scholarly journals Isolation and Characterization of a Rhizobium Bacterium Associated with the Toxic Dinoflagellate Gambierdiscus balechii

2019 ◽  
Author(s):  
Zhen Wu ◽  
Xiaohong Yang ◽  
Senjie Lin ◽  
Wai Hin Lee ◽  
Paul K.S. Lam
Keyword(s):  
16S Rdna ◽  
Net Primary Productivity ◽  
Future Research ◽  
Exponential Growth Phase ◽  
Sequencing Analysis ◽  
Nutrient Regeneration ◽  
Toxic Dinoflagellate ◽  
First Report ◽  
Isolation And Characterization ◽  
Encoding Gene

ABSTRACTAlgae-bacteria associations are increasingly being recognized to be important in shaping the growth of both algae and bacteria. Bacteria belonging to order Rhizobiales are important symbionts of legumes often developing as nodules on plant roots, but have not been widely documented in association with algae. Here, we detected, isolated, and characterized a Rhizobium species from the toxic benthic dinoflagellate Gambierdiscus culture. The sequence of 16S rDNA showed 99% identity with that of Rhizobium rosettiformans. To further characterize the bacterium, we amplified and sequenced a cell wall hydrolase (CWH)-encoding gene; phylogenetic analysis indicated that this sequence was similar to the homologs of Martellela sp. and Hoeflea sp, of order Rhizobiales. We performed PCR using nifH primers to determine whether this bacterium can fix N2; however, the results of sequencing analysis showed that it was closer to chlorophyllide a reductase-encoding gene (bchX), which is similar to nifH. Results of 16S rDNA qPCR showed that compared to that in the early exponential phase, the abundance of this bacterium increased during the late exponential growth phase of Gambierdiscus. When the dinoflagellate culture was subjected to N limitation, the abundance of the bacterium represented by both 16S rDNA and CWH increased. Based on these results and published literature, it is apparent that this Rhizobium bacterium benefits from the association with Gambierdiscus by hydrolyzing and utilizing the extracellular organic matter exudates released by the dinoflagellate. This is the first report of Rhizobium species being associated with dinoflagellates, which will shed light on the algae-bacteria relationships.IMPORTANCEPhytoplankton are the undisputed primary producers in the aquatic ecosystems and contribute approximately half of the global net primary productivity.Dinoflagellates are one of the most important phytoplankton in the marine ecosystems. Commonly, they do not exist autonomously in the marine environment but rather co-live with many bacteria that interact with dinoflagellates, producing a dynamic microbial ecosystem. Their interactions play a major role in important processes such as carbon fluxes and nutrient regeneration in the ocean, ultimately influencing the global carbon cycle and the climate. Hence, there is a need to understand the association and relationships between dinoflagellates and bacteria. Here, we tried to elucidate these interactions through isolating and characterizing a bacterium from a benthic toxic dinoflagellate culture. Our study is the first report of such bacterium being recorded to be associated with a dinoflagellate in this genus, providing new insights into the dinoflagellate-bacteria association for future research.

Isolation and Characterization of a Strain of Acidithiobacillus ferrooxidans

2013 ◽  
Vol 777 ◽  
pp. 242-246
Author(s):  
Ju Fang Xiao ◽  
Song Yan Qin ◽  
Peng Huang ◽  
Li Na Guo ◽  
Yi Chun Chen
Keyword(s):  
Acidithiobacillus Ferrooxidans ◽  
Oxidation Rate ◽  
Growth Process ◽  
Ph Value ◽  
Exponential Growth Phase ◽  
Sequencing Analysis ◽  
Isolation And Characterization ◽  
Potential Alternative ◽  
Acid Waste

An acidophilic strain was isolated from drainage in Shanxi coal mine, after 16SrDNA amplification and sequencing analysis, it was identified to be Acidithiobacillus ferrooxidans. The ferrous ion oxidation rate of At.f and pH value were studied during its growth, the results showed that, the strain entering into the exponential growth phase needed about 30 hours, and the oxidation rate was more than 99% after 60 hours. The pH value increased from 2.08 to 2.64 at first 30 hours and then decreased to 2.0, and finally maintained at 2.0 in the whole growth process. The isolated strain provided a potential alternative method to handle the steel-picking sulfuric acid waste liquor.

scholarly journals Discrepancies between Global Forest Net Primary Productivity Estimates Derived from MODIS and Forest Inventory Data and Underlying Factors

2021 ◽  
Vol 13 (8) ◽  
pp. 1441
Author(s):  
Jin Han Park ◽  
Jianbang Gan ◽  
Chan Park
Keyword(s):  
Low Income ◽  
Primary Productivity ◽  
Carbon Stock ◽  
Forest Cover ◽  
Net Primary Productivity ◽  
Estimation Methods ◽  
Future Research ◽  
Important Indicator ◽  
Sequestration Potential ◽  
Carbon Losses

The net primary productivity (NPP) of a forest is an important indicator of its potential for the provision of ecosystem services such as timber, carbon, and biodiversity. However, accurately and consistently quantifying global forest NPP remains a challenge in practice. We converted carbon stock changes using the Global Forest Resources Assessment (FRA) data and carbon losses associated with disturbances and timber removals into an NPP equivalent measurement (FRA NPP*) and compared it with the NPP derived from the MODIS satellite data (MOD17 NPP) for the world’s forests. We found statistically significant differences between the two NPP estimates, with the FRA NPP* being lower than the MOD17 NPP; the differences were correlated with forest cover, normalized difference vegetation index (NDVI), and GDP per capita in countries, and may also stem from the NPP estimation methods and scopes. While the former explicitly accounts for carbon losses associated with timber removals and disturbances, the latter better reflects the principles of photosynthesis. The discrepancies between the two NPP estimates increase in countries with a low income or low forest cover, calling for enhancing their forest resource assessment capacity. By identifying the discrepancies and underlying factors, we also provide new insights into the relationships between the MOD17 NPP and global forest carbon stock estimates, motivating and guiding future research to improve the robustness of quantifying global forest NPP and carbon sequestration potential.

scholarly journals Isolation and Characterization of Salt Tolerant Endophytic and Rhizospheric Plant Growth-Promoting Bacteria (PGPB) Associated with the Halophyte Plant (Sesuvium Verrucosum) Grown in KSA

2015 ◽  
Vol 3 (3) ◽  
pp. 552-560 ◽  
Author(s):  
Mohamed A.M. El-Awady ◽  
Mohamed M. Hassan ◽  
Yassin M. Al-Sodany
Keyword(s):  
Nitrogen Fixation ◽  
Acetic Acid ◽  
Plant Growth ◽  
Growth Promotion ◽  
Exponential Growth Phase ◽  
Plant Growth Promoting Bacteria ◽  
Salt Tolerant ◽  
Isolation And Characterization ◽  
Growth Promoting

This study was designed to isolate and characterize endophytic and rhizospheric bacteria associated with the halophyte plant Sesuvium verrucosum, grown under extreme salinity soil in Jeddah, Saudi Arabia. The plant growth promotion activities of isolated bacterial were evaluated in vitro. A total of 19 salt tolerant endophytic and rhizospheric bacterial isolates were obtained and grouped into six according to genetic similarity based on RAPD data. These six isolates were identified by amplification and partial sequences of 16S rDNA as Enterobacter cancerogenus,Vibrio cholerae, Bacillus subtilis, Escherichia coli and two Enterobacter sp. Isolates were then grown until exponential growth phase to evaluate the atmospheric nitrogen fixation, phosphate solubilization, and production of phytohormones such as indole-3-acetic acid, as well as 1-aminocyclopropane-1-carboxylate (ACC) deaminase activity. While, All of the six strains were negative for ACC deaminaseactivity, two isolates showed Nitrogen fixation activity, three isolates produce the plant hormone (Indole acetic acid) and two isolates have the activity of solubiliztion of organic phosphate. Among the six isolates, the isolate (R3) from the soil around the roots is able to perform the three previous growth promoting possibilities together and it is ideal for use in promoting the growth of plants under the high salinity conditions. This isolate is candidate to prepare a friendly biofertelizer that can be used for the improvement of the crops performance under salinity conditions.Int J Appl Sci Biotechnol, Vol 3(3): 552-560

Molecular analysis of the Penicillium marneffei glyceraldehyde-3-phosphate dehydrogenase-encoding gene (gpdA) and differential expression of gpdA and the isocitrate lyase-encoding gene (acuD) upon internalization by murine macrophages

2008 ◽  
Vol 57 (11) ◽  
pp. 1322-1328 ◽  
Author(s):  
Sophit Thirach ◽  
Chester R. Cooper ◽  
Nongnuch Vanittanakom
Keyword(s):  
Differential Expression ◽  
Isocitrate Lyase ◽  
Glyoxylate Cycle ◽  
Evolutionary Relationship ◽  
Amino Acid Sequences ◽  
Penicillium Marneffei ◽  
Macrophage Infection ◽  
Dimorphic Fungus ◽  
Isolation And Characterization ◽  
Encoding Gene

Penicillium marneffei is an intracellular dimorphic fungus that can cause a fatal disseminated disease in human immunodeficiency virus-infected patients. The factors that affect the pathogenicity of this fungus remain unclear. Here, we report the isolation and characterization of the gpdA cDNA and genomic clones encoding glyceraldehyde-3-phosphate dehydrogenase (GAPDH) in P. marneffei. Phylogenetic analysis of GAPDH amino acid sequences demonstrated the evolutionary relationship of P. marneffei to other fungi, including the intracellular pathogen Ajellomyces capsulatus. To assess the central importance of phagocytic cells in defence against P. marneffei infection, we used Northern blotting to investigate the response of the isocitrate lyase-encoding gene (acuD) and gpdA to nutrient deprivation inside macrophages. The results revealed that after macrophage internalization, the gene involved in the glyoxylate cycle, acuD, showed higher expression levels as early as 2 h from the start of co-incubation, and the differential expression could be observed again at 8 h after infection. In contrast, the expression of gpdA was downregulated in the yeast phase, as well as during macrophage infection after 2, 4 and 8 h of infection. The induction of P. marneffei acuD was shown to be coordinated with the downregulation of the glycolytic gpdA gene, implying that the cytoplasmic environment of macrophages is deficient in glucose and the glyoxylate pathway could be used by this pathogen to allow subsistence on two-carbon compounds within the host cell following its intracellular persistence.

scholarly journals Characterization of a Novel Fructosyltransferase from Lactobacillus reuteri That Synthesizes High-Molecular-Weight Inulin and Inulin Oligosaccharides

2002 ◽  
Vol 68 (9) ◽  
pp. 4390-4398 ◽  
Author(s):  
S. A. F. T. van Hijum ◽  
G. H. van Geel-Schutten ◽  
H. Rahaoui ◽  
M. J. E. C. van der Maarel ◽  
L. Dijkhuizen
Keyword(s):  
Molecular Weight ◽  
High Molecular Weight ◽  
Lactobacillus Reuteri ◽  
Bacterial Strains ◽  
Potential Health ◽  
Isolation And Characterization ◽  
A Cell ◽  
Encoding Gene ◽  
First Time

ABSTRACT Fructosyltransferase (FTF) enzymes produce fructose polymers (fructans) from sucrose. Here, we report the isolation and characterization of an FTF-encoding gene from Lactobacillus reuteri strain 121. A C-terminally truncated version of the ftf gene was successfully expressed in Escherichia coli. When incubated with sucrose, the purified recombinant FTF enzyme produced large amounts of fructo-oligosaccharides (FOS) with β-(2→1)-linked fructosyl units, plus a high-molecular-weight fructan polymer (>107) with β-(2→1) linkages (an inulin). FOS, but not inulin, was found in supernatants of L. reuteri strain 121 cultures grown on medium containing sucrose. Bacterial inulin production has been reported for only Streptococcus mutans strains. FOS production has been reported for a few bacterial strains. This paper reports the first-time isolation and molecular characterization of (i) a Lactobacillus ftf gene, (ii) an inulosucrase associated with a generally regarded as safe bacterium, (iii) an FTF enzyme synthesizing both a high molecular weight inulin and FOS, and (iv) an FTF protein containing a cell wall-anchoring LPXTG motif. The biological relevance and potential health benefits of an inulosucrase associated with an L. reuteri strain remain to be established.

scholarly journals First Report of an Aster Yellows Phytoplasma Associated with Cabbage in Southern Texas

Plant Disease ◽  
2001 ◽  
Vol 85 (4) ◽  
pp. 447-447 ◽  
Author(s):  
I.-M. Lee ◽  
R. A. Dane ◽  
M. C. Black ◽  
Noel Troxclair
Keyword(s):  
16S Rdna ◽  
Nested Pcr ◽  
Restriction Enzymes ◽  
Diagnostic Procedures ◽  
Acid Extraction ◽  
Insect Vector ◽  
Aster Yellows ◽  
First Report ◽  
Pcr Products ◽  
Aster Yellows Phytoplasma

In early spring 2000 carrot crops in southwestern Texas were severely infected by an outbreak of phyllody associated with aster yellows phytoplasma. Cabbage crops that had been planted adjacent to these carrot fields began to display previously unobserved symptoms characteristic of phytoplasma infection. Symptoms included purple discoloration in leaf veins and at the outer edges of leaves on cabbage heads. Proliferation of sprouts also occurred at the base of the stem and between leaf layers of some plants, and sprouts sometimes continued to proliferate on extended stems. About 5% of cabbage plants in the field exhibited these symptoms. Two symptomless and four symptomatic cabbage heads were collected in early April from one cabbage field. Veinal tissues were stripped from each sample and used for total nucleic acid extraction. To obtain specific and sufficient amount of PCR products for analysis, nested PCR was performed by using primer pairs (first with P1/P7 followed by R16F2n/R16R2) (1,2) universal for phytoplasma detection. A specific 16S rDNA fragment (about 1.2 kb) was strongly amplified from the four symptomatic but not from the two asymptomatic samples. The nested PCR products obtained from the four symptomatic samples were then analyzed by restriction fragment length polymorphism (RFLP) using the restriction enzymes MseI, HhaI, and HpaII, and the RFLP patterns were compared to the published patterns of known phytoplasmas (1). The resulting RFLP patterns were identical to those of a phytoplasma belonging to subgroup B of the aster yellows phytoplasma group (16SrI). These RFLP patterns were also evident in putative restriction sites observed in a 1.5 kbp nucleotide sequence of the 16S rDNA. This is the first report of aster yellows phytoplasma associated disease symptoms in cabbage in Texas. The occurrence of cabbage proliferation coincided with the presence of high populations of the insect vector, aster leafhopper. References: (1) I.-M. Lee et al. Int. J. Syst. Bacteriol. 48:1153, 1998. (2) B. Schneider et al. 1995. Molecular and Diagnostic Procedures in Mycoplasmology, Vol. I. Academic Press, San Diego, CA.

scholarly journals First Report on the Molecular Identification of Phytoplasma (16SrII-D) Associated with Witches' Broom of Kalmegh (Andrographis paniculata) in India

Plant Disease ◽  
2015 ◽  
Vol 99 (1) ◽  
pp. 155-155 ◽  
Author(s):  
S. T. Saeed ◽  
A. Khan ◽  
A. Samad
Keyword(s):  
16S Rdna ◽  
Nested Pcr ◽  
Disease Incidence ◽  
Antioxidant Properties ◽  
First Record ◽  
Andrographis Paniculata ◽  
Medicinal And Aromatic Plants ◽  
First Report ◽  
16S Rdna Sequence Analysis ◽  
Virtual Rflp

Andrographis paniculata (family Acanthaceae), also known as “King of Bitters” or Kalmegh, is an important medicinal plant used for the treatment of various diseases. It has antimicrobial, antiviral, anti-inflammatory, hepatoprotective, antidiabetic, antihyperglycemic, and antioxidant properties (1). During June 2014, while performing a routine survey of the commercial trial fields of Kalmegh at Central Institute of Medicinal and Aromatic Plants (CIMAP), Lucknow, India, typical phytoplasma disease symptoms such as virescence, proliferation, and witches' broom along with little leaf and stunted growth were observed. The disease incidence was estimated to be approximately 7 to 10%. To ascertain the presence of phytoplasma, 16 samples of leaves were collected from nine different field sites, and total genomic DNA was extracted from the symptomatic and symptomless Kalmegh plants by the CTAB method. Direct and nested PCR assays were performed targeting the 16S rDNA using generic phytoplasma primer pairs P1/P6 followed by R16F2n/R16R2 (2). Resulting bands of the expected size (1.5 kb and 1.2 kb, respectively) were amplified from symptomatic plants. No amplification was observed with DNA from asymptomatic plant samples. The purified nested PCR products were cloned into E. coli DH5α, using the pGEM-T Easy vector (Promega, United States) and sequenced with primers M13For/M13Rev using an automatic sequencer (ABI Prism, Perkin Elmer) at CIMAP. The sequence was analyzed by BLASTn and found to share 99% similarity with Echinacea witches'-broom phytoplasma and Sesame phyllody phytoplasma strain (GenBank Accession Nos. JF340080 and KF612966, respectively), which belong to the 16SrII-D group. The sequence was deposited in NCBI as GenBank Accession No. KM359410. A phylogenetic tree using MEGA v5.0 (4) was constructed with 16S rDNA; consensus sequences of phytoplasmas belonging to distinct groups revealed that the present phytoplasma clustered with the 16SrII group. iPhyClassifier software was used to perform sequence comparison and generate a virtual restriction fragment length polymorphism (RFLP) profile (5). On the basis of iPhyClassifier, the 16S rDNA sequence analysis of our isolate showed 99.2% similarity with that of the ‘Candidatus Phytoplasma australasiae’ reference strain (GenBank Accession No. Y10097), which belongs to 16Sr group II. The virtual RFLP pattern of F2n/R2 fragment was most similar to the 16SrII-D subgroup (similarity coefficient of 0.91) but showed a difference in profile with HpaI, HhaI, and MseI enzymes. Several bacterial/fungal and viral diseases have been reported on A. paniculata (3); however, to our knowledge, this is the first report of witches' broom disease in India and the first record of a 16SrII-D group phytoplasma on Kalmegh. Its presence in Kalmegh is of great significance due to its commercial interest. References: (1) S. Akbar. Altern. Med. Rev. 16:1, 2011. (2) D. E. Gundersen and M. Lee. Phytopathol. Mediterr. 35:144, 1996. (3) A. Khan and A. Samad. Plant Dis. 98:698, 2014. (4) K. Tamura et al. Mol. Biol. Evol. 28:2731, 2011. (5) Y. Zhao et al. Int. J. Syst. Evol. Microbiol. 59:2582, 2009.

scholarly journals First Report of Xylella fastidiosa in Peach in New Mexico

Plant Disease ◽  
2011 ◽  
Vol 95 (7) ◽  
pp. 871-871 ◽  
Author(s):  
J. J. Randall ◽  
J. French ◽  
S. Yao ◽  
S. F. Hanson ◽  
N. P. Goldberg
Keyword(s):  
New Mexico ◽  
Prunus Persica ◽  
Xylella Fastidiosa ◽  
Its Region ◽  
23S Rrna ◽  
Pcr Analysis ◽  
Sequencing Analysis ◽  
First Report ◽  
Dark Green ◽  
Branch Dieback

Xylella fastidiosa is a gram-negative bacterium that causes disease in a wide variety of plants such as grapes, citrus trees, oleanders, and elm and coffee trees. This bacterium is xylem limited and causes disease symptoms such as leaf scorch, stunting of plant growth, branch dieback, and fruit loss. The presence of X. fastidiosa was previously reported in New Mexico where it was found to be infecting chitalpa plants and grapevines (3). In the summer of 2010, peach (Prunus persica (L.) Batsch) trees from two locations in northern New Mexico exhibited leaf deformity and stunting, dark green venation, slight mottling, and branch dieback. Preliminary viral diagnostic screening was performed by Agdia (Elkhart, IN) on one symptomatic tree and it was negative for all viruses tested. Three trees from two different orchards tested positive for X. fastidiosa by ELISA and PCR analysis using X. fastidiosa-specific primer sets HL (1) and RST (2). Bacterial colonies were also cultured from these samples onto periwinkle wilt media. Eight colonies obtained from these three plants tested PCR positive using the X. fastidiosa-specific primers. The 16S ribosomal and 16S-23S rRNA internal transcribed spacer (ITS) region (557 nucleotides) (GenBank Accession No. HQ292776) along with the gyrase region (400 nucleotides) (GenBank Accession No. HQ292777) was amplified from the peach total DNA samples and the bacterial colonies. Sequencing analysis of these regions indicate that the X. fastidiosa found in peach is 100% similar to other X. fastidiosa multiplex isolates including isolates from peach, pecan, sycamore, and plum trees and 99% similar to the X. fastidiosa isolates previously found in New Mexico. Further analysis of the 16S ribosomal and 16S-23S rRNA ITS sequences with maximum likelihood phylogenetic analysis using Paup also groups the peach isolates into the X. fastidiosa multiplex subspecies. The gyrase sequence could not be used to differentiate the peach isolates into a subspecies grouping because of the lack of variability within the sequence. This X. fastidiosa multiplex subspecies could possibly be a threat to the New Mexico pecan industry since pecan infecting X. fastidiosa isolates belong to the same bacterial subspecies. It is not known if X. fastidiosa subspecies multiplex isolates from peach are capable of infecting pecans but they are closely genetically related. It is interesting to note that the isolates from peach are different than previously described X. fastidiosa isolates in New Mexico that were infecting chitalpa and grapes (3). X. fastidiosa has previously been described in peach; the disease is called “phony peach”. The peach trees exhibited stunting and shortened internodes as reported for “phony peach”. They also exhibited slight mottling and branch dieback that may be due to the environment in New Mexico or perhaps they are also exhibiting mineral deficiency symptoms in association with the X. fastidiosa disease. To our knowledge, this is the first report of X. fastidiosa in peach in New Mexico. References: (1) M. H. Francis et al. Eur. J. Plant Pathol. 115:203, 2006. (2) G. V. Minsavage et al. Phytopathology 84:456, 1994. (3) J. J. Randall et al. Appl. Environ. Microbiol. 75:5631, 2009.

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