Recovery of novel bacterial diversity from mangrove sediment

Liang, Jun-Bin; Chen, Yue‐Qin; Lan, C. Y.; Tam, N.F.Y.; Zan, Qijie; Huang, Li-Nan

doi:10.1007/s00227-006-0377-2

Cited by 100 publications

(68 citation statements)

References 37 publications

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“…Few studies on microbial diversity have been performed in benthic systems (Llobet-Brossa et al, 1998;Köpke et al, 2005;Có rdova-Kreylos et al, 2006;Wilms et al, 2006;Liang et al, 2007) and studies on the effect of bioturbation on microbial community structure remain extremely scarce (Plante and Wilde, 2004;Papaspyrou et al, 2005Papaspyrou et al, , 2006. Environmental parameters vary quickly, especially in coastal sediments.…”

Section: Discussionmentioning

confidence: 99%

Biodiversity of benthic microbial communities in bioturbated coastal sediments is controlled by geochemical microniches

2009

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We used a combination of field and laboratory approaches to address how the bioturbation activity of two crustaceans, the ghost shrimp Neotrypaea californiensis and the fiddler crab Uca crenulata, affects the microbial diversity in the seabed of a coastal lagoon (Catalina Harbor, Santa Catalina Island, CA, USA). Detailed geochemical analyses, including oxygen microsensor measurements, were performed to characterize environmental parameters. We used a whole-assemblage fingerprinting approach (ARISA: amplified ribosomal intergenic spacer analysis) to compare bacterial diversity along geochemical gradients and in relation to subsurface microniches. The two crustaceans have different burrowing behaviors. The ghost shrimp maintains complex, deepreaching burrows and permanently lives subterranean, supplying its burrow with oxygen-rich water. In contrast, the fiddler crab constructs simpler, J-shaped burrows, which it does not inhabit permanently and does not actively ventilate. Our goal was to address how varying environmental parameters affect benthic microbial communities. An important question in benthic microbial ecology has been whether burrows support similar or unique communities compared with the sediment surface. Our results showed that sediment surface microbial communities are distinct from subsurface assemblages and that different burrow types support diverse bacterial taxa. Statistical comparisons by canonical correspondence analysis indicated that the availability of oxidants (oxygen, nitrate, ferric iron) play a key role in determining the presence and abundance of different taxa. When geochemical parameters were alike, microbial communities associated with burrows showed significant similarity to sediment surface communities. Our study provides implications on the community structure of microbial communities in marine sediments and the factors controlling their distribution.

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Section: Discussionmentioning

confidence: 99%

Biodiversity of benthic microbial communities in bioturbated coastal sediments is controlled by geochemical microniches

2009

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“…Published sequences most similar (96%) to this cable bacteria cluster were from surface sediments of a subtropical mangrove habitat (Liang et al, 2007).…”

Section: Cable Bacteria Diversitymentioning

confidence: 97%

Succession of cable bacteria and electric currents in marine sediment

et al. 2014

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Filamentous Desulfobulbaceae have been reported to conduct electrons over centimetre-long distances, thereby coupling oxygen reduction at the surface of marine sediment to sulphide oxidation in sub-surface layers. To understand how these 'cable bacteria' establish and sustain electric conductivity, we followed a population for 53 days after exposing sulphidic sediment with initially no detectable filaments to oxygen. After 10 days, cable bacteria and electric currents were established throughout the top 15 mm of the sediment, and after 21 days the filament density peaked with a total length of 2 km cm À 2 . Cells elongated and divided at all depths with doubling times over the first 10 days of o20 h. Active, oriented movement must have occurred to explain the separation of O 2 and H 2 S by 15 mm. Filament diameters varied from 0.4-1.7 lm, with a general increase over time and depth, and yet they shared 16S rRNA sequence identity of 498%. Comparison of the increase in biovolume and electric current density suggested high cellular growth efficiency. While the vertical expansion of filaments continued over time and reached 30 mm, the electric current density and biomass declined after 13 and 21 days, respectively. This might reflect a breakdown of short filaments as their solid sulphide sources became depleted in the top layers of the anoxic zone. In conclusion, cable bacteria combine rapid and efficient growth with oriented movement to establish and exploit the spatially separated half-reactions of sulphide oxidation and oxygen consumption.

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“…disCussion although molecular approaches for assessing the microbial diversity in natural environments have been well developed and widely used in various types of environments (urakawa et al, 1999;iwamoto et al, 2000;araya et al, 2003;Bürgmann et al, 2004;Li et al, 2006;sousa et al, 2006;Muckian et al, 2007), our knowledge of the microbiology of mangrove ecosystems is still largely based on cultivation-dependent studies (holguin et al, 2001). Recently, the 16s rRna gene clone library was applied to investigate the bacterial composition in Futian mangrove swamp and the results showed that the surface sediments from subtropical mangrove swamp harbored a phylogenetically diverse population of organisms from the bacteria (Liang et al, 2007). in this study, dgge fingerprinting analysis provides an appropriate culture-independent approach for the rapid detection of the predominant microbial species and enables the simultaneous analysis of multiple samples.…”

Section: Microbial Community Composition In Relation To Environmentalmentioning

confidence: 87%

“…Most environmental bacteria cannot be cultured using current culture-based and traditional methods (Li et al, 2006). Molecular techniques based on culture-independent techniques such as denaturing gradient gel electrophoresis (dgge), automated ribosomal intergenic spacer analysis (aRisa) and terminal restriction fragment length polymorphism (TRFLP) have provided new tools for genetically identifying bacteria in all kinds of environmental systems, which has enhanced the knowledge of the in situ population structure of bacteria communities (Li et al, 2006;Liang et al, 2007;Muckian et al, 2007). as dgge can separate sequences of the same length with only a base difference, 16s rRna gene-dgge fingerprinting is particularly useful as an initial investigation to compare communities and identify the qualitative or most relatively abundant community members (Muyzer et al, 1993).…”

mentioning

confidence: 99%

Bacterial community structure of mangrove sediments in relation to environmental variables accessed by 16S rRNA gene-denaturing gradient gel electrophoresis fingerprinting

et al. 2009

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suMMaRY: Bacterial community structure and the relationship between environmental variables and microbial communities in the surface sediments of tropical mangrove ecosystems were investigated in sanya, hainan island, China. Profiles of bacterial communities were generated using culture-independent PCR-denaturing gradient gel electrophoresis (dgge), and the results were interpreted with multivariate statistical analysis. Findings suggested that microbial communities varied with sample collection sites and seasons. The samples collected from the same sample sites at the same time had more similar microbial communities except samples sh3 and aB5, which also had unique sediment quality. Canonical correspondence analysis (CCa) revealed that the organic carbon concentration of the sediments accounted for a significant amount of the variability in the bacterial community composition. Phylogenetic analysis was used to identify the major groups of the predominant bacterial phylotypes. 16s rRna gene-V3 fragments from 17 individual dgge bands were sequenced and the corresponding bacteria were found in mangrove sediments for the first time based on BLasT results. Predominant bacterial phylotypes clustered with various taxonomic groups, including Proteobacteria, Bacteroidetes, Gemmatimonadetes, Actinobacteria and Firmicutes.Keywords: bacterial community, mangrove sediments, denaturing gradient gel electrophoresis, multivariate statistics.ResuMen: Estructura de la comunidad bacteriana en sedimentos de manglares en relación a variables medioambientales mediante análisis de fragmentos del gen 16S rRNA y electroforesis en geles desnaturalizantes. -La estructura de la comunidad bacteriana y la relación entre variables ambientales y las comunidades microbianas de la superficie de sedimentos de los ecosistemas tropicales de manglares fueron investigados en sanya, hainan island, China. Los perfiles de las comunidades bacterianas fueron obtenidos utilizando electroforesis de gradiente de gel desnaturalizante (dgge), cultivo-independiente, y los resultados fueron interpretados con un análisis estadístico multivariante. Los resultados sugerían que las comunidades microbianas variaban con los lugares de muestreo y las estaciones. Las muestras recogidas en el mismo lugar de muestreo y al mismo tiempo tenían comunidades microbianas similares, excepto las muestras sh3 y aB5, que tenían diferente calidad de sedimentos. el análisis de correspondencia (CCa) mostró que la concentración de carbono orgánico en sedimentos explicaba una parte importante de la variabilidad en la composición de la comunidad bacteriana. Los análisis filogenéticos fueron usados para identificar los grupos más importantes de filotipos predominantes de bacterias. se secuenciaron fragmentos 16 rRna gene-V3 de 17 bandas individuales de dgge y las bacterias correspondientes fueron encontradas por primera vez en sedimentos de manglares en base a resultados de BLasT. Los filotipos de bacterias predominantes se agrupaban con varios grupos taxonómicos que incluyen Proteobacte...

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Recovery of novel bacterial diversity from mangrove sediment

Cited by 100 publications

References 37 publications

Biodiversity of benthic microbial communities in bioturbated coastal sediments is controlled by geochemical microniches

Biodiversity of benthic microbial communities in bioturbated coastal sediments is controlled by geochemical microniches

Succession of cable bacteria and electric currents in marine sediment

Bacterial community structure of mangrove sediments in relation to environmental variables accessed by 16S rRNA gene-denaturing gradient gel electrophoresis fingerprinting

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