scholarly journals Flavobacteria Blooms in Four Eutrophic Lakes: Linking Population Dynamics of Freshwater Bacterioplankton to Resource Availability

2007 ◽  
Vol 73 (11) ◽  
pp. 3511-3518 ◽  
Author(s):  
Alexander Eiler ◽  
Stefan Bertilsson
Keyword(s):  
Resource Availability ◽  
Bacterial Production ◽  
Fragment Length Polymorphism ◽  
Heterotrophic Bacteria ◽  
Phylogenetic Analyses ◽  
Polymorphism Analysis ◽  
Eutrophic Lakes ◽  
Specific Primers ◽  
Bacterial Populations ◽  
Bacterial Succession

ABSTRACT Heterotrophic bacteria are major contributors to biogeochemical cycles and influence water quality. Still, the lack of representative isolates and the few quantitative surveys leave the ecological role and significance of single bacterial populations to be revealed. Here we analyzed the diversity and dynamics of freshwater Flavobacteria populations in four eutrophic temperate lakes. From each lake, clone libraries were constructed using primers specific for either the class Flavobacteria or Bacteria. Sequencing of 194 Flavobacteria clones from 8 libraries revealed a diverse freshwater Flavobacteria community and distinct differences among lakes. Abundance and seasonal dynamics of Flavobacteria were assessed by quantitative PCR with class-specific primers. In parallel, the dynamics of individual populations within the Flavobacteria community were assessed with terminal restriction fragment length polymorphism analysis using identical primers. The contribution of Flavobacteria to the total bacterioplankton community ranged from 0.4 to almost 100% (average, 24%). Blooms where Flavobacteria represented more than 30% of the bacterioplankton were observed at different times in the four lakes. In general, high proportions of Flavobacteria appeared during episodes of high bacterial production. Phylogenetic analyses combined with Flavobacteria community fingerprints suggested dominance of two Flavobacteria lineages. Both drastic alterations in total Flavobacteria and in community composition of this class significantly correlated with bacterial production, emphasizing that resource availability is an important driver of heterotrophic bacterial succession in eutrophic lakes.

scholarly journals Identification protocol for sixArmillariaspecies from northeastern North America

2010 ◽  
Vol 40 (3) ◽  
pp. 536-548 ◽  
Author(s):  
J. A. McLaughlin ◽  
T. Hsiang
Keyword(s):  
Dna Sequences ◽  
Fragment Length Polymorphism ◽  
Intergenic Spacer ◽  
Polymorphism Analysis ◽  
Specific Primers ◽  
Northeastern North America ◽  
Armillaria Ostoyae ◽  
Armillaria Gallica ◽  
Species Specific ◽  
Restriction Fragment Length

DNA sequences (~3 kb long) extending from the intergenic spacer 1 (IGS1) region to the 18S gene were obtained for isolates of Armillaria ostoyae , Armillaria calvescens , Armillaria gallica , and Armillaria sinapina . Additional investigation of 16 A. ostoyae, 11 Armillaria gemina , 21 A. calvescens, 18 A. gallica, and 15 A. sinapina isolates produced 117 sequences spanning the 3′ end of the IGS1 through the 5S gene and into the 5′ end of the IGS2 region. Additional sequences spanning the 3′ IGS2 to 5′ 18S gene region were obtained for two A. ostoyae, three A. gemina, two A. calvescens, two A. gallica, and three A. sinapina isolates. This is the first report of complete IGS2 sequences from Armillaria spp. A species identification protocol involving species-specific primers and restriction fragment length polymorphism analysis was devised based on species-specific polymorphisms. The protocol successfully identified all 16 A. ostoyae, 11 A. gemina, three of three Armillaria mellea , 18 A. gallica, 14 of 15 A. sinapina (11/12 diploid and 3/3 haploid), and 14 of 21 A. calvescens (13/15 diploid and 1/6 haploid) isolates included in this study. To the best of our knowledge, this success rate has not been matched by other methods.

Molecular analysis of ammonia-oxidizing bacterial populations in aerated-anoxic Orbal processes

2002 ◽  
Vol 46 (1-2) ◽  
pp. 273-280 ◽  
Author(s):  
H.-D. Park ◽  
J.M. Regan ◽  
D.R. Noguera
Keyword(s):  
Fragment Length Polymorphism ◽  
Ammonia Oxidation ◽  
Wastewater Treatment Plants ◽  
Phylogenetic Analyses ◽  
Amoa Gene ◽  
Ammonia Oxidizing Bacteria ◽  
Ammonia Monooxygenase ◽  
Anoxic Zone ◽  
Bacterial Populations ◽  
Nitrosomonas Oligotropha

Aerated-anoxic processes operate under the principle that small additions of oxygen to an anoxic reactor induce simultaneous nitrification and denitrification. In these systems, ammonia oxidation in the anoxic zone can easily account for 30–50% of the total nitrification in the reactor, even though the dissolved oxygen concentration is usually below detection limit. To investigate whether the nitrification efficiency in aerated-anoxic processes was due to the presence of specialized ammonia-oxidizing bacteria (AOB), an analysis of the AOB population in an aerated-anoxic Orbal process and a conventional nitrogen removal process was carried out using phylogenetic analyses based on the ammonia monooxygenase A (amoA) gene. Terminal restriction fragment length polymorphism (TRFLP) analyses revealed that Nitrosospira-like organisms were one of the major contributors to ammonia oxidation in a full-scale aerated-anoxic Orbal reactor. However, the relative populations of Nitrosospira-like and Nitrosomonas-like AOB were not constant and appeared to have seasonal variability. Cloning and sequence comparison of amoA gene fragments demonstrated that most of the AOB in the aerated-anoxic Orbal process belonged to the Nitrosospira sp. and Nitrosomonas oligotropha lineages. The abundance of Nitrosospira-like organisms in aerated-anoxic reactors is significant, since this group of AOB has not been usually associated with nitrification in wastewater treatment plants.

scholarly journals Genetic Diversity and Temporal Variation in the Cyanophage Community Infecting Marine Synechococcus Species in Rhode Island's Coastal Waters

2003 ◽  
Vol 69 (8) ◽  
pp. 4639-4647 ◽  
Author(s):  
Marcia F. Marston ◽  
Jennifer L. Sallee
Keyword(s):  
Rhode Island ◽  
Relative Abundance ◽  
Coastal Waters ◽  
Fragment Length Polymorphism ◽  
Phylogenetic Analyses ◽  
Sampling Period ◽  
Polymorphism Analysis ◽  
Seawater Samples ◽  
June July ◽  
Viral Isolates

ABSTRACT The cyanophage community in Rhode Island's coastal waters is genetically diverse and dynamic. Cyanophage abundance ranged from over 104 phage ml−1 in the summer months to less then 102 phage ml−1 during the winter months. Thirty-six distinct cyanomyovirus g20 genotypes were identified over a 3-year sampling period; however, only one to nine g20 genotypes were detected at any one sampling date. Phylogenetic analyses of g20 sequences revealed that the Rhode Island cyanomyoviral isolates fall into three main clades and are closely related to other known viral isolates of Synechococcus spp. Extinction dilution enrichment followed by host range tests and PCR restriction fragment length polymorphism analysis was used to detect changes in the relative abundance of cyanophage types in June, July, and August 2002. Temporal changes in both the overall composition of the cyanophage community and the relative abundance of specific cyanophage g20 genotypes were observed. In some seawater samples, the g20 gene from over 50% of isolated cyanophages could not be amplified by using the PCR primer pairs specific for cyanomyoviruses, which suggested that cyanophages in other viral families (e.g., Podoviridae or Siphoviridae) may be important components of the Rhode Island cyanophage community.

scholarly journals Distribution of Xanthomonas oryzae pv. oryzae Strains Virulent to Xa21 in Korea

1999 ◽  
Vol 89 (10) ◽  
pp. 928-933 ◽  
Author(s):  
S. W. Lee ◽  
S. H. Choi ◽  
S. S. Han ◽  
D. G. Lee ◽  
B. Y. Lee
Keyword(s):  
Population Structure ◽  
Restriction Fragment Length Polymorphism ◽  
Fragment Length Polymorphism ◽  
Flag Leaf ◽  
Xanthomonas Oryzae ◽  
Polymorphism Analysis ◽  
Regional Structure ◽  
Bacterial Populations ◽  
Pathogenicity Tests ◽  
Restriction Fragment Length

Strains of Xanthomonas oryzae pv. oryzae that are virulent to rice lines carrying the Xa21 resistance gene were widely distributed in Korea. A total of 105 strains collected during 1987 to 1996 in Korea was characterized by pathogenicity tests and restriction fragment length polymorphism analysis of the XorII methyltransferase (xorIIM) and avrXa10 genes. Although the lesion lengths on rice line IRBB21, which carries Xa21, decreased as plant age increased, resistance and susceptibility of the plants to 31 strains were clearly differentiated at the seedling (14, 21, and 28 days old), maximum tillering, and flag leaf stages. The resistance or susceptibility of seedlings was correlated with bacterial populations within an inoculated leaf. There was a significant change in the population structure of X. oryzae pv. oryzae with regard to virulence to Xa21 over the last 10 years; this change in population was confirmed by genome analysis. Lineage I, which is avirulent to Xa21 and does not have a genomic xorIIM homolog, was the predominant lineage found between 1987 and 1989, while lineage II, which is virulent to Xa21 and contains the xorIIM homolog, was predominant in strains collected between 1994 and 1995. Our results demonstrate that introduction of Xa21 into commercial rice should be based on the regional structure of X. oryzae pv. oryzae populations and suggest that Xa21 will not be useful in Korea.

scholarly journals Phytoplasma occurrence in apple trees in the Czech Republic

2011 ◽  
Vol 39 (No. 1) ◽  
pp. 7-12 ◽  
Author(s):  
R. Fialová ◽  
M. Navrátil ◽  
P. Válová
Keyword(s):  
Fragment Length Polymorphism ◽  
Rrna Gene ◽  
Polymorphism Analysis ◽  
Apple Proliferation ◽  
Chain Reaction ◽  
Apple Trees ◽  
The Czech Republic ◽  
High Incidence ◽  
Phytoplasma Infection ◽  
Polymerase Chain

The presence of phytoplasmas in apple trees with proliferation symptoms, rubbery wood symptoms and no symp­toms was determined by using polymerase chain reaction assays with primers amplifying phytoplasma 16S rRNA gene. Phytoplasmas were detected in all trees with proliferation symptoms. Positive tests for phytoplasma in the group of trees with rubbery wood symptoms and of those without symptoms revealed a relatively high incidence of latent phytoplasma infection. Using restriction fragment length polymorphism analysis, phytoplasma of the same identity – apple proliferation phytoplasma (subgroup 16SrX-A) – was recorded in all positively tested trees.  

Systematic evidence from gene duplication and regulation

1990 ◽  
Vol 3 (1) ◽  
pp. 145
Author(s):  
DJ Colgan
Keyword(s):  
Gene Duplication ◽  
Evolutionary History ◽  
Tandem Duplication ◽  
Fragment Length Polymorphism ◽  
Duplicate Genes ◽  
Polymorphism Analysis ◽  
Multiple Origins ◽  
The Family ◽  
History Of ◽  
Phylogenetic Hypotheses

This paper is a review of the use of information regarding the presence of duplicate genes and their regulation in systematics. The review concentrates on data derived from protein electrophoresis and restriction fragment length polymorphism analysis. The appearance of a duplication in a subset of a group of species implies that the members of the subset belong to the same clade. Suppression of the duplication may render this clade apparently paraphyletic, but may itself be informative of relations within the lineage through patterns of loss of expression in all, or some tissues, or through restrictions of the formation of functional heteropolymers in polymeric enzymes. Examples are given of studies which have used such information to establish phylogenetic hypotheses at the family level, to identify an auto- or allo-polyploid origin of polyploid species and to determine whether there have been single or multiple origins of such species. The likelihood of homoplasy in the patterns of appearance and regulation of duplicates depends on the molecular basis of the duplication. In particular, the contrast between the expected consequences of tandem duplication and the expression of pseudogenes emphasises the value of determining the mechanism of the original duplication. Many instances of sporadic gene duplication are now known, and polyploidisation is a common event in the evolutionary history of both plants and animals. So the opportunities to discover duplicationrelated characters will arise in many systematic studies. A program is presented to increase the chances that such useful information will be recognisable during the studies.

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