Molecular evidence for the presence of novel actinomycete lineages in a temperate forest soil

Mcveigh, H.; Munro, James B.; Embley, T. Martin

doi:10.1007/bf01574693

Cited by 64 publications

(68 citation statements)

References 42 publications

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“…Similar, confounding results have been reported for actinomycetes in terrestrial soils where cultivation-based studies have shown Streptomyces spp. to be cosmopolitan and dominant, whereas PCR-based molecular analyses have underestimated or failed to detect this important group of microorganisms (18). These results again emphasize the limitations of molecular techniques when working with spore-forming bacteria that spend a majority of their life cycle in a lysis-resistant resting stage interspersed with sporadic but ecologically important periods of growth.…”

Section: Discussionmentioning

confidence: 89%

Culture-Dependent and Culture-Independent Diversity within the Obligate Marine Actinomycete Genus Salinispora

Mincer

Fenical

Jensen

2005

Appl Environ Microbiol

121

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Salinispora is the first obligate marine genus within the order Actinomycetales and a productive source of biologically active secondary metabolites. Despite a worldwide, tropical or subtropical distribution in marine sediments, only two Salinispora species have thus far been cultivated, suggesting limited species-level diversity. To further explore Salinispora diversity and distributions, the phylogenetic diversity of more than 350 strains isolated from sediments collected around the Bahamas was examined, including strains cultured using new enrichment methods. A culture-independent method, using a Salinispora-specific seminested PCR technique, was used to detect Salinispora from environmental DNA and estimate diversity. Overall, the 16S rRNA gene sequence diversity of cultured strains agreed well with that detected in the environmental clone libraries. Despite extensive effort, no new species level diversity was detected, and 97% of the 105 strains examined by restriction fragment length polymorphism belonged to one phylotype (S. arenicola). New intraspecific diversity was detected in the libraries, including an abundant new phylotype that has yet to be cultured, and a new depth record of 1,100 m was established for the genus. PCR-introduced error, primarily from Taq polymerase, significantly increased clone library sequence diversity and, if not masked from the analyses, would have led to an overestimation of total diversity. An environmental DNA extraction method specific for vegetative cells provided evidence for active actinomycete growth in marine sediments while indicating that a majority of sediment samples contained predominantly Salinispora spores at concentrations that could not be detected in environmental clone libraries. Challenges involved with the direct sequence-based detection of spore-forming microorganisms in environmental samples are discussed.Bacteria belonging to the order Actinomycetales, commonly referred to as actinomycetes, perform significant biogeochemical roles in terrestrial soils and are highly valued for their unparalleled ability to produce biologically active secondary metabolites. These bacteria account for ca. 45% of the bioactive microbial metabolites discovered (3) and have played a central role in the development of the modern pharmaceutical industry. The immense biotechnological utility of actinomycetes has led to exhaustive surveys of cultivars from terrestrial habitats and an associated increase in the numbers of known compounds being rediscovered due to a high rate of redundancy in the strains isolated. Given recent advances in our understanding of marine actinomycetes (7, 13, 24; see also a recent issue of Antonie van Leeuwenhoek, vol. 87, 2005, de-voted to the subject), strains isolated from the marine environment represent a relatively unexplored frontier for the discovery of new actinomycete biodiversity and a resource for novel secondary metabolites.Recently, we reported the discovery of the first obligate marine actinomycete genus for which the name "Salinospora...

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Section: Discussionmentioning

confidence: 89%

Culture-Dependent and Culture-Independent Diversity within the Obligate Marine Actinomycete Genus Salinispora

Mincer

Fenical

Jensen

2005

Appl Environ Microbiol

121

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“…Semiquantitative fluorescence in situ hybridization results for Defluviicoccus-related organisms showed that 4.1% Ϯ 0.6% of the total biovolume hybridizing with the EUBmix probes (5a) also hybridized with the DF1020 probe (12) and that 67.7% Ϯ 3.0% hybridized with the PAOmix probes designed to target "Candidatus Accumulibacter phosphatis" (5,19). Furthermore, comparisons with a range of phenol-based extraction methods (3,4,7,11) with activated-sludge samples showed that our method was equal to or better than these as assessed by PCR targeting the same problematic populations (McIlroy et al, unpublished). Increased safety and a reduced number of pipetting steps make the method suitable for high-throughput analysis.…”

mentioning

confidence: 99%

Simple and Safe Method for Simultaneous Isolation of Microbial RNA and DNA from Problematic Populations

McIlroy

Porter

Seviour

et al. 2008

Appl Environ Microbiol

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“…In order to minimize this, two strategies are usually employed for analyzing microbial communities. These are the use of a "hot start program" 74) and a "touch down program" 19) , and these conditions can also be used in combination.…”

Section: Pcr Amplificationmentioning

confidence: 99%

Microbial Community Analysis of the Phytosphere Using Culture-Independent Methodologies

et al. 2007

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The phytosphere is an attractive habitat for microorganisms due to an abundance of nutrients and relative environmental stability. The microorganisms that occupy this habitat assist in the uptake of nutrients from soils and can exert considerable influence upon the overall health of the plant. Recent technical advances in environmental microbiology have enabled the tracing and assessment of these microorganisms using rapid and simple molecular techniques without any culture-dependent bias. We herein review the current status of these modern molecular techniques in the study of plant-associated microbes, and summarize the issues relevant to the phytosphere from the aspect of both basic and applied science.

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Molecular evidence for the presence of novel actinomycete lineages in a temperate forest soil

Cited by 64 publications

References 42 publications

Culture-Dependent and Culture-Independent Diversity within the Obligate Marine Actinomycete Genus Salinispora

Culture-Dependent and Culture-Independent Diversity within the Obligate Marine Actinomycete Genus Salinispora

Simple and Safe Method for Simultaneous Isolation of Microbial RNA and DNA from Problematic Populations

Microbial Community Analysis of the Phytosphere Using Culture-Independent Methodologies

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