Diversity of Microbial Communities

Atlas, Ronald M.

doi:10.1007/978-1-4684-8989-7_1

Cited by 147 publications

(73 citation statements)

References 102 publications

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“…Nevertheless, when considering ecological diversity and community structure, it is believed that species diversity is an important feature in maintaining a degree of stability within that community. Thus, it is expected that stable and resilient microbial communities must contain a certain level of diversity (3). As has been shown, the present results demonstrate a greater diversity in the DGGE profiles of dental plaque associated with no gingivitis.…”

Section: Discussionsupporting

confidence: 80%

Statistical Analyses of Complex Denaturing Gradient Gel Electrophoresis Profiles

et al. 2005

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Studies using molecular techniques have demonstrated that a culture-based approach can severely underestimate the bacterial diversity in most environments. One of the molecular techniques that has been applied in microbial ecology is denaturing gradient gel electrophoresis (DGGE). The purpose of this study was to investigate differences in the microbiota of plaque, using a number of analysis techniques, from children without gingivitis (n ‫؍‬ 30) and from those with gingivitis (n ‫؍‬ 30). Extracted DNA from gingival margin plaque was subjected to PCR targeting the 16S rRNA gene using universal primers. DGGE profiles were analyzed in three ways. (i) Bacterial diversity was compared between cohorts by using the Shannon-Wiener index (also known as the Shannon-Weaver index). (ii) A hierarchical cluster analysis of the banding patterns was calculated and expressed as a dendrogram. (iii) Individual DGGE bands and their intensities for both cohorts were compared using a logistic regression analysis. The Shannon-Wiener indices demonstrated a greater bacterial diversity associated with no-gingivitis plaque (P ‫؍‬ 0.009). Dendrograms demonstrated that seven clades associated with gingivitis and five clades associated with no gingivitis. The logistic regression demonstrated that one band was significantly associated with no gingivitis (P ‫؍‬ 0.001), while two bands were significantly associated with gingivitis (P ‫؍‬ 0.005 and P ‫؍‬ 0.042). In conclusion, this study demonstrates that the development of gingivitis might be accompanied by a decrease in bacterial diversity. Furthermore, we have demonstrated that logistic regression is a good statistical method for analyzing and characterizing DGGE profiles.

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Section: Discussionsupporting

confidence: 80%

Statistical Analyses of Complex Denaturing Gradient Gel Electrophoresis Profiles

et al. 2005

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“…This argument is supported by the ability of nitrifiers to withstand long periods of dormancy (Kowalchuk et al 1998) allowing different phylotypes to await favourable conditions. Previous studies investigating changing microbial communities have reported similar events; for example, Kaneko et al 1977, as referenced in (Atlas & Bartha 1998), found that, although the species reintroduced into arctic seas after winter ice melt may have been different to species present when the ice formed, the niches filled by these bacteria remained constant. The fact that the resident β-AOB communities is able to change rapidly and is diverse ensures that sediments maintain at least the potential for nitrification despite the apparently unfavourable conditions.…”

Section: Discussionmentioning

confidence: 73%

Effects of organic perturbation on marine sediment betaproteobacterial ammonia oxidizers and on benthic nitrogen biogeochemistry

Bissett

Cook²,

MacLeod

et al. 2009

Mar. Ecol. Prog. Ser.

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The failure of denitrification to remove nitrogen build-up from aquatic systems is often attributed to sediment chemical conditions inhibiting nitrification and therefore the supply of suitable substrates to be denitrified. We investigated the effects of organic fish farm pollution on nitrogencycle dynamics and betaproteobacterial ammonia-oxidizing bacteria (β-AOB) community structure to elucidate the potential role of the nitrifier community on nitrogen biogeochemistry in marine sediments. Porewater nitrogen concentrations, denitrification rates, β-AOB 16S rDNA gene quantification, denaturing gradient gel electrophoresis (DGGE) community fingerprints and infaunal counts were determined in samples collected from beneath fish cages and at adjacent, non-impacted control sites. The study was conducted over 2 full, 1 yr production cycles. Although nitrogen cycling was significantly altered beneath cages, changes appeared to result from a reduction in the proportion of ammonia nitrified rather than from inhibition of nitrification per se. DGGE revealed β-AOB communities shifted rapidly and remained diverse at both cage and reference sites. Quantitative PCR (qPCR) showed β-AOB numbers did not decline in absolute terms but did decline as a proportion of the total bacterial community at cage sites and at the end of the stocking periods. Sediment infaunal community analysis showed significant effects of organic loading and indicated more bioirrigation at impacted sites. Despite the induction of conditions thought to be detrimental to nitrification and to β-AOB (low oxygen, reduced sediments, low pH, and high sulphide concentrations), these communities remained diverse and apparently viable, perhaps a result of heavy sediment bioirrigation. However, despite the increase in denitrification, nitrogen left the sediment predominantly as ammonia, thus producing potential point sources of eutrophication.

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“…The cultivable bacterial diversity across the altitude showed variation in the region revealing spatial trend and correlation with soil parameters and forest types. The variability in population densities of cultivable soil bacteria can be attributed to soil properties, physicochemical conditions and vegetations which are among the most important factors that influence soil microbial growth, population density and diversity (Atlas 1984, Dimitriu & Grayston 2010). Alpine and sub-alpine regions situated at higher altitude with sparse vegetation represent different soil physico-chemical factors when compared to tropical and et al (2011) who had reported decrease in soil pH with increase in altitude.…”

Section: Discussionmentioning

confidence: 99%

Cultivable bacterial diversity along the altitudinal zonation and vegetation range of tropical Eastern Himalaya

Lyngwi

Koijam

Sharma

et al. 2013

RBT

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Abstract:The Northeastern part of India sprawls over an area of 262 379km 2 in the Eastern Himalayan range. This constitutes a biodiversity hotspot with high levels of biodiversity and endemism; unfortunately, is also a poorly known area, especially on its microbial diversity. In this study, we assessed cultivable soil bacterial diversity and distribution from lowlands to highlands (34 to 3 990m.a.s.l.). Soil physico-chemical parameters and forest types across the different altitudes were characterized and correlated with bacterial distribution and diversity. Microbes from the soil samples were grown in Nutrient, Muller Hinton and Luria-Bertani agar plates and were initially characterized using biochemical methods. Parameters like dehydrogenase and urease activities, temperature, moisture content, pH, carbon content, bulk density of the sampled soil were measured for each site. Representative isolates were also subjected to 16S rDNA sequence analysis. A total of 155 cultivable bacterial isolates were characterized which were analyzed for richness, evenness and diversity indices. The tropical and sub-tropical forests supported higher bacterial diversity compared to temperate pine, temperate conifer, and sub-alpine rhododendron forests. The 16S rRNA phylogenetic analysis revealed that Firmicutes was the most common group followed by Proteobacteria and Bacteroidetes. Species belonging to the genera Bacillus and Pseudomonas were the most abundant. Bacterial CFU showed positive but insignificant correlation with soil parameters like pH (r=0.208), soil temperature (r=0.303), ambient temperature (r=0.443), soil carbon content (r=0.525), soil bulk density (r=0.268), soil urease (r=0.549) and soil dehydrogenase (r=0.492). Altitude (r=-0.561) and soil moisture content (r=-0.051) showed negative correlation. Altitudinal gradient along with the vegetation and soil physico-chemical parameters were found to influence bacterial diversity and distribution. This study points out that this is a biome with a vast reservoir of bacteria which decrease with increasing altitudes, and highlights the microbiological importance of the poorly studied Eastern Himalayan range, justifying efforts to explore the prevalence of novel species in the biome. Rev. Biol. Trop. 61 (1): 467-490. Epub 2013 March 01.

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Diversity of Microbial Communities

Cited by 147 publications

References 102 publications

Statistical Analyses of Complex Denaturing Gradient Gel Electrophoresis Profiles

Statistical Analyses of Complex Denaturing Gradient Gel Electrophoresis Profiles

Effects of organic perturbation on marine sediment betaproteobacterial ammonia oxidizers and on benthic nitrogen biogeochemistry

Cultivable bacterial diversity along the altitudinal zonation and vegetation range of tropical Eastern Himalaya

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