scholarly journals Microbial Diversity and Heterogeneity in Sandy Subsurface Soils

2004 ◽  
Vol 70 (3) ◽  
pp. 1723-1734 ◽  
Author(s):  
Jizhong Zhou ◽  
Beicheng Xia ◽  
Heshu Huang ◽  
Anthony V. Palumbo ◽  
James M. Tiedje
Keyword(s):  
Principal Component ◽  
Small Subunit ◽  
Ssu Rdna ◽  
Community Diversity ◽  
Rrna Gene ◽  
Gram Positive Bacteria ◽  
Operational Taxonomic Units ◽  
Culture Independent ◽  
Air Force Base ◽  
Dover Air Force Base

ABSTRACT Microbial community diversity and heterogeneity in saturated and unsaturated subsurface soils from Abbott's Pit in Virginia (1.57, 3.25, and 4.05 m below surface) and Dover Air Force Base in Delaware (6.00 and 7.50 m below surface) were analyzed using a culture-independent small-subunit (SSU) rRNA gene (rDNA)-based cloning approach. Four to six dominant operational taxonomic units (OTUs) were identified in 33 to 100 unique SSU rDNA clones (constituting about 40 to 50% of the total number of SSU rDNA clones in the clone library) from the saturated subsurface samples, whereas no dominant OTUs were observed in the unsaturated subsurface sample. Less than 10% of the clones among samples from different depths at the same location were identical, and the proportion of overlapping OTUs was lower for the samples that were vertically far apart than for adjacent samples. In addition, no OTUs were shared between the Abbott's Pit and Dover samples. The majority of the clones (80%) had sequences that were less than 5% different from those in the current databases. Phylogenetic analysis indicated that most of the bacterial clones were affiliated with members of the Proteobacteria family (90%), gram-positive bacteria (3%), and members of the Acidobacteria family (3%). Principal component analysis revealed that samples from different geographic locations were well separated and that samples from the same location were closely grouped together. In addition, the nonsaturated subsurface samples from Abbott's Pit clustered together and were well separated from the saturated subsurface soil sample. Finally, the overall diversity of the subsurface samples was much lower than that of the corresponding surface soil samples.

scholarly journals Quantitative Measure of Small-Subunit rRNA Gene Sequences of the Kingdom Korarchaeota

1998 ◽  
Vol 64 (12) ◽  
pp. 5064-5066 ◽  
Author(s):  
Clifford F. Brunk ◽  
Nicole Eis
Keyword(s):  
Internal Standard ◽  
Pcr Amplification ◽  
Quantitative Measure ◽  
Pcr Primers ◽  
Small Subunit ◽  
Ssu Rdna ◽  
Rdna Sequence ◽  
Rrna Gene ◽  
Small Subunit Rrna ◽  
Rdna Sequences

ABSTRACT Comparative PCR amplification of small-subunit (SSU) rRNA gene (rDNA) sequences indicates substantial preferential PCR amplification of pJP27 sequences with korarchaeote-specific PCR primers. The coamplification of a modified SSU rDNA sequence can be used as an internal standard to determine the amount of a specific SSU rDNA sequence.

Molecular bacterial diversity and bioburden of commercial airliner cabin air

2007 ◽  
Vol 53 (11) ◽  
pp. 1259-1271 ◽  
Author(s):  
Myron T. La Duc ◽  
Tara Stuecker ◽  
Kasthuri Venkateswaran
Keyword(s):  
Bacterial Diversity ◽  
Rrna Gene ◽  
Human Respiratory Tract ◽  
Atp Assay ◽  
Gram Positive Bacteria ◽  
Air Impingement ◽  
Culture Independent ◽  
Bacterial Enumeration ◽  
Gradual Accumulation ◽  
Opportunistic Pathogenic

Culture-independent, biomarker-targeted bacterial enumeration and identification strategies were employed to estimate total bacterial burden and diversity within the cabin air of commercial airliners. Samples from each of 4 flights on 2 commercial carriers were collected via air-impingement. The total viable microbial population ranged from below detection limits to 4.1 × 106cells/m3of air, as assessed by the ATP assay. A gradual accumulation of microbes was observed from the time of passenger boarding through mid-flight, followed by a sharp decline in bacterial abundance and viability from the initiation of descent through landing. Representatives of the α-, β-, and γ-Proteobacteria, as well as Gram-positive bacteria, were isolated in varying abundance. Neisseria meningitidis rRNA gene sequences were retrieved in great abundance from Airline A followed by Streptococcus oralis/mitis sequences. Pseudomonas synxantha sequences dominated Airline B clone libraries, followed by those of N. meningitidis and S. oralis/mitis. The cabin air samples examined herein housed low bacterial diversity and were often dominated by a particular subset of bacteria: opportunistic pathogenic inhabitants of the human respiratory tract and oral cavity.

scholarly journals Abundant and Diverse Fungal Microbiota in the Murine Intestine

2006 ◽  
Vol 72 (1) ◽  
pp. 793-801 ◽  
Author(s):  
Alexandra J Scupham ◽  
Laura L. Presley ◽  
Bo Wei ◽  
Elizabeth Bent ◽  
Natasha Griffith ◽  
...  
Keyword(s):  
Small Subunit ◽  
Rrna Genes ◽  
Rrna Gene ◽  
Small Subunit Rrna ◽  
Culture Independent ◽  
Specific Pathogen ◽  
Health And Disease ◽  
Oligonucleotide Fingerprinting ◽  
Rrna Sequences

ABSTRACT Enteric microbiota play a variety of roles in intestinal health and disease. While bacteria in the intestine have been broadly characterized, little is known about the abundance or diversity of enteric fungi. This study utilized a culture-independent method termed oligonucleotide fingerprinting of rRNA genes (OFRG) to describe the compositions of fungal and bacterial rRNA genes from small and large intestines (tissue and luminal contents) of restricted-flora and specific-pathogen-free mice. OFRG analysis identified rRNA genes from all four major fungal phyla: Ascomycota, Basidiomycota, Chytridiomycota, and Zygomycota. The largest assemblages of fungal rRNA sequences were related to the genera Acremonium, Monilinia, Fusarium, Cryptococcus/Filobasidium, Scleroderma, Catenomyces, Spizellomyces, Neocallimastix, Powellomyces, Entophlyctis, Mortierella, and Smittium and the order Mucorales. The majority of bacterial rRNA gene clones were affiliated with the taxa Bacteroidetes, Firmicutes, Acinetobacter, and Lactobacillus. Sequence-selective PCR analyses also detected several of these bacterial and fungal rRNA genes in the mouse chow. Fluorescence in situ hybridization analysis with a fungal small-subunit rRNA probe revealed morphologically diverse microorganisms resident in the mucus biofilm adjacent to the cecal and proximal colonic epithelium. Hybridizing organisms comprised about 2% of the DAPI (4′,6-diamidino-2-phenylindole, dihydrochloride)-positive organisms in the mucus biofilm, but their abundance in fecal material may be much lower. These data indicate that diverse fungal taxa are present in the intestinal microbial community. Their abundance suggests that they may play significant roles in enteric microbial functions.

scholarly journals Phylogenetic Diversity of Gram-Positive Bacteria Cultured from Marine Sediments

2007 ◽  
Vol 73 (10) ◽  
pp. 3272-3282 ◽  
Author(s):  
Erin A. Gontang ◽  
William Fenical ◽  
Paul R. Jensen
Keyword(s):  
New Taxa ◽  
Marine Sediments ◽  
Sequence Data ◽  
Rrna Gene ◽  
Gram Positive ◽  
Gram Positive Bacteria ◽  
Operational Taxonomic Units ◽  
The Republic ◽  
Republic Of Palau ◽  
High Degree

ABSTRACT Major advances in our understanding of marine bacterial diversity have been gained through studies of bacterioplankton, the vast majority of which appear to be gram negative. Less effort has been devoted to studies of bacteria inhabiting marine sediments, yet there is evidence to suggest that gram-positive bacteria comprise a relatively large proportion of these communities. To further expand our understanding of the aerobic gram-positive bacteria present in tropical marine sediments, a culture-dependent approach was applied to sediments collected in the Republic of Palau from the intertidal zone to depths of 500 m. This investigation resulted in the isolation of 1,624 diverse gram-positive bacteria spanning 22 families, including many that appear to represent new taxa. Phylogenetic analysis of 189 representative isolates, based on 16S rRNA gene sequence data, indicated that 124 (65.6%) belonged to the class Actinobacteria while the remaining 65 (34.4%) were members of the class Bacilli. Using a sequence identity value of ≥98%, the 189 isolates grouped into 78 operational taxonomic units, of which 29 (37.2%) are likely to represent new taxa. The high degree of phylogenetic novelty observed during this study highlights the fact that a great deal remains to be learned about the diversity of gram-positive bacteria in marine sediments.

scholarly journals Streamlined and Abundant Bacterioplankton Thrive in Functional Cohorts

mSystems ◽  
2020 ◽  
Vol 5 (5) ◽  
Author(s):  
Rhiannon Mondav ◽  
Stefan Bertilsson ◽  
Moritz Buck ◽  
Silke Langenheder ◽  
Eva S. Lindström ◽  
...  
Keyword(s):  
Common Good ◽  
Natural Habitat ◽  
Single Species ◽  
Small Subunit ◽  
Rrna Gene ◽  
Culture Independent ◽  
Species Population ◽  
Peroxidase Enzyme ◽  
Catalase Peroxidase ◽  
Single Species Population

ABSTRACT While fastidious microbes can be abundant and ubiquitous in their natural communities, many fail to grow axenically in laboratories due to auxotrophies or other dependencies. To overcome auxotrophies, these microbes rely on their surrounding cohort. A cohort may consist of kin (ecotypes) or more distantly related organisms (community) with the cooperation being reciprocal or nonreciprocal and expensive (Black Queen hypothesis) or costless (by-product). These metabolic partnerships (whether at single species population or community level) enable dominance by and coexistence of these lineages in nature. Here we examine the relevance of these cooperation models to explain the abundance and ubiquity of the dominant fastidious bacterioplankton of a dimictic mesotrophic freshwater lake. Using both culture-dependent (dilution mixed cultures) and culture-independent (small subunit [SSU] rRNA gene time series and environmental metagenomics) methods, we independently identified the primary cohorts of actinobacterial genera “Candidatus Planktophila” (acI-A) and “Candidatus Nanopelagicus” (acI-B) and the proteobacterial genus “Candidatus Fonsibacter” (LD12). While “Ca. Planktophila” and “Ca. Fonsibacter” had no correlation in their natural habitat, they have the potential to be complementary in laboratory settings. We also investigated the bifunctional catalase-peroxidase enzyme KatG (a common good which “Ca. Planktophila” is dependent upon) and its most likely providers in the lake. Further, we found that while ecotype and community cooperation combined may explain “Ca. Planktophila” population abundance, the success of “Ca. Nanopelagicus” and “Ca. Fonsibacter” is better explained as a community by-product. Ecotype differentiation of “Ca. Fonsibacter” as a means of escaping predation was supported but not for overcoming auxotrophies. IMPORTANCE This study examines evolutionary and ecological relationships of three of the most ubiquitous and abundant freshwater bacterial genera: “Ca. Planktophila” (acI-A), “Ca. Nanopelagicus” (acI-B), and “Ca. Fonsibacter” (LD12). Due to high abundance, these genera might have a significant influence on nutrient cycling in freshwaters worldwide, and this study adds a layer of understanding to how seemingly competing clades of bacteria can coexist by having different cooperation strategies. Our synthesis ties together network and ecological theory with empirical evidence and lays out a framework for how the functioning of populations within complex microbial communities can be studied.

Morphological reports on two species of Dexiotricha (Ciliophora, Scuticociliatia), with a note on the phylogenetic position of the genus

2014 ◽  
Vol 64 (Pt_2) ◽  
pp. 680-688 ◽  
Author(s):  
Xinpeng Fan ◽  
Saleh A. Al-Farraj ◽  
Feng Gao ◽  
Fukang Gu
Keyword(s):  
Phylogenetic Analyses ◽  
Eastern China ◽  
Small Subunit ◽  
Ssu Rdna ◽  
Contractile Vacuole ◽  
Phylogenetic Position ◽  
Rrna Gene ◽  
Small Subunit Rrna ◽  
North West ◽  
Rdna Sequences

Two Dexiotricha species (Dexiotricha elliptica nov. comb. and Dexiotricha cf. granulosa), respectively isolated from soil north-west of Riyadh, Saudi Arabia, and freshwater in Shanghai, eastern China, were investigated using standard methods. The species Loxocephalus ellipticus Kahl, 1931 is reclassified here in the genus Dexiotricha and was characterized mainly by constantly showing 16 somatic kineties, three post-oral kineties with the middle one shortened, a contractile vacuole located subcaudally with an excretory pore near the posterior end of somatic kinety 2 and single caudal cilia. A Dexiotricha granulosa-like organism having a subcaudally located contractile vacuole and fewer somatic kineties was designated D. cf. granulosa. The small-subunit rRNA gene (SSU rDNA) sequences of these two species were characterized and their phylogenetic positions based on SSU rDNA sequences were revealed by means of Bayesian inference and maximum-likelihood analysis. Phylogenetic analyses confirmed Dexiotricha as a monophyletic genus and supported its assignment to the order Loxocephalida. However, its family assignment remains unsupported.

scholarly journals Fungal Diversity in Deep-Sea Hydrothermal Ecosystems

2009 ◽  
Vol 75 (20) ◽  
pp. 6415-6421 ◽  
Author(s):  
Thomas Le Calvez ◽  
Gaëtan Burgaud ◽  
Stéphane Mahé ◽  
Georges Barbier ◽  
Philippe Vandenkoornhuyse
Keyword(s):  
Deep Sea ◽  
Fungal Diversity ◽  
Terrestrial Ecosystems ◽  
Small Subunit ◽  
Culture Collection ◽  
Point Of View ◽  
Rrna Gene ◽  
Small Subunit Rrna ◽  
Culture Independent ◽  
Hydrothermal Ecosystems

ABSTRACT Deep-sea hydrothermal ecosystems are considered oases of life in oceans. Since the discovery of these ecosystems in the late 1970s, many endemic species of Bacteria, Archaea, and other organisms, such as annelids and crabs, have been described. Considerable knowledge has been acquired about the diversity of (micro)organisms in these ecosystems, but the diversity of fungi has not been studied to date. These organisms are considered key organisms in terrestrial ecosystems because of their ecological functions and especially their ability to degrade organic matter. The lack of knowledge about them in the sea reflects the widely held belief that fungi are terrestrial organisms. The first inventory of such organisms in deep-sea hydrothermal environments was obtained in this study. Fungal diversity was investigated by analyzing the small-subunit rRNA gene sequences amplified by culture-independent PCR using DNA extracts from hydrothermal samples and from a culture collection that was established. Our work revealed an unsuspected diversity of species in three of the five fungal phyla. We found a new branch of Chytridiomycota forming an ancient evolutionary lineage. Many of the species identified are unknown, even at higher taxonomic levels in the Chytridiomycota, Ascomycota, and Basidiomycota. This work opens the way to new studies of the diversity, ecology, and physiology of fungi in oceans and might stimulate new prospecting for biomolecules. From an evolutionary point of view, the diversification of fungi in the oceans can no longer be ignored.

scholarly journals Diversity of NC10 bacteria associated with sediments of submergedPotamogeton crispus(Alismatales: Potmogetonaceae)

PeerJ ◽  
2018 ◽  
Vol 6 ◽  
pp. e6041 ◽  
Author(s):  
Binghan Wang ◽  
Shanshan Huang ◽  
Liangmao Zhang ◽  
Jianwei Zhao ◽  
Guanglong Liu ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Community Diversity ◽  
Rrna Gene ◽  
Dominant Group ◽  
Potamogeton Crispus ◽  
Carbon And Nitrogen ◽  
Operational Taxonomic Units ◽  
Group A ◽  
Group B

BackgroundThe nitrite-dependent anaerobic methane oxidation (N-DAMO) pathway, which plays an important role in carbon and nitrogen cycling in aquatic ecosystems, is mediated by “CandidatusMethylomirabilis oxyfera” (M. oxyfera) of the NC10 phylum.M. oxyfera-like bacteria are widespread in nature, however, the presence, spatial heterogeneity and genetic diversity ofM. oxyferain the rhizosphere of aquatic plants has not been widely reported.MethodIn order to simulate the rhizosphere microenvironment of submerged plants,Potamogeton crispuswas cultivated using the rhizobox approach. Sediments from three compartments of the rhizobox: root (R), near-rhizosphere (including five sub-compartments of one mm width, N1–N5) and non-rhizosphere (>5 mm, Non), were sampled. The 16S rRNA gene library was used to investigate the diversity ofM. oxyfera-like bacteria in these sediments.ResultsMethylomirabilis oxyfera-like bacteria were found in all three sections, with all 16S rRNA gene sequences belonging to 16 operational taxonomic units (OTUs). A maximum of six OTUs was found in the N1 sub-compartment of the near-rhizosphere compartment and a minimum of four in the root compartment (R) and N5 near-rhizosphere sub-compartment. Indices of bacterial community diversity (Shannon) and richness (Chao1) were 0.73–1.16 and 4–9, respectively. Phylogenetic analysis showed that OTU1-11 were classified into group b, while OTU12 was in a new cluster of NC10.DiscussionOur results confirmed the existence ofM. oxyfera-like bacteria in the rhizosphere microenvironment of the submerged plantP. crispus. Group b ofM. oxyfera-like bacteria was the dominant group in this study as opposed to previous findings that both group a and b coexist in most other environments. Our results indicate that understanding the ecophysiology ofM. oxyfera-like bacteria group b may help to explain their existence in the rhizosphere sediment of aquatic plant.

scholarly journals Kinetic Bias in Estimates of Coastal Picoplankton Community Structure Obtained by Measurements of Small-Subunit rRNA Gene PCR Amplicon Length Heterogeneity

1998 ◽  
Vol 64 (11) ◽  
pp. 4522-4529 ◽  
Author(s):  
Marcelino Suzuki ◽  
Michael S. Rappé ◽  
Stephen J. Giovannoni
Keyword(s):  
Clone Library ◽  
Fluorescence Emission ◽  
Small Subunit ◽  
Ssu Rdna ◽  
Rrna Genes ◽  
Rrna Gene ◽  
Length Variation ◽  
Small Subunit Rrna ◽  
Gene Frequencies ◽  
Rdna Sequences

ABSTRACT Marine bacterioplankton diversity was examined by quantifying natural length variation in the 5′ domain of small-subunit (SSU) rRNA genes (rDNA) amplified by PCR from a DNA sample from the Oregon coast. This new technique, length heterogeneity analysis by PCR (LH-PCR), determines the relative proportions of amplicons originating from different organisms by measuring the fluorescence emission of a labeled primer used in the amplification reaction. Relationships between the sizes of amplicons and gene phylogeny were predicted by an analysis of 366 SSU rDNA sequences from cultivated marine bacteria and from bacterial genes cloned directly from environmental samples. LH-PCR was used to compare the distribution of bacterioplankton SSU rDNAs from a coastal water sample with that of an SSU rDNA clone library prepared from the same sample and also to examine the distribution of genes in the PCR products from which the clone library was prepared. The analysis revealed that the relative frequencies of genes amplified from natural communities are highly reproducible for replicate sets of PCRs but that a bias possibly caused by the reannealing kinetics of product molecules can skew gene frequencies when PCR product concentrations exceed threshold values.

scholarly journals Soil and Rhizosphere Bacterial Diversity in Maize Agro- Ecosystem

2017 ◽  
Vol 6 (3) ◽  
pp. 35 ◽  
Author(s):  
Maria Teresa Federici Rodriguez ◽  
Natalia Bajsa Valverde ◽  
Paula Lagurara ◽  
Santiago Revale ◽  
Jackson Antonio Marcondes de Souza ◽  
...  
Keyword(s):  
Bacterial Community ◽  
Management Practices ◽  
Denaturing Gradient Gel Electrophoresis ◽  
Community Diversity ◽  
Rrna Gene ◽  
Phenological Stages ◽  
Maize Production ◽  
Maize Cultivars ◽  
Culture Independent ◽  
Gradient Gel Electrophoresis

Management practices used in maize production have an impact on soil agro- ecosystems where different microbial communities coexist. Soil inhabiting bacteria are numerous and diverse, but we know very little about their ecological distribution. Here we analyzed the bacterial community diversity in the rhizosphere of two transgenic maize cultivars, in agricultural soil before sowing and in non-cultivated soil in an experimental site in the south region of Uruguay. We followed two culture-independent methods: DGGE (denaturing gradient gel electrophoresis) and 454-pyrosequencing of 16S rRNA gene amplicon. Through pyrosequencing, the three environments analyzed presented differences in terms of bacterial composition. However, no differences were found in the relative abundance of the ten most represented phyla in the rhizosphere of the two cultivars at different phenological stages. We found significant differences of Bacteroidetes, Gemmatimonadetes, Planctomycetes, Proteobacteria and Verrucomicrobia phyla when comparing agricultural and non-cultivated soils, as well as a significant enrichment of members of the phylum Gemmatimonadetes in all rhizosphere samples compared to soil. Through DGGE analysis we evidenced that maize rhizosphere bacterial communities changed at different phenological stages in both cultivars. We also provided baseline information about bacterial specific taxa within maize agro- ecosystem for further evaluation of possible rhizosphere bacterial community shifts of genetically modified maize cultivars under different management practices.

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