Bühring SI, Elvert M, Witte U.. The microbial community structure of different permeable sandy sediments characterized by the investigation of bacterial fatty acids and fluorescence in situ hybridization. Environ Microbiol 7: 281-293

Max Planck Institute for Marine Microbiology, Celsiusstr. 1, 28359 Bremen, Germany.
Environmental Microbiology (Impact Factor: 6.2). 03/2005; 7(2):281-93. DOI: 10.1111/j.1462-2920.2004.00710.x
Source: PubMed

ABSTRACT This study describes the microbial community structure of three sandy sediment stations that differed with respect to median grain size and permeability in the German Bight of the Southern North Sea. The microbial community was investigated using lipid biomarker analyses and fluorescence in situ hybridization. For further characterization we determined the stable carbon isotope composition of the biomarkers. Biomarkers identified belong to different bacterial groups such as members of the Cytophaga-Flavobacterium cluster and sulfate-reducing bacteria (SRB). To support these findings, investigations using different fluorescent in situ hybridization probes were performed, specifically targeting Cytophaga-Flavobacterium, gamma-Proteobacteria and different members of the SRB. Depth profiles of bacterial fatty acid relative abundances revealed elevated subsurface peaks for the fine sediment, whereas at the other sandy sediment stations the concentrations were less variable with depth. Although oxygen penetrates deeper into the coarser and more permeable sediments, the SRB biomarkers are similarly abundant, indicating suboxic to anoxic niches in these environments. We detected SRB in all sediment types as well as in the surface and at greater depth, which suggests that SRB play a more important role in oxygenated marine sediments than previously thought.

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Available from: Marcus Elvert, Sep 29, 2015
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    • "The results from our taxonomic characterization of the community (Figure 3) generally agree with previous results that suggest Proteobacteria (Gammaproteobacteria), Planctomycetes, and Bacteroidetes taxa dominate coastal sands [2,5,33,34]. Although not examined here in detail, the difference in environmental conditions in the Mississippi Sound estuarine system (west of Mobile Bay), which is protected by a series of barrier islands and receives large nutrient loads, from the remainder of the Gulf Coast (east of Mobile Bay) may partition this region into two environmental provinces that select for similar but distinct community compositions. "
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    ABSTRACT: Microorganisms associated with coastal sands serve as a natural biofilter, providing essential nutrient recycling in nearshore environments and acting to maintain coastal ecosystem health. Anthropogenic stressors often impact these ecosystems, but little is known about whether these disturbances can be identified through microbial community change. The blowout of the Macondo Prospect reservoir on April 20, 2010, which released oil hydrocarbons into the Gulf of Mexico, presented an opportunity to examine whether microbial community composition might provide a sensitive measure of ecosystem disturbance. Samples were collected on four occasions, beginning in mid-June, during initial beach oiling, until mid-November from surface sand and surf zone waters at seven beaches stretching from Bay St. Louis, MS to St. George Island, FL USA. Oil hydrocarbon measurements and NOAA shoreline assessments indicated little to no impact on the two most eastern beaches (controls). Sequence comparisons of bacterial ribosomal RNA gene hypervariable regions isolated from beach sands located to the east and west of Mobile Bay in Alabama demonstrated that regional drivers account for markedly different bacterial communities. Individual beaches had unique community signatures that persisted over time and exhibited spatial relationships, where community similarity decreased as horizontal distance between samples increased from one to hundreds of meters. In contrast, sequence analyses detected larger temporal and less spatial variation among the water samples. Superimposed upon these beach community distance and time relationships, was increased variability in bacterial community composition from oil hydrocarbon contaminated sands. The increased variability was observed among the core, resident, and transient community members, indicating the occurrence of community-wide impacts rather than solely an overprinting of oil hydrocarbon-degrading bacteria onto otherwise relatively stable sand population structures. Among sequences classified to genus, Alcanivorax, Alteromonas, Marinobacter, Winogradskyella, and Zeaxanthinibacter exhibited the largest relative abundance increases in oiled sands.
    PLoS ONE 09/2013; 8(9):e74265. DOI:10.1371/journal.pone.0074265 · 3.23 Impact Factor
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    • "Marine microbial communities are fundamental regulators of biogeochemical cycles, and their relationships with geochemical environments are at the center of marine microbial ecology and biogeochemistry (Falkowski et al., 2008; Strom, 2008). Although several molecular finger-printing methods have been applied to the investigation of sandy sediment microbial communities (Llobet- Brossa et al., 1998; Mills et al., 2003; Rusch et al., 2003; Buhring et al., 2005; Hewson et al., 2006; Hunter et al., 2006; Sørensen et al., 2007; Mills et al., 2008), our understanding of the impact of abiotic factors on microbial communities in sandy sediments remains limited. In particular, although biogeochemical redox stratification has been well documented in marine sediments (Canfield et al., 1993; Thamdrup et al., 1994), information on the correlation of microbial community composition with redox stratification in sediments, particularly marine sandy sediments, remains largely unknown (Urakawa et al., 2000; Edlund et al., 2008). "
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    ABSTRACT: Relationships between microbial communities and geochemical environments are important in marine microbial ecology and biogeochemistry. Although biogeochemical redox stratification has been well documented in marine sediments, its impact on microbial communities remains largely unknown. In this study, we applied denaturing gradient gel electrophoresis (DGGE) and clone library construction to investigate the diversity and stratification of bacterial communities in redox-stratified sandy reef sediments in a microcosm. A total of 88 Operational Taxonomic Units (OTU) were identified from 16S rRNA clone libraries constructed from sandy reef sediments in a laboratory microcosm. They were members of nine phyla and three candidate divisions, including Proteobacteria (Alpha-, Beta-, Gamma-, Delta-, and Epsilonproteobacteria), Actinobacteria, Acidobacteria, Bacteroidetes, Chloroflexi, Cyanobacteria, Firmicutes, Verrucomicrobia, Spirochaetes, and the candidate divisions WS3, SO31 and AO19. The vast majority of these phylotypes are related to clone sequences from other marine sediments, but OTUs of Epsilonproteobacteria and WS3 are reported for the first time from permeable marine sediments. Several other OTUs are potential new bacterial phylotypes because of their low similarity with reference sequences. Results from the 16S rRNA, gene clone sequence analyses suggested that bacterial communities exhibit clear stratification across large redox gradients in these sediments, with the highest diversity found in the anoxic layer (15–25 mm) and the least diversity in the suboxic layer (3–5 mm). Analysis of the nosZ, and amoA gene libraries also indicated the stratification of denitrifiers and nitrifiers, with their highest diversity being in the anoxic and oxic sediment layers, respectively. These results indicated that redox-stratification can affect the distribution of bacterial communities in sandy reef sediments.
    Chinese Journal of Oceanology and Limnology 11/2011; 29:1209-1223. DOI:10.1007/s00343-011-0316-z · 0.66 Impact Factor
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    • "However, as the investigations started to pay more attention to subsurface coastal sediments, the number of publications is currently increasing (Wilms et al., 2006). The previous microbiological studies on coastal marine sediments focused on vertical distribution of microbial communities (Bühring et al., 2005; Wilms et al., 2006). On the other hand, microbial communities can also be influenced by seasonality in the sediment's physical and chemical characteristics. "
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    ABSTRACT: Spatial (10 different locations) and temporal (2 years) changes in characteristics of the Marmara Sea Sediments were monitored to determine interactions between the chemical and microbial diversity. The sediments were rich in terms of hydrocarbon, nitrate, Ni and microbial cell content. Denitrifying, sulfate reducing, fermentative and methanogenic organisms were co-abundant in 15 cm below the sea floor. The local variations in the sediments' characteristics were more distinctive than the temporal ones. The sulfate and nitrate contents were the main drivers of the changes in the microbial community compositions. N and P were limited for microbial growth in the sediments, and their levels determined the total cell abundance and activity. Seasonal shifts in temperatures of the shallow sediments were also reflected in the active cell abundances. It was concluded that the Marmara Sea is a promising ecosystem for the further investigation of the ecologically important microbial processes.
    Marine Pollution Bulletin 09/2011; 62(11):2384-94. DOI:10.1016/j.marpolbul.2011.08.033 · 2.99 Impact Factor
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