Gene transfer among bacteria under conditions of nutrient depletion in simulated and natural aquatic environments

Goodman, Amanda E.

doi:10.1016/0168-6496(94)90025-6

Cited by 12 publications

(8 citation statements)

References 16 publications

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“…The data presented here show that phage‐encoded sequences are moving between biomes in recent evolutionary time. Genetic information could be carried by phages between environments and passed on to new hosts via transduction [30–33]. Therefore, movement of phages between environments may be responsible for the large amount of lateral gene transfer observed amongst microbes in different environments.…”

Section: Resultsmentioning

confidence: 99%

Global distribution of nearly identical phage-encoded DNA sequences

Breitbart

Miyake

Rohwer

2004

FEMS Microbiology Letters

196

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Phages, the most abundant biological entities on the planet, play important roles in biogeochemical cycling, horizontal gene transfer, and defining microbial community composition. However, very little is known about phage diversity or biogeography, and there has not yet been a systematic effort to compare the phages found in different ecosystems. Here, we report that T7‐like Podophage DNA polymerase sequences occur in every major biome investigated, including marine, freshwater, sediment, terrestrial, extreme, and metazoan‐associated. The majority of these sequences belong to a unique clade that is only distantly related to cultured isolates. Some identical T7‐like phage‐encoded DNA polymerase genes from this clade were >99% conserved at the nucleotide level in multiple different environments, suggesting that these phages are moving between biomes in recent evolutionary time and that the global genomic pool for T7‐like phages may be smaller than previously hypothesized.

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Section: Resultsmentioning

confidence: 99%

Global distribution of nearly identical phage-encoded DNA sequences

Breitbart

Miyake

Rohwer

2004

FEMS Microbiology Letters

196

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“…This ¢nding may be attributable to the relatively small sample size of both investigations, but could indicate the transient presence of speci¢c IS1 hosts. The presence of IS1 increases the potential for genetic rearrangements in IS1 hosts within the lake, particularly as horizontal transfer occurs in the natural environment [37], transposition can occur in resting bacteria [38], and transposition rates have been shown to increase in nutrient-limited conditions [39,40]. Given these circumstances the contribution of IS1 to genetic variations in these bacterial populations should not be underestimated.…”

Section: Discussionmentioning

confidence: 99%

Detection and distribution of insertion sequence 1 (IS1)-containing bacteria in the freshwater environment

Rhodes¹

2000

FEMS Microbiology Ecology

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The distribution of insertion sequence 1 (IS1)-containing bacteria was investigated in Windermere (Cumbria, UK), a freshwater body impacted by treated sewage discharge and run-off from the surrounding catchment. Culturable IS1-containing bacteria were recovered from the water column at three depths in Windermere North Basin (WNB) and South Basin (WSB), and from sediment at both sites (at the sediment surface in WSB and to a depth of 12^13 cm in WNB). Polymerase chain reaction amplification of IS1 and the Escherichia coli/ Shigella sp. specific gene uidA, from community DNA from shallow sediments, extended the detection limit beyond that of culture at both sites. This detection was extended further into deep sediment extracted from WNB as IS1 and uidA were detected in sub-samples to a depth of 4.7 and 2.3 m, respectively. Analysis of a representative subset of 90 IS1-carrying isolates recovered from water and sediment at both sites demonstrated 21 heterogeneous IS1 profiles with estimated copy numbers ranging from 1 to 16. Identification of the host bacteria showed that the element was confined mainly to Enterobacter spp. However, this study showed IS1 to be present in Citrobacter freundii for the first time. Plasmids were carried by 75.3% of enterobacterial isolates and four plasmids (2.6%) carried IS1. DNA sequence analysis of five IS1 clones demonstrated that IS1 isoforms from this study were similar ( s 89% nucleotide identity) to known IS1 isoforms. Two isoforms of IS1 from a single Enterobacter cloacae isolate differed by 6.7% at the nucleotide level suggesting that they had been acquired independently. ß : S 0 1 6 8 -6 4 9 6 ( 0 0 ) 0 0 0 7 7 -5

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“…This finding may be attributable to the relatively small sample size of both investigations, but could indicate the transient presence of specific IS 1 hosts. The presence of IS 1 increases the potential for genetic rearrangements in IS 1 hosts within the lake, particularly as horizontal transfer occurs in the natural environment [37], transposition can occur in resting bacteria [38], and transposition rates have been shown to increase in nutrient‐limited conditions [39,40]. Given these circumstances the contribution of IS 1 to genetic variations in these bacterial populations should not be underestimated.…”

Section: Discussionmentioning

confidence: 99%

Detection and distribution of insertion sequence 1 (IS1)-containing bacteria in the freshwater environment1

Rhodes

Saunders

Pickup

2000

FEMS Microbiology Ecology

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The distribution of insertion sequence 1 (IS1)‐containing bacteria was investigated in Windermere (Cumbria, UK), a freshwater body impacted by treated sewage discharge and run‐off from the surrounding catchment. Culturable IS1‐containing bacteria were recovered from the water column at three depths in Windermere North Basin (WNB) and South Basin (WSB), and from sediment at both sites (at the sediment surface in WSB and to a depth of 12–13 cm in WNB). Polymerase chain reaction amplification of IS1 and the Escherichia coli/Shigella sp. specific gene uidA, from community DNA from shallow sediments, extended the detection limit beyond that of culture at both sites. This detection was extended further into deep sediment extracted from WNB as IS1 and uidA were detected in sub‐samples to a depth of 4.7 and 2.3 m, respectively. Analysis of a representative subset of 90 IS1‐carrying isolates recovered from water and sediment at both sites demonstrated 21 heterogeneous IS1 profiles with estimated copy numbers ranging from 1 to 16. Identification of the host bacteria showed that the element was confined mainly to Enterobacter spp. However, this study showed IS1 to be present in Citrobacter freundii for the first time. Plasmids were carried by 75.3% of enterobacterial isolates and four plasmids (2.6%) carried IS1. DNA sequence analysis of five IS1 clones demonstrated that IS1 isoforms from this study were similar (>89% nucleotide identity) to known IS1 isoforms. Two isoforms of IS1 from a single Enterobacter cloacae isolate differed by 6.7% at the nucleotide level suggesting that they had been acquired independently.

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Gene transfer among bacteria under conditions of nutrient depletion in simulated and natural aquatic environments

Cited by 12 publications

References 16 publications

Global distribution of nearly identical phage-encoded DNA sequences

Global distribution of nearly identical phage-encoded DNA sequences

Detection and distribution of insertion sequence 1 (IS1)-containing bacteria in the freshwater environment

Detection and distribution of insertion sequence 1 (IS1)-containing bacteria in the freshwater environment1

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