scholarly journals Diversity of cultivable protease-producing bacteria and their extracellular proteases associated to scleractinian corals

PeerJ ◽  
2020 ◽  
Vol 8 ◽  
pp. e9055
Author(s):  
Hongfei Su ◽  
Zhenlun Xiao ◽  
Kefu Yu ◽  
Qinyu Huang ◽  
Guanghua Wang ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Serine Proteases ◽  
Organic Nitrogen ◽  
Vital Role ◽  
Scleractinian Corals ◽  
Rrna Gene ◽  
Bacterial Strains ◽  
16S Rrna Gene Sequences ◽  
Extracellular Proteases ◽  
Aspartic Proteases

Protease-producing bacteria play a vital role in degrading organic nitrogen in marine environments. However, the diversity of the bacteria and extracellular proteases has seldom been addressed, especially in communities of coral reefs. In this study, 136 extracellular protease-producing bacterial strains were isolated from seven genera of scleractinian corals from Luhuitou fringing reef, and their protease types were characterized. The massive coral had more cultivable protease-producing bacteria than branching or foliose corals. The abundance of cultivable protease-producing bacteria reached 106 CFU g−1 of coral. Phylogenetic analysis of 16S rRNA gene sequences revealed that the isolates were assigned to 24 genera, from which 20 corresponded to the phyla Firmicutes and Proteobacteria. Bacillus and Fictibacillus were retrieved from all coral samples. Moreover, Vibrio and Pseudovibrio were most prevalent in massive or foliose coral Platygyra and Montipora. In contrast, 11 genera were each identified in only one isolate. Nearly all the extracellular proteases from the bacteria were serine proteases or metalloproteases; 45.83% of isolates also released cysteine or aspartic proteases. These proteases had different hydrolytic ability against different substrates. This study represents a novel insight on the diversity of cultivable protease-producing bacteria and their extracellular proteases in scleractinian corals.

scholarly journals Identification of phenol- and p-cresol-producing intestinal bacteria by using media supplemented with tyrosine and its metabolites

2018 ◽  
Vol 94 (9) ◽  
Author(s):  
Yuki Saito ◽  
Tadashi Sato ◽  
Koji Nomoto ◽  
Hirokazu Tsuji
Keyword(s):  
Phylogenetic Analysis ◽  
Intestinal Bacteria ◽  
Acid Decarboxylase ◽  
Rrna Gene ◽  
Bacterial Strains ◽  
16S Rrna Gene Sequences ◽  
Metabolic Intermediates ◽  
Genomic Search ◽  
Tyrosine Phenol Lyase ◽  
The 16S Rrna Gene

AbstractTo identify intestinal bacteria that produce phenols (phenol and p-cresol), we screened 153 strains within 152 species in 44 genera by culture-based assay using broth media supplemented with 200 µM each of tyrosine and its predicted microbial metabolic intermediates (4-hydroxyphenylpyruvate, DL-4-hydroxyphenyllactate, 3-(p-hydroxyphenyl)propionate, 4-hydroxyphenylacetate and 4-hydroxybenzoate). Phenol-producing activity was found in 36 strains and p-cresol-producing activity in 55 strains. Fourteen strains had both types of activity. Phylogenetic analysis based on the 16S rRNA gene sequences of strains that produced 100 µM or more of phenols revealed that 16 phenol producers belonged to the Coriobacteriaceae, Enterobacteriaceae, Fusobacteriaceae and Clostridium clusters I and XIVa; four p-cresol-producing bacteria belonged to the Coriobacteriaceae and Clostridium clusters XI and XIVa; and one strain producing both belonged to the Coriobacteriaceae. A genomic search for protein homologs of enzymes involved in the metabolism of tyrosine to phenols in 10 phenol producers and four p-cresol producers, the draft genomes of which were available in public databases, predicted that phenol producers harbored tyrosine phenol-lyase or hydroxyarylic acid decarboxylase, or both, and p-cresol producers harbored p-hydroxyphenylacetate decarboxylase or tyrosine lyase, or both. These results provide important information about the bacterial strains that contribute to production of phenols in the intestine.

scholarly journals The Termite Group I Phylum Is Highly Diverse and Widespread in the Environment

2007 ◽  
Vol 73 (20) ◽  
pp. 6682-6685 ◽  
Author(s):  
Daniel P. R. Herlemann ◽  
Oliver Geissinger ◽  
Andreas Brune
Keyword(s):  
Phylogenetic Analysis ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Rrna Gene ◽  
Gene Sequences ◽  
16S Rrna Gene Sequences ◽  
Specific Primers ◽  
Environmental Distribution ◽  
Data Set ◽  
Group I

ABSTRACT The bacterial candidate phylum Termite Group I (TG-1) presently consists mostly of “Endomicrobia,” which are endosymbionts of flagellate protists occurring exclusively in the hindguts of termites and wood-feeding cockroaches. Here, we show that public databases contain many, mostly undocumented 16S rRNA gene sequences from other habitats that are affiliated with the TG-1 phylum but are only distantly related to “Endomicrobia.” Phylogenetic analysis of the expanded data set revealed several diverse and deeply branching lineages comprising clones from many different habitats. In addition, we designed specific primers to explore the diversity and environmental distribution of bacteria in the TG-1 phylum.

scholarly journals Description of Sphingobium fuliginis sp. nov., a phenanthrene-degrading bacterium from a fly ash dumping site, and reclassification of Sphingomonas cloacae as Sphingobium cloacae comb. nov.

2006 ◽  
Vol 56 (9) ◽  
pp. 2147-2152 ◽  
Author(s):  
Om Prakash ◽  
Rup Lal
Keyword(s):  
Phylogenetic Analysis ◽  
Fatty Acid ◽  
Fly Ash ◽  
16S Rrna ◽  
Dna Hybridization ◽  
Type Strain ◽  
Rrna Gene ◽  
16S Rrna Gene Sequences ◽  
Dumping Site ◽  
Degrading Bacterium

A phenanthrene-degrading bacterium, strain TKPT, was isolated from a fly ash dumping site of the thermal power plant in Panki, Kanpur, India, by an enrichment culture method using phenanthrene as the sole source of carbon and energy. Phylogenetic analysis based on 16S rRNA gene sequences indicated that the strain belonged to the genus Sphingobium, as it showed highest sequence similarity to Sphingobium herbicidovorans DSM 11019T (97.3 %) and Sphingomonas cloacae JCM 10874T (96.5 %), compared with only 91–93 % similarity to members of other genera such as Sphingomonas sensu stricto, Novosphingobium, Sphingopyxis and Sphingosinicella. In DNA–DNA hybridization experiments with strains that were closely related phylogenetically and in terms of 16S rRNA gene sequences, i.e. Sphingobium herbicidovorans DSM 11019T and Sphingomonas cloacae JCM 10874T, strain TKPT showed less than 70 % relatedness. Strain TKPT contained sphingoglycolipids SGL-1 and SGL-2 and 18 : 1ω7c as the predominant fatty acid, with 16 : 0 as a minor component and 14 : 0 2-OH as the major 2-hydroxy fatty acid. Thus, phylogenetic analysis, DNA–DNA hybridization, fatty acid and polar lipid profiles and differences in physiological and morphological features from the most closely related members of the Sphingobium group showed that strain TKPT represents a distinct species of Sphingobium. The name Sphingobium fuliginis sp. nov. is proposed, with the type strain TKPT (=MTCC 7295T=CCM 7327T). Sphingomonas cloacae JCM 10874T formed a coherent cluster with members of Sphingobium, did not reduce nitrate to nitrite and had a fatty acid profile similar to those of Sphingobium species; hence Sphingomonas cloacae should be transferred to the genus Sphingobium as Sphingobium cloacae comb. nov., with the type strain JCM 10874T (=DSM 14926T).

scholarly journals Asgard archaea are diverse, ubiquitous, and transcriptionally active microbes

2018 ◽  
Author(s):  
Mingwei Cai ◽  
Yang Liu ◽  
Zhichao Zhou ◽  
Yuchun Yang ◽  
Jie Pan ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Genomic Analysis ◽  
Phylogenetic Position ◽  
Rrna Gene ◽  
Gene Sequences ◽  
16S Rrna Gene Sequences ◽  
Group D ◽  
Origin Of Eukaryotes

AbstractAsgard is a newly proposed archaeal superphylum. Phylogenetic position of Asgard archaea and its relationships to the origin of eukaryotes is attracting increasingly research interest. However, in-depth knowledge of their diversity, distribution, and activity of Asgard archaea remains limited. Here, we used phylogenetic analysis to cluster the publicly available Asgard archaeal 16S rRNA gene sequences into 13 subgroups, including five previously unknown subgroups. These lineages were widely distributed in anaerobic environments, with the majority of 16S rRNA gene sequences (92%) originating from sediment habitats. Co-occurrence analysis revealed potential relationships between Asgard, Bathyarchaeota, and Marine Benthic Group D archaea. Genomic analysis suggested that Asgard archaea are potentially mixotrophic microbes with divergent metabolic capabilities. Importantly, metatranscriptomics confirmed the versatile lifestyles of Lokiarchaeota and Thorarchaeota, which can fix CO2using the tetrahydromethanopterin Wood-Ljungdahl pathway, perform acetogenesis, and degrade organic matters. Overall, this study broadens the understandings of Asgard archaea ecology, and also provides the first evidence to support a transcriptionally active mixotrophic lifestyle of Asgard archaea, shedding light on the potential roles of these microorganisms in the global biogeochemical cycling.

Kallotenue papyrolyticum gen. nov., sp. nov., a cellulolytic and filamentous thermophile that represents a novel lineage (Kallotenuales ord. nov., Kallotenuaceae fam. nov.) within the class Chloroflexia

2013 ◽  
Vol 63 (Pt_12) ◽  
pp. 4675-4682 ◽  
Author(s):  
Jessica K. Cole ◽  
Brandon A. Gieler ◽  
Devon L. Heisler ◽  
Maryknoll M. Palisoc ◽  
Amanda J. Williams ◽  
...  
Keyword(s):  
Carbon Sources ◽  
Rrna Gene ◽  
Bacterial Strains ◽  
16S Rrna Gene Sequences ◽  
Content Type ◽  
Link Type ◽  
Casamino Acids ◽  
Ph Range ◽  
Dense Liquid ◽  
Cellulose Filter

Several closely related, thermophilic and cellulolytic bacterial strains, designated JKG1T, JKG2, JKG3, JKG4 and JKG5, were isolated from a cellulolytic enrichment (corn stover) incubated in the water column of Great Boiling Spring, NV. Strain JKG1T had cells of diameter 0.7–0.9 µm and length ~2.0 µm that formed non-branched, multicellular filaments reaching >300 µm. Spores were not formed and dense liquid cultures were red. The temperature range for growth was 45–65 °C, with an optimum of 55 °C. The pH range for growth was pH 5.6–9.0, with an optimum of pH 7.5. JKG1T grew as an aerobic heterotroph, utilizing glucose, sucrose, xylose, arabinose, cellobiose, CM-cellulose, filter paper, microcrystalline cellulose, xylan, starch, Casamino acids, tryptone, peptone, yeast extract, acetate, citrate, lactate, pyruvate and glycerol as sole carbon sources, and was not observed to photosynthesize. The cells stained Gram-negative. Phylogenetic analysis using 16S rRNA gene sequences placed the new isolates in the class Chloroflexia , but distant from other cultivated members, with the highest sequence identity of 82.5 % to Roseiflexus castenholzii . The major quinone was menaquinone-9; no ubiquinones were detected. The major cellular fatty acids (>5 %) were C18 : 0, anteiso-C17 : 0, iso-C18 : 0, iso-C17 : 0, C16 : 0, iso-C16 : 0 and C17 : 0. The peptidoglycan amino acids were alanine, ornithine, glutamic acid, serine and asparagine. Whole-cell sugars included mannose, rhamnose, glucose, galactose, ribose, arabinose and xylose. Morphological, phylogenetic and chemotaxonomic results suggest that JKG1T is representative of a new lineage within the class Chloroflexia , which we propose to designate Kallotenue papyrolyticum gen. nov., sp. nov., Kallotenuaceae fam. nov., Kallotenuales ord. nov. The type strain of Kallotenue papyrolyticum gen. nov., sp. nov. is JKG1T ( = DSM 26889T = JCM 19132T).

scholarly journals Three novel lineages of ‘Candidatus Liberibacter africanus’ associated with native rutaceous hosts of Trioza erytreae in South Africa

2015 ◽  
Vol 65 (Pt_2) ◽  
pp. 723-731 ◽  
Author(s):  
Ronel Roberts ◽  
Emma T. Steenkamp ◽  
Gerhard Pietersen
Keyword(s):  
South Africa ◽  
Phylogenetic Analysis ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Sequence Data ◽  
Rrna Gene ◽  
Gene Sequences ◽  
16S Rrna Gene Sequences ◽  
Nucleotide Sequence Data ◽  
Trioza Erytreae

Greening disease of citrus in South Africa is associated with ‘Candidatus Liberibacter africanus’ (Laf), a phloem-limited bacterium vectored by the sap-sucking insect Trioza erytreae (Triozidae). Despite the implementation of control strategies, this disease remains problematic, suggesting the existence of reservoir hosts to Laf. The current study aimed to identify such hosts. Samples from 234 trees of Clausena anisata, 289 trees of Vepris lanceolata and 231 trees of Zanthoxylum capense were collected throughout the natural distribution of these trees in South Africa. Total DNA was extracted from samples and tested for the presence of liberibacters by a generic Liberibacter TaqMan real-time PCR assay. Liberibacters present in positive samples were characterized by amplifying and sequencing rplJ, omp and 16S rRNA gene regions. The identity of tree host species from which liberibacter sequences were obtained was verified by sequencing host rbcL genes. Of the trees tested, 33 specimens of Clausena, 17 specimens of Vepris and 10 specimens of Zanthoxylum tested positive for liberibacter. None of the samples contained typical citrus-infecting Laf sequences. Phylogenetic analysis of 16S rRNA gene sequences indicated that the liberibacters obtained from Vepris and Clausena had 16S rRNA gene sequences identical to that of ‘Candidatus Liberibacter africanus subsp. capensis’ (LafC), whereas those from Zanthoxylum species grouped separately. Phylogenetic analysis of the rplJ and omp gene regions revealed unique clusters for liberibacters associated with each tree species. We propose the following names for these novel liberibacters: ‘Candidatus Liberibacter africanus subsp. clausenae’ (LafCl), ‘Candidatus Liberibacter africanus subsp. vepridis’ (LafV) and ‘Candidatus Liberibacter africanus subsp. zanthoxyli’ (LafZ). This study did not find any natural hosts of Laf associated with greening of citrus. While native citrus relatives were shown to be infected with Laf-related liberibacters, nucleotide sequence data suggest that these are not alternative sources of Laf to citrus orchards, per se.

scholarly journals Microbial Diversity of the Brine-Seawater Interface of the Kebrit Deep, Red Sea, Studied via 16S rRNA Gene Sequences and Cultivation Methods

2001 ◽  
Vol 67 (7) ◽  
pp. 3077-3085 ◽  
Author(s):  
Wolfgang Eder ◽  
Linda L. Jahnke ◽  
Mark Schmidt ◽  
Robert Huber
Keyword(s):  
Phylogenetic Analysis ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Red Sea ◽  
Deep Sea ◽  
Rrna Gene ◽  
Strictly Anaerobic ◽  
Gene Sequences ◽  
16S Rrna Gene Sequences ◽  
Cultivation Methods

ABSTRACT The brine-seawater interface of the Kebrit Deep, northern Red Sea, was investigated for the presence of microorganisms using phylogenetic analysis combined with cultivation methods. Under strictly anaerobic culture conditions, novel halophiles were isolated. The new rod-shaped isolates belong to the halophilic genus Halanaerobiumand are the first representatives of the genus obtained from deep-sea, anaerobic brine pools. Within the genus Halanaerobium, they represent new species which grow chemoorganotrophically at NaCl concentrations ranging from 5 to 34%. The cellular fatty acid compositions are consistent with those of otherHalanaerobium representatives, showing unusually large amounts of Δ7 and Δ11 16:1 fatty acids. Phylogenetic analysis of the brine-seawater interface sample revealed the presence of various bacterial 16S rRNA gene sequences dominated by cultivated members of the bacterial domain, with the majority affiliated with the genusHalanaerobium. The new Halanaerobium 16S rRNA clone sequences showed the highest similarity (99.9%) to the sequence of isolate KT-8-13 from the Kebrit Deep brine. In this initial survey, our polyphasic approach demonstrates that novel halophiles thrive in the anaerobic, deep-sea brine pool of the Kebrit Deep, Red Sea. They may contribute significantly to the anaerobic degradation of organic matter enriched at the brine-seawater interface.

scholarly journals Oceanibulbus indolifex gen. nov., sp. nov., a North Sea alphaproteobacterium that produces bioactive metabolites

2004 ◽  
Vol 54 (4) ◽  
pp. 1177-1184 ◽  
Author(s):  
Irene Wagner-Döbler ◽  
Holger Rheims ◽  
Andreas Felske ◽  
Aymen El-Ghezal ◽  
Dirk Flade-Schröder ◽  
...  
Keyword(s):  
Fatty Acids ◽  
Phylogenetic Analysis ◽  
Fatty Acid ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
North Sea ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
Gene Sequences ◽  
16S Rrna Gene Sequences

A water sample from the North Sea was used to isolate the abundant heterotrophic bacteria that are able to grow on complex marine media. Isolation was by serial dilution and spread plating. Phylogenetic analysis of nearly complete 16S rRNA gene sequences revealed that one of the strains, HEL-45T, had 97·4 % sequence similarity to Sulfitobacter mediterraneus and 96·5 % sequence similarity to Staleya guttiformis. Strain HEL-45T is a Gram-negative, non-motile rod and obligate aerobe and requires sodium and 1–7 % sea salts for growth. It contains storage granules and does not produce bacteriochlorophyll. Optimal growth temperatures are 25–30 °C. The DNA base composition (G+C content) is 60·1 mol%. Strain HEL-45T has Q10 as the dominant respiratory quinone. The major polar lipids are phosphatidyl glycerol, diphosphatidyl glycerol, phosphatidyl choline, phosphatidyl ethanolamine and an aminolipid. The fatty acids comprise 18 : 1ω7c, 18 : 0, 16 : 1ω7c, 16 : 0, 3-OH 10 : 0, 3-OH 12 : 1 (or 3-oxo 12 : 0) and traces of an 18 : 2 fatty acid. Among the hydroxylated fatty acids only 3-OH 12 : 1 (or 3-oxo 12 : 0) appears to be amide linked, whereas 3-OH 10 : 0 appears to be ester linked. The minor fatty acid components (between 1 and 7 %) allow three subgroups to be distinguished in the Sulfitobacter/Staleya clade, placing HEL-45T into a separate lineage characterized by the presence of 3-OH 12 : 1 (or 3-oxo 12 : 0) and both ester- and amide-linked 16 : 1ω7c phospholipids. HEL-45T produces indole and derivatives thereof, several cyclic dipeptides and thryptanthrin. Phylogenetic analysis of 16S rRNA gene sequences and chemotaxonomic data support the description of a new genus and species, to include Oceanibulbus indolifex gen. nov., sp. nov., with the type strain HEL-45T (=DSM 14862T=NCIMB 13983T).

scholarly journals Photobacterium halotolerans sp. nov., isolated from Lake Martel in Spain

2006 ◽  
Vol 56 (5) ◽  
pp. 1067-1071 ◽  
Author(s):  
Raúl Rivas ◽  
Paula García-Fraile ◽  
Pedro F. Mateos ◽  
Eustoquio Martínez-Molina ◽  
Encarna Velázquez
Keyword(s):  
Phylogenetic Analysis ◽  
Saline Lake ◽  
Agar Medium ◽  
Novel Species ◽  
Rrna Gene ◽  
16S Rrna Gene Sequences ◽  
Marine Agar ◽  
Vibrio Proteolyticus ◽  
Arginine Dihydrolase ◽  
Distinct Lineage

A halotolerant bacterium was isolated from a saline lake located in Mallorca, Spain. Cells of the strain, designated MACL01T, were Gram-negative, rod-shaped and motile by means of polar flagella. Colonies of strain MACL01T were white to cream in TSA medium, turning brown after 7 days of incubation; they were blue in thiosulphate/citrate/bile salts/sucrose agar medium. A neighbour-joining phylogenetic analysis based on 16S rRNA gene sequences showed that strain MACL01T belongs to the genus Photobacterium, in which it forms a distinct lineage together with Photobacterium rosenbergii and Photobacterium ganghwense (showing 96.9 and 96.2 % similarity, respectively). The most closely related taxon according to phylogenetic analysis of the rpoA gene is also P. rosenbergii (90 % similarity). The recA gene also showed low similarity (83.7, 83.4 and 82.4 %, respectively) with respect to those of Vibrio proteolyticus LMG 3772T, Photobacterium leiognathii LMG 4228T and P. rosenbergii LMG 22223T. Neighbour-joining phylogenetic analysis of the rpoA and recA genes confirms that strain MACL01T belongs to the genus Photobacterium, forming a branch together with P. rosenbergii. Strain MACL01T was able to grow in 0–8 % NaCl. Growth occurred between 4 and 37 °C (optimum, 28 °C) and at pH 5–8.5. Luminescence was negative on marine agar. Strain MACL01T was found to be sensitive to the vibriostatic agent O/129. It reduced nitrate to nitrite, produced β-galactosidase and hydrolysed gelatin, but did not produce arginine dihydrolase, indole or acetoin. Strain MACL01T used several carbohydrates and fermented glucose, l-arabinose and sucrose. The most abundant fatty acids were summed feature 3 (32.6 %; comprising C16 : 1 ω7c and/or C15 : 0 iso 2-OH), C16 : 0 (21.2 %) and C18 : 1 ω7c (19.9 %). The G+C content of the genomic DNA was 49.8 mol%. On the basis of genotypic, phenotypic, chemotaxonomic and phylogenetic results, strain MACL01T (=LMG 22194T=CECT 5860T) should be classified as the type strain of a novel species of the genus Photobacterium, for which the name Photobacterium halotolerans sp. nov. is proposed.

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