Characterization of depth‐related population variation in microbial communities of a coastal marine sediment using 16S rDNA‐based approaches and quinone profiling

Urakawa, Hidetoshi; Yoshida, Tsutomu; Nishimura, Masahiko; Ohwada, Kenji

doi:10.1046/j.1462-2920.2000.00137.x

Cited by 122 publications

(92 citation statements)

References 49 publications

(64 reference statements)

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“…However, in the Hausstrand sands, OTU numbers were higher in the deeper layer (10-15 cm) as compared with the mid (5-10 cm) and upper (0-5 cm) layers (Supplementary Figure S5). Increased OTU numbers with depth have been described earlier for western Pacific, southern North Sea, as well as for Namibian coastal sediments, using various molecular techniques (for example, Urakawa et al, 2000;Franco et al, 2007;Julies, unpublished data). We hypothesize that the relationship between intermediate disturbance and diversity, which has been shown for a variety of organisms (for example, Connell, 1978;Townsend et al, 1997), but not yet tested on benthic microorganisms, might explain the apparent link between sediment depth and bacterial OTU numbers at our study site.…”

Section: Effects On Otu Numberssupporting

confidence: 53%

“…Sediment depth-related patterns in bacterial community structure were, for instance, detected for a variety of benthic habitats, such as cold seep sediments (Inagaki et al, 2002), the warm deep Mediterranean sea (Luna et al, 2004), the western Pacific coast (Urakawa et al 2000), the Antarctic continental shelves (Bowman and McCuaig, 2003), coral reef sediments , as well as for continental shelf sediments of the southern North Sea (Franco et al, 2007).…”

Section: Introductionmentioning

confidence: 99%

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Time- and sediment depth-related variations in bacterial diversity and community structure in subtidal sands

et al. 2009

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Bacterial community structure and microbial activity were determined together with a large number of contextual environmental parameters over 2 years in subtidal sands of the German Wadden Sea in order to identify the main factors shaping microbial community structure and activity in this habitat. Seasonal changes in temperature were directly reflected in bacterial activities and total community respiration, but could not explain variations in the community structure. Strong sediment depthrelated patterns were observed for bacterial abundances, carbon production rates and extracellular enzymatic activities. Bacterial community structure also showed a clear vertical variation with higher operational taxonomic unit (OTU) numbers at 10-15 cm depth than in the top 10 cm, probably because of the decreasing disturbance by hydrodynamic forces with sediment depth. The depthrelated variations in bacterial community structure could be attributed to vertical changes in bacterial abundances, chlorophyll a and NO 3 À , indicating that spatial patterns of microbes are partially environmentally controlled. Time was the most important single factor affecting microbial community structure with an OTU replacement of up to 47% over 2 years and a contribution of 34% to the total variation. A large part of this variation was not related to any environmental parameters, suggesting that temporal variations in bacterial community structure are caused by yet unknown environmental drivers and/or by stochastic events in coastal sand habitats. Principal ecosystem functions such as benthic oxygen consumption and extracellular hydrolysis of organic matter were, however, at a high level at all times, indicating functional redundancy in the microbial communities.

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Section: Effects On Otu Numberssupporting

confidence: 53%

Section: Introductionmentioning

confidence: 99%

Time- and sediment depth-related variations in bacterial diversity and community structure in subtidal sands

et al. 2009

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“…Several investigators have raised concerns about whether the DNA extract obtained is representative of the indigenous microflora and about the problems associated with PCR of 16S rDNA gene for the phylogenetic analysis, and therefore this will not be discussed here (Chandler et al 1997;Urakawa et al 2000). With the limitations of culture techniques, however, the sequenced-based phylogenetic techniques provide a less biased picture of the community composition than would any cultivation technique (Amann et al 1995).…”

Section: Discussionmentioning

confidence: 99%

High 16S rDNA bacterial diversity in glacial meltwater lake sediment, Bratina Island, Antarctica

Sjöling

Cowan

2003

Extremophiles

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The microbial diversity in maritime meltwater pond sediments from Bratina Island, Ross Sea, Antarctica was investigated by 16S rDNA-dependent molecular phylogeny. Investigations of the vertical distribution, phylogenetic composition, and spatial variability of Bacteria and Archaea in the sediment were carried out. Results revealed the presence of a highly diverse bacterial population and a significantly depthrelated composition. Assessment of 173 partial 16S rDNA clones analyzed by amplified rDNA restriction analysis (ARDRA) using tetrameric restriction enzymes (HinP1I 5'GVCGC3'and Msp I. 5'CVCGG3', BioLabs) revealed 153 different bacterial OTUs (operational tax-onomic units). However, only seven archaeal OTUs were detected, indicating low archaeal diversity. Based on ARDRA results, 30 bacterial clones were selected for sequencing and the sequenced clones fell into seven major lineages of the domain Bacteria; the a, y,and d subdivisions of Proteobacteria, the Cytophaga-Flavo-bacterium-Bacteroides, the Spirochaetaceae, and the Actinobacteria. All of the archaeal clones sequenced belonged to the group Crenarchaeota and phylogenetic analysis revealed close relationships with members ofthe deep-branching Group 1 Marine Archaea.

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“…Laterally and at large scales (cm to km, globally), the structure, composition and diversity of microbial communities are directly influenced by variation in environmental factors, including temperature, salinity, organic matter composition and concentration, sediment type and pH (Wilde and Plante, 2002;Köster et al, 2005;Hughes Martiny et al, 2006;Lozupone and Knight, 2007). Across smaller environmental scales (mm to cm), microbial community composition and function can vary considerably, in particular, with increasing sediment depth, driven primarily by changes in redox conditions and the availability of nutrients and organic matter (Jensen et al, 1993;Urakawa et al, 2000;Llobet-Brossa et al, 2002;Köpke et al, 2005;Köster et al, 2008;Böer et al, 2009;Jansen et al, 2009). …”

Section: Introductionmentioning

confidence: 99%

Bioturbating shrimp alter the structure and diversity of bacterial communities in coastal marine sediments

et al. 2010

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Bioturbation is a key process in coastal sediments, influencing microbially driven cycling of nutrients as well as the physical characteristics of the sediment. However, little is known about the distribution, diversity and function of the microbial communities that inhabit the burrows of infaunal macroorganisms. In this study, terminal-restriction fragment length polymorphism analysis was used to investigate variation in the structure of bacterial communities in sediment bioturbated by the burrowing shrimp Upogebia deltaura or Callianassa subterranea. Analyses of 229 sediment samples revealed significant differences between bacterial communities inhabiting shrimp burrows and those inhabiting ambient surface and subsurface sediments. Bacterial communities in burrows from both shrimp species were more similar to those in surface-ambient than subsurface-ambient sediment (R ¼ 0.258, Po0.001). The presence of shrimp was also associated with changes in bacterial community structure in surrounding surface sediment, when compared with sediments uninhabited by shrimp. Bacterial community structure varied with burrow depth, and also between individual burrows, suggesting that the shrimp's burrow construction, irrigation and maintenance behaviour affect the distribution of bacteria within shrimp burrows. Subsequent sequence analysis of bacterial 16S rRNA genes from surface sediments revealed differences in the relative abundance of bacterial taxa between shrimp-inhabited and uninhabited sediments; shrimp-inhabited sediment contained a higher proportion of proteobacterial sequences, including in particular a twofold increase in Gammaproteobacteria. Chao1 and ACE diversity estimates showed that taxon richness within surface bacterial communities in shrimp-inhabited sediment was at least threefold higher than that in uninhabited sediment. This study shows that bioturbation can result in significant structural and compositional changes in sediment bacterial communities, increasing bacterial diversity in surface sediments and resulting in distinct bacterial communities even at depth within the burrow. In an area of high macrofaunal abundance, this could lead to alterations in the microbial transformations of important nutrients at the sediment-water interface.

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Characterization of depth‐related population variation in microbial communities of a coastal marine sediment using 16S rDNA‐based approaches and quinone profiling

Cited by 122 publications

References 49 publications

Time- and sediment depth-related variations in bacterial diversity and community structure in subtidal sands

Time- and sediment depth-related variations in bacterial diversity and community structure in subtidal sands

High 16S rDNA bacterial diversity in glacial meltwater lake sediment, Bratina Island, Antarctica

Bioturbating shrimp alter the structure and diversity of bacterial communities in coastal marine sediments

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