Identification and characterization of humic substances-degrading bacterial isolates from an estuarine environment

Esham, E

doi:10.1016/s0168-6496(00)00078-7

Cited by 9 publications

(11 citation statements)

References 24 publications

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“…These organisms include members of the roseobacter group (3), Agrobacterium species (5,30,32), Acinetobacter species (11,31,42), and Bacillus species (23). 3,4-PCD activity has not been found in members of the rhodobacter group or the Halomonadaceae group (in which isolates SE37 and SE96 cluster), although both of these groups contain members capable of metabolizing aromatic compounds (9,35).…”

Section: Resultsmentioning

confidence: 99%

Diversity of the Ring-Cleaving Dioxygenase Gene pcaH in a Salt Marsh Bacterial Community

Buchan¹,

Neidle

Moran³

2001

Appl Environ Microbiol

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Degradation of lignin-related aromatic compounds is an important ecological process in the highly productive salt marshes of the southeastern United States, yet little is known about the mediating organisms or their catabolic pathways. Here we report the diversity of a gene encoding a key ring-cleaving enzyme of the ␤-ketoadipate pathway, pcaH, amplified from bacterial communities associated with decaying Spartina alterniflora, the salt marsh grass that dominates these coastal systems, as well as from enrichment cultures with aromatic substrates (p-hydroxybenzoate, anthranilate, vanillate, and dehydroabietate). Sequence analysis of 149 pcaH clones revealed 85 unique sequences. Thirteen of the 53 amino acid residues compared were invariant in the PcaH proteins, suggesting that these residues have a required catalytic or structural function. Fifty-eight percent of the clones matched sequences amplified from a collection of 36 bacterial isolates obtained from seawater, marine sediments, or senescent Spartina. Fifty-two percent of the pcaH clones could be assigned to the roseobacter group, a marine lineage of the class ␣-Proteobacteria abundant in coastal ecosystems. Another 6% of the clones matched genes retrieved from isolates belonging to the genera Acinetobacter, Bacillus, and Stappia, and 42% of the clones could not be assigned to a cultured bacterium based on sequence identity. These results suggest that the diversity of the genes encoding a single step in aromatic compound degradation in the coastal marsh examined is high.

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Section: Resultsmentioning

confidence: 99%

Diversity of the Ring-Cleaving Dioxygenase Gene pcaH in a Salt Marsh Bacterial Community

Buchan¹,

Neidle

Moran³

2001

Appl Environ Microbiol

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“…At present we can only speculate about the ecological role of Actinobacteria in different types of freshwaters. Members of this lineage might be able to utilize refractory humic substances, as is known for other gram-positive Bacteria, including actinobacterial genera (13,20). Humic substances are a prominent component of the dissolved organic carbon pool in many systems (6, 24) (e.g., in Lake Fuchskuhle) and an important carbon source for aquatic Bacteria (2,34).…”

Section: Abundant Freshwater Bacteria With Gram-positive Cell Walls?mentioning

confidence: 99%

An Improved Protocol for Quantification of Freshwater Actinobacteria by Fluorescence In Situ Hybridization

Sekar

Pernthaler

et al. 2003

Appl Environ Microbiol

278

253

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We tested a previously described protocol for fluorescence in situ hybridization of marine bacterioplankton with horseradish peroxidase-labeled rRNA-targeted oligonucleotide probes and catalyzed reporter deposition (CARD-FISH) in plankton samples from different lakes. The fraction of Bacteria detected by CARD-FISH was significantly lower than after FISH with fluorescently monolabeled probes. In particular, the abundances of aquatic Actinobacteria were significantly underestimated. We thus developed a combined fixation and permeabilization protocol for CARD-FISH of freshwater samples. Enzymatic pretreatment of fixed cells was optimized for the controlled digestion of gram-positive cell walls without causing overall cell loss. Incubations with high concentrations of lysozyme (10 mg ml ؊1 ) followed by achromopeptidase (60 U ml ؊1 ) successfully permeabilized cell walls of Actinobacteria for subsequent CARD-FISH both in enrichment cultures and environmental samples. Between 72 and >99% (mean, 86%) of all Bacteria could be visualized with the improved assay in surface waters of four lakes. For freshwater samples, our method is thus superior to the CARD-FISH protocol for marine Bacteria (mean, 55%) and to FISH with directly fluorochrome labeled probes (mean, 67%). Actinobacterial abundances in the studied systems, as detected by the optimized protocol, ranged from 32 to >55% (mean, 45%). Our findings confirm that members of this lineage are among the numerically most important Bacteria of freshwater picoplankton.

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“…Studies on bacterial isolates capable of utilizing humic substances have shown these bacteria to be phylogenetically and physiologically diverse. Aerobic isolates include α‐ and γ‐ Proteobacteria and Gram‐positive bacteria (Esham et al ., 2000) and anaerobic isolates include Proteobacteria of all subdivisions as well as Acidobacteria (Coates et al . 2002).…”

Section: Introductionmentioning

confidence: 99%

Effect of humic material on the bacterioplankton community composition in boreal lakes and mesocosms

Haukka

Heikkinen

Kairesalo

et al. 2005

Environmental Microbiology

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The bacterioplankton community composition in two Finnish forest lakes with different content of humic substances was studied by denaturing gradient gel electrophoresis (DGGE) and sequencing of the major bands. The same dominant bacterial phylotypes were detected in the bacterioplankton communities of clear-water Lake Ahvenlammi and humic Lake Sammalisto. For 4 years, in every water layer, Actinobacteria was the dominant and Verrucomicrobia the second most common phylum. In the hypolimnion, other dominant phyla were also found. We set up a mesocosm experiment to assess the effect of a sudden load of allochthonous humus extract to the bacterioplankton community composition. Changes in the bacterial communities were followed in four control and four humus extract-added mesocosms for 50 days. In the humic mesocosms the phylotypes of allochthonous Proteobacteria arriving with the humus extract were initially prevalent but disappeared during the first weeks. After this the Actinobacteria-dominated communities resembled the bacterioplankton communities of the control mesocosms and Lake Ahvenlammi. Towards the end of the experiment the community patterns in all the mesocosms started to change slightly because of erratic occurrence of new proteobacterial phylotypes. Thus the effects of a sudden load of allochthonous humic material and bacteria to the bacterioplankton community composition were transient.

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Identification and characterization of humic substances-degrading bacterial isolates from an estuarine environment

Cited by 9 publications

References 24 publications

Diversity of the Ring-Cleaving Dioxygenase Gene pcaH in a Salt Marsh Bacterial Community

Diversity of the Ring-Cleaving Dioxygenase Gene pcaH in a Salt Marsh Bacterial Community

An Improved Protocol for Quantification of Freshwater Actinobacteria by Fluorescence In Situ Hybridization

Effect of humic material on the bacterioplankton community composition in boreal lakes and mesocosms

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