scholarly journals Chitinase Gene Sequences Retrieved from Diverse Aquatic Habitats Reveal Environment-Specific Distributions

2004 ◽  
Vol 70 (12) ◽  
pp. 6977-6983 ◽  
Author(s):  
Gary R. LeCleir ◽  
Alison Buchan ◽  
James T. Hollibaugh
Keyword(s):  
Water Column ◽  
Chitinase Gene ◽  
Mono Lake ◽  
Hypersaline Lake ◽  
Sargasso Sea ◽  
Gene Sequences ◽  
Central Arctic Ocean ◽  
Sediment Samples ◽  
Group I ◽  
Chitinase Genes

ABSTRACT Chitin is an abundant biopolymer whose degradation is mediated primarily by bacterial chitinases. We developed a degenerate PCR primer set to amplify a ∼900-bp fragment of family 18, group I chitinase genes and used it to retrieve these gene fragments from environmental samples. Clone libraries of presumptive chitinase genes were created for nine water and six sediment samples from 10 aquatic environments including freshwater and saline lakes, estuarine water and sediments, and the central Arctic Ocean. Putative chitinase sequences were also retrieved from the Sargasso Sea metagenome sequence database. We were unable to obtain PCR product with these primers from an alkaline, hypersaline lake (Mono Lake, California). In total, 108 partial chitinase gene sequences were analyzed, with a minimum of 5 and a maximum of 13 chitinase sequences obtained from each library. All chitinase sequences were novel compared to previously identified sequences. Intralibrary sequence diversity was low, while we found significant differences between libraries from different water column samples and between water column and sediment samples. However, identical sequences were retrieved from samples collected at widely distributed locations that did not necessarily represent similar environments, suggesting homogeneity of chitinoclastic communities between some environments.

scholarly journals Selected Chitinase Genes in Cultured and Uncultured Marine Bacteria in the α- and γ-Subclasses of the Proteobacteria

2000 ◽  
Vol 66 (3) ◽  
pp. 1195-1201 ◽  
Author(s):  
Matthew T. Cottrell ◽  
Daniel N. Wood ◽  
Liying Yu ◽  
David L. Kirchman
Keyword(s):  
Marine Bacteria ◽  
Pcr Primers ◽  
Chitinase Gene ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Bacterial Strains ◽  
Chitin Degradation ◽  
Group I ◽  
Degrading Bacteria ◽  
Chitinase Genes

ABSTRACT PCR primers were patterned after chitinase genes in four γ-proteobacteria in the families Alteromonadaceae andEnterobacteriaceae (group I chitinases) and used to explore the occurrence and diversity of these chitinase genes in cultured and uncultured marine bacteria. The PCR results from 104 bacterial strains indicated that this type of chitinase gene occurs in two major groups of marine bacteria, α- and γ-proteobacteria, but not theCytophaga-Flavobacter group. Group I chitinase genes also occur in some viruses infecting arthropods. Phylogenetic analysis indicated that similar group I chitinase genes occur in taxonomically related bacteria. However, the overall phylogeny of chitinase genes did not correspond to the phylogeny of 16S rRNA genes, possibly due to lateral transfer of chitinase genes between groups of bacteria, but other mechanisms, such as gene duplication, cannot be ruled out. Clone libraries of chitinase gene fragments amplified from coastal Pacific Ocean and estuarine Delaware Bay bacterioplankton revealed similarities and differences between cultured and uncultured bacteria. We had hypothesized that cultured and uncultured chitin-degrading bacteria would be very different, but in fact, clones having nucleotide sequences identical to those of chitinase genes of cultured α-proteobacteria dominated both libraries. The other clones were similar but not identical to genes in cultured γ-proteobacteria, including vibrios and alteromonads. Our results suggest that a closer examination of chitin degradation by α-proteobacteria will lead to a better understanding of chitin degradation in the ocean.

scholarly journals The Termite Group I Phylum Is Highly Diverse and Widespread in the Environment

2007 ◽  
Vol 73 (20) ◽  
pp. 6682-6685 ◽  
Author(s):  
Daniel P. R. Herlemann ◽  
Oliver Geissinger ◽  
Andreas Brune
Keyword(s):  
Phylogenetic Analysis ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Rrna Gene ◽  
Gene Sequences ◽  
16S Rrna Gene Sequences ◽  
Specific Primers ◽  
Environmental Distribution ◽  
Data Set ◽  
Group I

ABSTRACT The bacterial candidate phylum Termite Group I (TG-1) presently consists mostly of “Endomicrobia,” which are endosymbionts of flagellate protists occurring exclusively in the hindguts of termites and wood-feeding cockroaches. Here, we show that public databases contain many, mostly undocumented 16S rRNA gene sequences from other habitats that are affiliated with the TG-1 phylum but are only distantly related to “Endomicrobia.” Phylogenetic analysis of the expanded data set revealed several diverse and deeply branching lineages comprising clones from many different habitats. In addition, we designed specific primers to explore the diversity and environmental distribution of bacteria in the TG-1 phylum.

Distribution of pathogenic vibrios and Vibrio spp. in the water column and sediment samples from the southern Gulf of Mexico

2021 ◽  
Vol 173 ◽  
pp. 113116
Author(s):  
Johanna Bernáldez-Sarabia ◽  
Marcial L. Lizárraga-Partida ◽  
Edna L. Hernández-López ◽  
Jahaziel Gasperin-Bulbarela ◽  
Alexei F. Licea-Navarro ◽  
...  
Keyword(s):  
Gulf Of Mexico ◽  
Water Column ◽  
Sediment Samples ◽  
Southern Gulf Of Mexico ◽  
Pathogenic Vibrios ◽  
Vibrio Spp

scholarly journals Chitinase Genes in Lake Sediments of Ardley Island, Antarctica

2005 ◽  
Vol 71 (12) ◽  
pp. 7904-7909 ◽  
Author(s):  
Xiang Xiao ◽  
Xuebin Yin ◽  
Jian Lin ◽  
Liguang Sun ◽  
Ziyong You ◽  
...  
Keyword(s):  
Bacterial Community ◽  
Lake Sediment ◽  
Sediment Core ◽  
Chitinase Gene ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Chitinolytic Bacteria ◽  
Organic Carbon Concentration ◽  
Gene Copies ◽  
Chitinase Genes

ABSTRACT A sediment core spanning approximately 1,600 years was collected from a lake on Ardley Island, Antarctica. The sediment core had been greatly influenced by penguin guano. Using molecular methods, the chitinolytic bacterial community along the sediment core was studied over its entire length. Primers targeting conserved sequences of the catalytic domains of family 18 subgroup A chitinases detected group A chitinases from a wide taxonomic range of bacteria. Using quantitative competitive PCR (QC-PCR), chitinase gene copies in each 1-cm section of the whole sediment column were quantified. QC-PCR determination of the chitinase gene copies indicated significant correlation with phosphorus and total organic carbon concentration, suggesting a historical connection between chitinase gene copies and the amount of penguin guano input into the lake sediment. Most of the chitinase genes cloned from the historic sediment core were novel. Analysis of the chitinase gene diversity in selected sediment layers and in the fresh penguin deposits indicated frequent shifts in the chitinolytic bacterial community over time. Sequence analysis of the 16S rRNA genes of chitinolytic bacteria isolated from the lake sediment revealed that the isolates belonged to Janthinobacterium species, Stenotrophomonas species of γ-Proteobacteria, Cytophaga species of the Cytophaga-Flexibacter-Bacteroides group, and Streptomyces and Norcardiopsis species of Actinobacteria. Chitinase gene fragments were cloned and sequenced from these cultivated chitinolytic bacteria. The phylogeny of the chitinase genes obtained from the isolates did not correspond well to that of the isolates, suggesting acquisition via horizontal gene transfer.

scholarly journals Chitinase Gene Positively Regulates Hypersensitive and Defense Responses of Pepper to Colletotrichum acutatum Infection

2020 ◽  
Vol 21 (18) ◽  
pp. 6624 ◽  
Author(s):  
Muhammad Ali ◽  
Quan-Hui Li ◽  
Tao Zou ◽  
Ai-Min Wei ◽  
Ganbat Gombojab ◽  
...  
Keyword(s):  
Defense Response ◽  
Defense Responses ◽  
Chitinase Gene ◽  
Colletotrichum Acutatum ◽  
Basal Resistance ◽  
Chitin Binding Domain ◽  
Pepper Leaves ◽  
Defense Response Genes ◽  
Chitinase Genes ◽  
Pepper Plants

Anthracnose caused by Colletotrichum acutatum is one of the most devastating fungal diseases of pepper (Capsicum annuum L.). The utilization of chitin-binding proteins or chitinase genes is the best option to control this disease. A chitin-binding domain (CBD) has been shown to be crucial for the innate immunity of plants and activates the hypersensitive response (HR). The CaChiIII7 chitinase gene has been identified and isolated from pepper plants. CaChiIII7 has repeated CBDs that encode a chitinase enzyme that is transcriptionally stimulated by C. acutatum infection. The knockdown of CaChiIII7 in pepper plants confers increased hypersensitivity to C. acutatum, resulting in its proliferation in infected leaves and an attenuation of the defense response genes CaPR1, CaPR5, and SAR8.2 in the CaChiIII7-silenced pepper plants. Additionally, H2O2 accumulation, conductivity, proline biosynthesis, and root activity were distinctly reduced in CaChiIII7-silenced plants. Subcellular localization analyses indicated that the CaChiIII7 protein is located in the plasma membrane and cytoplasm of plant cells. The transient expression of CaChiIII7 increases the basal resistance to C. acutatum by significantly expressing several defense response genes and the HR in pepper leaves, accompanied by an induction of H2O2 biosynthesis. These findings demonstrate that CaChiIII7 plays a prominent role in plant defense in response to pathogen infection.

Planktonic and Benthic Bacteriovorous Protozoa at Eleven Stations in Puget Sound and Adjacent Pacific Ocean

1969 ◽  
Vol 26 (2) ◽  
pp. 299-304 ◽  
Author(s):  
Bruce Lighthart
Keyword(s):  
Pacific Ocean ◽  
Water Column ◽  
Deep Sea ◽  
Heterotrophic Bacteria ◽  
Puget Sound ◽  
Ecological Role ◽  
Population Densities ◽  
Sediment Samples

Bacteriovorous Protozoa and heterotrophic bacteria quantitatively cultured from 31 samples collected at eight stations in Puget Sound and three in the adjacent Pacific Ocean (one station being 1520 m deep) ranges from undetectable to approximately 1000 Protozoa per ml and 5–80,000 bacteria/ml. Flagellates in the genera Bodo, Oikomonas, Monas, Rynchomonas, and Actinomonas were the most prevalent forms cultured. One ciliate and several sarcodinoids were also grown. The regression of predatory Protozoa on prey bacteria in sediment samples was calculated to be 580 bacteria for every bacteriovorous protozoan. Population densities of both bacteriovorous Protozoa and heterotrophic bacteria in the samples decreased from sediment to the water column, and from shore seaward. The ecological role of bacteriovorous Protozoa in the shallow and deep sea is discussed.

scholarly journals Comprehensive Analysis of the Chitinase Gene Family in Cucumber (Cucumis sativus L.): From Gene Identification and Evolution to Expression in Response to Fusarium oxysporum

2019 ◽  
Vol 20 (21) ◽  
pp. 5309 ◽  
Author(s):  
Ezra S. Bartholomew ◽  
Kezia Black ◽  
Zhongxuan Feng ◽  
Wan Liu ◽  
Nan Shan ◽  
...  
Keyword(s):  
Gene Family ◽  
Fusarium Oxysporum ◽  
Expression Patterns ◽  
Chitinase Gene ◽  
Cucumis Sativus L ◽  
Binding Domains ◽  
Organ Specific ◽  
Duplication Events ◽  
Chitinase Genes ◽  
Related Proteins

Chitinases, a subgroup of pathogenesis-related proteins, are responsible for catalyzing the hydrolysis of chitin. Accumulating reports indicate that chitinases play a key role in plant defense against chitin-containing pathogens and are therefore good targets for defense response studies. Here, we undertook an integrated bioinformatic and expression analysis of the cucumber chitinases gene family to identify its role in defense against Fusarium oxysporum f. sp. cucumerinum. A total of 28 putative chitinase genes were identified in the cucumber genome and classified into five classes based on their conserved catalytic and binding domains. The expansion of the chitinase gene family was due mainly to tandem duplication events. The expression pattern of chitinase genes was organ-specific and 14 genes were differentially expressed in response to F. oxysporum challenge of fusarium wilt-susceptible and resistant lines. Furthermore, a class I chitinase, CsChi23, was constitutively expressed at high levels in the resistant line and may play a crucial role in building a basal defense and activating a rapid immune response against F. oxysporum. Whole-genome re-sequencing of both lines provided clues for the diverse expression patterns observed. Collectively, these results provide useful genetic resource and offer insights into the role of chitinases in cucumber-F. oxysporum interaction.

scholarly journals Distribution and Diversity of Archaeal and Bacterial Ammonia Oxidizers in Salt Marsh Sediments

2009 ◽  
Vol 75 (23) ◽  
pp. 7461-7468 ◽  
Author(s):  
Nicole S. Moin ◽  
Katelyn A. Nelson ◽  
Alexander Bush ◽  
Anne E. Bernhard
Keyword(s):  
Salt Marsh ◽  
16S Rrna ◽  
New England ◽  
Water Column ◽  
Salt Marshes ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Group I ◽  
Marsh Sediments ◽  
Salt Marsh Sediments

ABSTRACT Diversity and abundance of ammonia-oxidizing Betaproteobacteria (β-AOB) and archaea (AOA) were investigated in a New England salt marsh at sites dominated by short or tall Spartina alterniflora (SAS and SAT sites, respectively) or Spartina patens (SP site). AOA amoA gene richness was higher than β-AOB amoA richness at SAT and SP, but AOA and β-AOB richness were similar at SAS. β-AOB amoA clone libraries were composed exclusively of Nitrosospira-like amoA genes. AOA amoA genes at SAT and SP were equally distributed between the water column/sediment and soil/sediment clades, while AOA amoA sequences at SAS were primarily affiliated with the water column/sediment clade. At all three site types, AOA were always more abundant than β-AOB based on quantitative PCR of amoA genes. At some sites, we detected 109 AOA amoA gene copies g of sediment−1. Ratios of AOA to β-AOB varied over 2 orders of magnitude among sites and sampling dates. Nevertheless, abundances of AOA and β-AOB amoA genes were highly correlated. Abundance of 16S rRNA genes affiliated with Nitrosopumilus maritimus, Crenarchaeota group I.1b, and pSL12 were positively correlated with AOA amoA abundance, but ratios of amoA to 16S rRNA genes varied among sites. We also observed a significant effect of pH on AOA abundance and a significant salinity effect on both AOA and β-ΑΟΒ abundance. Our results expand the distribution of AOA to salt marshes, and the high numbers of AOA at some sites suggest that salt marsh sediments serve as an important habitat for AOA.

scholarly journals Differential Expression of Eight Chitinase Genes in Medicago truncatula Roots During Mycorrhiza Formation, Nodulation, and Pathogen Infection

2000 ◽  
Vol 13 (7) ◽  
pp. 763-777 ◽  
Author(s):  
Peter Salzer ◽  
Athos Bonanomi ◽  
Katinka Beyer ◽  
Regina Vögeli-Lange ◽  
Roger A. Aeschbacher ◽  
...  
Keyword(s):  
Arbuscular Mycorrhiza ◽  
Medicago Truncatula ◽  
Glomus Intraradices ◽  
Chitinase Gene ◽  
Class I ◽  
Specific Class ◽  
Class Iii ◽  
Phytophthora Megasperma ◽  
Class Iii Chitinase ◽  
Chitinase Genes

Expression of eight different chitinase genes, representing members of five chitinase classes, was studied in Medicago truncatula roots during formation of arbuscular mycorrhiza with Glomus intraradices, nodulation with Rhizobium meliloti, and pathogen attack by Phytophthora megasperma f. sp. medicaginis, Fusarium solani f. sp. phaseoli (compatible interactions with root rot symptoms), Ascochyta pisi (compatible, symptomless), and F. solani f. sp. pisi (incompatible, nonhost interaction). In the compatible plant-pathogen interactions, expression of class I, II, and IV chitinase genes was enhanced. The same genes were induced during nodulation. Transcripts of class I and II chitinase genes accumulated transiently during early stages of the interaction, and transcripts of the class IV chitinase gene accumulated in mature nodules. The pattern of chitinase gene expression in mycorrhizal roots was markedly different: Expression of class I, II, and IV chitinase genes was not enhanced, whereas expression of three class III chitinase genes, with almost no basal expression, was strongly induced. Two of these three (Mtchitinase III-2 and Mtchitinase III-3) were not induced at all in interactions with pathogens and rhizobia. Thus, the expression of two mycorrhiza-specific class III chitinase genes can be considered a hallmark for the establishment of arbuscular mycorrhiza in Medicago truncatula.

Sign in / Sign up

Export Citation Format

Share Document