzed the microbiomes of seven lichen genera in two Colombian Paramos using 16S rRNA gene analyses and provide the first description of the bacterial communities associated with Cora and Hypotrachyna lichens. Paramo lichen microbiomes were diverse, and in some cases were distinguished based on the identity of the lichen host. The majority of the lichen-associated microorganisms were not present in all lichens sampled and could be considered transient or specialists. We also uncovered sixteen shared taxa that suggest a core lichen microbiome among this diverse group of lichens, broadening our concept of these symbiotic structures. Additionally, we identified strains producing compounds active against clinically relevant pathogens. These results indicate that lichen microbiomes from the Paramo ecosystem are diverse and host-specific but share a taxonomic core and can be a source of new bacterial taxa and antimicrobials.

scholarly journals Changes in the Active, Dead, and Dormant Microbial Community Structure Across a Pleistocene Permafrost Chronosequence

2018 ◽  
Author(s):  
Alex 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 metagenomic and 16S rRNA gene sequencing. However, these methods do not distinguish between 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 (19K, 27K, and 33K). Cell counts and analysis of 16S rRNA gene amplicons from live, dead, and dormant cells revealed how communities differ between these pools and how they change over geologic time. We found clear evidence that cells capable of forming endospores are not necessarily dormant and that the propensity to form endospores differed among taxa. Specifically, Bacilli are more likely to form endospores in response to long-term stressors associated with permafrost environmental conditions than members of Clostridia, which are more likely to persist as vegetative cells over geologic timescales. We also found that exogenous DNA preserved within permafrost does not bias DNA sequencing results since its removal did not significantly alter the microbial community composition. These results extend the findings of a previous study that showed permafrost age and ice content largely control microbial community diversity and cell abundances.ImportanceThe study of permafrost transcends the study of climate change and exobiology. Permafrost soils store more than half earth’s soil carbon despite covering ∽15% of the land area (Tarnocai et al 2009). This permafrost carbon is rapidly degraded following thaw (Tarnocai C et al 2009, Schuur et al 2015). Understanding microbial communities in permafrost will contribute to the knowledge base necessary to understand the rates and forms of permafrost C and N cycling post thaw. 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 permafrost we can focus efforts searching for evidence of life on cryogenic cosmic bodies. 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 across geologic timescales.

scholarly journals Microbial communities associated with the camel tick, Hyalomma dromedarii: 16S rRNA gene-based analysis

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Nighat Perveen ◽  
Sabir Bin Muzaffar ◽  
Ranjit Vijayan ◽  
Mohammad Ali Al-Deeb
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Microbial Communities ◽  
Bacterial Communities ◽  
Health Hazard ◽  
Illumina Miseq ◽  
Blood Feeding ◽  
Microbial Interactions ◽  
Rrna Gene ◽  
Hyalomma Dromedarii

Abstract Hyalomma dromedarii is an important blood-feeding ectoparasite that affects the health of camels. We assessed the profile of bacterial communities associated with H. dromedarii collected from camels in the eastern part of the UAE in 2010 and 2019. A total of 100 partially engorged female ticks were taken from tick samples collected from camels (n = 100; 50/year) and subjected to DNA extraction and sequencing. The 16S rRNA gene was amplified from genomic DNA and sequenced using Illumina MiSeq platform to elucidate the bacterial communities. Principle Coordinates Analysis (PCoA) was conducted to determine patterns of diversity in bacterial communities. In 2010 and 2019, we obtained 899,574 and 781,452 read counts and these formed 371 and 191 operational taxonomic units (OTUs, clustered at 97% similarity), respectively. In both years, twenty-five bacterial families with high relative abundance were detected and the following were the most common: Moraxellaceae, Enterobacteriaceae, Staphylococcaceae, Bacillaceae, Corynebacteriaceae, Flavobacteriaceae, Francisellaceae, Muribaculaceae, Neisseriaceae, and Pseudomonadaceae. Francisellaceae and Enterobacteriaceae coexist in H. dromedarii and we suggest that they thrive under similar conditions and microbial interactions inside the host. Comparisons of diversity indicated that microbial communities differed in terms of richness and evenness between 2010 and 2019, with higher richness but lower evenness in communities in 2010. Principle coordinates analyses showed clear clusters separating microbial communities in 2010 and 2019. The differences in communities suggested that the repertoire of microbial communities have shifted. In particular, the significant increase in dominance of Francisella and the presence of bacterial families containing pathogenic genera shows that H. dromedarii poses a serious health risk to camels and people who interact with them. Thus, it may be wise to introduce active surveillance of key genera that constitute a health hazard in the livestock industry to protect livestock and people.

Molecular characterization of the bacterial communities present in sheep's milk and cheese produced in South Brazilian Region via 16S rRNA gene metabarcoding sequencing

LWT ◽  
2021 ◽  
Vol 147 ◽  
pp. 111579
Author(s):  
Creciana M. Endres ◽  
Ícaro Maia S. Castro ◽  
Laura D. Trevisol ◽  
Juliana M. Severo ◽  
Michele B. Mann ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Molecular Characterization ◽  
Bacterial Communities ◽  
Rrna Gene

scholarly journals Sponge-Associated Bacteria Are Strictly Maintained in Two Closely Related but Geographically Distant Sponge Hosts

2011 ◽  
Vol 77 (20) ◽  
pp. 7207-7216 ◽  
Author(s):  
Naomi F. Montalvo ◽  
Russell T. Hill
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Bacterial Communities ◽  
Sponge Species ◽  
Rrna Gene ◽  
Gene Sequences ◽  
Associated Bacteria ◽  
Content Type ◽  
Key Species ◽  
Sponge Associated Bacteria

ABSTRACTThe giant barrel spongesXestospongiamutaandXestospongiatestudinariaare ubiquitous in tropical reefs of the Atlantic and Pacific Oceans, respectively. They are key species in their respective environments and are hosts to diverse assemblages of bacteria. These two closely related sponges from different oceans provide a unique opportunity to examine the evolution of sponge-associated bacterial communities. Mitochondrial cytochrome oxidase subunit I gene sequences fromX.mutaandX.testudinariashowed little divergence between the two species. A detailed analysis of the bacterial communities associated with these sponges, comprising over 900 full-length 16S rRNA gene sequences, revealed remarkable similarity in the bacterial communities of the two species. Both sponge-associated communities include sequences found only in the twoXestospongiaspecies, as well as sequences found also in other sponge species and are dominated by three bacterial groups,Chloroflexi,Acidobacteria, andActinobacteria. While these groups consistently dominate the bacterial communities revealed by 16S rRNA gene-based analysis of sponge-associated bacteria, the depth of sequencing undertaken in this study revealed clades of bacteria specifically associated with each of the twoXestospongiaspecies, and also with the genusXestospongia, that have not been found associated with other sponge species or other ecosystems. This study, comparing the bacterial communities associated with closely related but geographically distant sponge hosts, gives new insight into the intimate relationships between marine sponges and some of their bacterial symbionts.

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