Evidence for sedimenting particles as the origin of the microbial community in a coastal marine sediment

Novitsky, JA

doi:10.3354/meps060161

Cited by 24 publications

(19 citation statements)

References 11 publications

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“…Most forms of aquaculture contribute to enhanced sedimentation of organic material proximal to the culture units (Hall et al 1990, Jaramillo et al 1992. The annual mean sedimentation rate at the reference site (36.4 g dry wt m-* d-l) in Upper South Cove was in the range reported by Novitsky (1990) for nearby Halifax Harbour (26.2 to 55.2 g dry wt m-2 d-l), using sediment traps of the same design. The sedimentation rate for the mussel-line site (88.7 g dry wt m-2 d-l), Table 7.…”

Section: Sediment Respiration and Macrofaunamentioning

confidence: 56%

“…Carbon and nitrogen analyses were performed on 10 m1 subsamples of trap contents filtered onto silver filters (0.8 pm Hytrex membranes; Osmonics Inc., Minnetonka, MN, USA) with a Perkin Elmer model 185B CHN analyser. Further details of sediment traps can be found in Novitsky (1990).…”

Section: Methodsmentioning

confidence: 99%

“…Sedimentation was measured in acrylic tubes (6 cm i.d., 60 cm long) closed at the bottom with a rubber stopper. Eight tubes were secured in a weighted plastic box which was set on the sediment surface (Novitsky 1990). The traps were deployed between April 20, 1989 andApril 20, 1990 for periods which averaged 2 wk.…”

Section: Methodsmentioning

confidence: 99%

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Effects of suspended mussel culture (Mytilus spp.) on sedimentation, benthic respiration and sediment nutrient dynamics in a coastal bay

Hatcher¹,

Grant²,

Schofield³

1994

Mar. Ecol. Prog. Ser.

188

102

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Many studies have shown that the pnmary effect of shellfish culture on nearshore m a n n e systems is enhanced sedimentation T h~s study was d e s~g n e d to measure the effects of this enhanced sedimentation on the respiration and nutrlent fluxes of the benthic community and the coupling between the pelagic and b e n t h~c systems at a mussel culture s~t e (Mytllus edulls and M trossulus) In Upper South Cove, Nova Scotia, Canada There was a signif~cant association between chlorophyll In the water colun~n and sedimentation rate In Upper South Cove over the study year 1990, particularly under the mussel llnes, but the malority of the part~culate carbon and nitrogen whlch fell to the bottom was not Incorporated Into the sediments Suspended mussel culture had little Impact on sediment phosphorus dynamics The largest response of the sediment coinmunity to suspended mussel culture was ammonium release, whlch was higher under the mussel lines at all times of the year Over the year, the sedlments of the reference site were a net sink f o~ total dissolved nitrogen, whlle the sediments under the mussel line were a source

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Section: Sediment Respiration and Macrofaunamentioning

confidence: 56%

Section: Methodsmentioning

confidence: 99%

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Effects of suspended mussel culture (Mytilus spp.) on sedimentation, benthic respiration and sediment nutrient dynamics in a coastal bay

Hatcher¹,

Grant²,

Schofield³

1994

Mar. Ecol. Prog. Ser.

188

102

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“…4). Novitsky (1990) reported that marine sedimenting particles may influence sediment bacterial communities. This phylogenetic group was also found in marine sedimenting particles (Rath et al, 1998).…”

Section: Verrucomicrobiamentioning

confidence: 99%

Microbial diversity in marine sediments from Sagami Bay and Tokyo Bay, Japan, as determined by 16S rRNA gene analysis The DDBJ accession numbers for the sequences reported in this paper are AB022607–AB022642.

1999

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16S rDNA clone libraries were analysed to investigate the microbial diversity in marine sediments from Sagami Bay (stations SA, water depth of 1159 m, and SB, 1516 m) and Tokyo Bay (station TK, 43 m). A total of 197 clones was examined by amplified rDNA restriction analysis (ARDRA) using three fourbase-specific restriction enzymes (HhaI, RsaI and HaeIII). In SA, 57 RFLP types were detected from 77 clones. In SB, 17 RFLP types were detected from 62 clones. In TK, 21 RFLP types were detected from 58 clones. The genotypic diversity among the three sampling sites was 0958, 0636 and 0821, respectively, indicating that the microbial diversity of SA was higher than at the other two stations. At SA, the most abundant RFLP type constituted 10 % of all clones. The samples from SB and TK had dominant RFLP types which constituted 60 % and 38 % of the total clone libraries, respectively. The community structure of SA included many single-type clones, which were found only once in the clone libraries. This structure contrasted with that of the other two stations. Thirty-seven clones were selected and sequenced according to dendrograms derived from ARDRA, to cover most of the microbial diversity in the clone libraries. No clones were identical to any of the known 16S rRNA sequences or to each other. All sequences had S848 % similarity to rDNA sequences retrieved from the DNA databases. Sequenced clones fell into five major lineages of the domain Bacteria : the gamma, delta and epsilon Proteobacteria, Gram-positive bacteria and the division Verrucomicrobia. At SA, the Verrucomicrobia and the three subclasses of the Proteobacteria were found. Most clone sequences belonged to the gamma Proteobacteria. The high-GC Gram-positive bacteria and the gamma subclass of the Proteobacteria were common at both SB and TK. Although the depths of SB and TK were very different, the community diversity inferred from ARDRA and the taxonomic position of the dominant clones were similar. All clones belonging to the high-GC Gram-positive bacteria collected from both SB and TK fell into the same cluster and are regarded as members of an unknown actinomycete group. The clone compositions were different at each sampling site, and clones of the gamma Proteobacteria and high-GC Gram-positive bacteria were dominant.

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“…Marine sediments probably represent some of the most complex microbial habitats on earth: in these sediments, complex microbial communities arise through the merging of indigenous microorganisms present in marine sediments and external organisms transported from the water column or the terrestrial environment (Novitsky 1990). Although studying the microbial diversity and microbial population is essential for under-standing biogeochemical cycles, limited information is available because of the limitation of traditional cultivation techniques for assessing microbial diversity and population in marine sediments.…”

Section: Introductionmentioning

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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Evidence for sedimenting particles as the origin of the microbial community in a coastal marine sediment

Cited by 24 publications

References 11 publications

Effects of suspended mussel culture (Mytilus spp.) on sedimentation, benthic respiration and sediment nutrient dynamics in a coastal bay

Effects of suspended mussel culture (Mytilus spp.) on sedimentation, benthic respiration and sediment nutrient dynamics in a coastal bay

Microbial diversity in marine sediments from Sagami Bay and Tokyo Bay, Japan, as determined by 16S rRNA gene analysis The DDBJ accession numbers for the sequences reported in this paper are AB022607–AB022642.

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

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