Microbial community patterns of potential substrate utilization: a comparison of salt marsh, sand dune, and seawater-irrigated agronomic systems

Goodfriend, Wendy

doi:10.1016/s0038-0717(97)00167-3

Cited by 36 publications

(14 citation statements)

References 31 publications

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“…Microorganisms are typically plated on laboratory culture media, and different types of colonies are identified with biochemical or morphological methods (11,12). Microbial communities can also be analyzed with carbon-source utilization patterns through the application of environmental samples into BIOLOG microplates (13,14). Other methods, including fatty acid methyl ester (FAME), phospholipid fatty acid ester (PLFA), C 0 t 1/2 curve analysis, and denaturing gradient gel electrophoresis (DGGE) have also been applied to analyze microbial communities with or without culturing microbes (15)(16)(17)(18)(19).…”

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confidence: 99%

Microbial phyllosphere populations are more complex than previously realized

Yang

Crowley

Borneman

et al. 2001

Proc. Natl. Acad. Sci. U.S.A.

328

229

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Phyllosphere microbial communities were evaluated on leaves of field-grown plant species by culture-dependent and -independent methods. Denaturing gradient gel electrophoresis (DGGE) with 16S rDNA primers generally indicated that microbial community structures were similar on different individuals of the same plant species, but unique on different plant species. Phyllosphere bacteria were identified from Citrus sinesis (cv. Valencia) by using DGGE analysis followed by cloning and sequencing of the dominant rDNA bands. Of the 17 unique sequences obtained, database queries showed only four strains that had been described previously as phyllosphere bacteria. Five of the 17 sequences had 16S similarities lower than 90% to database entries, suggesting that they represent previously undescribed species. In addition, three fungal species were also identified. Very different 16S rDNA DGGE banding profiles were obtained when replicate cv. Valencia leaf samples were cultured in BIOLOG EcoPlates for 4.5 days. All of these rDNA sequences had 97-100% similarity to those of known phyllosphere bacteria, but only two of them matched those identified by the culture independent DGGE analysis. Like other studied ecosystems, microbial phyllosphere communities therefore are more complex than previously thought, based on conventional culture-based methods.A ll plant species in natural habitats have associated epiphytic microflora comprising the so-called phyllosphere (1, 2). The composition and quantity of nutrients, including carbohydrates, organic acids, and amino acids that support the growth of epiphytic bacteria, are affected by the plant species, leaf age, leaf physiological status, and the presence of tissue damage (3). Similarly, host plants, leaf age, leaf position, physical environmental condition, and availability of immigrant inoculum have also been suggested to be involved in determining species of microbes in the phyllosphere (4-7).There has been much interest in life forms that inhabit extreme environments such as the phyllosphere. With the repeated, rapid alteration of environmental conditions occurring on leaf surfaces, the phyllosphere has been recognized as a hostile environment to bacteria (8). Leaf surfaces are often dry and temperatures can reach 40-55°C under intense sunlight. During the night, however, leaves are frequently wet with dew and at relatively cool temperatures (5-10°C). Strong UV radiation during the day and sparse nutritional (oligotrophic) conditions also contribute to stressful conditions in the phyllosphere (8). More than 85 different species of microorganisms in 37 genera have been reported in the phyllospheres of rye, olive, sugar beet, and wheat, all by culture-based methods (8-10). Most of these bacteria establish large populations with no apparent effect on the plant, but a few of them can infect the leaves and cause disease (1).Microbial ecologists have devoted much effort to investigating microbial diversity and studying biological interactions between species in the environment. Microor...

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mentioning

confidence: 99%

Microbial phyllosphere populations are more complex than previously realized

Yang

Crowley

Borneman

et al. 2001

Proc. Natl. Acad. Sci. U.S.A.

328

229

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“…The functional classification of microbial communities based on carbon substrate utilization pattern (Biolog ECO MicroPlate) has been frequently used for examining of community-level physiological functions (Garland and Mills 1991). Potential microbial functional diversity is defined as the number and type carbon substrate sources used by the microbial community (Goodfriend 1998). Functional diversity is a valuable parameter for comparison of differences in ecosystems, habitats, or sites.…”

Section: Introductionmentioning

confidence: 99%

Effects of seawater irrigation on soil microbial community structure and physiological function

Chaudhary

Rathore

Jha

2016

Int. J. Environ. Sci. Technol.

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Irrigation with diluted seawater would be an alternative water resource which can play an important role under scarce resources of freshwater for promoting agricultural production in coastal areas. Salvadora persica Linn. was irrigated with different concentrations of seawater (0, 10, 20, 40, 60, 80 and 100 % seawater), and their effect on plant growth, nutrient contents in soil and plants, shift in soil microbial community structure (phospholipid fatty acid; PLFA) and community-level physiological profiling (CLPP, Biolog ECO MicroPlate) were studied. Plant dry matter was significantly increased with all seawater treatments, and highest increase was at 20 % seawater treatment. Sodium and chloride contents were significantly increased, whereas ratios of K/Na and Ca/Na were significantly decreased in plants with seawater irrigation. Soil electrical conductivity (EC), available K and Na were significantly increased with increasing the concentration of seawater. Total PLFA concentration and PLFA profile of soils were used as indices of total microbial biomass and community composition, respectively. The concentrations of total PLFA, gram-positive, gram-negative and actinomycetes biomarker PLFAs were significantly reduced at 20, 40, 80 and 40 % concentrations of seawater, respectively. The application of different concentrations of seawater induced a clear shift in the soil microbial community structure toward the bacterial abundance. The microbial community structure and community-level physiological profiling in seawater irrigation treatments had significantly differentiated. It can be concluded that irrigation with different concentrations of seawater had significant impact on soil chemical and microbial properties which is attributed due to the salinity stress.

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“…Distinctive colour patterns in the reaction well array have been reported and described for soils from different ecosystems and plant communities as well as agricultural soil with different management regimes [10,11,12]. As an example, Goodfriend [13] determined that microbial community substrate utilization refl ected similarity in habitat type rather than geographical infl uences in different saline systems (salt marsh, sand dune, and seawater irrigated agronomic systems). Limited studies have been made on soil microbial community activity due to consistent long-term experimental soil management within a site or to the fl exible on-farm soil management and no work has been done on casing soil.…”

Section: Introductionmentioning

confidence: 99%

Evaluation of in situ functional activity of casing soils during growth cycle of mushroom (Agaricus bisporus (Lange) Imbach) employing community level physiological profiles (CLPPs)

Choudhary¹,

Agarwal²,

Johri

2009

Indian J Microbiol

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Community level physiological profi les (CLPPs) have been rarely applied to mushroom compost ecosystem, probably for the lack of standardized methodology. Recently, however CLPPs have been employed as a tool to investigate the degree of maturity of compost (Mondini and Insam, 2005, Compost Science and Utilization, 13(1): 27-33). The potential of CLPPs to detect compost maturity test is considerably signifi cant in that it provides sensitivity and the simplicity of the assay. The aim of this work was to investigate the maturity of casing that comprised of farm yard manure and spent compost and infl uence of casing type on the behaviour of bacterial community during the growth cycle of mushroom Agaricus bisporus (Lange) Imbach employing standardized inoculum density and effects of different data interpretation based on the kinetics of colour formation. Casing samples of different age were extracted at a particular dilution and then inoculated in 96 well microtitre plates. Optical density (OD) in well was measured at 590 nm every 24 hours for 5 days. Principal component analysis (PCA) was performed by employing OD values at fi xed average well colour development (AWCD). PCA of fresh samples showed that classifi cation and ordination of samples according to their age were signifi cant with fi xed AWCD.

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Microbial community patterns of potential substrate utilization: a comparison of salt marsh, sand dune, and seawater-irrigated agronomic systems

Cited by 36 publications

References 31 publications

Microbial phyllosphere populations are more complex than previously realized

Microbial phyllosphere populations are more complex than previously realized

Effects of seawater irrigation on soil microbial community structure and physiological function

Evaluation of in situ functional activity of casing soils during growth cycle of mushroom (Agaricus bisporus (Lange) Imbach) employing community level physiological profiles (CLPPs)

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