Primer selection impacts specific population abundances but not community dynamics in a monthly time-series 16S rRNA gene amplicon analysis of coastal marine bacterioplankton

AbstractTraditional methods for monitoring the microbiological quality of water focus on the detection of fecal indicator bacteria such as Escherichia coli, often tested as a weekly grab sample. To understand the stability of E.coli concentrations over time, we evaluated three approaches to measuring E. coli levels in water: microbial culture using Colilert, quantitative PCR for uidA and next-generation sequencing of the 16S rRNA gene. Two watersheds, one impacted by agricultural and the other by urban activities, were repeatedly sampled over a simultaneous ten-hour period during each of the four seasons. Based on 16S rRNA gene deep sequencing, each watershed showed different microbial community profiles. The bacterial microbiomes varied with season, but less so within each 10-hour sampling period. Enterobacteriaceae comprised only a small fraction (<1%) of the total community. The qPCR assay detected significantly higher quantities of E. coli compared to the Colilert assay and there was also variability in the Colilert measurements compared to Health Canada’s recommendations for recreational water quality. From the 16S data, other bacteria such as Prevotella and Bacteroides showed promise as alternative indicators of fecal contamination. A better understanding of temporal changes in watershed microbiomes will be important in assessing the utility of current biomarkers of fecal contamination, determining the best timing for sample collection, as well as searching for additional microbial indicators of the health of a watershed.

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Development of a 16S rRNA gene-based microarray for the detection of marine bacterioplankton community

Acta Oceanologica Sinica ◽

10.1007/s13131-017-1055-6 ◽

2017 ◽

Vol 36 (10) ◽

pp. 106-114 ◽

Cited By ~ 1

Author(s):

Wei Zhao ◽

Jingjing Wang ◽

Yajie Liang ◽

Zhiyong Huang

Keyword(s):

16S Rrna ◽

16S Rrna Gene ◽

Rrna Gene ◽

Marine Bacterioplankton ◽

Bacterioplankton Community

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Trichomes form genotype-specific microbial hotspots in the phyllosphere of tomato

Environmental Microbiome ◽

10.1186/s40793-020-00364-9 ◽

2020 ◽

Vol 15 (1) ◽

Author(s):

Peter Kusstatscher ◽

Wisnu Adi Wicaksono ◽

Alessandro Bergna ◽

Tomislav Cernava ◽

Nick Bergau ◽

...

Keyword(s):

16S Rrna ◽

16S Rrna Gene ◽

Community Dynamics ◽

Statistical Tests ◽

Central Element ◽

Shannon Index ◽

Gene Copy ◽

Rrna Gene ◽

Core Microbiome ◽

Defense Strategies

Abstract Background The plant phyllosphere is a well-studied habitat characterized by low nutrient availability and high community dynamics. In contrast, plant trichomes, known for their production of a large number of metabolites, are a yet unexplored habitat for microbes. We analyzed the phyllosphere as well as trichomes of two tomato genotypes (Solanum lycopersicum LA4024, S. habrochaites LA1777) by targeting bacterial 16S rRNA gene fragments. Results Leaves, leaves without trichomes, and trichomes alone harbored similar abundances of bacteria (108–109 16S rRNA gene copy numbers per gram of sample). In contrast, bacterial diversity was found significantly increased in trichome samples (Shannon index: 4.4 vs. 2.5). Moreover, the community composition was significantly different when assessed with beta diversity analysis and corresponding statistical tests. At the bacterial class level, Alphaproteobacteria (23.6%) were significantly increased, whereas Bacilli (8.6%) were decreased in trichomes. The bacterial family Sphingomonadacea (8.4%) was identified as the most prominent, trichome-specific feature; Burkholderiaceae and Actinobacteriaceae showed similar patterns. Moreover, Sphingomonas was identified as a central element in the core microbiome of trichome samples, while distinct low-abundant bacterial families including Hymenobacteraceae and Alicyclobacillaceae were exclusively found in trichome samples. Niche preferences were statistically significant for both genotypes and genotype-specific enrichments were further observed. Conclusion Our results provide first evidence of a highly specific trichome microbiome in tomato and show the importance of micro-niches for the structure of bacterial communities on leaves. These findings provide further clues for breeding, plant pathology and protection as well as so far unexplored natural pathogen defense strategies.

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Microbial community dynamics based on 16S rRNA gene profiles in a Pacific Northwest estuary and its tributaries

FEMS Microbiology Ecology ◽

10.1016/j.femsec.2004.10.016 ◽

2005 ◽

Vol 52 (1) ◽

pp. 115-128 ◽

Cited By ~ 72

Author(s):

Anne E. Bernhard ◽

Debbie Colbert ◽

James McManus ◽

Katharine G. Field

Keyword(s):

Microbial Community ◽

16S Rrna ◽

16S Rrna Gene ◽

Pacific Northwest ◽

Community Dynamics ◽

Rrna Gene ◽

Microbial Community Dynamics ◽

Gene Profiles

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Trichomes form genotype-specific microbial hotspots in the phyllosphere of tomato

10.21203/rs.3.rs-25108/v1 ◽

2020 ◽

Author(s):

Peter Kusstatscher ◽

Wisnu Adi Wicaksono ◽

Alessandro Bergna ◽

Tomislav Cernava ◽

Nick Bergau ◽

...

Keyword(s):

16S Rrna ◽

16S Rrna Gene ◽

Community Dynamics ◽

Statistical Tests ◽

Central Element ◽

Shannon Index ◽

Gene Copy ◽

Rrna Gene ◽

Core Microbiome ◽

Defense Strategies

Abstract Background The plant phyllosphere is a well-studied habitat characterized by low nutrient availability and high community dynamics. In contrast, plant trichomes, known for their production of a large number of metabolites, are a yet unexplored habitat for microbes. We analyzed the phyllosphere as well as trichomes of two tomato genotypes (Solanum lycopersicum LA4024, S. habrochaites LA1777) by targeting bacterial 16S rRNA gene fragments.Results Leaves, leaves without trichomes, and trichomes alone harbored similar abundances of bacteria (108- 109 16S rRNA gene copy numbers per gram of sample). In contrast, bacterial diversity was found significantly increased in trichome samples (Shannon index: 4.4 vs. 2.5). Moreover, the community composition was significantly different when assessed with beta diversity analysis and corresponding statistical tests. At the bacterial class level, Alphaproteobacteria (23.6%) were significantly increased, whereas Bacilli (8.6%) were decreased in trichomes. The bacterial family Sphingomonadacea (8.4%) was identified as the most prominent, trichome-specific taxa; Burkholderiaceae and Actinobacteria showed similar pattern. Moreover, Sphingomonas was identified as a central element in the core microbiome of trichome samples, while distinct low-abundant bacterial families including Hymenobacteraceae and Alicyclobacillaceae were exclusively found in trichome samples. Niche preferences were statistically significant for both genotypes and genotype-specific enrichments were further observed.Conclusion Our results provide first evidence of a highly specific trichome microbiome in tomato and show the importance of micro-niches for the structure of bacterial communities on leaves. These findings provide further clues for breeding, plant pathology and protection as well as so far unexplored natural pathogen defense strategies.

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Microbial Community Dynamics and Stability during an Ammonia-Induced Shift to Syntrophic Acetate Oxidation

Applied and Environmental Microbiology ◽

10.1128/aem.00166-14 ◽

2014 ◽

Vol 80 (11) ◽

pp. 3375-3383 ◽

Cited By ~ 83

Author(s):

Jeffrey J. Werner ◽

Marcelo L. Garcia ◽

Sarah D. Perkins ◽

Kevin E. Yarasheski ◽

Samuel R. Smith ◽

...

Keyword(s):

16S Rrna ◽

16S Rrna Gene ◽

Community Dynamics ◽

Ammonia Concentration ◽

Stable Operation ◽

Rrna Gene ◽

Acetate Oxidation ◽

16S Rrna Gene Analysis ◽

Phylogenetic Structure ◽

Syntrophic Acetate Oxidation

ABSTRACTAnaerobic digesters rely on the diversity and distribution of parallel metabolic pathways mediated by complex syntrophic microbial communities to maintain robust and optimal performance. Using mesophilic swine waste digesters, we experimented with increased ammonia loading to induce a shift from aceticlastic methanogenesis to an alternative acetate-consuming pathway of syntrophic acetate oxidation. In comparison with control digesters, we observed shifts in bacterial 16S rRNA gene content and in functional gene repertoires over the course of the digesters' 3-year operating period. During the first year, under identical startup conditions, all bioreactors mirrored each other closely in terms of bacterial phylotype content, phylogenetic structure, and evenness. When we perturbed the digesters by increasing the ammonia concentration or temperature, the distribution of bacterial phylotypes became more uneven, followed by a return to more even communities once syntrophic acetate oxidation had allowed the experimental bioreactors to regain stable operation. The emergence of syntrophic acetate oxidation coincided with a partial shift from aceticlastic to hydrogenotrophic methanogens. Our 16S rRNA gene analysis also revealed that acetate-fed enrichment experiments resulted in communities that did not represent the bioreactor community. Analysis of shotgun sequencing of community DNA suggests that syntrophic acetate oxidation was carried out by a heterogeneous community rather than by a specific keystone population with representatives of enriched cultures with this metabolic capacity.

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Molecular analyses of the diversity in marine bacterioplankton assemblages along the coastline of the northeastern Gulf of Mexico

Canadian Journal of Microbiology ◽

10.1139/w10-069 ◽

2010 ◽

Vol 56 (10) ◽

pp. 853-863 ◽

Cited By ~ 4

Author(s):

Ola A. Olapade

Keyword(s):

In Situ Hybridization ◽

16S Rrna ◽

16S Rrna Gene ◽

Gulf Of Mexico ◽

Fluorescence In Situ Hybridization ◽

Community Diversity ◽

Rrna Gene ◽

Marine Bacterioplankton ◽

Northeastern Gulf Of Mexico

Bacterial community diversity in marine bacterioplankton assemblages were examined in 3 coastal locations along the northeastern Gulf of Mexico (GOM) using 16S rRNA gene libraries and fluorescence in situ hybridization approaches. The majority of the sequences (30%–60%) were similar to the 16S rRNA gene sequences of unknown bacteria; however, the operational taxonomic units from members of the Cyanobacteria, Proteobacteria, and Bacteroidetes were also present at the 3 GOM sites. Overall, sequence diversity was more similar between the Gulf sites of Carrabelle and Ochlockonee than between either of the Gulf sites and Apalachicola Bay. Fluorescence in situ hybridization analyses revealed the quantitative predominance of members of the Alphaproteobacteria subclass and the Cytophaga – Flavobacterium cluster within the bacterioplankton assemblages. In general, the study further reveals the presence of many bacterial taxa that have been previously found to be dominant in coastal marine environments. Differences observed in the representation of the various bacterial phylogenetic groups among the GOM coastal sites could be partly attributed to dynamic variations in several site-specific conditions, including intermittent tidal events, nutrient availability, and anthropogenic influences.

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