scholarly journals Cross-Ocean Distribution of Rhodobacterales Bacteria as Primary Surface Colonizers in Temperate Coastal Marine Waters

2007 ◽  
Vol 74 (1) ◽  
pp. 52-60 ◽  
Author(s):  
Hongyue Dang ◽  
Tiegang Li ◽  
Mingna Chen ◽  
Guiqiao Huang
Keyword(s):  
Atlantic Coast ◽  
Adaptation Strategy ◽  
Current Data ◽  
Control Surface ◽  
Rrna Gene ◽  
Multivariate Statistical ◽  
Surface Colonization ◽  
Bacterial Surface ◽  
West Pacific Ocean ◽  
Bacterial Assemblages

ABSTRACT Bacterial surface colonization is a universal adaptation strategy in aquatic environments. However, neither the identities of early colonizers nor the temporal changes in surface assemblages are well understood. To determine the identities of the most common bacterial primary colonizers and to assess the succession process, if any, of the bacterial assemblages during early stages of surface colonization in coastal water of the West Pacific Ocean, nonnutritive inert materials (glass, Plexiglas, and polyvinyl chloride) were employed as test surfaces and incubated in seawater off the Qingdao coast in the spring of 2005 for 24 and 72 h. Phylogenetic analysis of the 16S rRNA gene sequences amplified from the recovered surface-colonizing microbiota indicated that diverse bacteria colonized the submerged surfaces. Multivariate statistical cluster analyses indicated that the succession of early surface-colonizing bacterial assemblages followed sequential steps on all types of test surfaces. The Rhodobacterales, especially the marine Roseobacter clade members, formed the most common and dominant primary surface-colonizing bacterial group. Our current data, along with previous studies of the Atlantic coast, indicate that the Rhodobacterales bacteria are the dominant and ubiquitous primary surface colonizers in temperate coastal waters of the world and that microbial surface colonization follows a succession sequence. A conceptual model is proposed based on these findings, which may have important implications for understanding the structure, dynamics, and function of marine biofilms and for developing strategies to harness or control surface-associated microbial communities.

scholarly journals Abrupt Temporal Fluctuations in the Chicken Fecal Microbiota Are Explained by Its Gastrointestinal Origin

2012 ◽  
Vol 78 (8) ◽  
pp. 2941-2948 ◽  
Author(s):  
M. Sekelja ◽  
I. Rud ◽  
S. H. Knutsen ◽  
V. Denstadli ◽  
B. Westereng ◽  
...  
Keyword(s):  
Barrier Function ◽  
16S Rrna Gene Sequencing ◽  
Fecal Microbiota ◽  
Pathogen Transmission ◽  
Rrna Gene ◽  
Multivariate Statistical ◽  
Content Type ◽  
Factors Affecting ◽  
Temporal Fluctuations ◽  
Gastric Barrier

ABSTRACTOne of the main challenges in understanding the composition of fecal microbiota is that it can consist of microbial mixtures originating from different gastrointestinal (GI) segments. Here, we addressed this challenge for broiler chicken feces using a direct 16S rRNA gene-sequencing approach combined with multivariate statistical analyses. Broiler feces were chosen because of easy sampling and the importance for pathogen transmission to the human food chain. Feces were sampled daily for 16 days from chickens with and without a feed structure-induced stimulation of the gastric barrier function. Overall, we found four dominant microbial phylogroups in the feces. Two of the phylogroups were related to clostridia, one to lactobacilli, and one toEscherichia/Shigella. The relative composition of these phylogroups showed apparent stochastic temporal fluctuations in feces. Analyses of dissected chickens at the end of the experiment, however, showed that the two clostridial phylogroups were correlated to the microbiota in the cecum/colon and the small intestine, while the upper gut (crop and gizzard) microbiota was correlated to the lactobacillus phylogroup. In addition, chickens with a stimulated gizzard also showed less of the proximate GI dominating bacterial group in the feces, supporting the importance of the gastric barrier function. In conclusion, our results suggest that GI origin is a main determinant for the chicken fecal microbiota composition. This knowledge will be important for future understanding of factors affecting shedding of both harmful and beneficial gastrointestinal bacteria through feces.

scholarly journals An advanced multivariate statistical approach to study coastal sediment data

2006 ◽  
Vol 4 (1) ◽  
pp. 68-80 ◽  
Author(s):  
Pavlina Simeonova ◽  
Costel Sarbu ◽  
Thomas Spanos ◽  
Vasil Simeonov ◽  
Stefan Tsakovski
Keyword(s):  
Atlantic Coast ◽  
Large Data ◽  
Data Interpretation ◽  
Coastal Sediment ◽  
Multivariate Statistical ◽  
Data Set ◽  
The Usa ◽  
Multivariate Statistical Approach ◽  
Scatter Plots ◽  
Sediment Data

AbstractThe present paper deals with the application of classical and fuzzy principal components analysis to a large data set from coastal sediment analysis. Altogether 126 sampling sites from the Atlantic Coast of the USA are considered and at each site 16 chemical parameters are measured. It is found that four latent factors are responsible for the data structure (“natural”, “anthropogenic”, “bioorganic”, and “organic anthropogenic”). Additionally, estimating the scatter plots for factor scores revealed the similarity between the sampling sites. Geographical and urban factors are found to contribute to the sediment chemical composition. It is shown that the use of fuzzy PCA helps for better data interpretation especially in case of outliers.

scholarly journals Fecal Bacterial Microbiota of Healthy Free-Ranging, Healthy Corralled, and Chronic Diarrheic Corralled Rhesus Macaques (Macaca mulatta)

2021 ◽  
Vol 71 (2) ◽  
pp. 152-165
Author(s):  
Nicole R Compo ◽  
Luis Mieles-Rodriguez ◽  
Diego E Gomez
Keyword(s):  
Gut Microbiota ◽  
Rhesus Macaques ◽  
Current Data ◽  
Rrna Gene ◽  
Primate Research ◽  
Gastrointestinal Microbiota ◽  
Healthy Humans ◽  
Bacterial Microbiota ◽  
Health And Development ◽  
Free Ranging

A clinical challenge to nearly every primate facility in North America is chronic idiopathic diarrhea (CID), the pathogenesis of which has yet to be fully elucidated. However, wild macaques appear resistant to CID, a trend that we observed in the free-ranging population of the Caribbean Primate Research Center. The gastrointestinal microbiota has been shown to have a significant role in the pathogenesis of disease and in maintaining normal health and development of the gut. In humans, chronic diarrhea is associated with alteration of the gut microbiota, which has lower bacterial diversity than does the microbiota of healthy humans. The current study was designed to describe and compare the fecal bacterial microbiota of healthy corralled, CID corralled, and healthy, free-ranging macaques. Fresh fecal samples were collected from healthy corralled (HC; n = 30) and CID (n = 27) rhesus macaques and from healthy macaques from our free-ranging colony (HF; n = 43). We excluded macaques that had received antibiotics during the preceding 60 d (90 d for healthy animals). Bacterial DNA was extracted, and the V4 region of the 16S rRNA gene was sequenced and compared with known databases. The relative abundance of Proteobacteria was higher in CID animals than HC animals, but otherwise few differences were found between these 2 groups. HF macaques were differentially enriched with Christensenellaceae and Helicobacter, which are highly associated with a 'healthy' gut in humans, as compared to corralled animals, whereas CID animals were enriched with Proteobacteria, which are associated with dysbiosis in other species. These results indicate that environment has a greater influence than health status on the gut microbiota. Furthermore, the current data provided targets for future studies on potential clinical interventions, such as probiotics and fecal transplants.

scholarly journals Effects of Caribbean sponge secondary metabolites on bacterial surface colonization

2005 ◽  
Vol 40 ◽  
pp. 191-203 ◽  
Author(s):  
SR Kelly ◽  
E Garo ◽  
PR Jensen ◽  
W Fenical ◽  
JR Pawlik
Keyword(s):  
Secondary Metabolites ◽  
Surface Colonization ◽  
Bacterial Surface

scholarly journals Tad pili play a dynamic role in Caulobacter crescentus surface colonization

2019 ◽  
Author(s):  
Matteo Sangermani ◽  
Isabelle Hug ◽  
Nora Sauter ◽  
Thomas Pfohl ◽  
Urs Jenal
Keyword(s):  
Caulobacter Crescentus ◽  
Optical Trap ◽  
Natural Environments ◽  
Surface Attachment ◽  
Surface Colonization ◽  
Bacterial Surface ◽  
Controlled Flow ◽  
Mechanical Sensing

ABSTRACTBacterial surface attachment is mediated by rotary flagella and filamentous appendages called pili. Here, we describe the role of Tad pili during surface colonization of Caulobacter crescentus. Using an optical trap and microfluidic controlled flow conditions as a mimic of natural environments, we demonstrate that Tad pili undergo repeated cycles of extension and retraction. Within seconds after establishing surface contact, pili reorient cells into an upright position promoting walking-like movements against the medium flow. Pili-mediated positioning of the flagellated pole close to the surface facilitates motor-mediated mechanical sensing and promotes anchoring of the holdfast, an adhesive substance that affords long-term attachment. We present evidence that the second messenger c-di-GMP regulates pili dynamics during surface encounter in distinct ways, promoting increased activity at intermediate levels and retraction of pili at peak concentrations. We propose a model, in which flagellum and Tad pili functionally interact and together impose a ratchet-like mechanism that progressively drives C. crescentus cells towards permanent surface attachment.

scholarly journals Patiriisocius marinistellae gen. nov., sp. nov., isolated from the starfish Patiria pectinifera, and reclassification of Ulvibacter marinus as a member of the genus Patiriisocius comb. nov.

2020 ◽  
Vol 70 (7) ◽  
pp. 4119-4129 ◽  
Author(s):  
Keisuke Kawano ◽  
Natsumi Ushijima ◽  
Minoru Kihara ◽  
Hideomi Itoh
Keyword(s):  
Type Species ◽  
Amino Acid Identity ◽  
Current Data ◽  
Rrna Gene ◽  
Aerobic Bacterium ◽  
Phenotypic Properties ◽  
Content Type ◽  
Relationship Analysis ◽  
Link Type ◽  
Patiria Pectinifera

A marine strain, designated KK4T, was isolated from the surface of a starfish, Patiria pectinifera, which was collected from seawater off the coast of Hokkaido, Japan. Strain KK4T is a Gram-stain-negative, non-spore-forming, rod-shaped, aerobic bacterium that forms yellow-pigmented colonies. A phylogenetic relationship analysis, based on 16S rRNA gene sequences, revealed that strain KK4T was closely related to Ulvibacter marinus IMCC12008T, Ulvibacter antarcticus IMCC3101T and Ulvibacter litoralis KMM 3912T, with similarities of 96.9, 95.8 and 95.6 %, respectively, but low sequence similarities (<94 %) among other genera in the family Flavobacteriaceae . Genomic similarities between strain KK4T and the three Ulvibacter type strains based on average nucleotide identity and digital DNA–DNA hybridization values were lower than the species delineation thresholds. Moreover, phylogenetic tree based on genome sequences showed that strain KK4T was clustered with U. marinus IMCC12008T and formed a branch independent from the cluster including type species of the genera Ulvibacter , Marixanthomonas , Marinirhabdus , Aureitalea and Aequorivita . Amino acid identity values between strain KK4T/ U. marinus IMCC12008T and the neighbour type species/strains were 61.9–68.2% and 61.5–67.4 %, which were lower than the genus delineation threshold, implying the novel genus status of strain KK4T. Strain KK4T growth occurred at pH 6.0–9.0, 4–30 °C and in NaCl concentrations of 0.5–5.0 %, and optimally at pH 7.0, 25 °C and 3.0 %, respectively. Unlike Ulvibacter strains, strain KK4T could assimilate glucose, mannose, galactose and acetate. The major quinone and fatty acids were menaquinone-6 and iso-C15 : 0 (27.5 %), iso-C15 : 1 G (22.5 %) and iso-C17 : 0 3-OH (12.8 %), respectively. Based on genetic, phylogenetic and phenotypic properties, strain KK4T represents a novel species of the genus Patiriisocius, for which the name Patiriisocius marinistellae gen. nov., sp. nov. is proposed. The type strain is KK4T (=JCM 33344T=KCTC 72225T). In addition, based on the current data, Ulvibacter marinus should be reclassified as Patiriisocius marinus comb. nov.

scholarly journals Loktanella agnita sp. nov. and Loktanella rosea sp. nov., from the north-west Pacific Ocean

2005 ◽  
Vol 55 (5) ◽  
pp. 2203-2207 ◽  
Author(s):  
Elena P. Ivanova ◽  
Natalia V. Zhukova ◽  
Anatoly M. Lysenko ◽  
Nataliya M. Gorshkova ◽  
Alexander F. Sergeev ◽  
...  
Keyword(s):  
Pacific Ocean ◽  
Sea Water ◽  
Sequence Similarity ◽  
Carbon Sources ◽  
Tween 80 ◽  
Rrna Gene ◽  
North West ◽  
Temperature Range ◽  
West Pacific Ocean ◽  
The North

One whitish and four pinkish strains of Gram-negative, non-motile, aerobic bacteria were isolated from sea-water and sediment samples collected in Chazhma Bay (Sea of Japan, Pacific Ocean). Analysis of 16S rRNA gene sequences revealed that these strains belonged to the ‘Alphaproteobacteria’, having highest sequence similarity of about 94–97 % with species of the genus Loktanella. None of the strains degraded gelatin, casein, chitin, agar, DNA or starch and they had limited ability to utilize carbon sources. The four pinkish strains, Fg36T, Fg1, Fg116 and Fg117, degraded Tween 80. Sea-water strain R10SW5T grew at 3–6 % NaCl and a temperature range of 8–35 °C, whilst strains Fg36T, Fg1, Fg116 and Fg117 grew at NaCl concentrations of 1–12 % and a temperature range of 4–35 °C. Phosphatidylglycerol (58/79 %), diphosphatidylglycerol (11/6 %) and phosphatidylcholine (28/22 %) were the major phospholipids. The predominant fatty acids were 16 : 0 (12·2/8·6 %) and 18 : 1ω7 (76·6/68·4 %). The DNA G+C content of strain R10SW5T was 59·1 mol% and those of the four pinkish strains ranged from 60·5 to 61·8 mol%. Based on the results of phenotypic, genotypic, chemotaxonomic and phylogenetic investigation, two novel species, Loktanella agnita sp. nov. and Loktanella rosea sp. nov., are proposed. The type strains are R10SW5T (=KMM 3788T=CIP 107883T) and Fg36T (=KMM 6003T=CIP 107851T=LMG 22534T), respectively.

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