Developing SSU rDNA metagenomic profiles of aquatic microbial communities for environmental assessments

Marshall, Michael M.; Amos, R.; Henrich, Vincent C.; Rublee, Parke A.

doi:10.1016/j.ecolind.2007.04.007

Cited by 23 publications

(14 citation statements)

References 63 publications

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“…Taxonomic levels representing species are commonly delineated at 97% 16S rRNA sequence similarity for prokaryotes and 97% rRNA sequence and rRNA related ITS (internal transcribed spacer) sequence similarity for fungi (Roselló‐Morak & Amann ; Schloss & Handelsman ; Marshal et al . ; Amend et al . ; Chu et al .…”

Section: Methodsmentioning

confidence: 99%

How species richness and total abundance constrain the distribution of abundance

2013

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The species abundance distribution (SAD) is one of the most intensively studied distributions in ecology and its hollow-curve shape is one of ecology's most general patterns. We examine the SAD in the context of all possible forms having the same richness (S) and total abundance (N), i.e. the feasible set. We find that feasible sets are dominated by similarly shaped hollow curves, most of which are highly correlated with empirical SADs (most R(2) values > 75%), revealing a strong influence of N and S on the form of the SAD and an a priori explanation for the ubiquitous hollow curve. Empirical SADs are often more hollow and less variable than the majority of the feasible set, revealing exceptional unevenness and relatively low natural variability among ecological communities. We discuss the importance of the feasible set in understanding how general constraints determine observable variation and influence the forms of predicted and empirical patterns.

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Section: Methodsmentioning

confidence: 99%

How species richness and total abundance constrain the distribution of abundance

2013

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“…refs. 44,128,154,155,177, early studies only) and microbial eukaryotes 137) or both 108) in the environment. Sequences obtained from the environment by direct amplification were described as the sole mean to provide information for at least 99% of the prokaryotes in natural communities 6) .…”

Section: Introductionmentioning

confidence: 99%

Global Sequencing: A Review of Current Molecular Data and New Methods Available to Assess Microbial Diversity

Christen

2008

Microb. Environ.

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Roughly estimating the diversity of life has for a long time been seen as a challenge. Sequences obtained from the environment by direct amplification are now seen as the sole mean to provide information for at least 99% of the prokaryotes in natural communities. Recent massive parallel sequencing technologies now allow to sequence nearly every sequence resulting from such amplification. Are we ready to deal with such a deluge of data? Using three recent publications (16S rRNA genes amplification in soil and seawater followed by massive parallel sequencing) as case examples, this review analyses the state of the field.

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“…Most of the microeukaryotes found in eutrophic lakes belonged to the functional groups of autotrophs, parasites, toxin producers, saprophytes, strict phagotrophs or mixotrophs. Taxa such as Fungi, Ciliophora, Cryptophytes and Chlorophytes are commonly found, suggesting a widespread prevalence of these microeukaryotes in eutrophic lakes (Marshall et al , 2008).…”

Section: Introductionmentioning

confidence: 99%

Microscopic eukaryotes living in a dying lake (Lake Koronia, Greece)

Genitsaris

Kormas

Moustaka‐Gouni

2009

FEMS Microbiology Ecology

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The morphological and phylogenetic diversity of the microscopic eukaryotes of the Lake Koronia water column was investigated during a mass kill of birds and fish in August-September 2004. The dominant morphospecies corresponded to the known toxin-producing species Prymnesium parvum, followed by Amoebidium sp., a taxon belonging to the group of parasitic Mesomycetozoea, and the common chlorophyte Pediastrum boryanum. Prymnesium exhibited heteromorphic life-cycle stages (flagellate and nonmotile coccoid cells). Phylogenetic analysis with 18S rRNA gene suggested that these heteromorphic stages belonged to the Platychrysis-Prymnesium monophyletic group. The most abundant phylotype was almost identical to P. boryanum. The fungal phylotypes were related to the Chytridiomycota, and the ciliate-like ones were closely related to Enchelys polynucleata and Pattersoniella vitiphila. Two phylotypes representing novel members belonging to the Jakobida and the Apicomplexa were also found. The microscopic eukaryotes of Lake Koronia include several organisms that are related to parasitic life modes.

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Developing SSU rDNA metagenomic profiles of aquatic microbial communities for environmental assessments

Cited by 23 publications

References 63 publications

How species richness and total abundance constrain the distribution of abundance

How species richness and total abundance constrain the distribution of abundance

Global Sequencing: A Review of Current Molecular Data and New Methods Available to Assess Microbial Diversity

Microscopic eukaryotes living in a dying lake (Lake Koronia, Greece)

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