How do Planktonic Particle Collection Methods Affect Bacterial Diversity Estimates and Community Composition in Oligo-, Meso- and Eutrophic Lakes?

Particles are hotspots of bacterial growth and nutrient recycling in aquatic ecosystems. In the study of particle-attached (PA) and/or free-living (FL) microbial assemblages, the first step is to separate particles from their surrounding water columns. Widely used collection techniques are filtration using different pore size filters, and centrifugation; however, it is unclear how the bacterial diversity, bacterial community structure (BCS) and taxonomic composition of PA assemblages are affected by different particle collection methods. To address this knowledge gap, we collected planktonic particles from eutrophic Lake Taihu, mesotrophic Lake Tianmu, and oligotrophic Lake Fuxian in China, using filtration with five pore size of filters (20, 10, 8.0, 5.0, and 3.0 μm), and centrifugation. Bacterial communities were then analyzed using Illumina MiSeq sequencing of the 16S rRNA gene. We found that PA collection method affected BCS significantly in all lakes. Centrifugation yielded the highest species diversity and lowest mean percentage of photoautotrophic Cyanobacteria in Lake Taihu, but not in the other two lakes, thus highlighting the potential compatibility of this method in the study of PA assemblage in eutrophic lakes. The high bacterial diversity and low relative percentage of Cyanobacteria was in samples retained on 5.0 μm filters in all lakes. These results suggest that collecting PA samples in lakes using filters with 5.0 μm pore size is the preferred protocol, if species diversity and heterotrophic bacteria are the top research priorities, when comparing bacterial communities in different trophic lakes at the same time. The present study offers the possibility of collecting PA samples using unified methods in oligotrophic to eutrophic lakes.

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Loss of bacterial diversity in the sinuses is associated with lower smell discrimination scores

Scientific Reports ◽

10.1038/s41598-020-73396-3 ◽

2020 ◽

Vol 10 (1) ◽

Author(s):

Kristi Biswas ◽

Brett Wagner Mackenzie ◽

Charlotte Ballauf ◽

Julia Draf ◽

Richard G. Douglas ◽

...

Keyword(s):

Bacterial Diversity ◽

Bacterial Communities ◽

Gene Sequencing ◽

16S Rrna Gene Sequencing ◽

Olfactory Dysfunction ◽

Rrna Gene ◽

Olfactory Loss ◽

Olfactory Impairment ◽

Rrna Gene Sequencing ◽

Normal Sense

Abstract Olfactory impairment affects ~ 20% of the population and has been linked to various serious disorders. Microbes in the nasal cavity play a key role in priming the physiology of the olfactory epithelium and maintaining a normal sense of smell by the host. The aim of this study was to explore the link between olfactory dysfunction and nasal bacterial communities. A total of 162 subjects were recruited for this study from a specialized olfactory dysfunction clinic and placed into one of three groups: anosmia, hyposmia or normosmia. Swabs from the nasal middle meatus were collected from each subject then processed for bacterial 16S rRNA gene sequencing. No overall differences in bacterial diversity or composition were observed between the three cohorts in this study. However, the relative abundances of Corynebacterium spp. and Streptococcus spp. were significantly (p < 0.05) different in subjects with olfactory loss. Furthermore, subjects with deficiencies in discriminating between smells (based on discrimination scores) had a lower bacterial diversity (Simpson’s evenness p < 0.05). While these results are preliminary in nature, potential bacterial biomarkers for olfactory loss were identified. These findings need to be further validated and biologically tested in animal models.

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Pyrosequencing analysis of free-living and attached bacterial communities in Meiliang Bay, Lake Taihu, a large eutrophic shallow lake in China

Canadian Journal of Microbiology ◽

10.1139/cjm-2014-0503 ◽

2015 ◽

Vol 61 (1) ◽

pp. 22-31 ◽

Cited By ~ 22

Author(s):

Xiangming Tang ◽

Linlin Li ◽

Keqiang Shao ◽

Boweng Wang ◽

Xianlei Cai ◽

...

Keyword(s):

Bacterial Communities ◽

Lake Taihu ◽

16S Rrna Genes ◽

Rrna Genes ◽

Eutrophic Lakes ◽

Free Living ◽

Bacterial Populations ◽

Meiliang Bay ◽

Taxonomic Groups ◽

High Level

To elucidate the relationship between particle-attached (PA, ≥5.0 μm) and free-living (FL, 0.2–5.0 μm) bacterial communities, samplings were collected seasonally from November 2011 to August 2012 in Meiliang Bay, Lake Taihu, China. We used 454 pyrosequencing of 16S rRNA genes to study bacterial diversity and structure of PA and FL communities. The analysis rendered 37 985 highly qualified reads, subsequently assigned to 1755 operational taxonomic units (97% similarity) for the 8 samples. Although 27 high-level taxonomic groups were obtained, the 3 dominant phyla (Proteobacteria, Actinobacteria, and Bacteroidetes) comprised about 75.9% and 82.4% of the PA and FL fractions, respectively. Overall, we found no significant differences between community types, as indicated by ANOSIM R statistics (R = 0.063, P > 0.05) and the Parsimony test (P = 0.222). Dynamics of bacterial communities were correlated with changes in concentrations of total suspended solids (TSS) and total phosphorus (TP). In summer, a significant taxonomic overlap in the 2 size fractions was observed when Cyanobacteria, a major contributor of TSS and TP, dominated in the water, highlighting the potential rapid exchange between PA and FL bacterial populations in large shallow eutrophic lakes.

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Effect of Geography and Captivity on Scat Bacterial Communities in the Imperiled Channel Island Fox

10.21203/rs.3.rs-384378/v1 ◽

2021 ◽

Author(s):

Nicole E Adams ◽

Madeleine A Becker ◽

Suzanne Edmands

Keyword(s):

Bacterial Diversity ◽

Bacterial Communities ◽

Captive Breeding ◽

Interdisciplinary Approach ◽

Amplicon Sequencing ◽

Rrna Gene ◽

Sample Collection ◽

Channel Island ◽

Island Fox ◽

Urocyon Littoralis

Abstract Background With developing understanding that host-associated microbiota play significant roles in individual health and fitness, taking an interdisciplinary approach combining microbiome research with conservation science is increasingly favored. Here we establish the scat microbiome of the imperiled Channel Island fox (Urocyon littoralis) and look at the effects of geography and captivity on the variation in bacterial communities. Results Using high throughput 16S rRNA gene amplicon sequencing, we discovered distinct bacterial communities in each island fox subspecies. Weight, timing of the sample collection, and sex contributed to the geographic patterns. We uncovered significant taxonomic differences and an overall decrease in bacterial diversity in captive versus wild foxes. Conclusions Understanding the drivers of microbial variation in this system provides a valuable lens through which to evaluate the health and conservation of these genetically depauperate foxes. The island-specific bacterial community baselines established in this study can make monitoring island fox health easier and understanding the implications of inter-island translocation clearer. The decrease in bacterial diversity within captive foxes could lead to losses in the functional services normally provided by commensal microbes and suggests that zoos and captive breeding programs would benefit from maintaining microbial diversity.

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Bacterial diversity associated with subalpine fir (Abies lasiocarpa) ectomycorrhizae following wildfire and salvage-logging in central British Columbia

Canadian Journal of Microbiology ◽

10.1139/w02-056 ◽

2002 ◽

Vol 48 (7) ◽

pp. 611-625 ◽

Cited By ~ 18

Author(s):

Madhukar B Khetmalas ◽

Keith N Egger ◽

Hugues B Massicotte ◽

Linda E Tackaberry ◽

M Jill Clapperton

Keyword(s):

Bacterial Diversity ◽

16S Rdna ◽

Bacterial Communities ◽

Restriction Analysis ◽

Rrna Gene ◽

Abies Lasiocarpa ◽

Gram Positive ◽

Salvage Logging ◽

Gram Positive Bacteria ◽

Significant Difference

To assess the effect of fire and salvage logging on the diversity of mycorrhizalbacterial communities, bacteria associated with Cenococcum, Thelephora, Tomentella, Russulaceae, and E-strain ectomycorrhizae (ECM) of Abies lasiocarpa seedlings were characterized using two approaches. First, bacteria were isolated and characterized by Biolog©, gas chromatography fatty acid methyl ester (GC-FAME), and amplified 16S rDNA restriction analysis (ARDRA). The bacterial communities retrieved from ECM from both sites were dominated by Proteobacteria (groups gamma and beta). Pseudomonas was the most common genus isolated, followed by Variovorax, Burkholderia, and Xanthomonas. Gram-positive isolates (mostly high-G+C Gram-positive bacteria) were more frequently retrieved on the burned-salvaged site, many commonly associated with the two ascomycete ECM, Cenococcum and E-strain. Pseudomonas species were retrieved more frequently from Thelephora. Although actinomycetes were isolated from all sites, almost no actinomycetes or other Gram-positive bacteria were isolated from either Thelephora or Tomentella. Second, amplified 16S rRNA gene sequences were amplified directly from root tips and then cloned into the plasmid vector pAMP1, followed by restriction analysis. This technique distinguished more genotypes than isolates retrieved by culturing methods, but generally, results were similar in that the largest proportion of the bacteria were putatively Gram-negative; putative Gram-positive bacteria were fewer and most were from the burnedsalvaged site. Direct cloning resulted in many patterns that did not match any identified isolates, suggesting that a large proportion of clones were unique or not culturable by the methods used. Analysis for both protocols showed no significant difference in bacterial diversity between the burnedsalvaged and unburned sites. Key words: rhizosphere bacteria, ARDRA, 16S rDNA, Biolog©, GC-FAME.

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Bacterial communities inside and in the vicinity of the Chinese Great Wall Station, King George Island, Antarctica

Antarctic Science ◽

10.1017/s095410200700003x ◽

2007 ◽

Vol 19 (1) ◽

pp. 11-16 ◽

Cited By ~ 15

Author(s):

Xiang Xiao ◽

Mingguang Li ◽

Ziyong You ◽

Fengping Wang

Keyword(s):

Bacterial Diversity ◽

Denaturing Gradient Gel Electrophoresis ◽

Heterotrophic Bacteria ◽

Soil Samples ◽

Rrna Gene ◽

Adjacent Area ◽

Molecular Approaches ◽

Cell Counts ◽

Two Samples ◽

Great Wall

Both bacterial culture and molecular approaches were used to investigate the bacterial diversity inside the Chinese Antarctic Great Wall Station and in its adjacent area. Heterotrophic bacteria were isolated from the samples using a direct plating method. γ-Proteobacteria, Actinobacteria, Flavobacteria and Firmicutes were isolated from these samples. In the three water samples, Pseudomonas species were dominant. In soil samples, Flavobacterium, Bacillus or Arthrobacter species dominated. Escherichia coli strains were isolated only in two samples from inside the station. Total cell counts in the six soil samples were semi-quantified by Quantitative Competitive-PCR of the 16S rRNA gene copies. The soil samples contained 105 to 109 cells g−1. Denaturing gradient gel electrophoresis (DGGE) was used further to investigate the bacterial diversity in the soil samples. A wider range of bacterial diversity including α-Proteobacteria, β-Proteobacteria, δ-Proteobacteria, γ-Proteobacteria, Flavobacteria, Actinobacteria and unclassified bacteria was discovered.

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Effect of Geography and Captivity on Scat Bacterial Communities in the Imperiled Channel Island Fox

Frontiers in Microbiology ◽

10.3389/fmicb.2021.748323 ◽

2021 ◽

Vol 12 ◽

Author(s):

Nicole E. Adams ◽

Madeleine A. Becker ◽

Suzanne Edmands

Keyword(s):

Bacterial Diversity ◽

Bacterial Communities ◽

Captive Breeding ◽

Interdisciplinary Approach ◽

Amplicon Sequencing ◽

Rrna Gene ◽

Sample Collection ◽

Channel Island ◽

Island Fox ◽

Urocyon Littoralis

With developing understanding that host-associated microbiota play significant roles in individual health and fitness, taking an interdisciplinary approach combining microbiome research with conservation science is increasingly favored. Here we establish the scat microbiome of the imperiled Channel Island fox (Urocyon littoralis) and examine the effects of geography and captivity on the variation in bacterial communities. Using high throughput 16S rRNA gene amplicon sequencing, we discovered distinct bacterial communities in each island fox subspecies. Weight, timing of the sample collection, and sex contributed to the geographic patterns. We uncovered significant taxonomic differences and an overall decrease in bacterial diversity in captive versus wild foxes. Understanding the drivers of microbial variation in this system provides a valuable lens through which to evaluate the health and conservation of these genetically depauperate foxes. The island-specific bacterial community baselines established in this study can make monitoring island fox health easier and understanding the implications of inter-island translocation clearer. The decrease in bacterial diversity within captive foxes could lead to losses in the functional services normally provided by commensal microbes and suggests that zoos and captive breeding programs would benefit from maintaining microbial diversity.

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

10.1101/181982 ◽

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.

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Bacterial Communities in Aquatic Sediment from Bukit Duabelas Raintforest and Oil Palm Plantation at Sumatra Indonesia

HAYATI Journal of Biosciences ◽

10.4308/hjb.25.2.85 ◽

2018 ◽

Vol 25 (2) ◽

pp. 85

Author(s):

Marini Wijayanti ◽

Aris Tri Wahyudi ◽

Munti Yuhana ◽

Martin Engelhaupt ◽

Anja Meryandini

Keyword(s):

16S Rrna ◽

Bacterial Diversity ◽

Oil Palm ◽

Bacterial Communities ◽

Total Carbon ◽

Available Phosphorus ◽

Rrna Gene ◽

Oil Palm Plantation ◽

Community Shift ◽

Aquatic Sediment

The diversity of bacterial communities in aquatic sediment of rainforest and oil palm plantation at Sumatra was studied using pyrosequencing of 16S rRNA gene and common biodiversity indices. Phylogenetic approach was used for revealing the community shift of bacterial phyla and genera in both areas. Ecological approach used soil pH, total Carbon (TC), total Nitrogen (TN), available Phosphorus (AP) measurement and bacterial diversity with Shanon and Simpson indices, and bacterial richness with Chao1-ACE indices and OTUs. Bacterial diversity and richness in aquatic sediment of forest area was higher than that ones in oil palm plantation area, although their pH, TC, and TN in both areas were not different significantly. The majority of sequences related to Proteobacteria (34.85%), Acidobacteria (32.67%), Nitrospirae (6.86%), Chloroflexi (4.31%), and Actinobacteria (4.02%) were from forest; whereas those related to Acidobacteria (46.10%), Proteobacteria (25.86%), Nitrospirae (9.20%), Chloroflexi (4.99%), and Actinobacteria (2.34%) invented from oil palm plantation. The genera of Alphaproteobacteria and Betaproteobacteria dominated in genera phylotype of bacterial 16S rRNA phylogenetic revealed both aquatic sediment of forest and oil palm plantation. The most genera in the phylogenetic tree from aquatic sediment of both areas was Burkholderia. The bacterial community shift in aquatic sediment of forest transformation indicated higher bacterial diversity index, richness index, some of phyla and genera in aquatic sediment from forest than from oil palm plantation.

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Diversity of habitats and bacterial communities support landscape-scale multifunctionality differently across seasons

10.7287/peerj.preprints.2036v1 ◽

2016 ◽

Cited By ~ 1

Author(s):

Christian Alsterberg ◽

Fabian Roger ◽

Kristina Sundbäck ◽

Jaanis Juhanson ◽

Stefan Hulth ◽

...

Keyword(s):

Species Diversity ◽

Bacterial Diversity ◽

Bacterial Communities ◽

Inorganic Nitrogen ◽

Gross Primary Production ◽

Habitat Diversity ◽

Ecosystem Functions ◽

Ruppia Maritima ◽

Resource Complementarity ◽

The Relationship

In this study, we demonstrate how changes in the diversity of habitat and bacterial communities affect landscape multifunctionality. Habitat diversity may beget species diversity by increasing niche availability and resource complementarity. Species diversity, in turn, generally promotes multifunctionality, i.e. the simultaneous performance of multiple ecosystem functions. However, the relationship between habitat diversity and functioning remains to be explicitly explored. In order to test the relationship between habitat diversity and multifunctionality we constructed experimental landscapes of four different habitats common in shallow-water sediment ecosystems: cyanobacterial mats, Ruppia maritima meadows, silty mud and sandy beach. We manipulated the diversity of these habitats over three consecutive seasons and measured bacterial diversity, benthic microalgal diversity and four functions related to marine nitrogen cycling (gross primary production, nitrogen fixation, denitrification and uptake of dissolved inorganic nitrogen). Our results showed that higher habitat and bacterial diversity, but not benthic microalgal diversity, increased landscape multifunctionality. However, the relative importance of habitat and bacterial diversity varied with season. Habitat diversity was generally the strongest driver, affecting multifunctionality directly in summer and indirectly via bacterial diversity in autumn. In spring, neither of the two aspects of diversity was important. Our study demonstrates the importance of considering temporal differences in both habitat and species diversity for landscape multifunctionality, and the importance of direct and indirect effects in mediating ecosystem functions. Habitat homogenization in concert with loss in biodiversity can thus be a driving force of declining ecosystem functioning and the services they underpin.

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