scholarly journals Diversity of Free-Living and Attached Bacteria in Offshore Western Mediterranean Waters as Depicted by Analysis of Genes Encoding 16S rRNA

1999 ◽  
Vol 65 (2) ◽  
pp. 514-522 ◽  
Author(s):  
Silvia G. Acinas ◽  
Josefa Antón ◽  
Francisco Rodríguez-Valera
Keyword(s):  
16S Rdna ◽  
Restriction Analysis ◽  
Western Mediterranean ◽  
Bacterial Cells ◽  
Free Living ◽  
Attached Bacteria ◽  
Genes Encoding ◽  
Community Fingerprinting ◽  
Close Relatives ◽  
Alteromonas Macleodii

ABSTRACT In a previous study (S. G. Acinas, F. Rodrı́guez-Valera, and C. Pedrós-Alió, FEMS Microbiol. Ecol. 24:27–40, 1997), community fingerprinting by 16S rDNA restriction analysis applied to Mediterranean offshore waters showed that the free-living pelagic bacterial community was very different from the bacterial cells aggregated or attached to particles of more than about 8 μm. Here we have studied both assemblages at three depths (5, 50, and 400 m) by cloning and sequencing the 16S rDNA obtained from the same samples, and we have also studied the samples by scanning electron microscopy to detect morphology patterns. As expected, the sequences retrieved from the assemblages were very different. The subsample of attached bacteria contained very little diversity, with close relatives of a well-known species of marine bacteria, Alteromonas macleodii, representing the vast majority of the clones at every depth. On the other hand, the free-living assemblage was highly diverse and varied with depth. At 400 m, close relatives of cultivated γProteobacteria predominated, but as shown by other authors, near the surface most clones were related to phylotypes described only by sequence, in which the α Proteobacteria of the SAR11 cluster predominated. The new technique of rDNA internal spacer analysis has been utilized, confirming these results. Clones representative of the A. macleodii cluster have been completely sequenced, producing a picture that fits well with the idea that they could represent a genus with at least two species and with a characteristic depth distribution.

Phylogeny based on 16S rDNA andnifHsequences ofRalstonia taiwanensisstrains isolated from nitrogen-fixing nodules ofMimosa pudica, in India

2004 ◽  
Vol 50 (5) ◽  
pp. 313-322 ◽  
Author(s):  
Subhash Chandra Verma ◽  
Soumitra Paul Chowdhury ◽  
Anil Kumar Tripathi
Keyword(s):  
16S Rdna ◽  
South India ◽  
Restriction Analysis ◽  
Cross Reaction ◽  
North India ◽  
Mimosa Pudica ◽  
Free Living ◽  
South Indian ◽  
Indian Isolates ◽  
Dinitrogenase Reductase

Bacterial symbionts present in the indeterminate-type nitrogen (N)-fixing nodules of Mimosa pudica grown in North and South India showed maximum similarity to Ralstonia taiwanensis on the basis of carbon-source utilization patterns and 16S rDNA sequence. Isolates from the nodules of M. pudica from North India and South India showed identical ARDRA (Amplified Ribosomal DNA Restriction Analysis) patterns with Sau3AI and RsaI, but AluI revealed dimorphy between the North Indian and South Indian isolates. Alignment of 16S rDNA sequences revealed similarity of North Indian isolates with an R. taiwanensis strain isolated from M. pudica in Taiwan, whereas South Indian isolates showed closer relatedness with the isolates from Mimosa diplotricha. Alignment of nifH sequences from both North Indian and South Indian isolates with that of the related isolates revealed their closer affinity to α-rhizobia, suggesting that nif genes in the β-rhizobia might have been acquired from α-rhizobia via lateral transfer during co-occupancy of nodules by α-rhizobia and progenitors of R. taiwanensis, members of the β-subclass of Proteobacteria. Immunological cross-reaction of the bacteroid preparation of M. pudica nodules showed strong a positive signal with anti-dinitrogenase reductase antibody, whereas a weak positive cross-reaction was observed with free-living R. taiwanensis grown microaerobically in minimal medium with and without NH4Cl. In spite of the expression of dinitrogenase reductase under free-living conditions, acetylene reduction was not observed under N-free conditions even after prolonged incubation.Key words: symbiotic nitrogen fixation, Mimosa pudica, rhizobia, phylogeny, 16S rDNA, nifH, Ralstonia taiwanensis.

scholarly journals Genome Sequence of the Polysaccharide-Degrading, Thermophilic Anaerobe Spirochaeta thermophila DSM 6192

2010 ◽  
Vol 192 (24) ◽  
pp. 6492-6493 ◽  
Author(s):  
Angel Angelov ◽  
Susanne Liebl ◽  
Meike Ballschmiter ◽  
Mechthild Bömeke ◽  
Rüdiger Lehmann ◽  
...  
Keyword(s):  
Genome Sequence ◽  
Complete Genome Sequence ◽  
Glycoside Hydrolase ◽  
Enzyme System ◽  
Cellulose Degradation ◽  
Carbohydrate Binding ◽  
Carbohydrate Binding Module ◽  
Free Living ◽  
Genome Data ◽  
Genes Encoding

ABSTRACT Spirochaeta thermophila is a thermophilic, free-living anaerobe that is able to degrade various α- and β-linked sugar polymers, including cellulose. We report here the complete genome sequence of S. thermophila DSM 6192, which is the first genome sequence of a thermophilic, free-living member of the Spirochaetes phylum. The genome data reveal a high density of genes encoding enzymes from more than 30 glycoside hydrolase families, a noncellulosomal enzyme system for (hemi)cellulose degradation, and indicate the presence of a novel carbohydrate-binding module.

scholarly journals Detection and Quantification of Superoxide Formed within the Periplasm of Escherichia coli

2006 ◽  
Vol 188 (17) ◽  
pp. 6326-6334 ◽  
Author(s):  
Sergei Korshunov ◽  
James A. Imlay
Keyword(s):  
Escherichia Coli ◽  
Pathogenic Bacteria ◽  
Phagocytic Cells ◽  
Free Living ◽  
E Coli ◽  
Superoxide Formation ◽  
Genes Encoding ◽  
Copper Zinc ◽  
Primary Substrate

ABSTRACT Many gram-negative bacteria harbor a copper/zinc-containing superoxide dismutase (CuZnSOD) in their periplasms. In pathogenic bacteria, one role of this enzyme may be to protect periplasmic biomolecules from superoxide that is released by host phagocytic cells. However, the enzyme is also present in many nonpathogens and/or free-living bacteria, including Escherichia coli. In this study we were able to detect superoxide being released into the medium from growing cultures of E. coli. Exponential-phase cells do not normally synthesize CuZnSOD, which is specifically induced in stationary phase. However, the engineered expression of CuZnSOD in growing cells eliminated superoxide release, confirming that this superoxide was formed within the periplasm. The rate of periplasmic superoxide production was surprisingly high and approximated the estimated rate of cytoplasmic superoxide formation when both were normalized to the volume of the compartment. The rate increased in proportion to oxygen concentration, suggesting that the superoxide is generated by the adventitious oxidation of an electron carrier. Mutations that eliminated menaquinone synthesis eradicated the superoxide formation, while mutations in genes encoding respiratory complexes affected it only insofar as they are likely to affect the redox state of menaquinone. We infer that the adventitious autoxidation of dihydromenaquinone in the cytoplasmic membrane releases a steady flux of superoxide into the periplasm of E. coli. This endogenous superoxide may create oxidative stress in that compartment and be a primary substrate of CuZnSOD.

scholarly journals Single cell genomics reveals plastid-lacking Picozoa are close relatives of red algae

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Max E. Schön ◽  
Vasily V. Zlatogursky ◽  
Rohan P. Singh ◽  
Camille Poirier ◽  
Susanne Wilken ◽  
...  
Keyword(s):  
Single Cell ◽  
Red Algae ◽  
Free Living ◽  
Plastid Evolution ◽  
Single Cell Genomics ◽  
Close Relatives ◽  
Globally Distributed ◽  
Eukaryotic Supergroup ◽  
Rare Group ◽  
Endosymbiotic Origin

AbstractThe endosymbiotic origin of plastids from cyanobacteria gave eukaryotes photosynthetic capabilities and launched the diversification of countless forms of algae. These primary plastids are found in members of the eukaryotic supergroup Archaeplastida. All known archaeplastids still retain some form of primary plastids, which are widely assumed to have a single origin. Here, we use single-cell genomics from natural samples combined with phylogenomics to infer the evolutionary origin of the phylum Picozoa, a globally distributed but seemingly rare group of marine microbial heterotrophic eukaryotes. Strikingly, the analysis of 43 single-cell genomes shows that Picozoa belong to Archaeplastida, specifically related to red algae and the phagotrophic rhodelphids. These picozoan genomes support the hypothesis that Picozoa lack a plastid, and further reveal no evidence of an early cryptic endosymbiosis with cyanobacteria. These findings change our understanding of plastid evolution as they either represent the first complete plastid loss in a free-living taxon, or indicate that red algae and rhodelphids obtained their plastids independently of other archaeplastids.

scholarly journals Factors mediating plastid dependency and the origins of parasitism in apicomplexans and their close relatives

2015 ◽  
Vol 112 (33) ◽  
pp. 10200-10207 ◽  
Author(s):  
Jan Janouškovec ◽  
Denis V. Tikhonenkov ◽  
Fabien Burki ◽  
Alexis T. Howe ◽  
Martin Kolísko ◽  
...  
Keyword(s):  
Plastid Genome ◽  
Sequence Data ◽  
Sister Group ◽  
Molecular Characteristics ◽  
Phylogenomic Analysis ◽  
Free Living ◽  
Plastid Genomes ◽  
Monophyletic Lineage ◽  
Causative Agents ◽  
Close Relatives

Apicomplexans are a major lineage of parasites, including causative agents of malaria and toxoplasmosis. How such highly adapted parasites evolved from free-living ancestors is poorly understood, particularly because they contain nonphotosynthetic plastids with which they have a complex metabolic dependency. Here, we examine the origin of apicomplexan parasitism by resolving the evolutionary distribution of several key characteristics in their closest free-living relatives, photosynthetic chromerids and predatory colpodellids. Using environmental sequence data, we describe the diversity of these apicomplexan-related lineages and select five species that represent this diversity for transcriptome sequencing. Phylogenomic analysis recovered a monophyletic lineage of chromerids and colpodellids as the sister group to apicomplexans, and a complex distribution of retention versus loss for photosynthesis, plastid genomes, and plastid organelles. Reconstructing the evolution of all plastid and cytosolic metabolic pathways related to apicomplexan plastid function revealed an ancient dependency on plastid isoprenoid biosynthesis, predating the divergence of apicomplexan and dinoflagellates. Similarly, plastid genome retention is strongly linked to the retention of two genes in the plastid genome, sufB and clpC, altogether suggesting a relatively simple model for plastid retention and loss. Lastly, we examine the broader distribution of a suite of molecular characteristics previously linked to the origins of apicomplexan parasitism and find that virtually all are present in their free-living relatives. The emergence of parasitism may not be driven by acquisition of novel components, but rather by loss and modification of the existing, conserved traits.

The ontogeny of trilobite segmentation: a comparative approach

Paleobiology ◽  
2006 ◽  
Vol 32 (4) ◽  
pp. 602-627 ◽  
Author(s):  
Nigel C. Hughes ◽  
Alessandro Minelli ◽  
Giuseppe Fusco
Keyword(s):  
Direct Development ◽  
Comparative Approach ◽  
Phase Boundaries ◽  
Free Living ◽  
Ancestral Condition ◽  
Morphological Transitions ◽  
Posterior Trunk ◽  
Close Relatives ◽  
Number Of Segments ◽  
Trunk Segments

Ontogenetic stages of trilobites have traditionally been recognized on the basis of the development of exoskeletal segmentation. The established protaspid, meraspid, and holaspid phases relate specifically to the development of articulated joints between exoskeletal elements. Transitions between these phases were marked by the first and last appearances of new trunk segment articulations. Here we propose an additional and complementary ontogenetic scheme based on the generation of new trunk segments. It includes an anamorphic phase during which new trunk segments appeared, and an epimorphic phase during which the number of segments in the trunk remained constant. In some trilobites an ontogenetic boundary can also be recognized at the first appearance of morphologically distinct posterior trunk segments. Comparison of the phase boundaries of these different aspects of segment ontogeny highlights rich variation in the segmentation process among Trilobita. Cases in which the onset of the holaspid phase preceded onset of the epimorphic phase are here termed protarthrous, synchronous onset of both phases is termed synarthromeric, and onset of the epimorphic phase before onset of the holaspid phase is termed protomeric. Although these conditions varied among close relatives and perhaps even intraspecifically in some cases, particular conditions may have been prevalent within some clades.Trilobites displayed hemianamorphic development that was accomplished over an extended series of juvenile and mature free-living instars. Although developmental schedules varied markedly among species, morphological transitions during trilobite development were generally regular, limited in scope, and extended over a large number of instars when compared with those of many living arthropods. Hemianamorphic, direct development with modest change between instars is also seen among basal members of the Crustacea, basal myriapods, pycnogonids, and in some fossil chelicerates. This mode may represent the ancestral condition of euarthropod development.

The dynamics of attached and free-living bacterial population in tropical coastal waters

2015 ◽  
Vol 66 (8) ◽  
pp. 701 ◽  
Author(s):  
Siew Wen Lee ◽  
Choon Weng Lee ◽  
Chui Wei Bong ◽  
Kumaran Narayanan ◽  
Edmund Ui-Hang Sim
Keyword(s):  
Coastal Waters ◽  
Bacterial Population ◽  
Bacterial Abundance ◽  
Large Fraction ◽  
Free Living ◽  
Water Port ◽  
Eutrophic Water ◽  
Attached Bacteria ◽  
Student’S T ◽  
Student’S T Test

We investigated the dynamics of attached and free-living bacterial abundance over a period of 18 months in tropical coastal waters of Malaysia. We measured the abundance at both oligotrophic coastal water (Port Dickson) and eutrophic estuary (Klang), and hypothesised that attached bacteria are predominant in eutrophic waters. We found that bacterial abundance was higher at Klang than Port Dickson (Student’s t-test: t=4.87, d.f.=19, P<0.001). Attached bacteria also formed a large fraction of the total bacteria at Klang (75% ±13s.d.) relative to Port Dickson (56% ±22), and showed preference for chlorophyll-a-based particles rather than total suspended solids. The bacterial community structure was clearly different between the two stations but was similar between the attached and free-living bacterial population. Our results showed the importance of attached bacteria in eutrophic water where they could play a major role in carbon and nutrient cycling.

Sign in / Sign up

Export Citation Format

Share Document