Molecular phylogenetic analysis of a soil microbial community in a soybean field

Ueda, Tadashi; Suga, Yasuhiro; Matsuguchi, Tatsuhiko

doi:10.1111/j.1365-2389.1995.tb01337.x

Cited by 134 publications

(128 citation statements)

References 32 publications

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“…The DNA extraction method described by Ueda et al (1995) was used with some modifications. We mixed approximately 20 g of sediment with an equal volume of 120 mM sodium phosphate buffer (pH 8.0) containing 5% SDS; the mixture was vigorously shaken in a plastic bottle for 40 min at 25°C.…”

Section: Methodsmentioning

confidence: 99%

Characterization of microbial communities in marine surface sediments by terminal-restriction fragment length polymorphism (T-RFLP) analysis and quinone profiling

Urakawa¹,

Yoshida²,

Nishimura³

et al. 2001

Mar. Ecol. Prog. Ser.

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We characterized microbial communities from Japanese coastal sediments by using terminal-restriction fragment length polymorphism (T-RFLP) analysis and quinone profiling. Surface sediments (0 to 2 cm) were collected from 5 different locations, Tokyo Bay (S1: water depth 15 m), Sagami Bay (S2: 1520 m; S3: 1133 m), Suruga Bay (S4: 1290 m), and Nankai Trough (S5: 4023 m). The length of terminal-restriction fragments (T-RFs) was estimated by an automated DNA sequencer. The average fragment numbers (mean ± SD) estimated from the 3 separate restriction analyses (Hha I, Rsa I and Msp I) were S1 = 74 ± 6.2, S2 = 28 ± 4.6, S3 = 27 ± 6.2, S4 = 73 ± 4.0, and S5 = 35 ± 2.1. Sixteen quinone homologs were detected from S2, S3, S4 and S5, while 17 homologs were found from S1. Major differences in the quinone profiles among sampling sites were primarily related to the relative abundance of quinone homologs. However, the difference in homolog number did not contribute to the change of profile in each sampling site. The appearance and disappearance of quinone homologs were only seen in minor components. Community profiles from T-RFLP analysis revealed that the microbial population in Sagami Bay (S2 and S3) and Nankai Trough (S5) were similar (16.8 to 25.8% divergence). On the other hand, sediments from Sagami Bay (S2 and S3) were closely related to each other (13.9% divergence), but quinone profiling of Nankai Trough sediment (S5) was not similar to those of Sagami Bay. It was assumed that this difference derived from different characteristics of the 2 techniques used. Thus, we found that the phylogenetic structures in S2, S3, and S5 were similar, but the relative abundance and physiological condition of the microbial populations was apparently different between Sagami Bay (S2 and S3) and Nankai Trough (S5). In this study, a combination of the methods T-RFLP and quinone profiling succeeded in characterizing the microbial community of marine sediments and it is likely that this approach will prove effective in future analyses of microbial communities in marine sediments.

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Section: Methodsmentioning

confidence: 99%

Characterization of microbial communities in marine surface sediments by terminal-restriction fragment length polymorphism (T-RFLP) analysis and quinone profiling

Urakawa¹,

Yoshida²,

Nishimura³

et al. 2001

Mar. Ecol. Prog. Ser.

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“…1992, DeLong et al 1994, McInerney et al 1995a, b. Preston et al 1996. Relatives also include 2 soil archaeal clones (Ueda et al 1995;see also RDP, Maidak et al 1994) as well as clones recently found in freshwater lake sediments (Hershberger et al 1996). The second group falls among the Euryarchaeota (contaming methanogens, halophiles, and some thermophiles; Woese 1987), is distantly related (<80'% sequence similarity) to Thermoplasma, and has also previously been reported from coastal and offshore marine plankton (DeLong 1992.…”

Section: Archaeamentioning

confidence: 99%

Widespread Archaea and novel Bacteria from the deep sea as shown by 16S rRNA gene sequences

Fuhrman¹,

Davis²

1997

Mar. Ecol. Prog. Ser.

230

189

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ABSTRACT. Marine microbial diversity is important yet poorly-known, due to low culturability and undersampling. However, 16s rRNA gene sequences cloned directly from biomass allow us to know what microbial types are present, irrespective of culturing, and to create probes suitable for biodiversity studies. Many sequences are needed for good probe design. Here we report on sequences from 57 deep sea clones, obtained by the polymerase chain reaction with 'universal' primers, from 500 m and 3000 m depths in the northeast Pacific and 1000 m depth in the subtropical Atlantic. The most common group, with 19 of the new sequences (10 Atlantic), was a recently reported crenarchaeal cluster, Group I. We also found 6 sequences in 2 other archaeal groups in the broad methanogen-halophile lineage; 2 of these were in a distinct lineage not previously reported. The bacterial sequences included 22 dispersed among the a and y Proteobacteria (8 related to SAR 1 l), 5 related to a previously reported broad group (Group A) of marine clones poorly affiliated with known (cultured and sequenced) major bacterial divisions, 6 in a second group with little affiliation to any previously reported division (we call this Group B), 1 In a third possible major novel group, 2 deeply branched with~n the 'Green Nonsulfur' lineage, and 1 branching with a soil clone. In contrast to the vast majority of the sequences, a cluster of 5 sequences was very close to a cultured marine proteobacterium, Alterornonas macleod~j. It appeared that 5 of the clones were chimeric, although this label is difficult to apply when sequences are only distantly related to those in the database, as was common. We conclude that the deep sea contains numerous novel and widespread major prokaryotic lineages. Given the huge volume of this habitat and typical bacteria.1 abundances, it appears that the previously unknown archaeal and bacterial groups may be the most abundant organisms on Earth.

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“…Also, short 16s rDNA clone sequences from a paddy field (Maidak et al, 1994), a soybean field (Ueda et al, 1995) and a marine environment (Fuhrman et al, 1993) were demonstrated to cluster with these actinobacterial sequences. Thus it has been concluded that this group of uncultured organisms might contribute to ecologically important processes (Rheims et al, 1996b).…”

Section: Introductionmentioning

confidence: 99%

Ribosome analysis reveals prominent activity of an uncultured member of the class Actinobacteria in grassland soils

et al. 1997

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A 16s rRNA-based molecular ecological study was performed to search for dominant bacterial sequences in Drentse A grassland soils (The Netherlands). In the first step, a library of 165 clones was generated from PCR-amplified 165 rDNA. By sequence comparison, clone DA079 and two other identical clones could be affiliated to a group of recently described uncultured Actinobacteria. This group contained 165 rDNA clone sequences obtained from different environments across the world. To determine whether such uncultured organisms were part of the physiologically active population in the soil, ribosomes were isolated from the environment and 16s rRNA was partially amplified via RT-PCR using conserved primers for members of the domain Bacteria. Subsequent sequence-specif ic separation by temperature-gradient gel electrophoresis (TGGE) generated fingerprints of the amplicons. Such community fingerprints were compared with the TGGE pattern of PCRamplified rDNA of clone DA079 which was generated with the same set of primers. One of the dominant fingerprint bands matched with the band obtained from the actinobacterial clone. Southern blot hybridization with a probe made from clone DA079 confirmed sequence identity of clone and fingerprint band. This is the first report that a member of the novel actinobacterial group may play a physiologically active role in a native microbial community.

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Molecular phylogenetic analysis of a soil microbial community in a soybean field

Cited by 134 publications

References 32 publications

Characterization of microbial communities in marine surface sediments by terminal-restriction fragment length polymorphism (T-RFLP) analysis and quinone profiling

Characterization of microbial communities in marine surface sediments by terminal-restriction fragment length polymorphism (T-RFLP) analysis and quinone profiling

Widespread Archaea and novel Bacteria from the deep sea as shown by 16S rRNA gene sequences

Ribosome analysis reveals prominent activity of an uncultured member of the class Actinobacteria in grassland soils

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