Community Structure In Sediments Research Articles

Microbial communities in wetlands of the Athabasca oil sands: genetic and metabolic characterization

Naphthenic acids are a complex family of naturally occurring cyclic and acyclic carboxylic acids that are present in the acidic fraction of petroleum. Naphthenic acids are acutely toxic to aquatic organisms. Previous studies showed that wetland sediments exposed to oil sands process water containing naphthenic acids had higher rates of naphthenic acid degradation in vitro compared with unexposed wetlands. In this study we compare the microbial community structures in sediments from wetlands exposed to different amounts of oil sands process water using BIOLOG, phospholipid fatty acid analysis and denaturing gradient gel electrophoresis of total bacterial DNA. Community profiles were compared using cluster analysis. BIOLOG profiles were primarily influenced by seasonal trends rather than naphthenic acids content. In contrast, phospholipid fatty acid analysis comparisons clustered communities that had higher levels of residual oil, although this association was not strong. In contrast, cluster diagrams produced from the denaturing gradient gel electrophoresis data clearly separated bacterial communities according to naphthenic acids concentrations, indicating that naphthenic acids content was a major influence on the composition of the bacterial community. In addition, denaturing gradient gel electrophoresis profiles indicated that naphthenic acids-exposed bacterial communities were homogeneous on a scale of meters, whereas unexposed (off-site) wetlands were less homogeneous.

Variation in microbial biomass and community structure in sediments of peter the great bay (sea of japan/east sea), as estimated from fatty acid biomarkers

Variation in the microbial biomass and community structure found in sediment of heavily polluted bays and the adjacent unpolluted areas were examined using phospholipid fatty acid analysis. Total microbial biomass and microbial community structure were responding to environmental determinants, sediment grain size, depth of sediment, and pollution due to petroleum hydrocarbons. The marker fatty acids of microeukaryotes and prokaryotes - aerobic, anaerobic, and sulfate-reducing bacteria -were detected in sediments of the areas studied. Analysis of the fatty acid profiles revealed wide variations in the community structure in sediments, depending on the extent of pollution, sediment depth, and sediment grain size. The abundance of specific bacterial fatty acids points to the dominance of prokaryotic organisms, whose composition differed among the stations. Fatty acid distributions in sediments suggest the high contribution of aerobic bacteria. Sediments of polluted sites were significantly enriched with anaerobic bacteria in comparison with clean areas. The contribution of this bacterial group increased with the depth of sediments. Anaerobic bacteria were predominantly present in muddy sediments, as evidenced from the fatty acid profiles. Relatively high concentrations of marker fatty acids of sulfate-reducing bacteria were associated with organic pollution in this site. Specific fatty acids of microeukaryotes were more abundant in surface sediments than in deeper sediment layers. Among the microeukaryotes, diatoms were an important component. Significant amounts of bacterial biomass, the predominance of bacterial biomarker fatty acids with abundance of anaerobic and sulfate-reducing bacteria are indicative of a prokaryotic consortium responsive to organic pollution.

Quantifying bioirrigation using ecological parameters: a stochastic approach†.

Irrigation by benthic macrofauna has a major influence on the biogeochemistry and microbial community structure of sediments. Existing quantitative models of bioirrigation rely primarily on chemical, rather than ecological, information and the depth-dependence of bioirrigation intensity is either imposed or constrained through a data fitting procedure. In this study, stochastic simulations of 3D burrow networks are used to calculate mean densities, volumes and wall surface areas of burrows, as well as their variabilities, as a function of sediment depth. Burrow networks of the following model organisms are considered: the polychaete worms Nereis diversicolor and Schizocardium sp., the shrimp Callianassa subterranea, the echiuran worm Maxmuelleria lankesteri, the fiddler crabs Uca minax, U. pugnax and U. pugilator, and the mud crabs Sesarma reticulatum and Eurytium limosum. Consortia of these model organisms are then used to predict burrow networks in a shallow water carbonate sediment at Dry Tortugas, FL, and in two intertidal saltmarsh sites at Sapelo Island, GA. Solute-specific nonlocal bioirrigation coefficients are calculated from the depth-dependent burrow surface areas and the radial diffusive length scale around the burrows. Bioirrigation coefficients for sulfate obtained from network simulations, with the diffusive length scales constrained by sulfate reduction rate profiles, agree with independent estimates of bioirrigation coefficients based on pore water chemistry. Bioirrigation coefficients for O2 derived from the stochastic model, with the diffusion length scales constrained by O2 microprofiles measured at the sediment/water interface, are larger than irrigation coefficients based on vertical pore water chemical profiles. This reflects, in part, the rapid attenuation with depth of the O2 concentration within the burrows, which reduces the driving force for chemical transfer across the burrow walls. Correction for the depletion of O2 in the burrows results in closer agreement between stochastically-derived and chemically-derived irrigation coefficient profiles.

Microenvironments and microbial community structure in sediments

The aim of this study was to explore the potential of a combined chemical and microbiological approach as part of a study of organic carbon oxidation processes in sediments. An assessment of microbiological diversity using molecular techniques was carried out in combination with high resolution chemical measurements at the sediment-water interface of a coastal lagoon affected by eutrophication in autumn 2000. There was a 0.2 mm overlap between the O2 and H2S profiles. pH showed a maximum just above the sediment-water interface coinciding with an oxygen maximum, suggesting photosynthetic activity, and a minimum coinciding with the O2-H2S interface. The redox potential was high in bottom water and surface sediment, reflecting the presence of oxygen and oxides, and reached low values after a step-wise decrease at -18 mm. Reduction of Fe occurred within the biofilm at the O2-H2S interface and was mostly due to reduction by H2S. The elevated concentrations of dissolved Mn in the oxic water may have been caused either by in situ production within organic aggregates or lateral water flow from sites nearby at which Mn2+ diffuses out of the sediment. Sequences related to sulphur chemolitotrophs were retrieved from the biofilm samples, which is consistent with the small overlap between O2 and H2S observed in this biofilm. Although the resolution of techniques used was different, sequencing results were consistent with chemical data in delineating the same horizons according to redox, pH or ecological properties.

Macrobenthos of Spartina foliosa (Pacific Cordgrass) Salt Marshes in Southern California: Community Structure and Comparison to a Pacific Mudflat and a Spartina alterniflora (Atlantic Smooth Cordgrass) Marsh

Environmental attributes (vegetation and sediment properties) of and macrofaunal community structure in sediments of five southern California Spartina foliosa marshes (San Diego Bay, Mission Bay, Upper Newport Bay, Bolsa Chica Lagoon, and Anaheim Bay) were examined during October 1994. Macrofaunal densities in Pacific S. foliosa marshes (avg. 122,268 indiv. m2>300 μm) were 3 to 10 times higher than observed in Atlantic S. alterniflora and S. anglica marshes. The macrofauna of S. foliosa marshes was composed mainly of enchytraeid, naidid, and tubificid oligochaetes (66%), with the enchytraeids dominant at all sites except Bolsa Chica Lagoon. Polychaetes, insects, and peracarid crustaceans accounted for most of the remaining fauna. Multivariate analyses indicated greatest faunal similarity between the two southernmost marshes (Mission Bay and San Diego Bay), and between Anaheim and Newport Bay marshes, with Bolsa Chica Lagoon exhibiting a distinct assemblage. There were strong positive associations of faunal abundance and composition with percent organic matter and percent open area, and negative associations with percent sand and dry weight of algae. For the vegetated marsh in Mission Bay, faunal comparisons were made with an adjacent mudflat and with a S. alterniflora marsh in North Carolina, USA. The unvegetated mudflat exhibited similar macrofaunal densities but higher species richness than the adjacent Spartina marsh. The macrofaunal assemblage of the Mission Bay S. foliosa marsh differed from that of the Atlantic S. alterniflora marsh and the Pacific mudflat in having a greater proportion of oligochaetes, especially Enchytraeidae, and fewer polychaetes. This study represents the first published description that we are aware of for macrofauna in S. foliosa vegetated marsh sediments. The findings document faunal variation among southern California embayments and suggest that differences in macrobenthic community structure occur between marsh and mudflat habitat as well as between east and west coast Spartina marshes. Observed differences may have significant implications for wetland conservation and restoration efforts.

Sediment community structure around a whale skeleton in the deep Northeast Pacific: Macrofaunal, microbial and bioturbation effects

Chemoautotrophic communities on lipid-rich whale skeletons are known from a total of 16 modern and fossil sites in the deep Pacific Ocean. While the attached fauna of modern whale bones has been studied, the impact of whale falls on surrounding sediment assemblages remains largely unevaluated. Using the research submersible Alvin, we sampled the sediment community at distances of 0, 0.5, 1, 2, 4, and ∼100 m from the lipid-rich skeleton of a 21 m balaenopterid on the 1240 m seafloor in Santa Catalina Basin. When sampled in 1988 and 1991, the skeleton had been on the seafloor for >4 yr and supported a large attached chemoautotrophic assemblage. Sedimentary organic content, microbial biomass and bacterial abundance were not significantly different near the skeleton than in background sediments, and pore-water sulfide concentrations were only modestly elevated (to ⩽20 μM) adjacent to the bones. The species composition of infaunal macrobenthos near the skeleton was similar to that in background sediments, providing little evidence of a specialized enrichment and/or sulfophilic assemblage. Nonetheless, macrofaunal abundance within 0.5 m of the skeleton was reduced by >40%, due to a decline in the paraonid polychaete Levinsenia oculata. The reduction in L. oculata (the community dominant) caused a sharp increase in rarefaction diversity near the skeleton. Bioturbation intensities, evaluated from 234Th profiles, were also dramatically reduced in sediments near the skeleton, as were rates of extracellular lipase activity. We postulate that reduced infaunal abundance and bioturbation near the skeleton resulted from the interference effects of vesicomyid clam-shell debris, and that the low bioturbation rates in turn limited extracellular lipase activity. We conclude that whale skeletons, and the remains of their associated chemoautotrophic assemblages, may physically impact nearby sediment communities for years after the organic and sulfide enrichment effects of whale falls have dissipated, yielding changes in infaunal diversity and bioturbation.

Comparative description of microbial community structure in surface sediments of eutrophic bays

Comparisons of microbial community structure in sediments of eutrophic areas such as Hiroshima Bay, Etauchi Bay, Osaka Bay and Kojima Lake in Japan were undertaken by analysing the phospholipid fatty acid (PLFA) composition in sediments. In addition, the PLFA composition of aerobic bacteria, anaerobic bacteria and sulphate reducing bacteria (SRB) were analysed to assess their contribution to sedimentary lipid. The monounsaturated PLFA and branched PLFA were predominantly present in aerobic bacteria, and anaerobic bacteria and SRB, respectively. The PLFA composition of sediments showed significant regional differences among the four study areas, indicating the significant difference in microbial community structure. The aerobic prokaryotes and eukaryotes were predominantly present in all the study areas except in Osaka Bay where the gram-positive bacteria and anaerobic bacteria were predominant. The characteristic PLFA of aerobic prokaryotes and eukaryotes were significantly higher in Kojima Lake than other areas whereas the biomarker PLFA of gram-positive bacteria were predominantly present in Osaka Bay than that in other areas. These significant variations in microbial community structure can be attributed to the differences in environmental perturbation.

Microbial community structure analysis of euxinic sediments using phospholipid fatty acid biomarkers

Microbial community structure in sediments, as determined by the phospholipid ester-linked fatty acid (PLFA) analysis, collected from Kojima Lake during summer and winter was described with reference to the environmental quality of the lake. A characteristic feature of the study area was the persistence of anoxia in summer and winter in the deeper area, and the sediments were under the reduced condition with high levels of sulfide, chemical oxygen demand, and low values of oxidation-reduction potential. PLFA profiles of the sediment were dominated by the saturated, branched and monounsaturated fatty acids. Small amounts (less than 5% of the total PLFA) of polyunsaturated fatty acids (biomarker fatty acids of microeukaryotes) and long chain fatty acids were detected in sediments. Total PLFA concentrations in sediments were higher in summer than in winter. Microbial community structure in the lake sediments was predominated by the prokaryotes, as evidenced from the larger amounts of bacterial biomarker fatty acids in the range of C10 to C20. The presence of signature fatty acids of sulfate reducing bacteria in sediments was consistent with the high levels of sulfide in the sediment and anoxic condition in the study area. PLFA showed significant differences in PLFA profiles between shallow and deeper areas, indicating the differences in the lipid contributing communities. However, no such a significant difference was observed between summer and winter.

Microbial community structure in sediments of a polluted bay as determined by phospholipid ester-linked fatty acids

Phospholipid ester-linked fatty acid (PLFA) composition in sediments were determined in order to understand the microbial community structure in a polluted bay. The PLFA pattern in sediments revealed the presence of aerobic and anaerobic bacteria, the composition of which differed among the stations. The community structure in sediments, as characterized by the composition of PLFA showed an absence of polyunsaturated fatty acids, except 18:2, signature fatty acids of microeukaryotes and a greater proportion of bacterial biomarker fatty acids. The results of Tukey's honestly significant difference test showed distinctive differences in the PLFA among the stations and also shifts in the microbial community structure in the bay. The significant patterns of PLFA in sediments with the virtual absence of lipid biomarkers for microeukaryotes and the relatively high proportions of bacterial biomarkers indicate the prokaryotic consortium responsive to organic contamination.

Variation in Microbial Biomass and Community Structure in Sediments of Eutrophic Bays as Determined by Phospholipid Ester-Linked Fatty Acids

[This corrects the article on p. 562 in vol. 58.].

Variation in Microbial Biomass and Community Structure in Sediments of Eutrophic Bays as Determined by Phospholipid Ester-Linked Fatty Acids

The distribution of phospholipid ester-linked fatty acids (PLFA) in sediments of eutrophic bays (Hiroshima Bay and Aki Nada) was studied to quantify the microbial biomass, community structure, and nutritional status. A total of 63 fatty acids in the range of C(10) to C(24) were determined. They consist of saturated fatty acids, branched fatty acids, monounsaturated fatty acids, and polyunsaturated fatty acids, and variation was revealed in the relative proportions of these fatty acids in sediments. On the basis of the PLFA concentration in sediments, the calculated microbial biomass showed variation (mean +/- standard deviation = 0.70 x 10 +/- 0.53 x 10 cells per g [dry weight] of sediment) in the eutrophic bays. In sediments, a higher amount of biomass was observed in the coastal area of Hiroshima Bay than that observed in the rest of the bay and adjacent Aki Nada. The microbial community structure of the present study area, as characterized by the PLFA profiles, showed very low percentages of polyunsaturated fatty acids and long-chain fatty acids characteristic of microeukary-otes and terrestrial input, respectively, and high percentages of fatty acids characteristic of bacteria. The distribution of PLFA profiles also showed the relative contribution of both aerobic and anaerobic bacteria, especially sulfate-reducing bacteria, in the study area. The relative proportions of PLFA revealed distinctive differences among the stations of the study area, as is evidenced from six clusters obtained for the PLFA profiles. The results of Tukey's honestly significant difference test further confirmed that the sediments in the coastal area of Hiroshima Bay were significantly enriched by a number of fatty acids when compared with other areas investigated where relatively few fatty acids were present in significant quantities. No marked variation in environmental parameters in the surface- and bottom-water samples was observed, indicating the absence of any water movement in the study area. Furthermore, low redox potential and the levels of sulfide in the sediment revealed the reduced condition of the sediment. The existing environmental conditions and pollution of the study area were attributed to the observed microbial community structure in the sediments.

Effect of epibenthic macropredators on community structure in subtidal organically enriched sediments in the inner Oslofjord

Predator exclusion experiments were performed on an unvegetated low-energy subtidal mudflat. Exclosures were maintained for periods from 2 to 5 mo to protect infauna from epibenthic macropredators. Recruitment was studied by plac~ng trays with azoic sediment on the bottom. Predation effects were determined by comparing faunal composition and abundance on natural sediment and in recruitment trays inside and outside the cages. Community structure was not affected by the cages. There was a tendency for several specles to increase In abundance inside the cages on the natural sediment, but only a few increases were significant. Habitat modifications under the cages were small. It is concluded that in the subtidal of the Oslofjord macropredators are not important in determining community structure in sediments, and that there is only a small effect of macropredators controlling densities of infauna.