Identifying numerically abundant culturable bacteria from complex communities: an example from a lignin enrichment culture

Abstract

Culturable bacteria that were numerically important members of a marine enrichment community were identified and characterized phylogenetically. Selective and nonselective isolation methods were used to obtain 133 culturable bacterial isolates from model marine communities enriched with the high-molecular-weight (lignin-rich) fraction of pulp mill effluent. The culture collection was screened against community DNA from the lignin enrichments by whole-genome hybridization methods, and three marine bacterial isolates were identified as being numerically important in the communities. One isolate was in the ␣-subclass of Proteobacteria, and the other two were in the ␥-subclass of Proteobacteria. Isolate-specific 16S rRNA oligonucleotide probes designed to precisely quantify the isolates in the lignin enrichment communities indicated contributions ranging from 2 to 32% of enrichment DNA, values nearly identical to those originally obtained by the simpler whole-genome hybridization method. Two 16S rRNA sequences closely related to that of one of the isolates, although not identical, were amplified via PCR from the seawater sample originally used to inoculate the enrichment medium. Partial sequences of 14 other isolates revealed significant phylogenetic diversity and unusual sequences among the culturable lignin enrichment bacteria, with the Proteobacteria, Cytophaga-Flavobacterium, and gram-positive groups represented.

New phylotypes of mesophilic filamentous anoxygenic phototrophic bacteria enriched from sulfide‐containing environments

“…giganteum (87% similarity). Similar matches between 16S rRNA gene sequences derived from culture-dependent and -independent techniques have been observed for organisms that are quantitatively abundant in the environment (Gonzalez et al, 1996;Gich et al, 2005).…”

Near real‐time, autonomous detection of marine bacterioplankton on a coastal mooring in Monterey Bay, California, using rRNA‐targeted DNA probes

“…Biotin-(C9)3-TGGTCCGTGTCTCAGTAC Cross reacts with many groups; not used in study Manz et al (1996) Malph-1_488 Capture Marine alphaproteobacteria Biotin-(C9)3-GCCGGGGTTTCTTTACCA Gel purified Gonzalez et al (1996) Gonzalez and Moran ( were run using different batches of arrays (data not shown). Samples prepared by the ESP were similar to if not more reactive than those prepared manually.…”

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

“…These prosthecate bacteria are typically characterized as oligotrophic bacteria that adhere to surfaces, and have been isolated from a variety of littoral marine sources including coastal regions in the western USA and India [22]. Isolate HS199 (week 2; Q-Proteobacteria) was most similar in 16S rRNA gene sequence to the aerobic marine bacterium Alteromonas macleodii [23] and was also closely related to an isolate obtained previously from a lignin enrichment culture of southeastern USA seawater [7]. A number of Gram-positive isolates (HS346 (week 2), HS503 (week 5), HS596 (week 5), HS406 (week 5), and HS410 (week 5)) were closely related to Paenibacillus lautus, a facultative anaerobe from soil [24] and Paenibacillus glucanolyticus, a soil-associated facultative anaerobe capable of hydrolyzing various L-glucans including carboxymethylcellulose [25].…”

“…Although our study is limited to only the culturable bacteria from the enrichment communities, it appears that organisms with a variety of phylogenetic af-¢liations are capable of degrading humic substances in the estuarine/marine environment. Gonzälez et al [7] likewise isolated bacteria associated with the K-Proteobacteria, Q-Proteobacteria, and the Cytophaga/Flavobacterium group Isolates presented as capable of utilizing aromatic compounds exhibited turbidity over three transfers in liquid medium and caused loss of absorbance in the medium in the 200^350-nm range. from marine enrichment cultures with a lignin derivative as the sole carbon source.…”

“…In part, this situation re£ects the general belief that readily cultured bacteria represent opportunistic species, rather than typical estuarine or marine organisms, and therefore that studies of isolates have little ecological relevance. Recently, it has been argued that typical marine bacteria can indeed be isolated [4,6] or that bacteria can be isolated which are closely related to ecologically important species and can therefore o¡er potential insights into their physiology [7]. In the case of humic substances-degrading bacteria, careful study of marine isolates could provide information on potential phylogenetic a¤liations and metabolic capabilities that allow growth on this complex substrate.…”