Communities In Marine Sediments Research Articles

The Effect of TBT on the Structure of a Marine Sediment Community – a Boxcosm Study

The effect of tri- n-butyl tin (TBT) on an intact marine sediment community after five months exposure was investigated. Changes in the structure of macro- and meiofauna communities were determined, as well as the functional diversity of the microbial community using BIOLOG microplates for Gram negative bacteria. Development of tolerance in the microbial community was investigated using Pollution Induced Community Tolerance (PICT) experiments with fluxes of nutrients as effect indicators. TBT affected the structure and recruitment of the macro- and meiofauna at nominal additions of 30–137 μmol TBT/m 2 sediment. Number of species, diversity, biomass and community similarity was reduced at these concentrations compared to control. Species that molt seemed to be the most tolerant since they were predominant in boxes that had received the highest TBT addition and echinoderms were the most sensitive species. Renewed addition of TBT in PICT experiments with sediment from each boxcosm showed that TBT had an effect on individual nutrient fluxes from all sediments. Analyses of the flux patterns revealed a memory of previous TBT exposure, either due to induced tolerance or other community conditioning.

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

MEPS Marine Ecology Progress Series Contact the journal Facebook Twitter RSS Mailing List Subscribe to our mailing list via Mailchimp HomeLatest VolumeAbout the JournalEditorsTheme Sections MEPS 220:47-57 (2001) - doi:10.3354/meps220047 Characterization of microbial communities in marine surface sediments by terminal-restriction fragment length polymorphism (T-RFLP) analysis and quinone profiling Hidetoshi Urakawa*, Tsutomu Yoshida, Masahiko Nishimura, Kouichi Ohwada** Ocean Research Institute, University of Tokyo, 1-15-1 Minamidai, Nakano-ku, Tokyo 164-8639, Japan *Present address: Civil and Environmental Engineering, University of Washington, 201 More Hall, Seattle, Washington 98195-2700, USA. **Present address: Faculty of Environmental and symbiotic Sciences, Prefectural University of Kumamoto, 3-1-100 Tsukide, Kumamoto 862-8502, Japan. E-mail: ohwada@pu-kumamoto.ac.jp ABSTRACT: 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 (HhaI, RsaI and MspI) 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. KEY WORDS: Microbial community · Marine sediment · Terminal-restriction fragment length polymorphism (T-RFLP) analysis · Quinone profiling Full text in pdf format PreviousNextExport citation RSS - Facebook - Tweet - linkedIn Cited by Published in MEPS Vol. 220. Online publication date: September 27, 2001 Print ISSN: 0171-8630; Online ISSN: 1616-1599 Copyright © 2001 Inter-Research.

Molecular and isotopic analysis of anaerobic methane-oxidizing communities in marine sediments

Convergent lines of molecular, carbon-isotopic, and phylogenetic evidence have previously indicated (Hinrichs, K.-U., Hayes, J.M., Sylva, S.P., Brewer, P.G., DeLong, E.F., 1999. Methane-consuming archaebacteria in marine sediments. Nature 398, 802–805.) that archaea are involved in the anaerobic oxidation of methane in sediments from the Eel River Basin, offshore northern California. Now, further studies of those same sediments and of sediments from a methane seep in the Santa Barbara Basin have confirmed and extended those results. Mass spectrometric and chromatographic analyses of an authentic standard of sn-2-hydroxyarchaeol (hydroxylated at C-3 in the sn-2 phytanyl moiety) have confirmed our previous, tentative identification of this compound but shown that the previously examined product was the mono-TMS, rather than di-TMS, derivative. Further analyses of 13C-depleted lipids, appreciably more abundant in samples from the Santa Barbara Basin, have shown that the archaeal lipids are accompanied by two sets of products that are only slightly less depleted in 13C. These are additional glycerol ethers and fatty acids. The alkyl substituents in the ethers (mostly monoethers, with some diethers) are non-isoprenoidal. The carbon-number distributions and isotopic compositions of the alkyl substituents and of the fatty acids are similar, suggesting strongly that they are produced by the same organisms. Their structures, n-alkyl and methyl-branched n-alkyl, require a bacterial rather than archaeal source. The non-isoprenoidal glycerol ethers are novel constituents in marine sediments but have been previously reported in thermophilic, sulfate- and nitrate-reducing organisms which lie near the base of the rRNA-based phylogenetic tree. Based on previous observations that the anaerobic oxidation of methane involves a net transfer of electrons from methane to sulfate, it appears likely that the non-archaeal, 13C-depleted lipids are products of one or more previously unknown sulfate-reducing bacteria which grow syntrophically with the methane-utilizing archaea. Their products account for 50% of the fatty acids in the sample from the Santa Barbara Basin. At all methane-seep sites examined, the preservation of aquatic products is apparently enhanced because the methane-oxidizing consortium utilizes much of the sulfate that would otherwise be available for remineralization of materials from the water column.

Horizontal heterogeneity of denitrifying bacterial communities in marine sediments by terminal restriction fragment length polymorphism analysis.

Although it is widely believed that horizontal patchiness exists in microbial sediment communities, determining the extent of variability or the particular members of the bacterial community which account for the observed differences among sites at various scales has not been routinely demonstrated. In this study, horizontal heterogeneity was examined in time and space for denitrifying bacteria in continental shelf sediments off Tuckerton, N.J., at the Rutgers University Long-Term Ecosystem Observatory (LEO-15). Characterization of the denitrifying community was done using PCR amplification of the nitrous oxide reductase (nosZ) gene combined with terminal restriction fragment length polymorphism analysis. Spatial scales from centimeters to kilometers were examined, while temporal variation was assayed over the course of 1995 to 1996. Sorenson's indices (pairwise similarity values) were calculated to permit comparison between samples. The similarities of benthic denitrifiers ranged from 0.80 to 0.85 for centimeter scale comparisons, from 0.52 to 0.79 for meter level comparisons, and from 0.23 to 0.53 for kilometer scale comparisons. Sorenson's indices for temporal comparisons varied from 0.12 to 0.74. A cluster analysis of the similarity values indicated that the composition of the denitrifier assemblages varied most significantly at the kilometer scale and between seasons at individual stations. Specific nosZ genes were identified which varied at centimeter, meter, or kilometer scales and may be associated with variability in meio- or macrofaunal abundance (centimeter scale), bottom topography (meter scale), or sediment characteristics (kilometer scale).

Nitrite reductase genes (nirK and nirS) as functional markers to investigate diversity of denitrifying bacteria in pacific northwest marine sediment communities.

Genetic heterogeneity of denitrifying bacteria in sediment samples from Puget Sound and two sites on the Washington continental margin was studied by PCR approaches amplifying nirK and nirS genes. These structurally different but functionally equivalent single-copy genes coding for nitrite reductases, a key enzyme of the denitrification process, were used as a molecular marker for denitrifying bacteria. nirS sequences could be amplified from samples of both sampling sites, whereas nirK sequences were detected only in samples from the Washington margin. To assess the underlying nir gene structure, PCR products of both genes were cloned and screened by restriction fragment length polymorphism (RFLP). Rarefraction analysis revealed a high level of diversity especially for nirS clones from Puget Sound and a slightly lower level of diversity for nirK and nirS clones from the Washington margin. One group dominated within nirK clones, but no dominance and only a few redundant clones were seen between sediment samples for nirS clones in both habitats. Hybridization and sequencing confirmed that all but one of the 228 putative nirS clones were nirS with levels of nucleotide identities as low as 45.3%. Phylogenetic analysis grouped nirS clones into three distinct subclusters within the nirS gene tree which corresponded to the two habitats from which they were obtained. These sequences had little relationship to any strain with known nirS sequences or to isolates (mostly close relatives of Pseudomonas stutzeri) from the Washington margin sediment samples. nirK clones were more closely related to each other than were the nirS clones, with 78.6% and higher nucleotide identities; clones showing only weak hybridization signals were not related to known nirK sequences. All nirK clones were also grouped into a distinct cluster which could not be placed with any strain with known nirK sequences. These findings show a very high diversity of nir sequences within small samples and that these novel nir clusters, some very divergent from known sequences, are not known in cultivated denitrifiers.

Changes in fatty acids of Pseudomonas nautica, a marine denitrifying bacterium, in response to n-eicosane as carbon source and various culture conditions

This study determined the effects of shifts in environmental conditions on the fatty acid composition of a sedimentary facultative anaerobic denitrifying marine bacteria (Pseudomonas nautica strain IP 617). The effects of carbon source (n-eicosane, sodium acetate and rich medium), temperature (13, 20 and 30°C), presence or lack of oxygen and growth phase (stationary and exponential) were investigated. As demonstrated by correspondence analysis, the effect of the various conditions tested, in descending order of importance, were carbon source>temperature>growth phase≥oxygen. Among the different growth substrates, n-eicosane (nC20) led to the most distinct FA profiles, characterised by high amounts of saturated and branched FA, the appearance of 20-carbon acids (20:1ω9 and 20:0) and a Δ10 methyl branched series with mainly the 10Me16:0. With regard to temperature effects, P. nautica showed a mean acyl chain length thermoregulation process for the major monounsaturated fatty acids which led to increased values of the ratio ΣC18:1/ΣC16:1 with increasing temperatures. The effect of growth phase and anaerobiosis were less marked. The analysis of bacterial fatty acids could enable the detection of hydrocarbonoclastic bacterial communities in marine sediments contaminated by hydrocarbons.

Changes in fatty acids of Pseudomonas nautica, a marine denitrifying bacterium, in response to n-eicosane as carbon source and various culture conditions

This study determined the effects of shifts in environmental conditions on the fatty acid composition of a sedimentary facultative anaerobic denitrifying marine bacteria ( Pseudomonas nautica strain IP 617). The effects of carbon source ( n-eicosane, sodium acetate and rich medium), temperature (13, 20 and 30°C), presence or lack of oxygen and growth phase (stationary and exponential) were investigated. As demonstrated by correspondence analysis, the effect of the various conditions tested, in descending order of importance, were carbon source>temperature>growth phase≥oxygen. Among the different growth substrates, n-eicosane ( nC 20) led to the most distinct FA profiles, characterised by high amounts of saturated and branched FA, the appearance of 20-carbon acids (20:1ω9 and 20:0) and a Δ 10 methyl branched series with mainly the 10Me16:0. With regard to temperature effects, P. nautica showed a mean acyl chain length thermoregulation process for the major monounsaturated fatty acids which led to increased values of the ratio ΣC 18:1/ΣC 16:1 with increasing temperatures. The effect of growth phase and anaerobiosis were less marked. The analysis of bacterial fatty acids could enable the detection of hydrocarbonoclastic bacterial communities in marine sediments contaminated by hydrocarbons.

Phylogenetic analysis of the bacterial communities in marine sediments.

For the phylogenetic analysis of microbial communities present in environmental samples microbial DNA can be extracted from the sample, 16S rDNA can be amplified with suitable primers and the PCR, and clonal libraries can be constructed. We report a protocol that can be used for efficient cell lysis and recovery of DNA from marine sediments. Key steps in this procedure include the use of a bead mill homogenizer for matrix disruption and uniform cell lysis and then purification of the released DNA by agarose gel electrophoresis. For sediments collected from two sites in Puget Sound, over 96% of the cells present were lysed. Our method yields high-molecular-weight DNA that is suitable for molecular studies, including amplification of 16S rRNA genes. The DNA yield was 47 micrograms per g (dry weight) for sediments collected from creosote-contaminated Eagle Harbor, Wash. Primers were selected for the PCR amplification of (eu)bacterial 16S rDNA that contained linkers with unique 8-base restriction sites for directional cloning. Examination of 22 16S rDNA clones showed that the surficial sediments in Eagle Harbor contained a phylogenetically diverse population of organisms from the Bacteria domain (G. J. Olsen, C. R. Woese, and R. Overbeek, J. Bacteriol. 176:1-6, 1994) with members of six major lineages represented: alpha, delta, and gamma Proteobacteria; the gram-positive high G+C content subdivision; clostridia and related organisms; and planctomyces and related organisms. None of the clones were identical to any representatives in the Ribosomal Database Project small subunit RNA database. The analysis of clonal representives in the first report using molecular techniques to determine the phylogenetic composition of the (eu)bacterial community present in coastal marine sediments.

Organic sedimentation and macrofauna as forcing factors in marine benthic nanofagellate communities

We investigated how benthic nanoflagellate communities in marine sediments respond to sedimentation of organic material and to the presence of macrofaunal organisms in controlled boxcosms. An input of 24 g C m(-2) resulted in a sharp increase in densities, from 93 to 477 × 10(3) flagellates cm(-3) within 11 days. At the onset, this increase was paralleled by enhanced bacterial production and bacterial numbers. When bacterial production collapsed, flagellate ingestion rates, varying from 17 to 67 bact flag(-1) h(-1), were sufficient to control bacterial abundance. The presence of macrofauna accelerated the burst in flagellate densities. With macrofauna the same maximum densities were reached, but later densities dropped to relatively low levels. Macrofaunal bioturbation resulted in higher flagellate densities deeper in the sediment (up to 1200% at 3 cm and up to 460% at 6 cm deep).