PMID- 27801907
OWN - NLM
STAT- MEDLINE
DCOM- 20170801
LR  - 20181202
IS  - 1751-7370 (Electronic)
IS  - 1751-7362 (Print)
IS  - 1751-7362 (Linking)
VI  - 11
IP  - 2
DP  - 2017 Feb
TI  - Geographic distribution at subspecies resolution level: closely related 
      Rhodopirellula species in European coastal sediments.
PG  - 478-489
LID - 10.1038/ismej.2016.123 [doi]
AB  - Members of the marine genus Rhodopirellula are attached living bacteria and 
      studies based on cultured Rhodopirellula strains suggested that three closely 
      related species R. baltica, 'R. europaea' and 'R. islandica' have a limited 
      geographic distribution in Europe. To address this hypothesis, we developed a 
      nested PCR for a single gene copy detection of a partial acetyl CoA synthetase 
      (acsA) from intertidal sediments collected all around Europe. Furthermore, we 
      performed growth experiments in a range of temperature, salinity and light 
      conditions. A combination of Basic Local Alignment Search Tool (BLAST) and 
      Minimum Entropy Decomposition (MED) was used to analyze the sequences with the 
      aim to explore the geographical distribution of the species and subspecies. MED 
      has been mainly used for the analysis of the 16S rRNA gene and here we propose a 
      protocol for the analysis of protein-coding genes taking into account the 
      degeneracy of the codons and a possible overestimation of functional diversity. 
      The high-resolution analysis revealed differences in the intraspecies community 
      structure in different geographic regions. However, we found all three species 
      present in all regions sampled and in agreement with growth experiments we 
      demonstrated that Rhodopirellula species do not have a limited geographic 
      distribution in Europe.
FAU - Zure, Marina
AU  - Zure M
AD  - Department of Microbiology, Max Planck Institute for Marine Microbiology, Bremen, 
      Germany.
FAU - Fernandez-Guerra, Antonio
AU  - Fernandez-Guerra A
AD  - Oxford e-Research Centre, University of Oxford, Oxford, UK.
AD  - Microbial Genomics and Bioinformatics Research Group, Max Planck Institute for 
      Marine Microbiology, Bremen, Germany.
FAU - Munn, Colin B
AU  - Munn CB
AD  - School of Marine Sciences and Engineering, University of Plymouth, Plymouth, UK.
FAU - Harder, Jens
AU  - Harder J
AD  - Department of Microbiology, Max Planck Institute for Marine Microbiology, Bremen, 
      Germany.
LA  - eng
PT  - Journal Article
DEP - 20161101
PL  - England
TA  - ISME J
JT  - The ISME journal
JID - 101301086
RN  - 0 (Bacterial Proteins)
RN  - 0 (DNA, Bacterial)
RN  - 0 (DNA, Ribosomal)
SB  - IM
MH  - Bacterial Proteins/genetics
MH  - DNA, Bacterial/chemistry/genetics
MH  - DNA, Ribosomal/chemistry/genetics
MH  - Europe
MH  - *Genetic Variation
MH  - Genome, Bacterial/*genetics
MH  - Geography
MH  - Geologic Sediments/*microbiology
MH  - High-Throughput Nucleotide Sequencing
MH  - Planctomycetales/*classification/genetics/isolation & purification
MH  - Polymerase Chain Reaction
MH  - Sequence Analysis, DNA
PMC - PMC5270564
EDAT- 2016/11/02 06:00
MHDA- 2017/08/02 06:00
PMCR- 2018/02/01
CRDT- 2016/11/02 06:00
PHST- 2016/06/02 00:00 [received]
PHST- 2016/07/19 00:00 [revised]
PHST- 2016/08/05 00:00 [accepted]
PHST- 2016/11/02 06:00 [pubmed]
PHST- 2017/08/02 06:00 [medline]
PHST- 2016/11/02 06:00 [entrez]
PHST- 2018/02/01 00:00 [pmc-release]
AID - ismej2016123 [pii]
AID - 10.1038/ismej.2016.123 [doi]
PST - ppublish
SO  - ISME J. 2017 Feb;11(2):478-489. doi: 10.1038/ismej.2016.123. Epub 2016 Nov 1.