scholarly journals Physiological and Biochemical Characterization of Isolated Bacteria from a Coccolithophore Chrysotila dentata (Prymnesiophyceae) Culture

Diversity ◽  
2021 ◽  
Vol 14 (1) ◽  
pp. 2
Author(s):  
Xueru Wang ◽  
Yang Liu ◽  
Jun Sun
Keyword(s):  
Biochemical Characterization ◽  
Starch Hydrolysis ◽  
Dilution Method ◽  
Rrna Gene ◽  
Sequencing Analysis ◽  
Free Living ◽  
Attached Bacteria ◽  
Urease Test ◽  
Physiological And Biochemical ◽  
Living Bacteria

Coccolithophores are involved in oceanic carbon and nitrogen cycles, and they also have an impact on global climate change. Chrysotila dentata have a complex and close relationship with phycosphere bacteria. In this study, culturable phycosphere bacteria (free-living bacteria and attached bacteria) are isolated from C. dentata by a gradient dilution method and identified based on the 16S rRNA gene sequencing analysis. The phylogenetic tree (neighbor-joining tree, N-J tree) was constructed using the bacterial sequences and closest related sequences from GenBank. Colony characteristics, Gram nature, and physiological and biochemical characteristics were obtained based on a series of tests, such as the sugar utilization (glucose, arabinose, xylose, maltose, and mannitol) test, Voges–Proskauer reaction, urease tests, gelatin liquefaction, Gram test, starch hydrolysis, among others. In this study, seven strains (CF1, CF2, CF3, CF5, CF6, and CF7) of free-living bacteria (CF) and five strains (CA1, CA2, CA3, CA4, and CA5) of attached bacteria (CA) are isolated and identified. We found that the culturable phycosphere bacteria of C. dentata were mainly α-proteobacteria and γ-proteobacteria, with a small part of the CFB (Cytophaga-Flexibacter-Bacteroides) group bacteria and firmicutes. In this study, most α-proteobacteria can utilize malonate and positive in the urease test, meanwhile they can grow in a 7% NaCl medium. Differently to α-proteobacteria, γ-proteobacteria are more reactive, and can utilize maltose, glucose, arabinose, malonate, aesculin, and starch hydrolysis. Meanwhile, γ-proteobacteria can growth in a 7% NaCl and pH 5.7 medium, and some bacteria of this strain were positive in nitrate reduction. Firmicutes are similar to γ-proteobacteria: they are similar in reactivity, as they can utilize maltose, glucose, arabinose, malonate, aesculin, and starch hydrolysis, and can growth in a 7% NaCl and pH 5.7 medium. The difference is that some of firmicutes were positive in gelatin liquefaction and can utilize mannitol. The CFB group of bacteria were only positive in malonate, aesculin, and starch hydrolysis. The above results provide basic experimental data for further studies on the relationship between the coccolithophores and culturable phycosphere bacteria.

Bacterial community structure in cooling water and biofilm in an industrial recirculating cooling water system

2013 ◽  
Vol 68 (4) ◽  
pp. 940-947 ◽  
Author(s):  
Jinmei Wang ◽  
Min Liu ◽  
Huijie Xiao ◽  
Wei Wu ◽  
Meijuan Xie ◽  
...  
Keyword(s):  
Community Structure ◽  
Bacterial Community ◽  
Water System ◽  
Cooling Water ◽  
Water Systems ◽  
Rrna Gene ◽  
Free Living ◽  
Cooling Water System ◽  
Attached Bacteria ◽  
Living Bacteria

Microbial fouling is a serious problem in open recirculating cooling water systems. The bacterial communities that cause it have not been fully understood. In this study, we analyzed the community structure of free-living bacteria and particle-attached bacteria in cooling water, and bacteria in biofilm collected from the wall of the water reservoir in an industrial recirculating cooling water system by construction of a 16S rRNA gene clone library. Based on amplified ribosomal DNA restriction analysis, clones of all three libraries were clustered into 45 operational taxonomic units (OTUs). Thirteen OTUs displaying 91–96% sequence similarity to a type strain might be novel bacterial species. Noted differences in community structure were observed among the three libraries. The relative species richness of the free-living bacteria in cooling water was much lower than that of particle-attached bacteria and bacteria in biofilm. The majority of the free-living bacterial community (99.0%) was Betaproteobacteria. The predominant bacteria in the particle-attached bacterial community were Alphaproteobacteria (20.5%), Betaproteobacteria (27.8%) and Planctomycetes (42.0%), while those in the biofilm bacterial community were Alphaproteobacteria (47.9%), Betaproteobacteria (11.7%), Acidobacteria (13.1%) and Gemmatimonadetes (11.3%). To control microbial fouling in industrial recirculating cooling water systems, additional physiological and ecological studies of these species will be essential.

scholarly journals Opening a next-generation black box: ecological trends for hundreds of species-like taxa uncovered within a single bacterial >99% 16S rRNA operational taxonomic unit

2021 ◽  
Author(s):  
Martin Hahn ◽  
Andrea Huemer ◽  
Alexandra Pitt ◽  
Matthias Hoetzinger
Keyword(s):  
16S Rrna ◽  
Sequence Similarity ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Rrna Gene ◽  
Taxon Richness ◽  
Large Set ◽  
Free Living ◽  
Environmental Distribution ◽  
Living Bacteria

Current knowledge on environmental distribution and taxon richness of free-living bacteria is mainly based on cultivation-independent investigations employing 16S rRNA gene sequencing methods. Yet, 16S rRNA genes are evolutionarily rather conserved, resulting in limited taxonomic and ecological resolutions provided by this marker. We used a faster evolving protein-encoding marker to reveal ecological patterns hidden within a single OTU defined by >99% 16S rRNA sequence similarity. The studied taxon, subcluster PnecC of the genus Polynucleobacter, represents a ubiquitous group of planktonic freshwater bacteria with cosmopolitan distribution, which is very frequently detected by diversity surveys of freshwater systems. Based on genome taxonomy and a large set of genome sequences, a sequence similarity threshold for delineation of species-like taxa could be established. In total, 600 species-like taxa were detected in 99 freshwater habitats scattered across three regions representing a latitudinal range of 3400 km (42°N to 71°N) and a pH gradient of 4.2 to 8.6. Besides the unexpectedly high richness, the increased taxonomic resolution revealed structuring of Polynucleobacter communities by a couple of macroecological trends, which was previously only demonstrated for phylogenetically much broader groups of bacteria. A unexpected pattern was the almost complete compositional separation of Polynucleobacter communities of Ca-rich and Ca-poor habitats, which strongly resembled the vicariance of plant species on silicate and limestone soils. The presented new cultivation-independent approach opened a window to an incredible, previously unseen diversity, and enables investigations aiming on deeper understanding of how environmental conditions shape bacterial communities and drive evolution of free-living bacteria.

Flavobacterium cutihirudinis sp. nov., isolated from the skin of the medical leech Hirudo verbana

2013 ◽  
Vol 63 (Pt_8) ◽  
pp. 2841-2847 ◽  
Author(s):  
S. P. Glaeser ◽  
H. Galatis ◽  
K. Martin ◽  
P. Kämpfer
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Type Species ◽  
Biochemical Characterization ◽  
Rrna Gene ◽  
Sequencing Analysis ◽  
Respiratory Quinone ◽  
Content Type ◽  
Link Type ◽  
Hirudo Verbana

A Gram-staining-negative, non-endospore-forming, yellow-pigmented strain (E89T) was isolated from the skin of the medical leech Hirudo verbana obtained from a leech farm located in Biebertal, Germany. 16S rRNA gene sequencing analysis showed that the isolate was grouped in the genus Flavobacterium . Strain E89T was most closely related to Flavobacterium chilense LM-09-FpT (98.2 %), Flavobacterium chungangense CJ7T (98.1 %), and Flavobacterium oncorhynchi 631-08T (98.1 %). 16S rRNA gene sequence similarities to all other species of the genus Flavobacterium were ≤97.4 %. A menaquinone of the type MK-6 was found to be the predominant respiratory quinone and the polar lipid profile consisted of the major compounds phosphatidylethanolamine, phosphatidylserine, two unidentified aminolipids, one unknown phospholipid and two unknown lipids. The fatty acid profile was composed of iso-C15 : 0, C15 : 0, summed feature 3 (C16 : 1ω7c and/or iso-C15 : 0 2-OH) found in major amounts and several hydroxylated fatty acids in smaller amounts, among them iso-C15 : 0 3-OH and iso-C17 : 0 3-OH. All these data support the allocation of the isolate in the genus Flavobacterium . Physiological/biochemical characterization and DNA–DNA hybridizations with the type strains of the most closely related species allowed a clear phenotypic and genotypic differentiation of the strain. Based on these data, strain E89T represents a novel species of the genus Flavobacterium , for which the name Flavobacterium cutihirudinis sp. nov. is proposed. The type strain is E89T ( = DSM 25795T = LMG 26922T = CIP 110374T).

The Potential of Free-Living Ground Water Bacteria to Degrade Aromatic Hydrocarbons and Heterocyclic Compounds

1988 ◽  
Vol 20 (3) ◽  
pp. 109-118 ◽  
Author(s):  
E. Arvin ◽  
B. Jensen ◽  
J. Aamand ◽  
C. Jørgensen
Keyword(s):  
Ground Water ◽  
Aromatic Hydrocarbons ◽  
Biomass Concentration ◽  
Nitrogen And Phosphorus ◽  
Free Living ◽  
Soil Fractions ◽  
Fine Soil ◽  
Attached Bacteria ◽  
Considerable Degradation ◽  
Living Bacteria

This study has documented that a considerable degradation potential related to aromatic hydrocarbons and aromatic nitrogen-, sulphur- and oxygen- containing compounds is associated with the free-living ground water bacteria. All studies were performed under aerobic conditions and with surplus of nitrogen and phosphorus. After a lag period, which differs considerably between locations upstream and downstream of hydrocarbon spills, the free-living bacteria are able to degrade the hydrocarbons to concentrations less than 1 µg/l. The bacteria from one site were able to degrade naphthalene according to a zero order reaction even at 1 µg/l. Preliminary experiments indicate that the free-living bacteria may have a relatively high activity compared to the attached bacteria when compared on the basis of the same total bacteria numbers. The hypothesis is put forward that, although the attached biomass concentration in the aquifer may be much higher than the free-living biomass, the latter is still very important for the degradation capability if the attached bacteria are fixed in the fine soil fractions (silt, etc), the reason being that the flow of water, and with this the flux of substrate, is relatively small to the attached bacteria due to low hydraulic conductivity in the fine soil fractions.

Limnoithona sinensis as refuge for bacteria: protection from UV radiation and chlorine disinfection in drinking water treatment

2014 ◽  
Vol 60 (11) ◽  
pp. 745-752 ◽  
Author(s):  
Tao Lin ◽  
Bo Cai ◽  
Wei Chen
Keyword(s):  
Drinking Water ◽  
Water Treatment ◽  
Uv Radiation ◽  
Bacterial Population ◽  
Drinking Water Treatment ◽  
Free Living ◽  
Surrounding Water ◽  
Chlorine Disinfection ◽  
Attached Bacteria ◽  
Living Bacteria

In this study, we tested the potential of Limnoithona sinensis to provide its attached bacteria refuge against disinfection. The experimental results indicated that in water devoid of zooplankton, both UV radiation and chlorine disinfection significantly decreased the viability of free-living bacteria. In the presence of L. sinensis, however, the attached bacteria could survive and rapidly recover from disinfection. This demonstrated that L. sinensis provided protection from external damage to various aquatic bacteria that were attached to its body. The surviving bacteria remained on L. sinensis after disinfection exposure, which enabled a rapid increase in the bacterial population followed by their subsequent release into the surrounding water. Compared with UV radiation, chlorine disinfection was more effective in terms of inactivating attached bacteria. Both UV radiation and chlorine disinfection had little effect in terms of preventing the spread of undesirable bacteria, due to the incomplete inactivation of the bacteria associated with L. sinensis.

Distribution of heterotrophic bacteria in relation to the concentration of particulate organic matter in seawater

1983 ◽  
Vol 29 (5) ◽  
pp. 570-575 ◽  
Author(s):  
Kimio Fukami ◽  
Usio Simidu ◽  
Nobuo Taga
Keyword(s):  
Organic Matter ◽  
Particulate Organic Matter ◽  
Heterotrophic Bacteria ◽  
Viable Count ◽  
Plate Count ◽  
Free Living ◽  
Count Method ◽  
Attached Bacteria ◽  
Geographical Scale ◽  
Living Bacteria

The relationship between the number of bacteria and the concentration of particulate organic carbon (POC) in seawater was investigated. In coastal seawater in summer, the POC concentration showed better correlation to the density of bacteria obtained by the viable plate count method (viable count, V.C.) than by the total direct count method (total count, T.C.). The number of attached bacteria (A) showed significant fluctuation, both laterally on a geographical scale and vertically in the water column; on the other hand, the number of free-living bacteria (F) was relatively constant. The POC concentration had a much higher correlation with A (r = 0.8795) than with T.C. (r = 0.7339), and had a low correlation with F (r = 0.6935). Moreover, a very good correlation was observed between the density of bacteria obtained by V.C. and A (r = 0.9153). These results indicate that when the concentration of particulate organic matter (POM) increases, some free-living bacteria become attached to POM, and grow on the surface of POM. These communities of attached bacteria have the ability to make colonies on plate media and can be counted as the "viable plate count."

scholarly journals Dynamics of Free-Living and Attached Bacterial Assemblages in Skeletonema sp. Diatom Cultures at Elevated Temperatures

2021 ◽  
Vol 8 ◽  
Author(s):  
Zichao Deng ◽  
Shouchang Chen ◽  
Ping Zhang ◽  
Xu Zhang ◽  
Jonathan M. Adams ◽  
...  
Keyword(s):  
Community Structure ◽  
Elevated Temperature ◽  
Bacterial Communities ◽  
Elevated Temperatures ◽  
Bacterial Species ◽  
Positive Interactions ◽  
Growth Stages ◽  
Free Living ◽  
Attached Bacteria ◽  
Living Bacteria

In the context of global warming, changes in phytoplankton-associated bacterial communities have the potential to change biogeochemical cycling and food webs in marine ecosystems. Skeletonema is a cosmopolitan diatom genus in coastal waters worldwide. Here, we grew a Skeletonema strain with its native bacterial assemblage at different temperatures and examined cell concentrations of Skeletonema sp. and free-living bacteria, dissolved organic carbon (DOC) concentrations of cultures, and the community structure of both free-living and attached bacteria at different culture stages. The results showed that elevated temperature increased the specific growth rates of both Skeletonema and free-living bacteria. Different growth stages had a more pronounced effect on community structure compared with temperatures and different physical states of bacteria. The effects of temperature on the structure of the free-living bacterial community were more pronounced compared with diatom-attached bacteria. Carbon metabolism genes and those for some specific amino acid pathways were found to be positively correlated with elevated temperature, which may have profound implications on the oceanic carbon cycle and the marine microbial loop. Network analysis revealed evidence of enhanced cooperation with an increase in positive interactions among different bacteria at elevated temperature. This may help the whole community to overcome the stress of elevated temperature. We speculate that different bacterial species may build more integrated networks with a modified functional profile of the whole community to cope with elevated temperature. This study contributes to an improved understanding of the response of diatom-associated bacterial communities to elevated temperature.

Pacificibacter maritimus gen. nov., sp. nov., isolated from shallow marine sediment

2011 ◽  
Vol 61 (6) ◽  
pp. 1375-1381 ◽  
Author(s):  
Lyudmila A. Romanenko ◽  
Naoto Tanaka ◽  
Vasily I. Svetashev ◽  
Nataliya I. Kalinovskaya
Keyword(s):  
Phylogenetic Analysis ◽  
New Genus ◽  
Biochemical Characterization ◽  
The Sea Of Japan ◽  
Rrna Gene ◽  
Sandy Sediment ◽  
Gene Sequence Analysis ◽  
Bacterium Strain ◽  
Physiological And Biochemical ◽  
Sequence Similarities

An aerobic, Gram-stain-negative, non-pigmented, non-motile bacterium, strain KMM 9031T, was isolated from a sandy sediment sample collected from the shore of the Sea of Japan and subjected to phenotypic and phylogenetic analysis. Based on comparative 16S rRNA gene sequence analysis, strain KMM 9031T constituted a separate phylogenetic line within the Roseobacter clade of the class Alphaproteobacteria, sharing highest sequence similarities with members of the genera Roseovarius (92.7–95.3 %), Pseudoruegeria (94.5 %), Sulfitobacter (92.7–94.4 %) and Thalassobacter (94.2–94.3 %). The predominant fatty acid of strain KMM 9031T was C18 : 1ω7c, with C16 : 0, C10 : 0 3-OH and C12 : 1 3-OH present in lesser amounts. The DNA G+C content of the isolate was 52.6 mol%. The major isoprenoid quinone was Q-10 and polar lipids comprised phosphatidylcholine, phosphatidylglycerol, diphosphatidylglycerol and two unknown lipids. On the basis of phylogenetic analysis and physiological and biochemical characterization, strain KMM 9031T represents a novel species in a new genus, for which the name Pacificibacter maritimus gen. nov., sp. nov. is proposed; the type strain is KMM 9031T ( = NRIC 0785T  = JCM 17096T).

scholarly journals ISOLATION AND IDENTIFICATION OF BACTERIOCIN PRODUCING MICROBES USING BIOCHEMICAL AND MOLECULAR TOOLS AND ANALYSIS OF ITS BIOPRESERVATION POTENTIAL

2016 ◽  
Vol 9 (9) ◽  
pp. 278
Author(s):  
Parmar Keshri Nandan ◽  
Anshita Nagar
Keyword(s):  
16S Rrna ◽  
Molecular Characterization ◽  
Developed Countries ◽  
Diffusion Method ◽  
Dilution Method ◽  
Rrna Gene ◽  
Accession Number ◽  
Isolation And Identification ◽  
16S Rrna Analysis ◽  
Urease Test

ABSTRACTObjective: Food safety is a matter of utmost importance in developing countries as well as in developed countries, so keeping this in mind this researchwork deals with the identification and characterization of bacteriocin producing microbes by using biochemical and molecular characterization. This study has also covered the biopreservation potential of bacteriocin produced by these microbes against sapodilla, tomato and banana as well.Methods: For the purpose of sample collection and isolation, samples of milk, curd and gangajal water were taken and bacteriocin producing microbes were isolated by using serial dilution method. Screening of bacteriocin producing microbe was done by antibacterial sensitivity test using agar well diffusion method against Bacillus amyloliquefaciens, Escherichia Coli, Staphylococcus aureus and Pseudomonas aeruginosa by determining their zone of inhibition. Biochemical characterization was done by using different tests, such as, catalase test, mannitol test, citrate test, gelatin test, maltose test, indole test, urease test, lactose test etc. Molecular characterization was done by using 16S rRNA gene sequencing. Preservative action of bacteriocinwas observed on fruits that comprise sapodilla, tomato and banana by spraying bacteriocin on them and analyzing their activities shows for at least10 days.Results: Microbes were found to be Enterococcus faecalis (Accession number KX011874) and Bacillus cereus (Accession number KX011875). Periodicobservatory studies reflect that using bacteriocin, banana can be preserved for nearly 6-7 days while sapodilla for 8-9 days and tomato for 9-10 days.Conclusion: From present study we would like to conclude that bacteriocins produced by microbes which is found in milk or curd can also be used asbiopreservatives for these defined fruits that is sapodilla, tomato and banana.Keywords: Bacteriocin, Biopreservation, 16S rRNA analysis.

Sign in / Sign up

Export Citation Format

Share Document