In an extended study on the biodiversity of rock-dwelling bacteria, the colony and cell morphology, physiology, protein patterns, and 16S rDNA sequences of 17 bacterial strains isolated from different surfaces of rocks, stones, and monuments and from various geographical locations were characterized. All except one strain, which was found to be a Bacillus, were members of the order Actinomycetales. The majority of the strains either were closely related to Geodermatophilus obscurus, which was also analyzed in this study, or formed a closely related sister taxon. All of these strains were isolated from the surface of marble in Namibia and Greece and from limestone from the Negev desert, Israel. One strain, G10, of Namibia origin was equidistantly related to Geodermatophilus obscurus, Frankia alni, Sporichthya polymorpha, and Acidothermus cellulolyticus. Three strains from rock varnish in the Mojave desert, California, were found to be highly related to Arthrobacter (formerly Micrococcus) agilis. All clusters could be confirmed from results of studies on morphological and physiological properties and from banding patterns of whole cell proteins. Based on the results of tests, four additional strains were assigned to the lineage defined by strain G10.

Five Merismopedia-like cyanobacterial strains were collected from microbial mats at Norderney Island, subcultured in the laboratory, and finally grown as unicyanobacterial cultures. As a sixth strain, Merismopedia glauca from the rising dbl quote, left (low)Sammlung von Algenkulturen" at Gottingen (SAG) was used for comparisons. According to morphological and physiological characteristics initially observed in the field and during initial subculturing, the five strains were assigned to the species Merismopedia glauca, Merismopedia punctata, or Merismopedia elegans. However, after prolonged maintenance under laboratory conditions, the formation of platelet-like colonies stopped, whereas cell sizes, production of extracellular polymeric substances, and division patterns were stably maintained. These physiological and morphological parameters allowed us to divide the six strains into two clusters. This division was further supported by the profiling of total cell protein and phycobilisomes using SDS-PAGE. The nearly complete 16S rDNA sequence of three of the six isolates was determined. The comparative sequencing analysis revealed an almost 100% identity of these three Merismopedia-like strains. The evolutionary distance dendrogram constructed placed this Merismopedia cluster into a common line of descent with Synechocystis sp. strain PCC6906. Based on the analysis of common stretches of 1,050 nucleotides, the overall similarity between the sequence types of rising dbl quote, left (low)Merismopedia" and rising dbl quote, left (low)Synechocystis" is 96-97%. The values of the different methods for taxonomic classification of unicyanobacterial strains, the relationship of the cyanobacterial genera Merismopedia, Synechococcus, Synechocystis, and Eucapsis sp., and the functional role of different Merismopedia morphologies within microbial mats are discussed. It is suggested that all analyzed Merismopedia strains be combined into one species, namely Merismopedia punctata Meyen (1839).

The psaE gene, encoding a 7.5 kDa peripheral protein of the photosystem I complex, has been cloned and characterized from the cyanobacterium Synechococcus sp. PCC 7002. The gene is transcribed as an abundant monocistronic transcript of approximately 325 nt. The PsaE protein has been overproduced in Escherichia coli, purified to homogeneity, and used to raise polyclonal antibodies. Mutant strains, in which the psaE gene was insertionally inactivated by interposon mutagenesis, were constructed and characterized. Although the PS I complexes of these strains were similar to those of the wild type, the strains grew more slowly under conditions which favour cyclic electron transport and could not grow at all under photoheterotrophic conditions. The results suggest that PsaE plays a role in cyclic electron transport in cyanobacteria.

Planktomarina temperata gen. nov., sp. nov., belonging to the globally distributed RCA cluster of the marine Roseobacter clade, isolated from the German Wadden Sea

The roles of individual bacterioplankton species in the re-mineralization of algal biomass are poorly understood. Evidence from molecular data had indicated that a spring diatom bloom in the German Bight of the North Sea in 2009 was followed by a rapid succession of uncultivated bacterioplankton species, including members of the genera Ulvibacter, Formosa, Polaribacter (class Flavobacteria) and Reinekea (class Gammaproteobacteria). We isolated strains from the same site during the diatom bloom in spring 2010 using dilution cultivation in an artificial seawater medium with micromolar substrate and nutrient concentrations. Flow cytometry demonstrated growth from single cells to densities of 10(4) -10(6) cells ml(-1) and a culturability of 35%. Novel Formosa, Polaribacter and Reinekea strains were isolated and had 16S rRNA gene sequence identities of > 99.8% with bacterioplankton in spring or summer 2009. Genomes of selected isolates were draft sequenced and used for read recruitment of metagenomes from bacterioplankton in 2009. Metagenome reads covered 93% of a Formosa clade B, 91% of a Reinekea and 74% of a Formosa clade A genome, applying a ≥ 94.5% nucleotide identity threshold. These novel strains represent abundant bacterioplankton species thriving on coastal phytoplankton blooms in the North Sea.

Total RNA was isolated from the diatom Cyclotella cryptica and separated into poly(A)+ and poly(A)- fractions. These fractions were subjected to in vitro translation/immunoprecipitation experiments using an antiserum directed against the predominant light-harvesting complex of Cy. cryptica (ccry antiserum) and a heterologous antiserum raised against the light-harvesting complex of the cryptophyte Cryptomonas maculata (cmac antiserum). From translation reactions programmed with poly(A)+ RNA the ccry-antiserum immunoprecipitated polypeptides with relative molecular weights (Mr) of 27000, 25000, 23000 and 21000, while the cmac-antiserum precipitated proteins with Mrs of 32500 and 27000, respectively. Subsequent cDNA synthesis and immunological screening of the cDNA library with both antisera resulted in the isolation of six cDNA clones encoding light-harvesting subunits. Full-length precursors were 199-210 amino acids in length and had Mrs of 20000-23000. The lengths of the putative signal peptides were 29 or 30 amino acids. Pairwise comparison revealed that the similarity between the clones ranged from 54-99% on the nucleotide level and from 36-99% at the amino acid level. In agreement with the data from the screens with the two antisera, the genes clustered into two groups. The data provide evidence that the genes constitute a heterogeneous multigene family and that the light-harvesting system of Cy. cryptica might be as complex as that of higher plants and green algae.

Large surface-to-volume ratios provide optimal nutrient uptake conditions for small microorganisms in oligotrophic habitats. The surface area can be increased with appendages. Here, we describe chains of interconnecting vesicles protruding from cells of strain Hel3_A1_48, affiliating with Formosa spp. within the Flavobacteriia and originating from coastal free-living bacterioplankton. The chains were up to 10 μm long and had vesicles emanating from the outer membrane with a single membrane and a size of 80 to 100 nm by 50 to 80 nm. Cells extruded membrane tubes in the exponential phase, whereas vesicle chains dominated on cells in the stationary growth phase. This formation is known as pearling, a physical morphogenic process in which membrane tubes protrude from liposomes and transform into chains of interconnected vesicles. Proteomes of whole-cell membranes and of detached vesicles were dominated by outer membrane proteins, including the type IX secretion system and surface-attached peptidases, glycoside hydrolases, and endonucleases. Fluorescein-labeled laminarin stained the cells and the vesicle chains. Thus, the appendages provide binding domains and degradative enzymes on their surfaces and probably storage volume in the vesicle lumen. Both may contribute to the high abundance of these Formosa-affiliated bacteria during laminarin utilization shortly after spring algal blooms. IMPORTANCE Microorganisms produce membrane vesicles. One synthesis pathway seems to be pearling that describes the physical formation of vesicle chains from phospholipid vesicles via extended tubes. Bacteria with vesicle chains had been observed as well as bacteria with tubes, but pearling was so far not observed. Here, we report the observation of, initially, tubes and then vesicle chains during the growth of a flavobacterium, suggesting biopearling of vesicle chains. The flavobacterium is abundant during spring bacterioplankton blooms developing after algal blooms and has a special set of enzymes for laminarin, the major storage polysaccharide of microalgae. We demonstrated with fluorescently labeled laminarin that the vesicle chains bind laminarin or contain laminarin-derived compounds. Proteomic analyses revealed surface-attached degradative enzymes on the outer membrane vesicles. We conclude that the large surface area and the lumen of vesicle chains may contribute to the ecological success of this marine bacterium.

Two additional cDNA clones containing genes which encode fucoxanthin chlorophyll a/c binding proteins (Fcps) of the centric diatom Cyclotella cryptica have been sequenced. The first cDNA clone containing fcp12 had an insert size of 871 base pairs (bp). The open reading frame (ORF) of 693 bp corresponds to a precursor protein of 231 amino acids with a molecular weight (Mr) of 25 200. For the mature Fcp12, a protein of 196 amino acids with a Mr of 21 700 is proposed. The second cDNA clone contained the fragmentary fcp4 with an insert of 805 bp. The ORF of 492 bp corresponds to a polypeptide of 164 amino acids with a Mr of 18 050. Phylogenetic analyses revealed that the proteins Fcp1, Fcp2, Fcp3 and Fcp5 are closely related to the Fcps of other diatoms, whereas Fcp6, Fcp7 and Fcp12 share the highest homology to the Fcp of the haptophyte Isochrysis galbana and to the light inducible proteins LI818r3 and LI818 of Chlamydomonas reinhardtii and Chlamydomonas eugametos. The subunit Fcp4 revealed some homology with the red algal LH subunits LhcaR1 and LhcaR2 of Porphyridium cruentum.