Total bacterial diversity in soil and sediment communities—A review

Torsvik, Vigdis; Sørheim, Roald; Goksøyr, Jostein

doi:10.1007/bf01574690

Cited by 399 publications

(261 citation statements)

References 48 publications

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“…It is estimated that 1 g of forest soil contains 4 Â 10 7 prokaryotic cells, whereas 1 g of grassland soil has 2 Â 10 9 prokaryotic cells (Daniel, 2005). DNA reassociation kinetic studies have estimated that 1 g of soil contains approximately 2000-18 000 genomes (Torsvik et al, 1996(Torsvik et al, , 1998Torsvik and Ovreas, 2002), suggesting that prokaryotic diversity in soil is extremely high. Owing to such high diversity, soil microbial communities are among the most difficult to characterize both phenotypically and genetically.…”

Section: Introductionmentioning

confidence: 99%

Reproducibility and quantitation of amplicon sequencing-based detection

et al. 2011

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To determine the reproducibility and quantitation of the amplicon sequencing-based detection approach for analyzing microbial community structure, a total of 24 microbial communities from a long-term global change experimental site were examined. Genomic DNA obtained from each community was used to amplify 16S rRNA genes with two or three barcode tags as technical replicates in the presence of a small quantity (0.1% wt/wt) of genomic DNA from Shewanella oneidensis MR-1 as the control. The technical reproducibility of the amplicon sequencing-based detection approach is quite low, with an average operational taxonomic unit (OTU) overlap of 17.2% ± 2.3% between two technical replicates, and 8.2% ± 2.3% among three technical replicates, which is most likely due to problems associated with random sampling processes. Such variations in technical replicates could have substantial effects on estimating b-diversity but less on a-diversity. A high variation was also observed in the control across different samples (for example, 66.7-fold for the forward primer), suggesting that the amplicon sequencing-based detection approach could not be quantitative. In addition, various strategies were examined to improve the comparability of amplicon sequencing data, such as increasing biological replicates, and removing singleton sequences and less-representative OTUs across biological replicates. Finally, as expected, various statistical analyses with preprocessed experimental data revealed clear differences in the composition and structure of microbial communities between warming and non-warming, or between clipping and non-clipping. Taken together, these results suggest that amplicon sequencing-based detection is useful in analyzing microbial community structure even though it is not reproducible and quantitative. However, great caution should be taken in experimental design and data interpretation when the amplicon sequencing-based detection approach is used for quantitative analysis of the b-diversity of microbial communities.

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Section: Introductionmentioning

confidence: 99%

Reproducibility and quantitation of amplicon sequencing-based detection

et al. 2011

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“…In most cases, microbes exist in taxonomically diverse communities, whose structure is determined by a complex interplay between environmental factors and ecological interactions among its community members 2,3 . Strong selection pressures for limiting resources have resulted in the evolution of diverse strategies to survive and reproduce under these conditions and gave rise to the stunning richness of ecological interactions that can be observed within microbial communities 4 .…”

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confidence: 99%

Metabolic cross-feeding via intercellular nanotubes among bacteria

et al. 2015

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Bacteria frequently exchange metabolites by diffusion through the extracellular environment, yet it remains generally unclear whether bacteria can also use cell-cell connections to directly exchange nutrients. Here we address this question by engineering cross-feeding interactions within and between Acinetobacter baylyi and Escherichia coli, in which two distant bacterial species reciprocally exchange essential amino acids. We establish that in a well-mixed environment E. coli, but likely not A. baylyi, can connect to other bacterial cells via membranederived nanotubes and use these to exchange cytoplasmic constituents. Intercellular connections are induced by auxotrophy-causing mutations and cease to establish when amino acids are externally supplied. Electron and fluorescence microscopy reveal a network of nanotubular structures that connects bacterial cells and enables an intercellular transfer of cytoplasmic materials. Together, our results demonstrate that bacteria can use nanotubes to exchange nutrients among connected cells and thus help to distribute metabolic functions within microbial communities.

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“…Torsvik et al (1996) mencionan que las modificaciones en la vegetación natural, así como el manejo de cultivos, inducen a una sucesión e inestabilidad de las poblaciones microbianas. Al igual que en la vegetación, las etapas primarias de sucesión de las comunidades microbianas estarían caracterizadas por la dominancia de unos pocos organismos y una baja diversidad.…”

Section: Cuadro 5 Resultados Principales De Las Enzimas De Restriccióunclassified

“…La información de campo (datos no mostrados) registrada para la cobertura de bosque mostró una alta diversidad de especies vegetales, siendo un indicativo de la variedad de sustratos ofrecidos para la actividad de muchos microorganismos en general, entre ellos los actinomicetos. Torsvik et al (1996) mencionaron que la alta variabilidad de micro-hábitats genera una mayor Fig. 6.…”

Section: Discussionunclassified

Comunidades de hongos actinomicetos en tres tipos de vegetación de la Amazonia colombiana: abundancia, morfotipos y el gen 16s ADNr

Cardona¹,

Peña‐Venegas²,

Ruiz‐García³

2008

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Communities of Actynomicetes fungy in three vegetation types of the Colombian Amazon:abundance, morphotypes and the 16s rDNA gene. Among soil microorganisms, Actinomycetes play an important role in the sustainability of natural and agricultural systems: decomposition of organic matter; degradation of recalcitrant compounds like lignin; nitrogen fixation; degradation of agricultural chemicals and biological control in plants and animals. We evaluated their diversity in soils under three different vegetation covers (pasture, tropical primary forest and stubble) at two depths in the Southern Colombian Amazon border. We collected five replicates per vegetation type (in each, three samples at 0-20cm and three at 20-30cm; for a total of 30 samples). Abundance and phenotypic diversity were determined by plate counting. Genomic DNA was extracted from the isolates: the 16s rDNA gene was amplified with specific primers, and its genetic diversity was estimated by means of an amplified restriction analysis (ARDRA). Actynomicetes abundance varied with vegetation and depth, possibly reflecting presence of earthworms, macro-fauna and physico-chemical characteristics associated to fertility, as well as organic matter, total bases, and optimal capacity to cationic interchange. Primary forests had the highest diversity. Sixteen morpho-types (six genera) were identified; Streptomyces was the most abundant everywhere. The heterogeneity of ARDRA patterns prevented species identification because of the intra-species variability in sequences of 16s rDNA operons. This community is a biological indicator of landscape alteration and could include new bio-active compounds of pharmaceutical interest. Rev. Biol. Trop. 57 (4): 1119-1139. Epub 2009 December 01.Keys words: Actynomicetes, pasture, tropical primary forest, stubble, 16S rDNA gen, ARDRA, phenotype and genetic diversity, Colombian Amazon.En el sur del trapecio de la Amazonía colombiana se observan procesos de "colonización" basados en modelos occidentales de producción, con agricultura intensiva (cultivos de bajo rendimiento) y desarrollo de una ganadería incipiente en paisajes no aptos para este uso (IGAC 1997). Esta intervención ha tenido como principales consecuencias la disminución de especies forestales, de especies animales, el aumento de los procesos erosivos del suelo y su consecuente degradación, la escasez de productos derivados del bosque y un gran desequilibrio ecológico inherente a la misma fragilidad del ecosistema (IGAC 1996).El sistema selvático tropical es considerado como el más grande de los sistemas vivientes, ya que alberga un número incalculable de especies diversas, a pesar de que cubre sólo el 10% de la superficie del planeta. De este modo, el Amazonas constituye el punto neurálgico de la biodiversidad en la Tierra. La cantidad de organismos que alberga es enorme. Se estima que más de la mitad de toda la biodiversidad del planeta se encuentra en esta región del

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Total bacterial diversity in soil and sediment communities—A review

Cited by 399 publications

References 48 publications

Reproducibility and quantitation of amplicon sequencing-based detection

Reproducibility and quantitation of amplicon sequencing-based detection

Metabolic cross-feeding via intercellular nanotubes among bacteria

Comunidades de hongos actinomicetos en tres tipos de vegetación de la Amazonia colombiana: abundancia, morfotipos y el gen 16s ADNr

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