Investigation of microbial community isolated from indoor artworks and air environment: identification, biodegradative abilities, and DNA typing.

PubMed

Pangallo, Domenico; Chovanová, Katarina; Simonovicová, Alexandra; Ferianc, Peter

2009-03-01

This study deals with establishing the characteristics of a microbial community isolated from indoor artworks and the surrounding air environment. It is one of the few studies on microbial degradation of indoor artworks. It shows the potential biodegradative risk that can occur if artworks are not exhibited and conserved in an appropriate environment. The microbial community isolated from the indoor artworks and air environment was examined by cultural and molecular methods. Different plate assays were used to screen the biodegradative activity of the isolated microflora: Remazol Brilliant Blue R, phenol red, and Azure B for the ligninolytic properties; Ostazin brilliant red H-3B for cellulose degradation; CaCO3 glucose agar for solubilization activity; and B4 agar for biomineralization. To type the bacterial and fungal isolates, 2 PCR methods, repetitive extragenic palindromes (REP) and random amplified microsatellite polymorphisms (RAMP) were used. The art objects were principally colonized by fungi. The most commonly isolated strains were represented by hyphomycetes of the genera Penicillium, Aspergillus, Cladosporium, and Chaetomium. Members of these genera showed intensive biodegradation activity, both on wood and on stone. Bacteria were predominant in the air, exhibiting complex communities, both in the air and on the artworks. The most frequently isolated genera were Bacillus and Staphylococcus with extensive biodegradation abilities. REP-PCR revealed high variability within strains belonging to the same genus. RAMP is a new PCR-based method, used in this research for the first time to cluster the microfilamentous fungi and to characterize and select especially Penicillium and Aspergillus strains, which were isolated in a large number.

Distribution, diversity and bioprospecting of bioactive compounds from cryptic fungal communities associated with endemic and cold-adapted macroalgae in Antarctica

USDA-ARS?s Scientific Manuscript database

We surveyed the distribution and diversity of fungi associated with eight macroalgae from Antarctica and their capability to produce bioactive compounds. The collections yielded 148 fungal isolates identified using molecular methods into 21 genera and 43 species. The most frequent taxa were Geomyces...

High diversity of non-sporulating moulds in respiratory specimens of immunocompromised patients: should all the species be reported when diagnosing invasive aspergillosis?

PubMed

Garcia-Hermoso, Dea; Alanio, Alexandre; Cabaret, Odile; Olivi, Martine; Foulet, Françoise; Cordonnier, Catherine; Costa, Jean-Marc; Bretagne, Stéphane

2015-09-01

Non-sporulating moulds (NSMs) isolated from respiratory specimens are usually discarded without further testing although they may have pathogenic effects in immunocompromised patients. The objective of this study was to determine the identity and frequency of NSMs in patients with haematological malignancies. We analysed the mycological results of 251 consecutive respiratory samples from 104 haematology patients. Yeast and sporulating moulds were identified at the genus/species level according to their phenotypic features. NSMs were identified by internal transcribed spacer (ITS) sequencing. We detected 179 positive samples, of which 10.1% (18/179) were mixtures of moulds and 26.3% (47/179) were mixtures of moulds and yeast. We identified 142 moulds belonging to 11 different genera/species or groups, with Aspergillus fumigatus (n = 50), Penicillium spp. (n = 31) and NSM (n = 24) being the most frequently isolated species. Twenty-two NSMs were successfully sequenced: 18 were basidiomycetes and six were ascomycetes, corresponding to 16 different genera/species. NSMs were isolated with A. fumigatus in the same sample or in a subsequent sample in five patients with probable invasive aspergillosis. The conclusion is that the respiratory specimens of immunocompromised patients frequently contain very diverse mould species that may increase the virulence of pathogenic species. Reporting all mould species isolated when diagnosing invasive fungal infection could test this hypothesis. © 2015 Blackwell Verlag GmbH.

Filamentous fungi isolated from sand and water of "Bairro Novo" and "Casa Caiada" beaches, Olinda, Pernambuco, Brazil.

PubMed

Gomes, D N F; Cavalcanti, M A Q; Fernandes, M J S; Lima, D M M; Passavante, J Z O

2008-08-01

Fungi comprehend a heterogeneous group of heterotrophic microorganisms that act as saprobes or parasites or, less frequently, as symbionts living in association with other organisms. They are cosmopolitan and important components of ecosystems. Considering the small number of Brazilian papers on the filamentous mycota in marine environments, and the need to improve knowledge of the diversity of these microfungi in "Casa Caiada" and "Bairro Novo" beaches, Olinda, PE, the aim of this work was to isolate and identify the fungi from sand and water samples of these ecosystems. Thirty two samplings of sand (surface and 20 cm deep) and water (surface and 1 m deep) were carried out during the dry and rainy seasons, in low and high tide. From each sand sample, a suspension was made with 50 g of sand diluted in 90 mL of sterilized distilled water. From each sand suspension and water sample, 0.5 mL was spread, in triplicate, onto Petri dishes containing Sabouraud Agar added of chloramphenicol. The plates were incubated at 28 degrees C (+/-2 degrees C). Fifty seven species were isolated, identified, and classified in 20 genera. Aspergillus and Penicillium were the most frequent genera in both sand and water, with a total of 11 and 19 species, respectively.

Identification of Mucorales isolates from soil using morphological and molecular methods

PubMed Central

Ziaee, A; Zia, M; Bayat, M; Hashemi, J

2016-01-01

Background and Purpose: Soil is the main habitat of saprophytic and pathogenic fungi. Mucoromycotina constitutes a large group of soil fungi, with certain opportunistic members causing systemic infections in immunocompromised hosts. The majority of human and animal infections are caused by the members of the genera Rhizopus, Mucor, Rhizomucor, Lichtheimia (Absidia), Cunninghamella, and Mortierella. Accordingly, in the present study, we aimed to isolate and identify the main genera of the order Mucorales, using molecular assays and morphological features. Materials and Methods: In total, 340 soil samples were collected from seven public parks throughout the city and sidewalk gardens in 14 municipal districts in Isfahan, Iran. All the samples were cultured on the appropriate media, incubated at 27°C for 2- 4 days, and examined daily for visible fungal growth. Polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) method was applied and macroscopic, microscopic, and physiological characteristics were assessed to identify fungal colonies. Results: 400 pure colonies, belonging to the orders Mucorales and Mortierellales, including the genera Lichtheimia, Rhizopus, Rhizomucor, Mucor, Cunninghamella, and Mortierella, were identified. The genus Rhizopus (35.5%) was the most frequent isolate, followed by Mucor (32.25%) and Rhizomucor (27.5%). Conclusion: The results emphasize the importance of opportunistic fungi in public areas and indicate the risk of exposure for immunocompromised individuals. PMID:28681007

Identification of Mucorales isolates from soil using morphological and molecular methods.

PubMed

Ziaee, A; Zia, M; Bayat, M; Hashemi, J

2016-03-01

Soil is the main habitat of saprophytic and pathogenic fungi. Mucoromycotina constitutes a large group of soil fungi, with certain opportunistic members causing systemic infections in immunocompromised hosts. The majority of human and animal infections are caused by the members of the genera Rhizopus , Mucor , Rhizomucor , Lichtheimia ( Absidia) , Cunninghamella, and Mortierella . Accordingly, in the present study, we aimed to isolate and identify the main genera of the order Mucorales, using molecular assays and morphological features . In total, 340 soil samples were collected from seven public parks throughout the city and sidewalk gardens in 14 municipal districts in Isfahan, Iran. All the samples were cultured on the appropriate media, incubated at 27°C for 2- 4 days, and examined daily for visible fungal growth. Polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) method was applied and macroscopic, microscopic, and physiological characteristics were assessed to identify fungal colonies. 400 pure colonies, belonging to the orders Mucorales and Mortierellales, including the genera Lichtheimia , Rhizopus, Rhizomucor, Mucor, Cunninghamella, and Mortierella, were identified . The genus Rhizopus (35.5%) was the most frequent isolate, followed by Mucor (32.25%) and Rhizomucor (27.5%). The results emphasize the importance of opportunistic fungi in public areas and indicate the risk of exposure for immunocompromised individuals.

Diversity and physiology of culturable bacteria associated with a coastal Antarctic ice core.

PubMed

Antony, Runa; Krishnan, K P; Laluraj, C M; Thamban, Meloth; Dhakephalkar, P K; Engineer, Anupama S; Shivaji, S

2012-06-20

Microbiological studies of polar ice at different depths may provide important comparisons, as they preserve records of microbial cells and past climate. In this study, we examined bacterial abundance, diversity and glaciochemical composition from three depths of an ice core from coastal Dronning Maud Land, East Antarctica. Higher bacterial abundance corresponded with high in situ sea-salt Na(+) and dust concentration, suggesting that bacteria might have been transported and deposited into ice along with dust particles and marine aerosols. Fourteen bacterial isolates belonging to the genera Methylobacterium, Brevundimonas, Paenibacillus, Bacillus and Micrococcus were retrieved. Frequent isolation of similar bacterial genera from different cold environments suggests that they possess features that enable survival and metabolism for extended periods of time at sub-zero temperatures. The highest number and diversity of recoverable bacteria was obtained from 49 m depth corresponding to 1926 AD and consisted of bacteria from 4 different genera whereas at 11 m (1989 AD) and 33 m (1953 AD) samples only species belonging to the genera Bacillus was recovered. Among the Bacillus species, Bacillus aryabhattai which has been reported only from the upper stratosphere, was isolated and is the first record from the Earth's surface. Methylobacterium was the most dominant genera at 49 m depth and its prevalence is attributable to a combination of high in situ methanesulfonate concentration, specialized metabolism and environmental hardiness of Methylobacterium. Some of the isolated bacteria were found to respire and grow using methanesulfonate, suggesting that they may utilize this substrate to sustain growth in ice. In addition, NO(3)(-) (2.93-3.69 μM), NH(4)(+) (1.45-3.90 μM) and PO(4)(3-) (0.01-0.75 μM) present in the ice could be potential sources fueling bacterial metabolism in this environment. It could be deduced from the study that variation in bacterial abundance and diversity was probably associated with the prevailing in situ conditions in ice. Copyright © 2012 Elsevier GmbH. All rights reserved.

The effect of different growth regimes on the endophytic bacterial communities of the fern, Dicksonia sellowiana hook (Dicksoniaceae).

PubMed

de Araújo Barros, Irene; Luiz Araújo, Welington; Lúcio Azevedo, João

2010-10-01

Endophytic bacteria associated with the fern Dicksonia sellowiana were investigated. The bacterial communities from the surface-sterilized pinnae and rachis segments of the plants from the Brazilian Atlantic Rainforest that grew in native field conditions were compared with the bacterial communities from plants grown in greenhouses and plants that were initially grown in greenhouses and then transferred to the forest. From 540 pinnae and 540 rachis segments, 163 (30.2%) and 346 (64.2%) were colonized by bacteria, respectively. The main bacterial genera and species that were isolated included Bacillus spp. ( B. cereus, B. megaterium, B. pumilus and B. subtilis ) , Paenibacillus sp. , Amphibacillus sp. , Gracilibacillus sp. , Micrococcus sp. and Stenotrophomonas spp. ( S. maltophilia and S. nitroreducens ). B. pumilus was the most frequently isolated bacterial species . Amphibacillus and Gracilibacillus were reported as endophytes for the first time. Other commonly found bacterial genera were not observed in D. sellowiana , which may reflect preferences of specific bacterial communities inside this fern or detection limitations due to the isolation procedures. Plants that were grown in greenhouses and plants that were reintroduced into the forest displayed more bacterial genera and species diversity than native field plants, suggesting that reintroduction shifts the bacterial diversity. Endophytic bacteria that displayed antagonistic properties against different microorganisms were detected, but no obvious correlation was found between their frequencies with plant tissues or with plants from different growth regimes. This paper reports the first isolation of endophytic bacteria from a fern.

The effect of different growth regimes on the endophytic bacterial communities of the fern, Dicksonia sellowiana hook (Dicksoniaceae)

PubMed Central

de Araújo Barros, Irene; Luiz Araújo, Welington; Lúcio Azevedo, João

2010-01-01

Endophytic bacteria associated with the fern Dicksonia sellowiana were investigated. The bacterial communities from the surface-sterilized pinnae and rachis segments of the plants from the Brazilian Atlantic Rainforest that grew in native field conditions were compared with the bacterial communities from plants grown in greenhouses and plants that were initially grown in greenhouses and then transferred to the forest. From 540 pinnae and 540 rachis segments, 163 (30.2%) and 346 (64.2%) were colonized by bacteria, respectively. The main bacterial genera and species that were isolated included Bacillus spp. ( B. cereus, B. megaterium, B. pumilus and B. subtilis ) , Paenibacillus sp. , Amphibacillus sp. , Gracilibacillus sp. , Micrococcus sp. and Stenotrophomonas spp. ( S. maltophilia and S. nitroreducens ). B. pumilus was the most frequently isolated bacterial species . Amphibacillus and Gracilibacillus were reported as endophytes for the first time. Other commonly found bacterial genera were not observed in D. sellowiana , which may reflect preferences of specific bacterial communities inside this fern or detection limitations due to the isolation procedures. Plants that were grown in greenhouses and plants that were reintroduced into the forest displayed more bacterial genera and species diversity than native field plants, suggesting that reintroduction shifts the bacterial diversity. Endophytic bacteria that displayed antagonistic properties against different microorganisms were detected, but no obvious correlation was found between their frequencies with plant tissues or with plants from different growth regimes. This paper reports the first isolation of endophytic bacteria from a fern. PMID:24031575

Identification of the bacterial community of maple sap by using amplified ribosomal DNA (rDNA) restriction analysis and rDNA sequencing.

PubMed

Lagacé, L; Pitre, M; Jacques, M; Roy, D

2004-04-01

The bacterial community of maple sap was characterized by analysis of samples obtained at the taphole of maple trees for the 2001 and 2002 seasons. Among the 190 bacterial isolates, 32 groups were formed according to the similarity of the banding patterns obtained by amplified ribosomal DNA restriction analysis (ARDRA). A subset of representative isolates for each ARDRA group was identified by 16S rRNA gene fragment sequencing. Results showed a wide variety of organisms, with 22 different genera encountered. Pseudomonas and Ralstonia, of the gamma- and beta-Proteobacteria, respectively, were the most frequently encountered genera. Gram-positive bacteria were also observed, and Staphylococcus, Plantibacter, and Bacillus were the most highly represented genera. The sampling period corresponding to 50% of the cumulative sap flow percentage presented the greatest bacterial diversity according to its Shannon diversity index value (1.1). gamma-Proteobacteria were found to be dominant almost from the beginning of the season to the end. These results are providing interesting insights on maple sap microflora that will be useful for further investigation related to microbial contamination and quality of maple products and also for guiding new strategies on taphole contamination control.

Culturable bacterial communities associated to Brazilian Oscarella species (Porifera: Homoscleromorpha) and their antagonistic interactions.

PubMed

Laport, Marinella Silva; Bauwens, Mathieu; de Oliveira Nunes, Suzanne; Willenz, Philippe; George, Isabelle; Muricy, Guilherme

2017-04-01

Sponges offer an excellent model to investigate invertebrate-microorganism interactions. Furthermore, bacteria associated with marine sponges represent a rich source of bioactive metabolites. The aim of this study was to characterize the bacteria inhabiting a genus of sponges, Oscarella, and their potentiality for antimicrobial production. Bacterial isolates were recovered from different Oscarella specimens, among which 337 were phylogenetically identified. The culturable community was dominated by Proteobacteria and Firmicutes, and Vibrio was the most frequently isolated genus, followed by Shewanella. When tested for antimicrobial production, bacteria of the 12 genera isolated were capable of producing antimicrobial substances. The majority of strains were involved in antagonistic interactions and inhibitory activities were also observed against bacteria of medical importance. It was more pronounced in some isolated genera (Acinetobacter, Bacillus, Photobacterium, Shewanella and Vibrio). These findings suggest that chemical antagonism could play a significant role in shaping bacterial communities within Oscarella, a genus classified as low-microbial abundance sponge. Moreover, the identified strains may contribute to the search for new sources of antimicrobial substances, an important strategy for developing therapies to treat infections caused by multidrug-resistant bacteria. This study was the first to investigate the diversity and antagonistic activity of bacteria isolated from Oscarella spp. It highlights the biotechnological potential of sponge-associated bacteria.

[Diversity of cultivable actinobacteria in Xinghu wetland sediments].

PubMed

Xue, Dong; Zhao, Guozhen; Yao, Qing; Zhao, Haiquan; Zhu, Honghui

2015-11-04

To study the diversity of cultivable actinobacteria in Xinghu wetland and screen actinobacteria with a pharmaceutical potential for producing biologically active secondary metabolites. We studied the diversity of actinobacteria isolated from Xinghu wetland by using different selective isolation media and methods. The high bioactive actinobacteria were identified and further investigated for the presence of polyketide synthases (PKS-I, PKS-II), nonribosomal peptide synthetases (NRPS), 3-amino-5-hydroxybenzoic acid synthases (AHBA) and 3-hydroxy-3-methylglutaryl Coenzyme A (HMG CoA) sequences by specific amplification. More than 300 actinobacteria were isolated, and 135 isolates were selected on the basis of their morphologies on different media and were further characterized by 16S rRNA gene sequencing. The isolates belonged to 7 orders, 10 families, 13 genera, Streptomyces was the most frequently isolated genus, followed by the genera Micromonospora and Nocardia. Twenty-four isolates showed high activity against Staphylococcus aureus and Escherichia coli, but there no strain displaying antagonistic activity against Salmonella sp. High frequencies of positive PCR amplification were obtained for PKS-I (16.7%, 4/24), PKS-II (62.5%,15/24), NRPS (16.7%, 4/24), HMG CoA (29.2%, 7/24) and AHBA (12.5%, 3/24) biosynthetic systems. High Performance Liquid Chromatography showed that strain XD7, XD114, XD128 produce lots of secondary metabolites. This study indicated that actinobacteria isolated from Xinghu wetland are abundant and have potentially beneficial and diverse bioactivities which should be pursued for their biotechnical promise.

Pencillium keratitis in an Immunocompetent Patient from Pune, Maharashtra, India.

PubMed

Vyawahare, Chanda Ratnakar; Misra, Rabindra Nath; Gandham, Nageswari Rajesh; Angadi, Kalpna Mohan; Paul, Retina

2014-07-01

The incidence of fungal keratitis is less common than bacterial and viral keratitis. However, it remains a diagnostic and therapeutic challenge. Delayed clinical diagnosis is common mainly because of lack of suspicion. Further slow growth of fungus increases the time for confirmed laboratory diagnosis. After accurate diagnosis, patient's management remains inadequate due to lack of availability of antifungal agents and its poor corneal penetration. Multitude of genera of molds and yeast have been identified in fungal keratitis. Due to their ubiquitous nature and easy isolation from the environment, their role in true pathogenesis is difficult to ascertain. Worldwide, incidence of fungal keratitis is rising at present. The predisposing factors comprises trauma, use of contact lenses and topical steroids. Filamentous fungi and dematiaceous fungi are the frequently encountered etiological agents of fungal keratitis. Dimorphic fungi are reported less frequently. Fungal keratitis tends to occur more frequently in young males and usually in winter and monsoon. Penicillium genera includes several species. By far Penicillium marneffei (P. marneffei) infection is most common, mainly associated with AIDS. A number of infections caused by species other than P. marneffei have been reported as well. Here we report a case of Penicillium keratitis in a young, HIV negative male farmer.

Algal diversity in North American desert soils

NASA Astrophysics Data System (ADS)

Flechtner, Valerie R.; Ng, Rainer A.; Johansen, Jeffrey R.; Antionio, Sheri

2005-09-01

Clonal isolates of cyanophytes were collected from several study sites in the Dugway Proving Ground and San Rafael Sell Overlook in Utah. We identified 32 taxa belonging to 24 cyanobacterial genera. Some taxa were widely distributed, occurring in all sites. For example, the members of the filamentous cyanobacterial genera Leptolyngbya, Microcoleus, Nostoc and Trichocoleus and members of the coccoid genus Aphanocapsa were common to all sites. On the other hand, members of the cyanobacterial genus Calothrix were rarely encountered at the Dugway site but were recovered frequently from the San Rafael site. We were able to compare disturbed and undisturbed sites located close together in the San Rafael Overlook. We found that the genera Spirirestis and Cyanosarcina, were found exclusively in the undisturbed site. A number of the taxa recovered could be identified only to the genus level because they did not match previously published species descriptions. Since we have recovered both prokaryotic eukaryotic taxa new to science in our previous work, it is quite likely that some of these isolates do indeed represent new cyanobacterial species. This study is the most extensive characterization of cyanobacteria from soil crusts in a semi-arid North American deserts. It expands our knowledge of the diversity of the cyanobacterial components of North American soil crusts.

Identification of the Bacterial Community of Maple Sap by Using Amplified Ribosomal DNA (rDNA) Restriction Analysis and rDNA Sequencing

PubMed Central

Lagacé, L.; Pitre, M.; Jacques, M.; Roy, D.

2004-01-01

The bacterial community of maple sap was characterized by analysis of samples obtained at the taphole of maple trees for the 2001 and 2002 seasons. Among the 190 bacterial isolates, 32 groups were formed according to the similarity of the banding patterns obtained by amplified ribosomal DNA restriction analysis (ARDRA). A subset of representative isolates for each ARDRA group was identified by 16S rRNA gene fragment sequencing. Results showed a wide variety of organisms, with 22 different genera encountered. Pseudomonas and Ralstonia, of the γ- and β-Proteobacteria, respectively, were the most frequently encountered genera. Gram-positive bacteria were also observed, and Staphylococcus, Plantibacter, and Bacillus were the most highly represented genera. The sampling period corresponding to 50% of the cumulative sap flow percentage presented the greatest bacterial diversity according to its Shannon diversity index value (1.1). γ-Proteobacteria were found to be dominant almost from the beginning of the season to the end. These results are providing interesting insights on maple sap microflora that will be useful for further investigation related to microbial contamination and quality of maple products and also for guiding new strategies on taphole contamination control. PMID:15066796

Intra-Genomic Heterogeneity in 16S rRNA Genes in Strictly Anaerobic Clinical Isolates from Periodontal Abscesses.

PubMed

Chen, Jiazhen; Miao, Xinyu; Xu, Meng; He, Junlin; Xie, Yi; Wu, Xingwen; Chen, Gang; Yu, Liying; Zhang, Wenhong

2015-01-01

Members of the genera Prevotella, Veillonella and Fusobacterium are the predominant culturable obligate anaerobic bacteria isolated from periodontal abscesses. When determining the cumulative number of clinical anaerobic isolates from periodontal abscesses, ambiguous or overlapping signals were frequently encountered in 16S rRNA gene sequencing chromatograms, resulting in ambiguous identifications. With the exception of the genus Veillonella, the high intra-chromosomal heterogeneity of rrs genes has not been reported. The 16S rRNA genes of 138 clinical, strictly anaerobic isolates and one reference strain were directly sequenced, and the chromatograms were carefully examined. Gene cloning was performed for 22 typical isolates with doublet sequencing signals for the 16S rRNA genes, and four copies of the rrs-ITS genes of 9 Prevotella intermedia isolates were separately amplified by PCR, sequenced and compared. Five conserved housekeeping genes, hsp60, recA, dnaJ, gyrB1 and rpoB from 89 clinical isolates of Prevotella were also amplified by PCR and sequenced for identification and phylogenetic analysis along with 18 Prevotella reference strains. Heterogeneity of 16S rRNA genes was apparent in clinical, strictly anaerobic oral bacteria, particularly in the genera Prevotella and Veillonella. One hundred out of 138 anaerobic strains (72%) had intragenomic nucleotide polymorphisms (SNPs) in multiple locations, and 13 strains (9.4%) had intragenomic insertions or deletions in the 16S rRNA gene. In the genera Prevotella and Veillonella, 75% (67/89) and 100% (19/19) of the strains had SNPs in the 16S rRNA gene, respectively. Gene cloning and separate amplifications of four copies of the rrs-ITS genes confirmed that 2 to 4 heterogeneous 16S rRNA copies existed. Sequence alignment of five housekeeping genes revealed that intra-species nucleotide similarities were very high in the genera Prevotella, ranging from 94.3-100%. However, the inter-species similarities were relatively low, ranging from 68.7-97.9%. The housekeeping genes rpoB and gyrB1 were demonstrated to be alternative classification markers to the species level based on intra- and inter-species comparisons, whereas based on phylogenetic tree rpoB proved to be reliable phylogenetic marker for the genus Prevotella.

Intra-Genomic Heterogeneity in 16S rRNA Genes in Strictly Anaerobic Clinical Isolates from Periodontal Abscesses

PubMed Central

Chen, Jiazhen; Miao, Xinyu; Xu, Meng; He, Junlin; Xie, Yi; Wu, Xingwen; Chen, Gang; Yu, Liying; Zhang, Wenhong

2015-01-01

Background Members of the genera Prevotella, Veillonella and Fusobacterium are the predominant culturable obligate anaerobic bacteria isolated from periodontal abscesses. When determining the cumulative number of clinical anaerobic isolates from periodontal abscesses, ambiguous or overlapping signals were frequently encountered in 16S rRNA gene sequencing chromatograms, resulting in ambiguous identifications. With the exception of the genus Veillonella, the high intra-chromosomal heterogeneity of rrs genes has not been reported. Methods The 16S rRNA genes of 138 clinical, strictly anaerobic isolates and one reference strain were directly sequenced, and the chromatograms were carefully examined. Gene cloning was performed for 22 typical isolates with doublet sequencing signals for the 16S rRNA genes, and four copies of the rrs-ITS genes of 9 Prevotella intermedia isolates were separately amplified by PCR, sequenced and compared. Five conserved housekeeping genes, hsp60, recA, dnaJ, gyrB1 and rpoB from 89 clinical isolates of Prevotella were also amplified by PCR and sequenced for identification and phylogenetic analysis along with 18 Prevotella reference strains. Results Heterogeneity of 16S rRNA genes was apparent in clinical, strictly anaerobic oral bacteria, particularly in the genera Prevotella and Veillonella. One hundred out of 138 anaerobic strains (72%) had intragenomic nucleotide polymorphisms (SNPs) in multiple locations, and 13 strains (9.4%) had intragenomic insertions or deletions in the 16S rRNA gene. In the genera Prevotella and Veillonella, 75% (67/89) and 100% (19/19) of the strains had SNPs in the 16S rRNA gene, respectively. Gene cloning and separate amplifications of four copies of the rrs-ITS genes confirmed that 2 to 4 heterogeneous 16S rRNA copies existed. Conclusion Sequence alignment of five housekeeping genes revealed that intra-species nucleotide similarities were very high in the genera Prevotella, ranging from 94.3–100%. However, the inter-species similarities were relatively low, ranging from 68.7–97.9%. The housekeeping genes rpoB and gyrB1 were demonstrated to be alternative classification markers to the species level based on intra- and inter-species comparisons, whereas based on phylogenetic tree rpoB proved to be reliable phylogenetic marker for the genus Prevotella. PMID:26103050

On the microbiological profile of traditional Portuguese sourdough.

PubMed

Rocha, J M; Malcata, F X

1999-12-01

Traditional manufacture of bread from maize has been noted to play important roles from both economic and social standpoints; however, enforcement of increasingly strict hygiene standards requires thorough knowledge of the adventitious microbiota of the departing dough. To this goal, sourdough as well as maize and rye flours from several geographic locations and in two different periods within the agricultural year were assayed for their microbiota in sequential steps of quantification and identification. More than 400 strains were isolated and taxonomic differentiation between them was via Biomerieux API galleries (375 of which were successfully identified) following preliminary biochemical and morphological screening. The dominant groups were yeasts and lactic acid bacteria (LAB). The most frequently isolated yeasts were Saccharomyces cerevisiae and Candida pelliculosa. The most frequently isolated LAB were (heterofermentative) Leuconostoc spp. and (homofermentative) Lactobacillus spp.; L. brevis, L. curvatus, and L. lactis ssp. lactis were the dominant species for the Lactobacillus genera; Lactococcus lactis ssp. lactis for lactococci; Enterococcus casseliflavus, E. durans, and E. faecium for enterococci; and Streptococcus constellantus and S. equinus for streptococci.

Cultivable fungi present in Antarctic soils: taxonomy, phylogeny, diversity, and bioprospecting of antiparasitic and herbicidal metabolites.

PubMed

Gomes, Eldon C Q; Godinho, Valéria M; Silva, Débora A S; de Paula, Maria T R; Vitoreli, Gislaine A; Zani, Carlos L; Alves, Tânia M A; Junior, Policarpo A S; Murta, Silvane M F; Barbosa, Emerson C; Oliveira, Jaquelline G; Oliveira, Fabio S; Carvalho, Camila R; Ferreira, Mariana C; Rosa, Carlos A; Rosa, Luiz H

2018-05-01

Molecular biology techniques were used to identify 218 fungi from soil samples collected from four islands of Antarctica. These consisted of 22 taxa of 15 different genera belonging to the Zygomycota, Ascomycota, and Basidiomycota. Mortierella, Antarctomyces, Pseudogymnoascus, and Penicillium were the most frequently isolated genera and Penicillium tardochrysogenum, Penicillium verrucosus, Goffeauzyma gilvescens, and Mortierella sp. 2 the most abundant taxa. All fungal isolates were cultivated using solid-state fermentation to obtain their crude extracts. Pseudogymnoascus destructans, Mortierella parvispora, and Penicillium chrysogenum displayed antiparasitic activities, whilst extracts of P. destructans, Mortierella amoeboidea, Mortierella sp. 3, and P. tardochrysogenum showed herbicidal activities. Reported as pathogenic for bats, different isolates of P. destructans exhibited trypanocidal activities and herbicidal activity, and may be a source of bioactive molecules to be considered for chemotherapy against neglected tropical diseases. The abundant presence of P. destructans in soils of the four islands gives evidence supporting that soils in the Antarctic Peninsula constitute a natural source of strains of this genus, including some P. destructans strains that are phylogenetically close to those that infect bats in North America and Europe/Palearctic Asia.

Identification and characterization of psychrotolerant coliform bacteria isolated from pasteurized fluid milk.

PubMed

Masiello, S N; Martin, N H; Trmčić, A; Wiedmann, M; Boor, K J

2016-01-01

The presence of coliform bacteria in pasteurized fluid milk typically indicates that product contamination occurred downstream of the pasteurizer, but it may also indicate pasteurization failure. Although coliform detection is frequently used as a hygiene indicator for dairy products, our understanding of the taxonomic and phenotypic coliform diversity associated with dairy products is surprisingly limited. Therefore, using Petrifilm Coliform Count plates (3M, St. Paul, MN), we isolated coliforms from high-temperature, short-time (HTST)-pasteurized fluid milk samples from 21 fluid milk processing plants in the northeast United States. Based on source information and initial characterization using partial 16S rDNA sequencing, 240 nonredundant isolates were obtained. The majority of these isolates were identified as belonging to the genera Enterobacter (42% of isolates), Hafnia (13%), Citrobacter (12%), Serratia (10%), and Raoultella (9%); additional isolates were classified into the genera Buttiauxella, Cedecea, Kluyvera, Leclercia, Pantoea, and Rahnella. A subset of 104 representative isolates was subsequently characterized phenotypically. Cold growth analysis in skim milk broth showed that all isolates displayed at least a 2-log increase over 10 d at 6°C; the majority of isolates (n=74) displayed more than a 5-log increase. In total, 43% of the representative isolates displayed lipolysis when incubated on spirit blue agar at 6°C for 14 d, whereas 71% of isolates displayed proteolysis when incubated on skim milk agar at 6°C for 14 d. Our data indicate that a considerable diversity of coliforms is found in HTST-pasteurized fluid milk and that a considerable proportion of these coliforms have phenotypic characteristics that will allow them to cause fluid milk spoilage. Copyright © 2016 American Dairy Science Association. Published by Elsevier Inc. All rights reserved.

Ochratoxigenic fungi associated with green coffee beans (Coffea arabica L.) in conventional and organic cultivation in Brazil.

PubMed

de Fátima Rezende, Elisângela; Borges, Josiane Gonçalves; Cirillo, Marcelo Ângelo; Prado, Guilherme; Paiva, Leandro Carlos; Batista, Luís Roberto

2013-01-01

The genera Aspergillus comprises species that produce mycotoxins such as aflatoxins, ochratoxins and patulin. These are cosmopolitan species, natural contaminants of agricultural products. In coffee grains, the most important Aspergillus species in terms of the risk of presenting mycotoxins belong to the genera Aspergillus Section Circumdati and Section Nigri. The purpose of this study was to assess the occurrence of isolated ochratoxigenic fungi of coffee grains from organic and conventional cultivation from the South of Minas Gerais, Brazil, as well as to evaluate which farming system presents higher contamination risk by ochratoxin A (OTA) produced by fungi. Thirty samples of coffee grains (Coffea arabica L.) were analysed, being 20 of them of conventional coffee grains and 10 of them organic. The microbiological analysis was done with the Direct Plating Technique in a Dichloran Rose Bengal Chloramphenicol Agar (DRBC) media. The identification was done based on the macro and micro morphological characteristics and on the toxigenic potential with the Plug Agar technique. From the 30 samples analysed, 480 filamentous fungi of the genera Aspergillus of the Circumdati and Nigri Sections were isolated. The ochratoxigenic species identified were: Aspergillus auricoumus, A. ochraceus, A. ostianus, A. niger and A. niger Aggregate. The most frequent species which produces ochratoxin A among the isolated ones was A. ochraceus, corresponding to 89.55%. There was no significant difference regarding the presence of ochratoxigenic A. ochreceus between the conventional and organic cultivation systems, which suggests that the contamination risk is similar for both cultivation systems.

Ochratoxigenic fungi associated with green coffee beans (Coffea arabica L.) in conventional and organic cultivation in Brazil

PubMed Central

de Fátima Rezende, Elisângela; Borges, Josiane Gonçalves; Cirillo, Marcelo Ângelo; Prado, Guilherme; Paiva, Leandro Carlos; Batista, Luís Roberto

2013-01-01

The genera Aspergillus comprises species that produce mycotoxins such as aflatoxins, ochratoxins and patulin. These are cosmopolitan species, natural contaminants of agricultural products. In coffee grains, the most important Aspergillus species in terms of the risk of presenting mycotoxins belong to the genera Aspergillus Section Circumdati and Section Nigri. The purpose of this study was to assess the occurrence of isolated ochratoxigenic fungi of coffee grains from organic and conventional cultivation from the South of Minas Gerais, Brazil, as well as to evaluate which farming system presents higher contamination risk by ochratoxin A (OTA) produced by fungi. Thirty samples of coffee grains (Coffea arabica L.) were analysed, being 20 of them of conventional coffee grains and 10 of them organic. The microbiological analysis was done with the Direct Plating Technique in a Dichloran Rose Bengal Chloramphenicol Agar (DRBC) media. The identification was done based on the macro and micro morphological characteristics and on the toxigenic potential with the Plug Agar technique. From the 30 samples analysed, 480 filamentous fungi of the genera Aspergillus of the Circumdati and Nigri Sections were isolated. The ochratoxigenic species identified were: Aspergillus auricoumus, A. ochraceus, A. ostianus, A. niger and A. niger Aggregate. The most frequent species which produces ochratoxin A among the isolated ones was A. ochraceus, corresponding to 89.55%. There was no significant difference regarding the presence of ochratoxigenic A. ochreceus between the conventional and organic cultivation systems, which suggests that the contamination risk is similar for both cultivation systems. PMID:24294225

Isolation and enzyme bioprospection of endophytic bacteria associated with plants of Brazilian mangrove ecosystem.

PubMed

Castro, Renata A; Quecine, Maria Carolina; Lacava, Paulo T; Batista, Bruna D; Luvizotto, Danice M; Marcon, Joelma; Ferreira, Anderson; Melo, Itamar S; Azevedo, João L

2014-01-01

The mangrove ecosystem is a coastal tropical biome located in the transition zone between land and sea that is characterized by periodic flooding, which confers unique and specific environmental conditions on this biome. In these ecosystems, the vegetation is dominated by a particular group of plant species that provide a unique environment harboring diverse groups of microorganisms, including the endophytic microorganisms that are the focus of this study. Because of their intimate association with plants, endophytic microorganisms could be explored for biotechnologically significant products, such as enzymes, proteins, antibiotics and others. Here, we isolated endophytic microorganisms from two mangrove species, Rhizophora mangle and Avicennia nitida, that are found in streams in two mangrove systems in Bertioga and Cananéia, Brazil. Bacillus was the most frequently isolated genus, comprising 42% of the species isolated from Cananéia and 28% of the species from Bertioga. However, other common endophytic genera such as Pantoea, Curtobacterium and Enterobacter were also found. After identifying the isolates, the bacterial communities were evaluated for enzyme production. Protease activity was observed in 75% of the isolates, while endoglucanase activity occurred in 62% of the isolates. Bacillus showed the highest activity rates for amylase and esterase and endoglucanase. To our knowledge, this is the first reported diversity analysis performed on endophytic bacteria obtained from the branches of mangrove trees and the first overview of the specific enzymes produced by different bacterial genera. This work contributes to our knowledge of the microorganisms and enzymes present in mangrove ecosystems.

Occurrence, diversity, and host association of intestinal Campylobacter, Arcobacter, and Helicobacter in reptiles.

PubMed

Gilbert, Maarten J; Kik, Marja; Timmerman, Arjen J; Severs, Tim T; Kusters, Johannes G; Duim, Birgitta; Wagenaar, Jaap A

2014-01-01

Campylobacter, Arcobacter, and Helicobacter species have been isolated from many vertebrate hosts, including birds, mammals, and reptiles. Multiple studies have focused on the prevalence of these Epsilonproteobacteria genera in avian and mammalian species. However, little focus has been given to the presence within reptiles, and their potential zoonotic and pathogenic roles. In this study, occurrence, diversity, and host association of intestinal Epsilonproteobacteria were determined for a large variety of reptiles. From 2011 to 2013, 444 cloacal swabs and fecal samples originating from 417 predominantly captive-held reptiles were screened for Epsilonproteobacteria. Campylobacter, Arcobacter, and Helicobacter genus specific PCRs were performed directly on all samples. All samples were also cultured on selective media and screened for the presence of Epsilonproteobacteria. Using a tiered approach of AFLP, atpA, and 16S rRNA sequencing, 432 Epsilonproteobacteria isolates were characterized at the species level. Based on PCR, Campylobacter, Arcobacter, and Helicobacter were detected in 69.3% of the reptiles; 82.5% of the chelonians, 63.8% of the lizards, and 58.0% of the snakes were positive for one or more of these genera. Epsilonproteobacteria were isolated from 22.1% of the reptiles and were isolated most frequently from chelonians (37.0%), followed by lizards (19.6%) and snakes (3.0%). The most commonly isolated taxa were Arcobacter butzleri, Arcobacter skirrowii, reptile-associated Campylobacter fetus subsp. testudinum, and a putative novel Campylobacter taxon. Furthermore, a clade of seven related putative novel Helicobacter taxa was isolated from lizards and chelonians. This study shows that reptiles carry various intestinal Epsilonproteobacteria taxa, including several putative novel taxa.

Occurrence, Diversity, and Host Association of Intestinal Campylobacter, Arcobacter, and Helicobacter in Reptiles

PubMed Central

Gilbert, Maarten J.; Kik, Marja; Timmerman, Arjen J.; Severs, Tim T.; Kusters, Johannes G.; Duim, Birgitta; Wagenaar, Jaap A.

2014-01-01

Campylobacter, Arcobacter, and Helicobacter species have been isolated from many vertebrate hosts, including birds, mammals, and reptiles. Multiple studies have focused on the prevalence of these Epsilonproteobacteria genera in avian and mammalian species. However, little focus has been given to the presence within reptiles, and their potential zoonotic and pathogenic roles. In this study, occurrence, diversity, and host association of intestinal Epsilonproteobacteria were determined for a large variety of reptiles. From 2011 to 2013, 444 cloacal swabs and fecal samples originating from 417 predominantly captive-held reptiles were screened for Epsilonproteobacteria. Campylobacter, Arcobacter, and Helicobacter genus specific PCRs were performed directly on all samples. All samples were also cultured on selective media and screened for the presence of Epsilonproteobacteria. Using a tiered approach of AFLP, atpA, and 16S rRNA sequencing, 432 Epsilonproteobacteria isolates were characterized at the species level. Based on PCR, Campylobacter, Arcobacter, and Helicobacter were detected in 69.3% of the reptiles; 82.5% of the chelonians, 63.8% of the lizards, and 58.0% of the snakes were positive for one or more of these genera. Epsilonproteobacteria were isolated from 22.1% of the reptiles and were isolated most frequently from chelonians (37.0%), followed by lizards (19.6%) and snakes (3.0%). The most commonly isolated taxa were Arcobacter butzleri, Arcobacter skirrowii, reptile-associated Campylobacter fetus subsp. testudinum, and a putative novel Campylobacter taxon. Furthermore, a clade of seven related putative novel Helicobacter taxa was isolated from lizards and chelonians. This study shows that reptiles carry various intestinal Epsilonproteobacteria taxa, including several putative novel taxa. PMID:24988130

Identification of microorganisms isolated from jet fuel systems.

PubMed

Edmonds, P; Cooney, J J

1967-03-01

Seventy-two samples from jet aircraft fuel systems were examined for microbial contamination. Ten contaminated samples yielded 43 microorganisms which were classified into nine genera of bacteria and three genera of fungi. The predominant types, comprising about 37% of the isolated cultures, were identified as Bacillus spp. The remaining cultures were distributed among 11 genera, each of which represented 2 to 9% of the total isolates. Four cultures could not be assigned to a genus on the basis of the diagnostic criteria used. Only five isolates, in the genera Pseudomonas and Hormodendrum (Cladosporium), grew abundantly in a mineral salts solution with JP-4 fuel as the sole source of carbon. The presence of fuel utilizers in a fuel system may be a better index to potential problems that have been correlated with microbial contamination than the presence of aerobic sporeforming bacilli.

Oral microflora and their relation to risk factors in HIV+ patients with oropharyngeal candidiasis.

PubMed

Sharifzadeh, A; Khosravi, A R; Shokri, H; Asadi Jamnani, F; Hajiabdolbaghi, M; Ashrafi Tamami, I

2013-06-01

The purpose of this study was to determine the prevalence of oral microflora and association of oral candidiasis and multiple risk factors in HIV(+) patients. The present study included 100 HIV-infected patients participated in Imam Khomeini Hospital, Tehran, Iran for Oropharyngeal candidiasis (OPC) and HIV. We assessed the presence or absence of OPC, and samples were obtained from the oral cavity and direct microscopic examination, gram staining and culture on standard microbiological media were performed in all patients. CD4(+) cell count/CD4(+) percentage were also calculated. The demographic characteristics showed that the patients had a mean age of 32.3 years old, 78% male and 22% female. Patients belonging to 'O(+)' blood group (27%) were more prone to develop OPC. A total of 460 bacterial colonies were obtained and Streptococcus mutans (15.4%) was the most frequently isolated species in the HIV(+) patients, followed by Staphylococcus epidermidis (12.8%) and Corynebacterium (8.7%). In addition, 254 yeasts (from four different genera) were isolated from the patient under study. Candida species (94.4%) were the most frequently obtained genera, followed by Saccharomyces (2.4%), Kluyveromyces and Cryptococcus (1.6% for both) species. Candida albicans (37.2%) was the most common species isolated from HIV(+) patients with OPC and its frequency was significantly higher than that of other Candida species (P<0.05). Candida glabrata, C. dubliniensis, C. tropicalis, C. parapsilosis, C. krusei, C. lusitaniae, C. guilliermondii and C. norvegensis were also identified. Forty percent of the patients had angular cheilitis as the most frequent clinical variant. The mean CD4(+) cell counts were 154.5 cells/μL, with a range of 8 to 611 cells/μL. Thirty percent patients had a CD4(+) cell count between 101 and 200 cells/μL (28.7% of total yeasts isolated). Yeast and bacteria counts did not differ statistically among HIV(+) patients' subgroups with different levels of CD4(+) cells counts. Our results showed that yeasts of the genus Candida were isolated at a comparable rate from the oral cavity of HIV(+) patients and there was no significant difference of the variables CD4(+) cell count and yeast counts. The findings of this study would be helpful in any further study, which, if done prospectively on a large cohort, can be confirmatory. Copyright © 2013. Published by Elsevier SAS.

Isolation of bacterial skin flora of healthy sheep, with comparison between frequent and minimal human handling.

PubMed

Haarstad, Amy C; Eisenschenk, Melissa C; Heinrich, Nicole A; Weese, J Scott; McKeever, Patrick J

2014-06-01

Few data are available regarding skin bacterial flora of healthy sheep and meticillin-resistant Staphylococcus carriage. To compare skin, ear and mucosal bacterial populations between minimally and frequently handled sheep; to determine whether the frequency of meticillin-resistant Staphylococcus aureus varied between groups. One hundred and three healthy feedlot and show sheep from eight farms. Swabs were collected from the dorsum, right ear and right nostril of each sheep. Two groups from each farm were evaluated, except from one farm, which had only one group. Bacterial isolates were identified to the genus or species level using phenotypic analysis or matrix-associated laser desorption/ionization time-of-flight mass spectrometry. Antimicrobial susceptibility testing and spa typing were performed on isolates of S. aureus. Sixteen bacterial genera were identified and 11 staphylococcal species, including S. aureus. The skin and mucosal bacterial flora were compared between the groups. The only statistically significant difference in bacteria was Streptococcus spp. on the dorsum (P = 0.0088), with carriage being more common in frequently handled sheep. Antimicrobial susceptibility testing did not find meticillin-resistant S. aureus. There was no significant difference in S. aureus carriage in the ear (P = 0.33), nostril (P = 0.43) or dorsum (P = 0.053) between frequently and minimally handled sheep. The S. aureus isolates belonged to six different spa types. Three were of the ST398 lineage. Sheep are a potential source of livestock-associated meticillin-sensitive Staphylococcus aureus ST398. © 2014 ESVD and ACVD.

Contents of microscopic fungi in dusts coming from cereal analysis laboratories.

PubMed

Szwajkowska-Michalek, Lidia; Stuper, Kinga; Lakomy, Piotr; Matysiak, Anna; Perkowski, Juliusz

2010-01-01

Microscopic fungi - components of bioaerosol found in the workplace environment of individuals employed in the agricultural sector - constitute a considerable hazard for their health. This study includes quantitative and qualitative analyses of mycobionta contained in 20 samples of dusts collected from laboratories conducting analyses of cereals. A total of 27 species of viable microscopic fungi were isolated. The most frequently isolated genera Penicillium and Aspergillus, accounting for 27 percent and 26 percent of analyzed isolates. The content of fungal biomass was determined quantitatively using a fungal marker, ergosterol (ERG). Concentrations of this metabolite for all samples ranged from 0.48 mg/kg-212.36 mg/kg. Based on the analyses, it may be stated that the concentration of microfungi in settled dust from laboratories conducting analyses of cereals was varied, and in several cases markedly exceeded admissible concentration levels.

Identity and Behavior of Xylem-Residing Bacteria in Rough Lemon Roots of Florida Citrus Trees †

PubMed Central

Gardner, John M.; Feldman, Albert W.; Zablotowicz, Robert M.

1982-01-01

An aseptic vacuum extraction technique was used to obtain xylem fluid from the roots of rough lemon (Citrus jambhiri Lush.) rootstock of Florida citrus trees. Bacteria were consistently isolated from vascular fluid of both healthy and young tree decline-affected trees. Thirteen genera of bacteria were found, the most frequently occurring genera being Pseudomonas (40%), Enterobacter (18%), Bacillus, Corynebacterium, and other gram-positive bacteria (16%), and Serratia (6%). Xylem bacterial counts fluctuated seasonally. Bacterial populations ranged from 0.1 to 22 per mm3 of root tissue (about 102 to 2 × 104 bacteria per g of xylem) when bacterial counts were made on vascular fluid, but these numbers were 10- to 1,000-fold greater when aseptically homogenized xylem tissue was examined similarly. Some of the resident bacteria (4%) are potentially phytopathogenic. It is proposed that xylem bacteria have an important role in the physiology of citrus. PMID:16346030

A new selective enrichment procedure for isolating Pasteurella multocida from avian and environmental samples

USGS Publications Warehouse

Moore, M.K.; Cicnjak-Chubbs, L.; Gates, R.J.

1994-01-01

A selective enrichment procedure, using two new selective media, was developed to isolate Pasteurella multocida from wild birds and environmental samples. These media were developed by testing 15 selective agents with six isolates of P. multocida from wild avian origin and seven other bacteria representing genera frequently found in environmental and avian samples. The resulting media—Pasteurella multocida selective enrichment broth and Pasteurella multocida selective agar—consisted of a blood agar medium at pH 10 containing gentamicin, potassium tellurite, and amphotericin B. Media were tested to determine: 1) selectivity when attempting isolation from pond water and avian carcasses, 2) sensitivity for detection of low numbers of P. multocida from pure and mixed cultures, 3) host range specificity of the media, and 4) performance compared with standard blood agar. With the new selective enrichment procedure, P. multocida was isolated from inoculated (60 organisms/ml) pond water 84% of the time, whereas when standard blood agar was used, the recovery rate was 0%.

Evaluation of the Biolog MicroStation system for yeast identification

NASA Technical Reports Server (NTRS)

McGinnis, M. R.; Molina, T. C.; Pierson, D. L.; Mishra, S. K.

1996-01-01

One hundred and fifty-nine isolates representing 16 genera and 53 species of yeasts were processed with the Biolog MicroStation System for yeast identification. Thirteen genera and 38 species were included in the Biolog database. For these 129 isolates, correct identifications to the species level were 13.2, 39.5 and 48.8% after 24, 48 and 72 hours incubation at 30 degrees C, respectively. Three genera and 15 species which were not included in the Biolog database were also tested. Of the 30 isolates studied, 16.7, 53.3 and 56.7% of the isolates were given incorrect names from the system's database after 24,48 and 72 h incubation at 30 degrees C, respectively. The remaining isolates of this group were not identified.

Brachiaria Grasses (Brachiaria spp.) harbor a diverse bacterial community with multiple attributes beneficial to plant growth and development.

PubMed

Mutai, Collins; Njuguna, Joyce; Ghimire, Sita

2017-10-01

Endophytic and plant-associated bacteria were isolated from plants and rhizoplane soil of naturally grown Brachiaria grasses at International Livestock Research Institute in Nairobi, Kenya. Eighty-four bacterial strains were isolated from leaf tissues, root tissues, and rhizoplane soil on nutrient agar and 869 media. All bacterial strains were identified to the lowest possible taxonomic unit using 16S rDNA primers and were characterized for the production of Indole-3-acetic acid, hydrogen cyanide, and ACC deaminase; phosphate solubilization; siderophore production; antifungal properties; and plant biomass production. The 16S rDNA-based identification grouped these 84 bacterial strains into 3 phyla, 5 classes, 8 orders, 12 families, 16 genera, and 50 unique taxa. The four most frequently isolated genera were Pseudomonas (23), Pantoea (17), Acinetobacter (9), and Enterobacter (8). The functional characterization of these strains revealed that 41 of 84 strains had a minimum of three plant beneficial properties. Inoculation of maize seedlings with Acinetobacter spp., Microbacterium spp., Pectobacterium spp., Pseudomonas spp., and Enterobacter spp. showed positive effects on seedling biomass production. The ability of Brachiaria grasses to host genetically diverse bacteria, many of them with multiple plant growth-promoting attributes, might have contributed to high biomass production and adaptation of Brachiaria grasses to drought and low fertility soils. © 2017 International Livestock Research Institute. MicrobiologyOpen published by John Wiley & Sons Ltd.

Evaluation of the routine antimicrobial susceptibility testing results of clinically significant anaerobic bacteria in a Slovenian tertiary-care hospital in 2015.

PubMed

Jeverica, Samo; Kolenc, Urša; Mueller-Premru, Manica; Papst, Lea

2017-10-01

The aim of our study was to determined antimicrobial susceptibility profiles of 2673 clinically significant anaerobic bacteria belonging to the major genera, isolated in 2015 in a large tertiary-care hospital in Slovenia. The species identification was performed by MALDI-TOF mass spectrometry. Antimicrobial susceptibility was determined immediately at the isolation of the strains against: penicillin, co-amoxiclav, imipenem, clindamycin and metronidazole, using gradient diffusion methodology and EUCAST breakpoints. The most frequent anaerobes were Bacteroides fragilis group with 31% (n = 817), Gram positive anaerobic cocci (GPACs) with 22% (n = 589), Prevotella with 14% (n = 313) and Propionibacterium with 8% (n = 225). Metronidazole has retained full activity (100%) against all groups of anaerobic bacteria intrinsically susceptible to it. Co-amoxiclav and imipenem were active against most tested anaerobes with zero or low resistance rates. However, observed resistance to co-amoxiclav (8%) and imipenem (1%) is worrying especially among B. fragilis group isolates. High overall resistance (23%) to clindamycin was detected in our study and was highest among the genera Prevotella, Bacteroides, Parabacteroides, GPACs and Clostridium. Routine testing of antimicrobial susceptibility of clinically relevant anaerobic bacteria is feasible and provides good surveillance data. Copyright © 2017 The Authors. Published by Elsevier Ltd.. All rights reserved.

Mycobiota of ground red pepper and their aflatoxigenic potential.

PubMed

Ham, Hyeonheui; Kim, Sosoo; Kim, Min-Hee; Lee, Soohyung; Hong, Sung Kee; Ryu, Jae-Gee; Lee, Theresa

2016-12-01

To investigate contamination of ground red pepper with fungi and mycotoxin, we obtained 30 ground red pepper samples from 15 manufacturers in the main chili-pepper-producing areas in Korea. Fungal contamination was evaluated by spreading diluted samples on potato dextrose agar plates. The total fungi counts ranged from 0 to 7.3 × 10 3 CFU/g. In the samples, the genus Aspergillus had the highest incidence, while Paecilomyces was isolated most frequently. The next most frequent genera were Rhizopus, Penicillium, Cladosporium, and Alternaria. Within Aspergillus, A. ruber was predominant, followed by A. niger, A. amstelodami, A. ochraceus, A. terreus, A. versicolor, A. flavus, and A. fumigatus. The samples were analyzed for aflatoxins, ochratoxin A, and citrinin by ultra-perfomance liquid chromatography (UPLC) with a fluorescence detector. Ochratoxin A was detected from three samples at 1.03‒2.08 μg/kg, whereas no aflatoxins or citrinin were detected. To test the potential of fungal isolates to produce aflatoxin, we performed a PCR assay that screened for the norB-cypA gene for 64 Aspergillus isolates. As a result, a single 800-bp band was amplified from 10 A. flavus isolates, and one Aspergillus sp. isolate. UPLC analyses confirmed aflatoxin production by nine A. flavus isolates and one Aspergillus sp. isolate, which produced total aflatoxins at 146.88‒909.53 μg/kg. This indicates that continuous monitoring of ground red pepper for toxigenic fungi is necessary to minimize mycotoxin contamination.

Mycobiota variation in stored rice straw and its cellulolytic profile.

PubMed

El-Metwally, Mohammad Magdy; Ghoneem, Khalid Mohammad; Saber, Wesam El-Din Ismail Ali

2014-09-01

Rice Straw (RS) one of most important agrowaste worldwide. Variation in mycobiota inhabiting long stored RS and its cellulolytic profile were studied. The highest number of fungi (23 species) was recovered from 1st storage period (1-3 year). Alternaria alternata, Aspergillus sp., Cladosporium herbarum, Fusarium incarnatum, Geotrichum candidum, Penicillium sp., Stemphylium lycopersici and Ulocladium atrum are the most frequent genera. Among 21 fungal species recovered in the 2nd period (3-5 year), Cladosporium herbarum, Fusarium incarnatum, Stemphylium lycopersici and Ulocladium atrum recorded 100% frequency, whereas Ulocladium atrum, Veticillium lecanii, Stemphylium lycopersici and Penicillium sp., were the most frequent species in the 3rd period (> 5 years). Regarding the pathogenic fungal isolates, Nigrospora oryzae was the most frequent with high intensity in all samples of the three storage periods, whereas Alternaria padwikii reached the highest frequency and intensity in the 1st period and absent the 2nd and 3rd ones. The isolated fungal species showed a high production of cellulases comparing to previous studies with positive and significant correlation between FPase from one side and CMCase (r = 0.634, p ≤ 0.05) and β-glucosidase (r = 0.775, p ≤ 0.05) from the other side.

Phylogenetic identification of fungi isolated from the marine sponge Tethya aurantium and identification of their secondary metabolites.

PubMed

Wiese, Jutta; Ohlendorf, Birgit; Blümel, Martina; Schmaljohann, Rolf; Imhoff, Johannes F

2011-01-01

Fungi associated with the marine sponge Tethya aurantium were isolated and identified by morphological criteria and phylogenetic analyses based on internal transcribed spacer (ITS) regions. They were evaluated with regard to their secondary metabolite profiles. Among the 81 isolates which were characterized, members of 21 genera were identified. Some genera like Acremonium, Aspergillus, Fusarium, Penicillium, Phoma, and Trichoderma are quite common, but we also isolated strains belonging to genera like Botryosphaeria, Epicoccum, Parasphaeosphaeria, and Tritirachium which have rarely been reported from sponges. Members affiliated to the genera Bartalinia and Volutella as well as to a presumably new Phoma species were first isolated from a sponge in this study. On the basis of their classification, strains were selected for analysis of their ability to produce natural products. In addition to a number of known compounds, several new natural products were identified. The scopularides and sorbifuranones have been described elsewhere. We have isolated four additional substances which have not been described so far. The new metabolite cillifuranone (1) was isolated from Penicillium chrysogenum strain LF066. The structure of cillifuranone (1) was elucidated based on 1D and 2D NMR analysis and turned out to be a previously postulated intermediate in sorbifuranone biosynthesis. Only minor antibiotic bioactivities of this compound were found so far.

Phylogeny of anaerobic fungi (phylum Neocallimastigomycota), with contributions from yak in China.

PubMed

Wang, Xuewei; Liu, Xingzhong; Groenewald, Johannes Z

2017-01-01

The phylum Neocallimastigomycota contains eight genera (about 20 species) of strictly anaerobic fungi. The evolutionary relationships of these genera are uncertain due to insufficient sequence data to infer their phylogenies. Based on morphology and molecular phylogeny, thirteen isolates obtained from yak faeces and rumen digesta in China were assigned to Neocallimastix frontalis (nine isolates), Orpinomyces joyonii (two isolates) and Caecomyces sp. (two isolates), respectively. The phylogenetic relationships of the eight genera were evaluated using complete ITS and partial LSU sequences, compared to the ITS1 region which has been widely used in this phylum in the past. Five monophyletic lineages corresponding to six of the eight genera were statistically supported. Isolates of Caecomyces and Cyllamyces were present in a single lineage and could not be separated properly. Members of Neocallimastigomycota with uniflagellate zoospores represented by Piromyces were polyphyletic. The Piromyces-like genus Oontomyces was consistently closely related to the traditional Anaeromyces, and separated the latter genus into two clades. The phylogenetic position of the Piromyces-like genus Buwchfawromyces remained unresolved. Orpinomyces and Neocallimastix, sharing polyflagellate zoospores, were supported as sister genera in the LSU phylogeny. Apparently ITS, specifically ITS1 alone, is not a good marker to resolve the generic affinities of the studied fungi. The LSU sequences are easier to align and appear to work well to resolve generic relationships. This study provides a comparative phylogenetic revision of Neocallimastigomycota isolates known from culture and sequence data.

Multilocus sequence identification of Penicillium species in cork bark during plank preparation for the manufacture of stoppers.

PubMed

Serra, Rita; Peterson, Stephen; Venâncio, Armando

2008-04-01

Despite several studies reporting Penicillium as one of the most frequent fungal genera in cork planks, the isolates were rarely identified to species level. We conducted a detailed study to identify Penicillium species from the field to the factory environment prior to and after boiling the cork planks. A total of 84 samples were analyzed. Of the 486 Penicillium isolates phenotypically identified, 32 representative or unusual strains were selected for identification by multilocus DNA sequence type. Cork proved to be a rich source of Penicillium biodiversity. A total of 30 taxa were recognized from cork including rarely seen species and 6 phylogenetically unique groups. Spores of some species lodged deep in cork can survive the boiling process. P. glabrum, P. glandicola and P. toxicarium, species with high CFU numbers in the field, are still frequently present in cork after boiling. Other species are killed by the boiling treatment and replaced by Penicillium species originating from the factory environment. Species known to contribute to cork taint were isolated at all stages. Good manufacturing practices are necessary at all stages in the preparation of cork planks to minimize the load of Penicillium species that produce cork taint.

Deterioration and spoilage of peanuts and desiccated coconuts from two sub-Saharan tropical East African countries due to the associated mycobiota and their degradative enzymes.

PubMed

Ismail, M A

2001-01-01

A broad variety of fungi (84 species belonging to 36 genera) were identified with more taxa infesting peanut seed samples from two tropical countries (29 genera and 61 species) compared to those found in desiccated coconuts (20 genera and 55 species) on both DRBC and DG18 media. This may be due to the higher moisture levels in peanuts (5.07-7.97%) compared with coconuts (1.5-4.17%). More taxa and propagules were recovered on DG18 in both cases. The dominant fungi from both substrates on both isolation media were Aspergillus and Penicillium, with other fungi from only one substrate/medium. The aflatoxigenic species (A. flavus) dominated Kenyan samples more so than Ugandan samples on both substrates. However only 71.5% and 87.5% of the peanut kernels, on DRBC and DG18, respectively, were found to be infested with fungi. The aflatoxigenic species (A. flavus/parasiticus) were found in 75% of the samples, however only 15.75% and 13% of the kernels analyzed were infested. The most frequently isolated species from peanuts were A. niger followed by A. flavus and M. phaseolina. E. repens, E. amstelodami, E. rubrum and E. chevalieri dominated peanut seeds on DG18, and R. stolonifer, A. parasiticus, F. solani, L. theobromae and P. chrysogenum on DRBC. The mean count of fungal propagules in coconut samples were approximately 0.7 x 10(3) and 0.8 x 10(3) on DRBC and DG18, respectively, with a high proportion of those propagules recorded for the aflatoxigenic species (about 0. 17 x 10(3) and 0.25 x 10(3) colonies/g). The mycobiota of desiccated coconut was dominated by A. niger, A. flavus and P. chrysogenum. Also A. ochraceus, P. waksmanii, Paecilomyces variotii, P. islandicum and R. mucilaginosa were more frequent on DRBC, while, species of Cladosporium. Chrysosporium and Eurotium were more frequent on DG18. Enzyme indices (or the activities) for each specific strain, when determined after 5 and 8 days of incubation, proved to be similar. A recommendation is given. The proteolytic and lipolytic potentialities of the most commonly encountered species from both peanuts and coconuts were studied. The most interesting observation is that most of the positive isolates, in both commodities had high enzymic activity compared to those reported earlier for isolates of the same species. Such capabilities suggest that these commodities are expected to deteriorate, since climatic conditions in tropical areas favour fungal proliferation. Emphasis on the proper harvesting, drying, handling, transportation and/or storage; and also education of the populace, especially those are dealing with these foods, should be taken into consideration by the relevant authorities. The contaminated foods constitute a health hazard for human consumption.

[Correlation between positive skin tests to molds, total IgE, and specific IgE using ELISA and mold cultures from the environment of the pediatric allergy patient].

PubMed

García Caballero, R; Nader, O; Morfin Maciel, B

2001-01-01

The aim of this study was to made a correlation between allergic symptoms, positive skin prick test to fungi, total and specific IgE and mold culture in the patient's environmental. There were included 35 children (3-16 years), with skin prick test positive to fungi. The most frequent were: Rhizopus, Aspergillus, Cladosporium and Candida. Total and specific IgE were measured with ELISA, with titers high in 77.2% and 31.4% respectively. Fungal cultures were collected from dwellings and schools. The most frequently isolated mold genera were Cladosporium, Alternaria and Penicillium in the same proportion in both places: dwellings and schools. We concluded fungi are commonly found in children's environment.

Fungi Isolated From House Flies (Diptera: Muscidae) on Penned Cattle in South Texas

PubMed Central

Ysquierdo, Cherity A.; Olafson, Pia U.; Thomas, Donald B.

2017-01-01

Abstract Musca domestica L. were collected from cattle diagnosed with bovine ringworm to evaluate the potential of the house fly to disseminate Trichophyton verrucosum E. Bodin, a fungal dermatophyte that is the causative agent for ringworm in cattle. Fungal isolates were cultured from 45 individual flies on supplemented Sabouraud dextrose agar, and isolates were identified using morphological and microscopic approaches. Each isolate was identified further by PCR amplification of the ribosomal DNA locus with fungal-specific primers and subsequent amplicon sequencing. Trichophyton verrucosum was not identified using these approaches. However, 35 different fungal species representing 17 genera were cultured from collected flies, including several species that are allergenic and pathogenic to humans and animals. Several species within the fungal orders Hypocreales, Microascales, Onygenales, Saccharomycetales, Xylaniales, and Agaricales were observed for the first time on house flies. The most frequent fungus recovered was Cladosporium cladosporoides Fresen, which is known to be a ubiquitous, airborne allergen to humans. PMID:28399217

Three new anascosporic genera of the Saccharomycotina: Danielozyma gen. nov., Deakozyma gen. nov. and Middelhovenomyces gen. nov.

USDA-ARS?s Scientific Manuscript database

Three new non-ascosporic, ascomycetous yeast genera are proposed based on their isolation from currently described species and genera. Phylogenetic placement of the genera was determined from analysis of nuclear gene sequences for D1/D2 large subunit rRNA, small subunit rRNA, translation elongation...

Characterization of arsenic resistant bacteria from arsenic rich groundwater of West Bengal, India.

PubMed

Sarkar, Angana; Kazy, Sufia K; Sar, Pinaki

2013-03-01

Sixty-four arsenic (As) resistant bacteria isolated from an arsenic rich groundwater sample of West Bengal were characterized to investigate their potential role in subsurface arsenic mobilization. Among the isolated strains predominance of genera Agrobacterium/Rhizobium, Ochrobactrum and Achromobacter which could grow chemolitrophically and utilize arsenic as electron donor were detected. Higher tolerance to As(3+) [maximum tolerable concentration (MTC): ≥10 mM], As(5+) (MTC: ≥100 mM) and other heavy metals like Cu(2+), Cr(2+), Ni(2+) etc. (MTC: ≥10 mM), presence of arsenate reductase and siderophore was frequently observed among the isolates. Ability to produce arsenite oxidase and phosphatase enzyme was detected in 50 and 34 % of the isolates, respectively. Although no direct correlation among taxonomic identity of bacterial strains and their metabolic abilities as mentioned above was apparent, several isolates affiliated to genera Ochrobactrum, Achromobacter and unclassified Rhizobiaceae members were found to be highly resistant to As(3+) and As(5+) and positive for all the test properties. Arsenate reductase activity was found to be conferred by arsC gene, which in many strains was coupled with arsenite efflux gene arsB as well. Phylogenetic incongruence between the 16S rRNA and ars genes lineages indicated possible incidence of horizontal gene transfer for ars genes. Based on the results we propose that under the prevailing low nutrient condition inhabitant bacteria capable of using inorganic electron donors play a synergistic role wherein siderophores and phosphatase activities facilitate the release of sediment bound As(5+), which is subsequently reduced by arsenate reductase resulting into the mobilization of As(3+) in groundwater.

Diversity and antibacterial activity of culturable actinobacteria isolated from five species of the South China Sea gorgonian corals.

PubMed

Zhang, Xiao-Yong; He, Fei; Wang, Guang-Hua; Bao, Jie; Xu, Xin-Ya; Qi, Shu-Hua

2013-06-01

This study describes the diversity and antibacterial activity of culturable actinobacteria isolated from five species of gorgonian corals (Echinogorgia aurantiaca, Melitodes squamata, Muricella flexuosa, Subergorgia suberosa, and Verrucella umbraculum) collected in shallow water of the South China Sea. A total of 123 actinobacterial isolates were recovered using ten different isolation media, and assigned to 11 genera, including Streptomyces and Micromonospora as the dominant genera, followed by Nocardia, Verrucosispora, Nocardiopsis, Rhodococcus, Pseudonocardia, Agrococcus, Saccharomonospora, Saccharopolyspora and Dietzia. Comparable analysis indicated that the numbers of actinobacterial genera and isolates from the five gorgonian coral species varied significantly. It was found that 72 isolates displayed antibacterial activity against at least one indicator bacterium, and the antibacterial strains isolated from different gorgonians had almost the same proportion (~50 %). These results provide direct evidence for the hypotheses that gorgonian coral species contain large and diverse communities of actinobacteria, and suggest that many gorgonian-associated actinobacteria could produce some antibacterial agents to protect their hosts against pathogens. To our knowledge, this is the first report about the diversity of culturable actinobacteria isolated from gorgonian corals.

Fungi of virgin and cultivated soil of Salhiah Desert, Egypt.

PubMed

el-Gindy, A A; Saad, R R

1990-01-01

27 species and 13 genera of fungi were identified from virgin and cultivated soil of Salhiah. The most abundant species of phosphate solubilizing fungi were Aspergillus nidulans, A. niger, A flavus, Penicillium lilacinum, P. frequentans and Fusarium moniliforme. On cellulose agar the most prevalent species were Chaetomium bostrychodes, C. olivaceum, Humicola fuscoatra, Aspergillus flavus, A. nidulans, A. niger, A. ochraceus, Fusarium solani and F. oxysporum. On xylan agar Aspergillus fumigatus, A. ochraceus, A. niger, A. versicolor and Penicillium frequentans were the most frequent species. On lignin agar only two species were isolated. These are Aspergillus niger and Humicola fuscoatra.

Unexpected diversity of basidiomycetous endophytes in sapwood and leaves of Hevea.

PubMed

Martin, Rachael; Gazis, Romina; Skaltsas, Demetra; Chaverri, Priscila; Hibbett, David

2015-01-01

Research on fungal endophytes has expanded dramatically in recent years, but little is known about the diversity and ecological roles of endophytic basidiomycetes. Here we report the analysis of 310 basidiomycetous endophytes isolated from wild and planted populations of the rubber tree genus, Hevea. Species accumulation curves were nonasymptotic, as in the majority of endophyte surveys, indicating that more sampling is needed to recover the true diversity of the community. One hundred eighteen OTUs were delimited, representing nine orders of Basidiomycota (Agaricales, Atheliales, Auriculariales, Cantharellales, Hymenochaetales, Polyporales, Russulales, Septobasidiales, Tremellales). The diversity of basidiomycetous endophytes found inhabiting wild populations of Hevea was comparable to that present in plantations. However, when samples were segregated by tissue type, sapwood of wild populations was found to contain a higher number of species than sapwood of planted trees. Seventy-five percent of isolates were members of the Polyporales, the majority in the phlebioid clade. Most of the species belong to clades known to cause a white-rot type of wood decay. Two species in the insect-associated genus Septobasidium were isolated. The most frequently isolated genera included Bjerkandera, Ceriporia, Phanerochaete, Phlebia, Rigidoporus, Tinctoporellus, Trametes (Polyporales), Peniophora, Stereum (Russulales) and Coprinellus (Agaricales), all of which have been reported as endophytes from a variety of hosts, across wide geographic locations. Literature records on the geographic distribution and host association of these genera revealed that their distribution and substrate affinity could be extended if the endophytic niche was investigated as part of fungal biodiversity surveys. © 2015 by The Mycological Society of America.

Phylogenetic Identification of Fungi Isolated from the Marine Sponge Tethya aurantium and Identification of Their Secondary Metabolites

PubMed Central

Wiese, Jutta; Ohlendorf, Birgit; Blümel, Martina; Schmaljohann, Rolf; Imhoff, Johannes F.

2011-01-01

Fungi associated with the marine sponge Tethya aurantium were isolated and identified by morphological criteria and phylogenetic analyses based on internal transcribed spacer (ITS) regions. They were evaluated with regard to their secondary metabolite profiles. Among the 81 isolates which were characterized, members of 21 genera were identified. Some genera like Acremonium, Aspergillus, Fusarium, Penicillium, Phoma, and Trichoderma are quite common, but we also isolated strains belonging to genera like Botryosphaeria, Epicoccum, Parasphaeosphaeria, and Tritirachium which have rarely been reported from sponges. Members affiliated to the genera Bartalinia and Volutella as well as to a presumably new Phoma species were first isolated from a sponge in this study. On the basis of their classification, strains were selected for analysis of their ability to produce natural products. In addition to a number of known compounds, several new natural products were identified. The scopularides and sorbifuranones have been described elsewhere. We have isolated four additional substances which have not been described so far. The new metabolite cillifuranone (1) was isolated from Penicillium chrysogenum strain LF066. The structure of cillifuranone (1) was elucidated based on 1D and 2D NMR analysis and turned out to be a previously postulated intermediate in sorbifuranone biosynthesis. Only minor antibiotic bioactivities of this compound were found so far. PMID:21731550

Radiation of Pollination Systems in the Iridaceae of sub-Saharan Africa

PubMed Central

GOLDBLATT, PETER; MANNING, JOHN C.

2006-01-01

• Background Seventeen distinct pollination systems are known for genera of sub-Saharan African Iridaceae and recurrent shifts in pollination system have evolved in those with ten or more species. Pollination by long-tongued anthophorine bees foraging for nectar and coincidentally acquiring pollen on some part of their bodies is the inferred ancestral pollination strategy for most genera of the large subfamilies Iridoideae and Crocoideae and may be ancestral for the latter. Derived strategies include pollination by long-proboscid flies, large butterflies, night-flying hovering and settling moths, hopliine beetles and sunbirds. Bee pollination is diverse, with active pollen collection by female bees occurring in several genera, vibratile systems in a few and non-volatile oil as a reward in one species. Long-proboscid fly pollination, which is apparently restricted to southern Africa, includes four separate syndromes using different sets of flies and plant species in different parts of the subcontinent. Small numbers of species use bibionid flies, short-proboscid flies or wasps for their pollination; only about 2 % of species use multiple pollinators and can be described as generalists. • Scope Using pollination observations for 375 species and based on repeated patterns of floral attractants and rewards, we infer pollination mechanisms for an additional 610 species. Matching pollination system to phylogeny or what is known about species relationships based on shared derived features, we infer repeated shifts in pollination system in some genera, as frequently as one shift for every five or six species of southern African Babiana or Gladiolus. Specialized systems using pollinators of one pollination group, or even a single pollinator species are the rule in the family. Shifts in pollination system are more frequent in genera of Crocoideae that have bilaterally symmetric flowers and a perianth tube, features that promote adaptive radiation by facilitating precise shifts in pollen placement, in conjunction with changes in flower colour, scent and tube length. • Conclusions Diversity of pollination systems explains in part the huge species diversity of Iridaceae in sub-Saharan Africa, and permits species packing locally. Pollination shifts are, however, seen as playing a secondary role in speciation by promoting reproductive isolation in peripheral, ecologically distinct populations in areas of diverse topography, climate and soils. Pollination of Iridaceae in Eurasia and the New World, where the family is also well represented, is poorly studied but appears less diverse, although pollination by both pollen- and oil-collecting bees is frequent and bird pollination rare. PMID:16377653

Radiation of pollination systems in the Iridaceae of sub-Saharan Africa.

PubMed

Goldblatt, Peter; Manning, John C

2006-03-01

Seventeen distinct pollination systems are known for genera of sub-Saharan African Iridaceae and recurrent shifts in pollination system have evolved in those with ten or more species. Pollination by long-tongued anthophorine bees foraging for nectar and coincidentally acquiring pollen on some part of their bodies is the inferred ancestral pollination strategy for most genera of the large subfamilies Iridoideae and Crocoideae and may be ancestral for the latter. Derived strategies include pollination by long-proboscid flies, large butterflies, night-flying hovering and settling moths, hopliine beetles and sunbirds. Bee pollination is diverse, with active pollen collection by female bees occurring in several genera, vibratile systems in a few and non-volatile oil as a reward in one species. Long-proboscid fly pollination, which is apparently restricted to southern Africa, includes four separate syndromes using different sets of flies and plant species in different parts of the subcontinent. Small numbers of species use bibionid flies, short-proboscid flies or wasps for their pollination; only about 2 % of species use multiple pollinators and can be described as generalists. Using pollination observations for 375 species and based on repeated patterns of floral attractants and rewards, we infer pollination mechanisms for an additional 610 species. Matching pollination system to phylogeny or what is known about species relationships based on shared derived features, we infer repeated shifts in pollination system in some genera, as frequently as one shift for every five or six species of southern African Babiana or Gladiolus. Specialized systems using pollinators of one pollination group, or even a single pollinator species are the rule in the family. Shifts in pollination system are more frequent in genera of Crocoideae that have bilaterally symmetric flowers and a perianth tube, features that promote adaptive radiation by facilitating precise shifts in pollen placement, in conjunction with changes in flower colour, scent and tube length. Diversity of pollination systems explains in part the huge species diversity of Iridaceae in sub-Saharan Africa, and permits species packing locally. Pollination shifts are, however, seen as playing a secondary role in speciation by promoting reproductive isolation in peripheral, ecologically distinct populations in areas of diverse topography, climate and soils. Pollination of Iridaceae in Eurasia and the New World, where the family is also well represented, is poorly studied but appears less diverse, although pollination by both pollen- and oil-collecting bees is frequent and bird pollination rare.

Phylogenetic diversity of culturable fungi in the Heshang Cave, central China

PubMed Central

Man, Baiying; Wang, Hongmei; Xiang, Xing; Wang, Ruicheng; Yun, Yuan; Gong, Linfeng

2015-01-01

Caves are nutrient-limited and dark subterranean ecosystems. To date, attention has been focused on geological research of caves in China, whilst indigenous microbial diversity has been insufficiently characterized. Here, we report the fungal diversity in the pristine, oligotrophic, karst Heshang Cave, central China, using a culture-dependent method coupled with the analysis of the fungal rRNA-ITS gene sequences. A total of 194 isolates were obtained with six different media from 14 sampling sites of sediments, weathered rocks, and bat guanos. Phylogenetic analysis clustered the 194 sequenced isolates into 33 genera within 15 orders of three phyla, Ascomycota, Basidiomycota, and Zygomycota, indicating a high degree of fungal diversity in the Heshang Cave. Notably, 16 out of the 36 fungal genera were also frequently observed in solution caves around the world and 23 genera were previously found in carbonate cave, indicating potential similarities among fungal communities in cave ecosystems. However, 10 genera in this study were not reported previously in any solution caves, thus expanding our knowledge about fungal diversity in cave ecosystems. Moreover, culturable fungal diversity varied from one habitat to another within the cave, being the highest in sediments, followed by weathered rocks and bat guanos as indicated by α-diversity indexes. At the genus level, Penicillium accounted for 40, 54, and 52% in three habitats of sediments, weathered rocks, and bat guanos, respectively. Trichoderma, Paecilomyces, and Aspergillus accounted for 9, 22, and 37% in the above habitats, correspondingly. Despite of the dominance of Penicillium in all samples, β-diversity index indicated significant differences between each two fungal communities in the three habitats in view of both the composition and abundance. Our study is the first report on fungal communities in a natural pristine solution cave system in central China and sheds light on fungal diversity and functions in cave ecosystems. PMID:26539184

Fungi from Admiralty Bay (King George Island, Antarctica) Soils and Marine Sediments.

PubMed

Wentzel, Lia Costa Pinto; Inforsato, Fábio José; Montoya, Quimi Vidaurre; Rossin, Bruna Gomes; Nascimento, Nadia Regina; Rodrigues, André; Sette, Lara Durães

2018-06-19

Extreme environments such as the Antarctic can lead to the discovery of new microbial taxa, as well as to new microbial-derived natural products. Considering that little is known yet about the diversity and the genetic resources present in these habitats, the main objective of this study was to evaluate the fungal communities from extreme environments collected at Aldmiralty Bay (Antarctica). A total of 891 and 226 isolates was obtained from soil and marine sediment samples, respectively. The most abundant isolates from soil samples were representatives of the genera Leucosporidium, Pseudogymnoascus, and a non-identified Ascomycota NIA6. Metschnikowia sp. was the most abundant taxon from marine samples, followed by isolates from the genera Penicillium and Pseudogymnoascus. Many of the genera were exclusive in marine sediment or terrestrial samples. However, representatives of eight genera were found in both types of samples. Data from non-metric multidimensional scaling showed that each sampling site is unique in their physical-chemical composition and fungal community. Biotechnological potential in relation to enzymatic production at low/moderate temperatures was also investigated. Ligninolytic enzymes were produced by few isolates from root-associated soil. Among the fungi isolated from marine sediments, 16 yeasts and nine fungi showed lipase activity and three yeasts and six filamentous fungi protease activity. The present study permitted increasing our knowledge on the diversity of fungi that inhabit the Antarctic, finding genera that have never been reported in this environment before and discovering putative new species of fungi.

Recovery and phylogenetic diversity of culturable fungi associated with marine sponges Clathrina luteoculcitella and Holoxea sp. in the South China Sea.

PubMed

Ding, Bo; Yin, Ying; Zhang, Fengli; Li, Zhiyong

2011-08-01

Sponge-associated fungi represent an important source of marine natural products, but little is known about the fungal diversity and the relationship of sponge-fungal association, especially no research on the fungal diversity in the South China Sea sponge has been reported. In this study, a total of 111 cultivable fungi strains were isolated from two South China Sea sponges Clathrina luteoculcitella and Holoxea sp. using eight different media. Thirty-two independent representatives were selected for analysis of phylogenetic diversity according to ARDRA and morphological characteristics. The culturable fungal communities consisted of at least 17 genera within ten taxonomic orders of two phyla (nine orders of the phylum Ascomycota and one order of the phylum Basidiomycota) including some potential novel marine fungi. Particularly, eight genera of Apiospora, Botryosphaeria, Davidiella, Didymocrea, Lentomitella, Marasmius, Pestalotiopsis, and Rhizomucor were isolated from sponge for the first time. Sponge C. luteoculcitella has greater culturable fungal diversity than sponge Holoxea sp. Five genera of Aspergillus, Davidiella, Fusarium, Paecilomyces, and Penicillium were isolated from both sponges, while 12 genera of Apiospora, Botryosphaeria, Candida, Marasmius, Cladosporium, Didymocrea, Hypocrea, Lentomitella, Nigrospora, Pestalotiopsis, Rhizomucor, and Scopulariopsis were isolated from sponge C. luteoculcitella only. Order Eurotiales especially genera Penicillium, Aspergillus, and order Hypocreales represented the dominant culturable fungi in these two South China Sea sponges. Nigrospora oryzae strain PF18 isolated from sponge C. luteoculcitella showed a strong and broad spectrum antimicrobial activities suggesting the potential for antimicrobial compounds production.

Isolation and molecular identification of lactic acid bacteria and Bifidobacterium spp. from faeces of the blue-fronted Amazon parrot in Brazil.

PubMed

Allegretti, L; Revolledo, L; Astolfi-Ferreira, C S; Chacón, J L; Martins, L M; Seixas, G H F; Ferreira, A J P

2014-12-01

In Brazil, the blue-fronted Amazon parrot (Amazona aestiva) is a common pet. The faecal microbiota of these birds include a wide variety of bacterial species, the majority of which belong to the Gram-positive lactic acid bacteria (LAB) clade. The aim of this study was to investigate differences in the diversity and abundance of LAB and Bifidobacterium spp. in the cloacae between wild and captive birds and to select, identify and characterise LAB for consideration as a parrot probiotic. Cloacal swabs were collected from 26 wild and 26 captive birds. Bacterial DNA was extracted, and the 16S rRNA genes were amplified. The numbers of PCR-positive Enterococcus, Pediococcus, and Lactobacillus species isolated from wild and captive birds were significantly different (P<0.05). Enterococcus was the most frequently isolated genus, followed by Pediococcus, Lactobacillus, Lactococcus and Bifidobacterium. Enterococcus faecium, Pediococcus pentosaceus, Lactococcus lactis, Lactobacillus coryniformis, Lactobacillus sanfranciscensis and Bifidobacterium bifidum were the most frequently isolated species from all birds. This study increases our understanding of the faecal microbiota, and may help to improve the nutrition and habitat management of captive and wild parrots. The bacterial population identified in the faecal microbiota of clinically healthy wild and captive parrots can serve as a database to analyse variations in the gut microbiota of pathogen-infected parrots and to develop probiotics specific to these genera.

Thermophilic spore-forming bacteria isolated from spoiled canned food and their heat resistance. Results of a French ten-year survey.

PubMed

André, S; Zuber, F; Remize, F

2013-07-15

Thermal processing of Low Acid Canned Foods (LACF), which are safe and shelf-stable at ambient temperature for several years, results in heat inactivation of all vegetative microorganisms and the partial or total inactivation of spores. Good Manufacturing Hygienic Practices include stability tests for managing the pathogen risk related to surviving mesophilic bacterial spores. LACF are also often submitted to additional incubation conditions, typically 55 °C for 7 days, to monitor spoilage by thermophiles. In this study we identified the bacterial species responsible for non-stability after prolonged at 55 °C of incubation of LACF from 455 samples collected from 122 French canneries over 10 years. Bacteria were identified by microsequencing or a recent developed tool for group-specific PCR detection (SporeTraQ™). A single species was identified for 93% of examined samples. Three genera were responsible for more than 80% of all non-stability cases: mostly Moorella (36%) and Geobacillus (35%), and less frequently Thermoanaerobacterium (10%). The other most frequent bacterial genera identified were Bacillus, Thermoanaerobacter, Caldanaerobius, Anoxybacillus, Paenibacillus and Clostridium. Species frequency was dependent on food category, i.e. vegetables, ready-made meals containing meat, seafood or other recipes, products containing fatty duck, and related to the intensity of the thermal treatment applied in these food categories. The spore heat resistance parameters (D or δ and z values) from 36 strains isolated in this study were determined. Taken together, our results single out the species most suitable for use as indicators for thermal process settings. This extensively-documented survey of the species that cause non-stability at 55 °C in LACF will help canneries to improve the management of microbial contamination. Copyright © 2013 Elsevier B.V. All rights reserved.

Diversity and antibiotic resistance patterns of Sphingomonadaceae isolates from drinking water.

PubMed

Vaz-Moreira, Ivone; Nunes, Olga C; Manaia, Célia M

2011-08-15

Sphingomonadaceae (n = 86) were isolated from a drinking water treatment plant (n = 6), tap water (n = 55), cup fillers for dental chairs (n = 21), and a water demineralization filter (n = 4). The bacterial isolates were identified based on analysis of the 16S rRNA gene sequence, and intraspecies variation was assessed on the basis of atpD gene sequence analysis. The isolates were identified as members of the genera Sphingomonas (n = 27), Sphingobium (n = 28), Novosphingobium (n = 12), Sphingopyxis (n = 7), and Blastomonas (n = 12). The patterns of susceptibility to five classes of antibiotics were analyzed and compared for the different sites of isolation and taxonomic groups. Colistin resistance was observed to be intrinsic (92%). The highest antibiotic resistance prevalence values were observed in members of the genera Sphingomonas and Sphingobium and for beta-lactams, ciprofloxacin, and cotrimoxazole. In tap water and in water from dental chairs, antibiotic resistance was more prevalent than in the other samples, mainly due to the predominance of isolates of the genera Sphingomonas and Sphingobium. These two genera presented distinct patterns of association with antibiotic resistance, suggesting different paths of resistance development. Antibiotic resistance patterns were often related to the species rather than to the site or strain, suggesting the importance of vertical resistance transmission in these bacteria. This is the first study demonstrating that members of the family Sphingomonadaceae are potential reservoirs of antibiotic resistance in drinking water.

Red Soils Harbor Diverse Culturable Actinomycetes That Are Promising Sources of Novel Secondary Metabolites

PubMed Central

Guo, Xiaoxuan; Liu, Ning; Li, Xiaomin; Ding, Yun; Shang, Fei; Gao, Yongsheng; Ruan, Jisheng

2015-01-01

Red soils, which are widely distributed in tropical and subtropical regions of southern China, are characterized by low organic carbon, high content of iron oxides, and acidity and, hence, are likely to be ideal habitats for acidophilic actinomycetes. However, the diversity and biosynthetic potential of actinomycetes in such habitats are underexplored. Here, a total of 600 actinomycete strains were isolated from red soils collected in Jiangxi Province in southeast China. 16S rRNA gene sequence analysis revealed a high diversity of the isolates, which were distributed into 26 genera, 10 families, and 7 orders within the class Actinobacteria; these taxa contained at least 49 phylotypes that are likely to represent new species within 15 genera. The isolates showed good physiological potentials for biosynthesis and biocontrol. Chemical screening of 107 semirandomly selected isolates spanning 20 genera revealed the presence of at least 193 secondary metabolites from 52 isolates, of which 125 compounds from 39 isolates of 12 genera were putatively novel. Macrolides, polyethers, diketopiperazines, and siderophores accounted for most of the known compounds. The structures of six novel compounds were elucidated, two of which had a unique skeleton and represented characteristic secondary metabolites of a putative novel Streptomyces phylotype. These results demonstrate that red soils are rich reservoirs for diverse culturable actinomycetes, notably members of the families Streptomycetaceae, Pseudonocardiaceae, and Streptosporangiaceae, with the capacity to synthesize novel bioactive compounds. PMID:25724963

Characteristics of the cultivable bacteria from sediments associated with two deep-sea hydrothermal vents in Okinawa Trough.

PubMed

Sun, Qing-lei; Wang, Ming-qing; Sun, Li

2015-12-01

In this study, different culture-dependent methods were used to examine the cultivable heterotrophic bacteria in the sediments associated with two deep-sea hydrothermal vents (named HV1 and HV2) located at Iheya Ridge and Iheya North in Okinawa Trough. The two vents differed in morphology, with HV1 exhibiting diffuse flows while HV2 being a black smoker with a chimney-like structure. A total of 213 isolates were identified by near full-length 16S rRNA gene sequence analysis. Of these isolates, 128 were from HV1 and 85 were from HV2. The bacterial community structures were, in large parts, similar between HV1 and HV2. Nevertheless, differences between HV1 and HV2 were observed in one phylum, one class, 4 orders, 10 families, and 20 genera. Bioactivity analysis revealed that 25 isolates belonging to 9 different genera exhibited extracellular protease activities, 21 isolates from 11 genera exhibited extracellular lipase activities, and 13 isolates of 8 genera displayed antimicrobial activities. This is the first observation of a large population of bacteria with extracellular bioactivities existing in deep-sea hydrothermal vents. Taken together, the results of this study provide new insights into the characteristics of the cultivable heterotrophic bacteria in deep-sea hydrothermal ecosystems.

Trypanosomatidae: a spliced-leader-derived probe specific for the genus Phytomonas.

PubMed

Teixeira, M M; Serrano, M G; Nunes, L R; Campaner, M; Buck, G A; Camargo, E P

1996-12-01

We probed DNA from all trypanosomatid genera by slot blot hybridization with an oligonucleotide (SL3') complementary to a sequence of the Phytomonas spliced-leader or mini-exon RNA. The 19-nucleotide probe target site was previously shown to be highly conserved among a limited number of Phytomonas isolates, but diverges in other kinetoplastid genera. Our examination of 84 isolates of various genera of trypanosomatids showed hybridization of this probe exclusively with isolates from plants or insects which could, by morphological, biochemical, and molecular criteria, be considered to belong to the genus Phytomonas. In contrast, no hybridization was observed with flagellates of the genera Blastocrithidia, Crithidia, Endotrypanum, Herpetomonas, Leptomonas, Leishmania, and Trypanosoma. The method detected DNA quantities as low as 50 ng using either radioactive or nonradioactive probes, and was effective with as few as 10(4) intact flagellates. Together, these results suggest that this probe will serve as a convenient marker for taxonomic and epidemiological studies requiring reliable identification of Phytomonas spp. in plants or in putative insect vectors.

Exploration of cultivable fungal communities in deep coal-bearing sediments from ∼1.3 to 2.5 km below the ocean floor.

PubMed

Liu, Chang-Hong; Huang, Xin; Xie, Tian-Ning; Duan, Ning; Xue, Ya-Rong; Zhao, Tan-Xi; Lever, Mark A; Hinrichs, Kai-Uwe; Inagaki, Fumio

2017-02-01

Although subseafloor sediments are known to harbour a vast number of microbial cells, the distribution, diversity, and origins of fungal populations remain largely unexplored. In this study, we cultivated fungi from 34 of 47 deep coal-associated sediment samples collected at depths ranging from 1289 to 2457 m below the seafloor (mbsf) off the Shimokita Peninsula, Japan (1118 m water depth). We obtained a total of 69 fungal isolates under strict contamination controls, representing 61 Ascomycota (14 genera, 23 species) and 8 Basidiomycota (4 genera, 4 species). Penicillium and Aspergillus relatives were the most dominant genera within the Ascomycetes, followed by the members of genera Cladosporium, Hamigera, Chaetomium, Eutypella, Acremonium, Aureobasidium, Candida, Eurotium, Exophiala, Nigrospora, Bionectria and Pseudocercosporella. Four Basidiomycota species were identified as genera Schizophyllum, Irpex, Bjerkandera and Termitomyces. Among these isolates, Cladosporium sphaerospermum and Aspergillus sydowii relatives were isolated from a thin lignite coal-sandstone formation at 2457 mbsf. Our results indicate that these cultivable fungal populations are indigenous, originating from past terrigenous environments, which have persisted, possibly as spores, through ∼20 million years of depositional history. © 2017 Society for Applied Microbiology and John Wiley & Sons Ltd.

[Diversity of Bacillus species inhabiting on the surface and endophyte of lichens collected from Wuyi Mountain].

PubMed

Ge, Cibin; Liu, Bo; Che, Jianmei; Chen, Meichun; Liu, Guohong; Wei, Jiangchun

2015-05-04

The present work reported the isolation, identification and diversity of Bacillus species colonizing on the surface and endophyte in lichens collected from Wuyi Mountain. Nine lichen samples of Evernia, Stereocaulon, Menegazzia and other 6 genera belonging to 7 families were collected from Wuyi mountain nature reserve. The bacillus-like species colonizing on the surface and endophyte in these lichens were isolated and identified by 16S rRNA gene sequence analysis. There was no bacillus-like species isolated from Evernia, Ramalina and Lecarona. A total of 34 bacillus-like bacteria were isolated from another 6 lichen samples. These bacteria were identified as 24 species and were classified into Bacillus, Paenibacillus, Brevibacillus, Lysinibacillus and Viridiibacillus. Paenibacillus and Bacillus are the dominant genera, and accounting for 41. 2% and 35. 3% of all isolated bacteria respectively. Brevibacillus, Lysinibacillus and Viridiibacillu were first reported being isolated from lichens. There were different species and quantity of bacillus colonizing on the surface and endophyte in different lichens. The quantity of bacillus colonizing on the surface of Physcia was more than 3.85 x 10(6) cfu/g and was the largest in the isolated bacteria, while the species of bacillus colonizing on the surface and endophyte in Stereocaulon was the most abundant. Most of the isolated bacteria were colonizing on (in) one lichen genera, but Paenibacillus taichungensis, Paenibacillus odorifer, Brevibacillus agri, Lysinibacillus xylanilyticus was respectively colonizing on (in) 2-3 lichen genera and Bacillus mycoides was colonizing on (in) Menegazzia, Cladonia Physcia, and Stereocaulon. There are species and quantity diversity of bacillus colonizing on (in) lichens.

Keratinophilic fungi and other moulds associated with air-dust particles from Egypt.

PubMed

Abdel-Hafez, S I; Moubasher, A H; Barakat, A

1990-01-01

One-hundred and eleven species and three species varieties belonging to 39 genera were collected from 50 dust samples on the five media used at 28 degrees C. Using the hair-baiting technique with horse hair, 10 species of Chrysosporium were isolated: C. asperatum, C. state of Arthroderma tuberculatum, C. indicum, C. inops, C. keratinophilum, C. merdarium, C. pannorum, C. queenslandicum, C. tropicum and C. xerophilum. True dermatophytes were isolated: Trichophyton verrucosum and Trichophyton sp. Also, numerous fungi tolerating high levels of cycloheximide were encountered, such as members of Acremonium, Aspergillus and Penicillium. On plates of glucose or cellulose Czapek-Dox agar (free from sucrose) the most frequent fungi were: Alternaria alternata, Aspergillus flavus, A. flavus var. columnaris, A. fumigatus, A. niger, A. ochraceus, A. sydowii, A. terreus, Chaetomium globosum, Cladosporium herbarum, Emericella nidulans, Fusarium oxysporum, Mucor hiemalis, Penicillium chrysogenum, P. oxalicum, Scopulariopsis brevicaulis and Ulocladium atrum. On plates of 50% sucrose or 10 and 20% NaCl-Czapek's agar, some interesting species were frequently encountered: Eurotium amstelodami, E. chevalieri, E. halophilicum, E. montevidensis, E. repens, E. rubrum and Scopulariopsis halophilica. The isolated fungi have been tested for osmophilicity and halophilicity, they showed different rates of growth on sucrose and sodium chloride-Czapek's medium of various osmotic potential.

Fungi isolated from flue-cured tobacco sold in Southeast United States, 1968-1970.

PubMed

Welty, R E

1972-09-01

Flue-cured tobacco leaves, from low- and middle-stalk positions, offered for sale in each of two markets, within each of five tobacco types, were evaluated for moisture content (MC) and filamentous fungi during August through October in 1968, 1969, and 1970. Alternaria alternata, Penicillium cyclopium, Aspergillus niger, Aspergillus repens, and Aspergillus flavus were most frequently isolated from cultured tissue. Other filamentous fungi that grew from the tissue included species from four genera of field fungi and seven species of storage fungi. Although the MC ranged from 11.0 to 22.5%, it averaged 16.4, 16.8, and 15.9% for samples taken in 1968, 1969, and 1970, respectively. Average populations of fungi per sample over the three years ranged from 0 to 1,528,500 colonies/g of tobacco.

Fungi Isolated from Flue-Cured Tobacco Sold in Southeast United States, 1968-1970

PubMed Central

Welty, Ronald E.

1972-01-01

Flue-cured tobacco leaves, from low- and middle-stalk positions, offered for sale in each of two markets, within each of five tobacco types, were evaluated for moisture content (MC) and filamentous fungi during August through October in 1968, 1969, and 1970. Alternaria alternata, Penicillium cyclopium, Aspergillus niger, Aspergillus repens, and Aspergillus flavus were most frequently isolated from cultured tissue. Other filamentous fungi that grew from the tissue included species from four genera of field fungi and seven species of storage fungi. Although the MC ranged from 11.0 to 22.5%, it averaged 16.4, 16.8, and 15.9% for samples taken in 1968, 1969, and 1970, respectively. Average populations of fungi per sample over the three years ranged from 0 to 1,528,500 colonies/g of tobacco. PMID:4627970

Antimicrobial effect of probiotics on bacterial species from dental plaque.

PubMed

Zambori, Csilla; Morvay, Attila Alexandru; Sala, Claudia; Licker, Monica; Gurban, Camelia; Tanasie, Gabriela; Tirziu, Emil

2016-03-31

The antimicrobial role of probiotic Lactobacillus casei subspecies casei DG (L. casei DG) and of the mix culture of probiotic Lactobacillus acidophilus LA-5 and Bifidobacterium BB-12 was tested on species of Staphylococcus, Streptococcus, Pasteurella, and Neisseria genera from supragingival sites from dogs with dental disease of different breed, age, sex, weight, and diet. The research was conducted on these four genera because of their importance in zoonotic infections after dog bites. Species from Staphylococcus, Streptococcus, Pasteurella, and Neisseria genera were isolated and identified. To test the antimicrobial efficacy of L. casei DG and the mixed culture of probiotic L. acidophilus LA-5 and Bifidobacterium bifidum BB-12 on the pathogenic species, the agar overlay method was used. L. casei DG had a bactericidal effect on all analyzed species isolated from Staphylococcus, Streptococcus, Pasteurella, and Neisseria genera after 24 hours of incubation. The mixed probiotic culture made up of L. acidophilus LA-5 and Bifidobacterium BB-12 species had no bactericidal effect on the species of Staphylococcus and Streptococcus genera, which were resistant. However, it had a bacteriostatic effect on several species of Pasteurella and Neisseria genera. This work highlights the antimicrobial potential of probiotics in vitro, demonstrating that the probiotic L. casei DG has a bactericidal effect on all analyzed species isolated from dental plaque and that the mix culture of probiotic L. acidophilus LA-5 and Bifidobacterium BB-12 has only a bacteriostatic effect.

Isolation and characterization of marine bacteria capable of utilizing phthalate.

PubMed

Iwaki, Hiroaki; Nishimura, Ayaka; Hasegawa, Yoshie

2012-03-01

Eleven phthalate-degrading bacterial strains were isolated from seawater collected off the coast of Japan. The isolates were found to be most closely related to the marine bacterial genera Alteromonas, Citreicella, Marinomonas, Marinovum, Pelagibaca, Rhodovulum, Sulfitobacter, Thalassobius, Thalassococcus, Thalassospira, and Tropicibacter. For the first time, members of these genera were shown to be capable of growth on phthalate. The plate assay for visual detection of phthalate dioxygenase activity and PCR detection of a possible gene encoding 4,5-dihydroxyphthalate decarboxylase indicated that phthalate is degraded via 4,5-dihydroxyphthalate to protocatechuate in all the isolates.

Black-pigmented gram-negative anaerobes in endodontic infections.

PubMed

Haapasalo, M

1993-03-01

Necrotic dental root canal infections are polymicrobial infections dominated by anaerobic bacteria. The number of different species in one canal is usually low, approx. 4-7 species. The species isolated most frequently belong to the genera Prevotella, Porphyromonas, Fusobacterium, Peptostreptococcus, Eubacterium and Streptococcus. The frequency of isolation of black-pigmented Gram-negative anaerobes in endodontic infections varies from 25% to > 50%. Pr. intermedia is the most commonly found pigmented species, followed by Pr. denticola and two Porphyromonas species, P. gingivalis and P. endodontalis. Several studies have shown that P. gingivalis and P. endodontalis are closely related to the presence of acute symptoms in endodontic infections, whereas other black-pigmented Gram-negative anaerobes are not. However, several other species may also be involved in acute infections. Moreover, Porphyromonas species have occasionally been isolated from cases with no symptoms. Although Porphyromonas spp. are clearly related to symptoms at the beginning of therapy, they are not important for the prognosis of the treatment.

Diversity and Antibiotic Resistance Patterns of Sphingomonadaceae Isolates from Drinking Water▿

PubMed Central

Vaz-Moreira, Ivone; Nunes, Olga C.; Manaia, Célia M.

2011-01-01

Sphingomonadaceae (n = 86) were isolated from a drinking water treatment plant (n = 6), tap water (n = 55), cup fillers for dental chairs (n = 21), and a water demineralization filter (n = 4). The bacterial isolates were identified based on analysis of the 16S rRNA gene sequence, and intraspecies variation was assessed on the basis of atpD gene sequence analysis. The isolates were identified as members of the genera Sphingomonas (n = 27), Sphingobium (n = 28), Novosphingobium (n = 12), Sphingopyxis (n = 7), and Blastomonas (n = 12). The patterns of susceptibility to five classes of antibiotics were analyzed and compared for the different sites of isolation and taxonomic groups. Colistin resistance was observed to be intrinsic (92%). The highest antibiotic resistance prevalence values were observed in members of the genera Sphingomonas and Sphingobium and for beta-lactams, ciprofloxacin, and cotrimoxazole. In tap water and in water from dental chairs, antibiotic resistance was more prevalent than in the other samples, mainly due to the predominance of isolates of the genera Sphingomonas and Sphingobium. These two genera presented distinct patterns of association with antibiotic resistance, suggesting different paths of resistance development. Antibiotic resistance patterns were often related to the species rather than to the site or strain, suggesting the importance of vertical resistance transmission in these bacteria. This is the first study demonstrating that members of the family Sphingomonadaceae are potential reservoirs of antibiotic resistance in drinking water. PMID:21705522

Molecular characterization of antibiotic resistance in cultivable multidrug-resistant bacteria from livestock manure.

PubMed

Yang, Qingxiang; Tian, Tiantian; Niu, Tianqi; Wang, Panliang

2017-10-01

Diverse antibiotic-resistance genes (ARGs) are frequently reported to have high prevalence in veterinary manure samples due to extensive use of antibiotics in farm animals. However, the characteristics of the distribution and transmission of ARGs among bacteria, especially among different species of multiple antibiotic-resistant bacteria (MARB), have not been well explored. By applying high-throughput sequencing methods, our study uncovered a vast MARB reservoir in livestock manure. The genera Escherichia, Myroides, Acinetobacter, Proteus, Ignatzschineria, Alcaligenes, Providencia and Enterococcus were the predominant cultivable MARB, with compositions of 40.6%-85.7%. From chicken manure isolates, 33 MARB were selected for investigation of the molecular characteristics of antibiotic resistance. A total of 61 ARGs and 18 mobile genetic elements (MGEs) were investigated. We found that 47 ARGs were widely distributed among the 33 MARB isolates. Each isolate carried 27-36 genes responsible for resistance to eight classes of antibiotics frequently used in clinic or veterinary settings. ARGs to the six classes of antibiotics other than streptogramins and vancomycin were present in all 33 MARB isolates with a prevalence of 80%-100%. A total of 12 MGEs were widely distributed among the 33 MARB, with intI1, IS26, ISaba1, and ISEcp1 simultaneously present in 100% of isolates. In addition, 9 gene cassettes within integrons and ISCR1 were detected among MARB isolates encoding resistance to different antibiotic classes. This is the first report revealing the general co-presence of multiple ARGs, various MGEs and ARG cassettes in different species of individual MARB isolates in chicken manure. The results highlight a much higher risk of ARGs spreading through livestock manure to humans than we expected. Copyright © 2017 Elsevier Ltd. All rights reserved.

Phytate degradation by fungi and bacteria that inhabit sawdust and coffee residue composts.

PubMed

Fathallh Eida, Mohamed; Nagaoka, Toshinori; Wasaki, Jun; Kouno, Kenji

2013-01-01

Phytate is the primary source of organic phosphorus, but it cannot be directly utilized by plants and is strongly adsorbed by the soil, reducing bioavailability. Composting is a process used to improve the bioavailability of phytate in organic wastes through degradation by microorganisms. In this study, we aimed to investigate the phytate-degrading ability of fungi and bacteria that inhabit sawdust compost and coffee residue compost, and their contribution to the composting process. In the plate assay, the fungi that formed clear zones around their colonies belonged to the genera Mucor, Penicillium, Galactomyces, Coniochaeta, Aspergillus, and Fusarium, while the bacteria belonged to the genera Pseudomonas, Enterobacter, Chitinophaga, and Rahnella. Eight fungal isolates (genera Mucor, Penicillium, Galactomyces, and Coniochaeta) and four bacterial isolates (genera Pseudomonas, Enterobacter, and Rahnella) were selected to evaluate phytase activity in their liquid culture and their ability to degrade phytate in organic materials composed of mushroom media residue and rice bran. The selected fungi degraded phytate in organic materials to varying degrees. Penicillium isolates showed the highest degradation ability and Coniochaeta isolate exhibited relatively high degradation ability. The clear zone diameters of these fungal isolates displayed significantly positive and negative correlations with inorganic and phytate phosphorus contents in the organic materials after incubation, respectively; however, none of the selected bacteria reduced phytate phosphorus in organic materials. It is therefore possible that fungi are major contributors to phytate degradation during composting.

Korean indigenous bacterial species with valid names belonging to the phylum Actinobacteria.

PubMed

Bae, Kyung Sook; Kim, Mi Sun; Lee, Ji Hee; Kang, Joo Won; Kim, Dae In; Lee, Ji Hee; Seong, Chi Nam

2016-12-01

To understand the isolation and classification state of actinobacterial species with valid names for Korean indigenous isolates, isolation source, regional origin, and taxonomic affiliation of the isolates were studied. At the time of this writing, the phylum Actinobacteria consisted of only one class, Actinobacteria, including five subclasses, 10 orders, 56 families, and 330 genera. Moreover, new taxa of this phylum continue to be discovered. Korean actinobacterial species with a valid name has been reported from 1995 as Tsukamurella inchonensis isolated from a clinical specimen. In 1997, Streptomyces seoulensis was validated with the isolate from the natural Korean environment. Until Feb. 2016, 256 actinobacterial species with valid names originated from Korean territory were listed on LPSN. The species were affiliated with three subclasses (Acidimicrobidae, Actinobacteridae, and Rubrobacteridae), four orders (Acidimicrobiales, Actinomycetales, Bifidobacteriales, and Solirubrobacterales), 12 suborders, 36 families, and 93 genera. Most of the species belonged to the subclass Actinobacteridae, and almost of the members of this subclass were affiliated with the order Actinomycetales. A number of novel isolates belonged to the families Nocardioidaceae, Microbacteriaceae, Intrasporangiaceae, and Streptomycetaceae as well as the genera Nocardioides, Streptomyces, and Microbacterium. Twenty-six novel genera and one novel family, Motilibacteraceae, were created first with Korean indigenous isolates. Most of the Korean indigenous actionobacterial species were isolated from natural environments such as soil, seawater, tidal flat sediment, and fresh-water. A considerable number of species were isolated from artificial resources such as fermented foods, wastewater, compost, biofilm, and water-cooling systems or clinical specimens. Korean indigenous actinobacterial species were isolated from whole territory of Korea, and especially a large number of species were from Jeju, Gyeonggi, Jeonnam, Daejeon, and Chungnam. A large number of novel actinobacterial species continue to be discovered since the Korean government is encouraging the search for new bacterial species and researchers are endeavoring to find out novel strains from extreme or untapped environments.

A primary assessment of the endophytic bacterial community in a xerophilous moss (Grimmia montana) using molecular method and cultivated isolates

PubMed Central

Liu, Xiao Lei; Liu, Su Lin; Liu, Min; Kong, Bi He; Liu, Lei; Li, Yan Hong

2014-01-01

Investigating the endophytic bacterial community in special moss species is fundamental to understanding the microbial-plant interactions and discovering the bacteria with stresses tolerance. Thus, the community structure of endophytic bacteria in the xerophilous moss Grimmia montana were estimated using a 16S rDNA library and traditional cultivation methods. In total, 212 sequences derived from the 16S rDNA library were used to assess the bacterial diversity. Sequence alignment showed that the endophytes were assigned to 54 genera in 4 phyla (Proteobacteria, Firmicutes, Actinobacteria and Cytophaga/Flexibacter/Bacteroids). Of them, the dominant phyla were Proteobacteria (45.9%) and Firmicutes (27.6%), the most abundant genera included Acinetobacter, Aeromonas, Enterobacter, Leclercia, Microvirga, Pseudomonas, Rhizobium, Planococcus, Paenisporosarcina and Planomicrobium. In addition, a total of 14 species belonging to 8 genera in 3 phyla (Proteobacteria, Firmicutes, Actinobacteria) were isolated, Curtobacterium, Massilia, Pseudomonas and Sphingomonas were the dominant genera. Although some of the genera isolated were inconsistent with those detected by molecular method, both of two methods proved that many different endophytic bacteria coexist in G. montana. According to the potential functional analyses of these bacteria, some species are known to have possible beneficial effects on hosts, but whether this is the case in G. montana needs to be confirmed. PMID:24948927

The occurrence of molds in patients with chronic sinusitis.

PubMed

Twarużek, Magdalena; Soszczyńska, Ewelina; Winiarski, Piotr; Zwierz, Aleksander; Grajewski, Jan

2014-05-01

Chronic rhinosinusitis (CRS) is a common inflammatory condition of nasal and paranasal sinus mucosa. Although pathogenic bacteria were postulated as main etiological factor responsible for most cases of CRS, the involvement of molds was recently proved in some cases. The aim of the study was to conduct mycological analysis of material obtained from patients operated on due to chronic sinusitis. The study included 107 patients, 45 women and 62 men. During the surgery, a fragment of mucosa from the region of the ethmoid bulla was obtained as microbiological characteristics of this material closely resemble those of sinus mucosa. In addition, maxillary sinus lavage was obtained. The control group comprised patients without chronic sinusitis. The dithiothreitol solution method was used for the lavage examination. The tissue material (mucosal fragment from the region of the ethmoid bulla) was incubated in 2% liquid Sabouraud medium for 24 h. The material was inoculated onto culture media. The presence of molds was detected in 67% of examined samples. Overall, 41 species belonging to 12 genera were isolated. The most frequently detected genera included Penicillium spp. (46%) and Aspergillus spp. (16%). In addition, Cladosporium spp. (11%), Fusarium spp. (7%), Acremonium spp. (4%), Eurotium spp. (4%), Alternaria spp. (2%), Chaetomium spp. (1%), Geotrichum spp. (1%), Verticillium spp. (1%), Rhizopus spp. (1%), and some unidentified colonies (5%) were isolated. Penicillium crustosum, Penicillium citrinum, Aspergillus niger, Cladosporium cladosporioides, and Fusarium verticillioides were the most prevalent species.

Microbiota on spoiled vegetables and their characterization.

PubMed

Lee, Dong Hwan; Kim, Jin-Beom; Kim, Mihyun; Roh, Eunjung; Jung, Kyusuk; Choi, Minseon; Oh, Changsik; Choi, Jaehyuk; Yun, Jongchul; Heu, Sunggi

2013-08-01

Spoilage causes vegetables to deteriorate and develop unpleasant characteristics. Approximately 30 % of fresh vegetables are lost to spoilage, mainly due to colonization by bacteria. In the present study, a total of 44 bacterial isolates were obtained from a number of spoiled vegetables. The isolates were identified and classified into 20 different species of 14 genera based on fatty acid composition, biochemical tests, and 16S rDNA sequence analyses. Pseudomonas spp. were the species most frequently isolated from the spoiled vegetables. To evaluate the spoilage ability of each species, a variety of fresh vegetables were treated with each isolate and their degree of maceration was observed. In addition, the production of plant cell wall-degrading enzymes (PCWDEs), such as cellulase, xylanase, pectate lyase, and polygalacturonase, was compared among isolates to investigate their potential associations with spoilage. Strains that produce more PCWDEs cause spoilage on more diverse plants, and pectinase may be the most important enzyme among PCWDEs for vegetable spoilage. Most gram-negative spoilage bacteria produced acylated homoserine lactone, a quorum-sensing signal molecule, suggesting that it may be possible to use this compound effectively to prevent or slow down the spoilage of vegetables contaminated with diverse bacteria.

Occurrence of toxigenic fungi and determination of mycotoxins by HPLC-FLD in functional foods and spices in China markets.

PubMed

Kong, Weijun; Wei, Riwei; Logrieco, Antonio F; Wei, Jianhe; Wen, Jing; Xiao, Xiaohe; Yang, Meihua

2014-03-01

Twenty-four samples including 14 functional foods and 10 spices obtained from Chinese markets were examined for their mould profile. The mycotoxin contamination levels were also determined by an optimized HPLC-FLD method. 124 fungal isolates belonging to four different genera were recovered with Aspergillus and Penicillium as predominant fungi, with an incidence of 66.1% and 15.3%, respectively. In functional foods Aspergillus niger section (57.1%) was isolated more frequently, followed by Aspergillus flavi section (50.0%) and Aspergillus ochraceus section (21.4%), with the most contaminated samples being Coix seeds. Similar fungal presence and frequency were encountered in spice with A. niger section group (60.0%) and A. flavi section (40.0%) as main fungi. Cumin and Pricklyash peel samples showed the highest fungal contamination. Four functional foods and three spices were found to be positive at low levels for mycotoxins including aflatoxin B1 (up to 0.26μg/kg) and ochratoxin A (OTA) (5.0μg/kg). The more frequently detected mycotoxin was AFB1 (16.7%). Copyright © 2013 Elsevier Ltd. All rights reserved.

Diversity and biological activities of the bacterial community associated with the marine sponge Phorbas tenacior (Porifera, Demospongiae).

PubMed

Dupont, S; Carré-Mlouka, A; Descarrega, F; Ereskovsky, A; Longeon, A; Mouray, E; Florent, I; Bourguet-Kondracki, M L

2014-01-01

The diversity of the cultivable microbiota of the marine sponge Phorbas tenacior frequently found in the Mediterranean Sea was investigated, and its potential as a source of antimicrobial, antioxidant and antiplasmodial compounds was evaluated. The cultivable bacterial community was studied by isolation, cultivation and 16S rRNA gene sequencing. Twenty-three bacterial strains were isolated and identified in the Proteobacteria (α or γ classes) and Actinobacteria phyla. Furthermore, three different bacterial morphotypes localized extracellularly within the sponge tissues were revealed by microscopic observations. Bacterial strains were assigned to seven different genera, namely Vibrio, Photobacterium, Shewanella, Pseudomonas, Ruegeria, Pseudovibrio and Citricoccus. The strains affiliated to the same genus were differentiated according to their genetic dissimilarities using random amplified polymorphic DNA (RAPD) analyses. Eleven bacterial strains were selected for evaluation of their bioactivities. Three isolates Pseudovibrio P1Ma4, Vibrio P1MaNal1 and Citricoccus P1S7 revealed antimicrobial activity; Citricoccus P1S7 and Vibrio P1MaNal1 isolates also exhibited antiplasmodial activity, while two Vibrio isolates P1Ma8 and P1Ma5 displayed antioxidant activity. These data confirmed the importance of Proteobacteria and Actinobacteria associated with marine sponges as a reservoir of bioactive compounds. This study presents the first report on the diversity of the cultivable bacteria associated with the marine sponge Phorbas tenacior, frequently found in the Mediterranean Sea. Evaluation of the antiplasmodial, antimicrobial and antioxidant activities of the isolates has been investigated and allowed to select bacterial strains, confirming the importance of Proteobacteria and Actinobacteria as sources of bioactive compounds. © 2013 The Society for Applied Microbiology.

Bacteriological analysis of the digestive tube of the mud snail (Bullacta exarata Philippi) and its rearing shoal

NASA Astrophysics Data System (ADS)

Wang, Guoliang; Zheng, Tianlun; Lu, Tongxia; Wang, Yinong; Yu, Hong; Jin, Shan

2002-10-01

The bacterial flora in the digestive tube of Bullacta exarata Philippi and its rearing shoal were investigated. A total of 157 strains of heterotrophic bacteria, isolated from crop, stomach intestine and other parts of the digestive tube, mainly belong to the genera Photobacterium, Bacillus, Pseudomonas Vibrio and some genera of the family Enterobacteriaceae. There are significantly more varieties of bacteria in crop than in stomach and intestine. A total of 173 strains of bacteria were isolated from the rearing shoal, belonging to 13 genera. The 5 predominant genera, such as Bacillus and Photobacterium, are the same as those in the digestive tube, but greatly differ in percentages. The number of heterotrophic bacteria and Vibrio in rearing shoal change in line with the alteration of the temperature, and are significantly affected by the use of pesticides.

Phytate Degradation by Fungi and Bacteria that Inhabit Sawdust and Coffee Residue Composts

PubMed Central

Eida, Mohamed Fathallh; Nagaoka, Toshinori; Wasaki, Jun; Kouno, Kenji

2013-01-01

Phytate is the primary source of organic phosphorus, but it cannot be directly utilized by plants and is strongly adsorbed by the soil, reducing bioavailability. Composting is a process used to improve the bioavailability of phytate in organic wastes through degradation by microorganisms. In this study, we aimed to investigate the phytate-degrading ability of fungi and bacteria that inhabit sawdust compost and coffee residue compost, and their contribution to the composting process. In the plate assay, the fungi that formed clear zones around their colonies belonged to the genera Mucor, Penicillium, Galactomyces, Coniochaeta, Aspergillus, and Fusarium, while the bacteria belonged to the genera Pseudomonas, Enterobacter, Chitinophaga, and Rahnella. Eight fungal isolates (genera Mucor, Penicillium, Galactomyces, and Coniochaeta) and four bacterial isolates (genera Pseudomonas, Enterobacter, and Rahnella) were selected to evaluate phytase activity in their liquid culture and their ability to degrade phytate in organic materials composed of mushroom media residue and rice bran. The selected fungi degraded phytate in organic materials to varying degrees. Penicillium isolates showed the highest degradation ability and Coniochaeta isolate exhibited relatively high degradation ability. The clear zone diameters of these fungal isolates displayed significantly positive and negative correlations with inorganic and phytate phosphorus contents in the organic materials after incubation, respectively; however, none of the selected bacteria reduced phytate phosphorus in organic materials. It is therefore possible that fungi are major contributors to phytate degradation during composting. PMID:23100024

Airborne Bacteria in an Urban Environment

PubMed Central

Mancinelli, Rocco L.; Shulls, Wells A.

1978-01-01

Samples were taken at random intervals over a 2-year period from urban air and tested for viable bacteria. The number of bacteria in each sample was determined, and each organism isolated was identified by its morphological and biochemical characteristics. The number of bacteria found ranged from 0.013 to 1.88 organisms per liter of air sampled. Representatives of 19 different genera were found in 21 samples. The most frequently isolated organisms and their percent of occurence were Micrococcus (41%), Staphylococcus (11%), and Aerococcus (8%). The bacteria isolated were correlated with various weather and air pollution parameters using the Pearson product-moment correlation coefficient method. Statistically significant correlations were found between the number of viable bacteria isolated and the concentrations of nitric oxide (−0.45), nitrogen dioxide (+0.43), and suspended particulate pollutants (+0.56). Calculated individually, the total number of Micrococcus, Aerococcus, and Staphylococcus, number of rods, and number of cocci isolated showed negative correlations with nitric oxide and positive correlations with nitrogen dioxide and particulates. Statistically significant positive correlations were found between the total number of rods isolated and the concentration of nitrogen dioxide (+0.54) and the percent relative humidity (+0.43). The other parameters tested, sulfur dioxide, hydrocarbons, and temperature, showed no significant correlations. Images PMID:677875

Antimicrobial and Herbal Drug Resistance in Enteric Bacteria Isolated from Faecal Droppings of Common House Lizard/Gecko (Hemidactylus frenatus).

PubMed

Singh, Bhoj R; Singh, Vidya; Ebibeni, N; Singh, Raj K

2013-01-01

From 194 faecal dropping samples of common house geckos collected from offices (60), houses (88), integrated farm units (IFS,18) and hostels, guest houses, and dining rooms of different canteen/mess (HGM, 28), 326 bacterial isolates of enteric bacteria belonging to 17 genera and 34 species were detected. Escherichia coli were the most frequently (39) isolated followed by Citrobacter freundii (33), Klebsiella pneumonia (27), Salmonella indica (12), Enterobacter gergoviae (12), and Ent. agglomerans (11). Other important bacteria isolated from gecko droppings were Listonella damsela (2), Raoultella terrigena (3), S. salamae (2), S. houtenae (3), Edwardsiella tarda (4), Edwardsiella hoshinae (1), and Klebsiella oxytoca (2). Of the 223 isolates tested for antimicrobial drug sensitivity, 27 (12.1%) had multiple drug resistance (MDR). None of the salmonellae or edwardsiellae had MDR however, MDR strains were significantly more common among Escherichia spp. (P = 1.9 × 10(-5)) and isolates from IFS units (P = 3.58 × 10(-23)). The most effective herbal drug, Ageratum conyzoides extract, inhibited growth of only 27.8% of strains tested followed by ethanolic extract of Zanthoxylum rhetsa (13.9%), eucalyptus oil (5.4%), patchouli oil (5.4%), lemongrass oil (3.6%), and sandalwood oil (3.1%), and Artemisia vulgaris essential oil (3.1%).

Culturable bacterial diversity at the Princess Elisabeth Station (Utsteinen, Sør Rondane Mountains, East Antarctica) harbours many new taxa.

PubMed

Peeters, Karolien; Ertz, Damien; Willems, Anne

2011-07-01

We studied the culturable heterotrophic bacterial diversity present at the site of the new Princess Elisabeth Station at Utsteinen (Dronning Maud Land, East Antarctica) before construction. About 800 isolates were picked from two terrestrial microbial mat samples after incubation on several growth media at different temperatures. They were grouped using rep-PCR fingerprinting and partial 16S rRNA gene sequencing. Phylogenetic analysis of the complete 16S rRNA gene sequences of 93 representatives showed that the isolates belonged to five major phyla: Actinobacteria, Bacteroidetes, Proteobacteria, Firmicutes and Deinococcus-Thermus. Isolates related to the genus Arthrobacter were the most prevalent whereas the genera Hymenobacter, Deinococcus, Cryobacterium and Sphingomonas were also recovered in high numbers in both samples. A total of 35 different genera were found, the majority of which has previously been reported from Antarctica. For the genera Aeromicrobium, Aurantimonas, Rothia, Subtercola, Tessaracoccus and Xylophilus, this is the first report in Antarctica. In addition, numerous potential new species and new genera were recovered; many of them currently restricted to Antarctica, particularly in the phyla Bacteroidetes and Deinococcus-Thermus. Copyright © 2011 Elsevier GmbH. All rights reserved.

Identification of fungal phytopathogens using Fourier transform infrared-attenuated total reflection spectroscopy and advanced statistical methods

NASA Astrophysics Data System (ADS)

Salman, Ahmad; Lapidot, Itshak; Pomerantz, Ami; Tsror, Leah; Shufan, Elad; Moreh, Raymond; Mordechai, Shaul; Huleihel, Mahmoud

2012-01-01

The early diagnosis of phytopathogens is of a great importance; it could save large economical losses due to crops damaged by fungal diseases, and prevent unnecessary soil fumigation or the use of fungicides and bactericides and thus prevent considerable environmental pollution. In this study, 18 isolates of three different fungi genera were investigated; six isolates of Colletotrichum coccodes, six isolates of Verticillium dahliae and six isolates of Fusarium oxysporum. Our main goal was to differentiate these fungi samples on the level of isolates, based on their infrared absorption spectra obtained using the Fourier transform infrared-attenuated total reflection (FTIR-ATR) sampling technique. Advanced statistical and mathematical methods: principal component analysis (PCA), linear discriminant analysis (LDA), and k-means were applied to the spectra after manipulation. Our results showed significant spectral differences between the various fungi genera examined. The use of k-means enabled classification between the genera with a 94.5% accuracy, whereas the use of PCA [3 principal components (PCs)] and LDA has achieved a 99.7% success rate. However, on the level of isolates, the best differentiation results were obtained using PCA (9 PCs) and LDA for the lower wavenumber region (800-1775 cm-1), with identification success rates of 87%, 85.5%, and 94.5% for Colletotrichum, Fusarium, and Verticillium strains, respectively.

Potential of endophytic fungi as biocontrol agents of Duponchelia fovealis (Zeller) (Lepidoptera:Crambidae).

PubMed

Amatuzzi, R F; Cardoso, N; Poltronieri, A S; Poitevin, C G; Dalzoto, P; Zawadeneak, M A; Pimentel, I C

2017-11-09

This study reports the first assessment of endophytic fungi isolated from strawberry leaves and selection of isolates for the control of Duponchelia fovealis, a new pest of strawberries. A total of 400 strawberry leaves of the cultivar 'Albion' were collected in four commercial farms. Leaves were disinfected, cut in fragments, and placed on Petri dishes containing potato dextrose agar media with tetracycline and incubated for 30 days. Following this time, 517 fungal colonies were isolated, and thirteen genera were identified: Cladosporium, Aspergillus, Nigrospora, Fusarium, Trichoderma, Chaetomium, Alternaria, Paecilomyces, Penicillium, Ulocladium, Bipolaris, Diaporthe, and Phoma. Eight isolates belonging to the genera Aspergillus, Diaporthe, Paecilomyces, and Cladosporium were selected for pathogenicity bioassays against third instar larvae of D. fovealis. Isolates of Paecilomyces induced the highest mortality rates.

Microbiota from Litopenaeus vannamei: digestive tract microbial community of Pacific white shrimp (Litopenaeus vannamei).

PubMed

Tzuc, Jaqueline Tuyub; Escalante, Diana Rendíz; Rojas Herrera, Rafael; Gaxiola Cortés, Gabriela; Ortiz, Maria Leticia Arena

2014-01-01

Bacteria capable of producing different extracellular enzymes of potential relevance in digestive processes were isolated from the stomach, hepatopancreas and intestine of Pacific white shrimp Litopenaeus vannamei. A total of 64 strains with proteolytic activity were isolated and grouped into 16 clusters based on morphological characteristics: 4 groups were isolated from the intestine; 5 from the hepatopancreas; and 7 from the stomach. Molecular methods (16S rRNA gene amplification and sequencing) and phenotypic criteria (Gram stain, catalase and oxidase tests, cell and colony morphology) were used to identify strains, which corresponded to Pseudoalteromonas and Vibrio genera. These genera are reported to form part of the digestive tract microbial community in shrimp. Both genera were isolated from all three tested tissues. One member of each morphologic group was selected for analysis of the presence of amylases, lipases/esterases and chitinases. Most of the strains had all the tested enzymes, indicating that the L. vannamei digestive tract microbiotic flora includes groups which have the potential to contribute to the degradation of dietary components.

Effect of Sample Preparation on the Discrimination of Bacterial Isolates Cultured in Liquid Nutrient Media Using Laser-Induced Breakdown Spectroscopy (LIBS).

PubMed

Gamble, Gary R; Park, Bosoon; Yoon, Seung-Chul; Lawrence, Kurt C

2016-03-01

Laser-induced breakdown spectroscopy (LIBS) is used as the basis for discrimination between two genera of gram-negative bacteria and two genera of gram-positive bacteria representing pathogenic threats commonly found in poultry processing rinse waters. Because LIBS-based discrimination relies primarily upon the relative proportions of inorganic cell components including Na, K, Mg, and Ca, this study aims to determine the effects of trace mineral content and pH found in the water source used to isolate the bacteria upon the reliability of the resulting discriminant analysis. All four genera were cultured using tryptic soy agar (TSA) as the nutrient medium, and were grown under identical environmental conditions. The only variable introduced is the source water used to isolate the cultured bacteria. Cultures of each bacterium were produced using deionized (DI) water under two atmosphere conditions, reverse osmosis (RO) water, tap water, phosphate buffered saline (PBS) water, and TRIS buffered water. After 3 days of culture growth, the bacteria were centrifuged and washed three times in the same water source. Bacteria were then freeze dried, mixed with microcrystalline cellulose, and a pellet was made for LIBS analysis. Principal component analysis (PCA) was used to extract related variations in LIBS spectral data among the four bacteria genera and six water types used to isolate the bacteria, and Mahalanobis discriminant analysis (MDA) was used for classification. Results indicate not only that the four genera can be discriminated from each other in each water type, but that each genus can be discriminated by water type used for isolation. It is concluded that in order for LIBS to be a reliable and repeatable method for discrimination of bacteria grown in liquid nutrient media, care must be taken to insure that the water source used in purification of the culture be precisely controlled regarding pH, ionic strength, and proportionate amounts of mineral cations present. © The Author(s) 2016.

Identities of Arthrobacter spp. and Arthrobacter-Like Bacteria Encountered in Human Clinical Specimens▿

PubMed Central

Mages, Irene S.; Frodl, Reinhard; Bernard, Kathryn A.; Funke, Guido

2008-01-01

After the initial description of Arthrobacter spp. isolated from clinical specimens in the mid-1990s, very few further reports on Arthrobacter spp. have appeared in the clinical microbiology literature. The aim of the present study was to elucidate the distribution of Arthrobacter spp. and Arthrobacter-like bacteria encountered in clinical specimens by studying 50 consecutively isolated or received strains of large-colony-forming, whiteish-grayish, non-cheese-like-smelling, nonfermentative gram-positive rods by applying phenotypic methods as well as 16S rRNA gene sequencing. We observed a very heterogenous distribution, with the 50 strains belonging to 20 different taxa and each of 13 strains as a single representative of its particular taxon. Thirty-eight strains represented true Arthrobacter strains, 7 strains belonged to the genus Brevibacterium, 2 were Microbacterium species, and each of 3 single strains was a member of the rarely encountered genera Pseudoclavibacter, Leucobacter, and Brachybacterium, respectively. A. cumminsii (n = 14) and A. oxydans (n = 11) were the most frequently found species. The present report describes the first three A. aurescens strains isolated from human clinical specimens. Comprehensive antimicrobial susceptibility data are given for the 38 Arthrobacter isolates. PMID:18650355

Analysis of endophytic fungi in roots of Santalum album Linn. and its host plant Kuhnia rosmarinifolia Vent.*

PubMed Central

Sun, Si-sheng; Chen, Xiao-mei; Guo, Shun-xing

2014-01-01

Santalum album Linn. is an evergreen and hemi-parasitic tree, the heartwood-sandalwood of which was used during a long history in traditional Chinese medicine. Kuhnia rosmarinifolia Vent. is a good host for 1- or 2-year-old growing S. album. The interaction between S. album and K. rosmarinifolia is still little known. Many studies have been carried out on a number of plants for identification and diversity of endophytes. In this study, in total 25 taxa of endophytic fungi were isolated from the roots of S. album and the roots of K. rosmarinifolia. The most frequently isolated genera were Penicillium sp. 1 and Fusarium sp. 1 in the roots of S. album and K. rosmarinifolia, respectively. S. album is a root parasite of K. rosmarinifolia. The interesting result is that they apparently do not share the same endophytic fungi isolates. This study for the first time explored the content of endophytic fungi from S. album and K. rosmarinifolia, which provides important information for further studies. PMID:24510703

Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry: a new possibility for the identification and typing of anaerobic bacteria.

PubMed

Nagy, Elizabeth

2014-01-01

Anaerobic bacteria predominate in the normal flora of humans and are important, often life-threatening pathogens in mixed infections originating from the indigenous microbiota. The isolation and identification of anaerobes by phenotypic and DNA-based molecular methods at a species level is time-consuming and laborious. Following the successful adaptation of the matrix-assisted laser desorption/ionization time-of-flight mass spectrometry for the routine laboratory identification of bacteria, the extensive development of a database has been initiated to use this method for the identification of anaerobic bacteria. Not only frequently isolated anaerobic species, but also newly recognized and taxonomically rearranged genera and species can be identified using direct smear samples or whole-cell protein extraction, and even phylogenetically closely related species can be identified correctly by means of matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. Typing of anaerobic bacteria on a subspecies level, determination of antibiotic resistance and direct identification of blood culture isolates will revolutionize anaerobe bacteriology in the near future.

Identification and catabolic activity of well-derived gasoline-degrading bacteria from a contaminated aquifer.

PubMed Central

Ridgway, H F; Safarik, J; Phipps, D; Carl, P; Clark, D

1990-01-01

Approximately 300 gasoline-degrading bacteria were isolated from well water and core material from a shallow coastal aquifer contaminated with unleaded gasoline. Identification of 244 isolates revealed four genera: Pseudomonas, Alcaligenes, Nocardia, and Micrococcus, with pseudomonads making up 86.9% of bacteria identified. A total of 297 isolates was sorted into 111 catabolic groups on the basis of aerobic growth responses on 15 gasoline hydrocarbons. Each test hydrocarbon was degraded by at least one isolate. Toluene, p-xylene, ethylbenzene, and 1,2,4-trimethylbenzene were most frequently utilized as growth substrates, whereas cyclic and branched alkanes were least utilized. Most isolates were able to grow on 2 or 3 different hydrocarbons, and nearly 75% utilized toluene as a sole source of carbon and energy. Isolates were remarkably specific for hydrocarbon usage, often catabolizing only one of several closely related compounds. A subset of 220 isolates was sorted into 51 groups by polyacrylamide gel electrophoresis. Pseudomonas aeruginosa was partitioned into 16 protein-banding groups (i.e., subspecies) whose catabolic activities were largely restricted to substituted aromatics. Different members of subspecies groups defined by protein-banding pattern analysis often exhibited different growth responses on the same hydrocarbon, implying marked strain diversity. The catabolic activities of well-derived, gasoline-degrading bacteria associated with this contaminated aquifer are consonant with in situ adaptation at the site. PMID:2268163

Identification and catabolic activity of well-derived gasoline-degrading bacteria from a contaminated aquifer

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ridgway, H.F.; Safarik, J.; Phipps, D.

1990-11-01

Approximately 300 gasoline-degrading bacteria were isolated from well water and core material from a shallow coastal aquifer contaminated with unleaded gasoline. Identification of 244 isolates revealed four genera: Pseudomonas, Alcaligenes, Nocardia, and Micrococcus, with pseudomonads making up 86.9% of bacteria identified. A total of 297 isolates was sorted into 111 catabolic groups on the basis of aerobic growth responses on 15 gasoline hydrocarbons. Each test hydrocarbon was degraded by at least one isolate. Toluene, p-xylene, ethylbenzene, and 1,2,4-trimethylbenzene were most frequently utilized as growth substrates, whereas cyclic and branched alkanes were least utilized. Most isolates were able to grow onmore » 2 or 3 different hydrocarbons, and nearly 75% utilized toluene as a sole source of carbon and energy. Isolates were remarkably specific for hydrocarbon usage, often catabolizing only one of several closely related compounds. A subset of 220 isolates was sorted into 51 groups by polyacrylamide gel electrophoresis. Pseudomonas aeruginosa was partitioned into 16 protein-banding groups (i.e., subspecies) whose catabolic activities were largely restricted to substituted aromatics. Different members of subspecies groups defined by protein-banding pattern analysis often exhibited different growth responses on the same hydrocarbon, implying marked strain diversity. The catabolic activities of well-derived, gasoline-degrading bacteria associated with this contaminated aquifer are consonant with in situ adaptation at the site.« less

Lead (Pb) bioaccumulation; genera Bacillus isolate S1 and SS19 as a case study

NASA Astrophysics Data System (ADS)

Arifiyanto, Achmad; Apriyanti, Fitria Dwi; Purwaningsih, Puput; Kalqutny, Septian Hary; Agustina, Dyah; Surtiningsih, Tini; Shovitri, Maya; Zulaika, Enny

2017-06-01

Lead (Pb) includes a group of large heavy metal in nature was toxic either on animal or human and did not provide an advantage function biologically. Bacillus isolates S1 and SS19 known resistant to lead up to 50 mg / L PbCl2. In this research will be examined whether genera Bacillus isolates S1 and SS19 could accumulate metal lead (Pb), their capability in accumulating and profile protein differences when the bacteria genera Bacillus isolates S1 and SS19 get exposed metal lead (Pb). Inoculum at age ± 9 hours are used, with a Nutrient Broth (NB) containing 50, 75 and 100 mg / L PbCl2. Inductively Coupled Plasma Atomic Emission Spectrometry (ICP) used to assessed Pb2+ concentrations. Bioaccumulation levels of Pb2+ by Bacillus isolate S1 and SS19 related to the distinction of beginning concentration to the final concentration. Bacillus isolate S1 achieved 53% and 51% bioaccumulation efficiency rate in lead presence concentration (75 and 100 mg/L) and 51% (50 mg/L). Another way Bacillus isolate SS19 was able to accumulate 57% (50 mg/L PbCl2) and kept stable on 36% bioaccumulation efficiency rate (75 and 100 mg/L PbCl2). Regarding SDS-PAGE electrophoresis protein profile result, protein in ± 127 kDa, molecule mass detected in the presence of Lead for Bacillus isolate S1.

Mycobiota and mycotoxins in bee pollen collected from different areas of Slovakia.

PubMed

Kačániová, Miroslava; Juráček, Miroslav; Chlebo, Róbert; Kňazovická, Vladimíra; Kadasi-Horáková, Miriam; Kunová, Simona; Lejková, Jadža; Haščík, Peter; Mareček, Ján; Simko, Milan

2011-01-01

Contamination by microscopic fungi and mycotoxins in different bee pollen samples, which were stored under three different ways of storing as freezing, drying and UV radiation, was investigated. During spring 2009, 45 samples of bee-collected pollen were gathered from beekeepers who placed their bee colonies on monocultures of sunflower, rape and poppy fields within their flying distance. Bee pollen was collected from bees' legs by special devices placed at the entrance to hives. Samples were examined for the concentration and identification of microscopic fungi able to grow on Malt and Czapek-Dox agar and mycotoxins content [deoxynivalenol (DON), T-2 toxin (T-2), zearalenone (ZON) and total aflatoxins (AFL), fumonisins (FUM), ochratoxins (OTA)] by direct competitive enzyme-linked immunosorbent assays (ELISA). The total number of microscopic fungi in this study ranged from 2.98 ± 0.02 in frozen sunflower bee pollen to 4.06 ± 0.10 log cfu.g(-1) in sunflower bee pollen after UV radiation. In this study, 449 isolates belonging to 21 fungal species representing 9 genera were found in 45 samples of bee pollen. The total isolates were detected in frozen poppy pollen 29, rape pollen 40, sunflower pollen 80, in dried poppy pollen 12, rape pollen 36, sunflower 78, in poppy pollen after UV radiation treatment 54, rape 59 and sunflower 58. The most frequent isolates of microscopic fungi found in bee pollen samples of all prevalent species were Mucor mucedo (49 isolates), Alternaria alternata (40 isolates), Mucor hiemalis (40 isolates), Aspergillus fumigatus (33 isolates) and Cladosporium cladosporioides (31 isolates). The most frequently found isolates were detected in sunflower bee pollen frozen (80 isolates) and the lowest number of isolates was observed in poppy bee pollen dried (12 isolates). The most prevalent mycotoxin of poppy bee pollen was ZON (361.55 ± 0.26 μg.kg(-1)), in rape bee pollen T-2 toxin (265.40 ± 0.18 μg.kg(-1)) and in sunflower bee pollen T-2 toxin (364.72 ± 0.13 μg.kg(-1)) in all cases in frozen samples.

Genetic analysis of Phytophthora nicotianae populations from different hosts using microsatellite markers

USDA-ARS?s Scientific Manuscript database

Two hundred thirty-one isolates of P. nicotianae representing 14 populations from different host genera, including agricultural crops (Citrus, Nicotiana, and Lycopersicon), potted ornamental species in nurseries (Lavandula, Convolvulus, Myrtus, Correa and Ruta) and other plant genera of lesser econo...

Bergbambos and Oldeania, new genera of African bamboos (Poaceae, Bambusoideae)

PubMed Central

Stapleton, Chris M. A.

2013-01-01

Abstract Two new monotypic genera, Bergbambos and Oldeania are described for African temperate bamboo species in the tribe Arundinarieae, after a comparison of their morphological characteristics with those of similar species from Asia. Morphological differences are supported by their isolated geographical distributions. Molecular evidence does not support the inclusion of these species in related Asian genera, recognising them instead as distinct lineages. New combinations Bergbambos tessellata and Oldeania alpina are made. PMID:24198715

Fungal dissemination by housefly (Musca domestica L.) and contamination of food commodities in rural areas of South Africa.

PubMed

Phoku, J Z; Barnard, T G; Potgieter, N; Dutton, M F

2016-01-18

Several insects that act as vectors, including houseflies (Musca domestica L.), are often considered to be an important source of fungal contamination in human foods. Houseflies are also involved in the transmission of bacterial pathogens that may pose a serious hazard to human health. Thus, the rural population of South Africa, as typified by that in the Gauteng Province investigated in this study, is at high risk from fungal exposure disseminated by houseflies and it is therefore important to assess the role of flies in contaminating various food commodities. Eighty four samples of houseflies (captured from households and pit toilets) were studied for their potential to carry fungal spores into food commodities. The fungi occurring in samples of raw maize (15) and porridge (19) were also assessed. Fungal isolates were identified based on morphological characteristics by conventional identification methods. Fifteen genera of fungi were isolated and identified, of which Aspergillus, Fusarium, Penicillium, Cladosporium, Moniliella and Mucor were the most prevalent in all three sample types analysed. The incidence rates of fungal contamination per total fungal count isolated in houseflies, maize and porridge were recorded with mean fungal load of 2×10(8) CFU/ml, 1×10(7)CFU/g and 2×10(7)CFU/g respectively. Additionally, A. flavus, A. parasiticus, F. verticillioides, F. proliferatum, P. verrucosum, P. aurantiogriseum and M. suaveolens were the most frequent fungal isolates in houseflies with incidence rate of 34%, 11%, 27%, 21%, 22%, 17% and 32% respectively. F. verticillioides, A. flavus, A. niger and P. oslonii were the most prevalent species contaminating porridge and maize with incidence rate of 23%, 32%, 16% and 28% in maize samples, while incidence rates of 59%, 15% and 29% were recorded in porridge samples with the exception of F. verticillioides. The prevalence of these genera of fungi may pose serious health risks. Copyright © 2015 Elsevier B.V. All rights reserved.

The Black Yeast Exophiala dermatitidis and Other Selected Opportunistic Human Fungal Pathogens Spread from Dishwashers to Kitchens

PubMed Central

Zupančič, Jerneja; Novak Babič, Monika; Zalar, Polona; Gunde-Cimerman, Nina

2016-01-01

We investigated the diversity and distribution of fungi in nine different sites inside 30 residential dishwashers. In total, 503 fungal strains were isolated, which belong to 10 genera and 84 species. Irrespective of the sampled site, 83% of the dishwashers were positive for fungi. The most frequent opportunistic pathogenic species were Exophiala dermatitidis, Candida parapsilosis sensu stricto, Exophiala phaeomuriformis, Fusarium dimerum, and the Saprochaete/Magnusiomyces clade. The black yeast E. dermatitidis was detected in 47% of the dishwashers, primarily at the dishwasher rubber seals, at up to 106 CFU/cm2; the other fungi detected were in the range of 102 to 105 CFU/cm2. The other most heavily contaminated dishwasher sites were side nozzles, doors and drains. Only F. dimerum was isolated from washed dishes, while dishwasher waste water contained E. dermatitidis, Exophiala oligosperma and Sarocladium killiense. Plumbing systems supplying water to household appliances represent the most probable route for contamination of dishwashers, as the fungi that represented the core dishwasher mycobiota were also detected in the tap water. Hot aerosols from dishwashers contained the human opportunistic yeast C. parapsilosis, Rhodotorula mucilaginosa and E. dermatitidis (as well as common air-borne genera such as Aspergillus, Penicillium, Trichoderma and Cladosporium). Comparison of fungal contamination of kitchens without and with dishwashers revealed that virtually all were contaminated with fungi. In both cases, the most contaminated sites were the kitchen drain and the dish drying rack. The most important difference was higher prevalence of black yeasts (E. dermatitidis in particular) in kitchens with dishwashers. In kitchens without dishwashers, C. parapsilosis strongly prevailed with negligible occurrence of E. dermatitidis. F. dimerum was isolated only from kitchens with dishwashers, while Saprochaete/Magnusiomyces isolates were only found within dishwashers. We conclude that dishwashers represent a reservoir of enriched opportunistic pathogenic species that can spread from the dishwasher into the indoor biome. PMID:26867131

Identification of coliform genera recovered from water using different technologies.

PubMed

Fricker, C R; Eldred, B J

2009-12-01

Methods for the detection of coliforms in water have changed significantly in recent years with procedures incorporating substrates for the detection of beta-d-galactosidase becoming more widely used. This study was undertaken to determine the range of coliform genera detected with methods that rely on lactose fermentation and compare them to those recovered using methods based upon beta-d-galactosidase. Coliform isolates were recovered from sewage-polluted water using m-endo, membrane lauryl sulfate broth, tergitol TTC agar, Colilert-18, ChromoCult and ColiScan for primary isolation. Organisms were grouped according to whether they had been isolated based upon lactose fermentation or beta-d-galactosidase production. A wide range of coliform genera were detected using both types of methods. There was considerable overlap between the two groups, and whilst differences were seen between the genera isolated with the two method types, no clear pattern emerged. Substantial numbers of 'new' coliforms (e.g. Raoutella spp.) were recovered using both types of methods. The results presented here confirm that both methods based on lactose fermentation or detection of beta-d-galactosidase activity recover a range of coliform organisms. Any suggestion that only methods which are based upon fermentation of lactose recover organisms of public health or regulatory significance cannot be substantiated. Furthermore, the higher recovery of coliform organisms from sewage-polluted water using methods utilizing beta-d-galactosidase-based methods does not appear to be because of the recovery of substantially more 'new' coliforms.

[Toxocara canis eggs as bait for soil fungus in a subtropical city].

PubMed

Bojanich, María Viviana; Sarmiento, María Mercedes; Giusiano, Gustavo; Mangiaterra, Magdalena; Basualdo, Juan Ángel

2015-01-01

The use of different isolation techniques allows the recovery of fungi based on their ability to use selective substrates. The sprinkle method is a technique for the recovery of nematophagous fungi in the soil. These fungi are natural predators of nematodes and are widely distributed in nature. To detect possible fungi with nematophagous ability in the soil of city parks in Corrientes (Argentina). The soil samples were taken from an area of ground between two trees and to no more than 2cm deep. The isolation was performed according to the sprinkle method with Toxocara canis eggs as bait. Eighteen soil samples were collected, and 6 genera and 8 species of fungi were isolated. The sprinkle method, simple and efficient, has the advantage of using a small amount of untreated soil for the isolation of fungi that can grow on the eggs of geohelminths. The genera Bipolaris, Fusarium, Purpureocillium, Curvularia, Phoma and Scytalidium were isolated in this study. No other studies describing the interaction between the genera Curvularia, Phoma and Scytalidium with nematode eggs have been found in the literature, thus more studies are required to determine what is their real action on these eggs. Copyright © 2014 Revista Iberoamericana de Micología. Published by Elsevier Espana. All rights reserved.

Diversity, Biogeography, and Biodegradation Potential of Actinobacteria in the Deep-Sea Sediments along the Southwest Indian Ridge

PubMed Central

Chen, Ping; Zhang, Limin; Guo, Xiaoxuan; Dai, Xin; Liu, Li; Xi, Lijun; Wang, Jian; Song, Lei; Wang, Yuezhu; Zhu, Yaxin; Huang, Li; Huang, Ying

2016-01-01

The phylum Actinobacteria has been reported to be common or even abundant in deep marine sediments, however, knowledge about the diversity, distribution, and function of actinobacteria is limited. In this study, actinobacterial diversity in the deep sea along the Southwest Indian Ridge (SWIR) was investigated using both 16S rRNA gene pyrosequencing and culture-based methods. The samples were collected at depths of 1662–4000 m below water surface. Actinobacterial sequences represented 1.2–9.1% of all microbial 16S rRNA gene amplicon sequences in each sample. A total of 5 actinobacterial classes, 17 orders, 28 families, and 52 genera were detected by pyrosequencing, dominated by the classes Acidimicrobiia and Actinobacteria. Differences in actinobacterial community compositions were found among the samples. The community structure showed significant correlations to geochemical factors, notably pH, calcium, total organic carbon, total phosphorus, and total nitrogen, rather than to spatial distance at the scale of the investigation. In addition, 176 strains of the Actinobacteria class, belonging to 9 known orders, 18 families, and 29 genera, were isolated. Among these cultivated taxa, 8 orders, 13 families, and 15 genera were also recovered by pyrosequencing. At a 97% 16S rRNA gene sequence similarity, the pyrosequencing data encompassed 77.3% of the isolates but the isolates represented only 10.3% of the actinobacterial reads. Phylogenetic analysis of all the representative actinobacterial sequences and isolates indicated that at least four new orders within the phylum Actinobacteria were detected by pyrosequencing. More than half of the isolates spanning 23 genera and all samples demonstrated activity in the degradation of refractory organics, including polycyclic aromatic hydrocarbons and polysaccharides, suggesting their potential ecological functions and biotechnological applications for carbon recycling. PMID:27621725

Enhanced Detoxification of Arsenic Under Carbon Starvation: A New Insight into Microbial Arsenic Physiology.

PubMed

Nandre, Vinod S; Bachate, Sachin P; Salunkhe, Rahul C; Bagade, Aditi V; Shouche, Yogesh S; Kodam, Kisan M

2017-05-01

Nutrient availability in nature influenced the microbial ecology and behavior present in existing environment. In this study, we have focused on isolation of arsenic-oxidizing cultures from arsenic devoid environment and studied effect of carbon starvation on rate of arsenite oxidation. In spite of the absence of arsenic, a total of 40 heterotrophic, aerobic, arsenic-transforming bacterial strains representing 18 different genera were identified. Nineteen bacterial species were isolated from tannery effluent and twenty-one from tannery soil. A strong co-relation between the carbon starvation and arsenic oxidation potential of the isolates obtained from the said niche was observed. Interestingly, low carbon content enhanced the arsenic oxidation ability of the strains across different genera in Proteobacteria obtained. This represents the impact of physiological response of carbon metabolism under metal stress conditions. Enhanced arsenic-oxidizing ability of the strains was validated by the presence of aio gene and RT-PCR, where 0.5- to 26-fold up-regulation of arsenite oxidase gene in different genera was observed. The cultures isolated from tannery environment in this study show predominantly arsenic oxidation ability. This detoxification of arsenic in lack of carbon content can aid in effective in situ arsenic bioremediation.

Bioprospecting from cultivable bacterial communities of marine sediment and invertebrates from the underexplored Ubatuba region of Brazil.

PubMed

Tangerina, Marcelo M P; Correa, Hebelin; Haltli, Brad; Vilegas, Wagner; Kerr, Russell G

2017-01-01

Shrimp fisheries along the Brazilian coast have significant environmental impact due to high by-catch rates (21 kg per kilogram of shrimp). Typically discarded, by-catch contains many invertebrates that may host a great variety of bacterial genera, some of which may produce bioactive natural products with biotechnological applications. Therefore, to utilize by-catch that is usually discarded we explored the biotechnological potential of culturable bacteria of two abundant by-catch invertebrate species, the snail Olivancillaria urceus and the sea star Luidia senegalensis. Sediment from the collection area was also investigated. Utilizing multiple isolation approaches, 134 isolates were obtained from the invertebrates and sediment. Small-subunit rRNA (16S) gene sequencing revealed that the isolates belonged to Proteobacteria, Firmicutes and Actinobacteria phyla and were distributed among 28 genera. Several genera known for their capacity to produce bioactive natural products (Micromonospora, Streptomyces, Serinicoccus and Verrucosispora) were retrieved from the invertebrate samples. To query the bacterial isolates for their ability to produce bioactive metabolites, all strains were fermented and fermentation extracts profiled by UP LC-HRMS and tested for antimicrobial activity. Four strains exhibited antimicrobial activity against methicillin-resistant Staphylococcus aureus (MRSA) and Staphylococcus warneri.

Four new diterpenoid alkaloids from Aconitum japonicum subsp. subcuneatum.

PubMed

Yamashita, Hiroshi; Takeda, Keiko; Haraguchi, Machiko; Abe, Yuki; Kuwahara, Natsumi; Suzuki, Shota; Terui, Ayaka; Masaka, Takumi; Munakata, Naoko; Uchida, Mariko; Nunokawa, Masashi; Kaneda, Kyousuke; Goto, Masuo; Lee, Kuo-Hsiung; Wada, Koji

2018-01-01

Diterpenoid alkaloids with remarkable chemical properties and biological activities are frequently found in plants of the genera Aconitum, Delphinium, and Garrya. Accordingly, several diterpenoid alkaloid constituents of Aconitum and Delphinium plants as well as their derivatives exhibited cytotoxic activity against lung, prostate, nasopharyngeal, and vincristine-resistant nasopharyngeal cancer cell lines. Four new C 19 -diterpenoid alkaloids, 14-anisoyllasianine (1), 14-anisoyl-N-deethylaconine (2), N-deethylaljesaconitine A (3), and N-deethylnevadensine (4), together with 17 known C 19 - and C 20 -diterpenoid alkaloids, were isolated in a phytochemical investigation of rhizoma of Aconitum japonicum THUNB. subsp. subcuneatum (NAKAI) KADOTA. Their structures were elucidated by extensive spectroscopic methods including NMR (1D and 2D), IR, and MS (HRMS). Eight known diterpenoid alkaloids, lipoaconitine, lipomesaconitine, aconine, nevadenine, talatisamine, nevadensine, ryosenamine, and dehydrolucidusculine, were isolated the first time from A. japonicum subsp. subcuneatum. Three of the new C 19 -diterpenoid alkaloids (1, 3, 4) and six of the known diterpenoid alkaloids were evaluated for cytotoxic activity against five human tumor cell lines.

Effects of inoculating Lachnum and Cadophora isolates on the growth of Vaccinium corymbosum.

PubMed

Bizabani, Christine; Dames, Joanna

2015-12-01

The roots of ericaceous plants harbour a diversity of fungal taxa, which confer eco-physiological benefits to the host. Some of the fungi have been established to form ericoid mycorrhizal (ERM) associations and enhance plant growth in certain ericaceous genera. Although, Lachnum and Cadophora isolates have frequently been identified from the roots of this family, the status of their association and functional roles is still vague. The aims of this study were to identify Lachnum and Cadophora isolates; determine the root-fungal interactive structures formed in associations with Vaccinium corymbosum L. (blueberry) hosts and to examine inoculation effects of the fungal associates using several varieties of the blueberry. Lachnum and Cadophora were isolated and identified from Erica cerinthoides L. and Erica demmissa Klotzsch ex Benth using morphological and molecular techniques. Micropropagated blueberry varieties (Bluecrop, Elliott, Spartan, Chandler and Brightwell) were inoculated with respective fungi and plant growth evaluated. Both fungi colonised the roots and did not have any pathogenic effect. Lachnum isolate did not form any particular mycorrhizal structures whereas; Cadophora inoculated plants showed typical ericoid mycorrhizal coils. Inoculation with both fungi enhanced the shoot growth of Brightwell and Elliott varieties. However neutral effects were observed in the remaining varieties. In conclusion, Cadophora and Lachnum isolates have potential to promote growth of selected blueberry varieties. Copyright © 2015 Elsevier GmbH. All rights reserved.

Insights on the Effects of Heat Pretreatment, pH, and Calcium Salts on Isolation of Rare Actinobacteria from Karstic Caves

PubMed Central

Fang, Bao-Zhu; Salam, Nimaichand; Han, Ming-Xian; Jiao, Jian-Yu; Cheng, Juan; Wei, Da-Qiao; Xiao, Min; Li, Wen-Jun

2017-01-01

The phylum Actinobacteria is one of the most ubiquitously present bacterial lineages on Earth. In the present study, we try to explore the diversity of cultivable rare Actinobacteria in Sigangli Cave, Yunnan, China by utilizing a combination of different sample pretreatments and under different culture conditions. Pretreating the samples under different conditions of heat, setting the isolation condition at different pHs, and supplementation of media with different calcium salts were found to be effective for isolation of diverse rare Actinobacteria. During our study, a total of 204 isolates affiliated to 30 genera of phylum Actinobacteria were cultured. Besides the dominant Streptomyces, rare Actinobacteria of the genera Actinocorallia, Actinomadura, Agromyces, Alloactinosynnema, Amycolatopsis, Beutenbergia, Cellulosimicrobium, Gordonia, Isoptericola, Jiangella, Knoellia, Kocuria, Krasilnikoviella, Kribbella, Microbacterium, Micromonospora, Mumia, Mycobacterium, Nocardia, Nocardioides, Nocardiopsis, Nonomuraea, Oerskovia, Pseudokineococcus, Pseudonocardia, Rhodococcus, Saccharothrix, Streptosporangium, and Tsukamurella were isolated from these cave samples. PMID:28848538

Quantitative analysis of oxyresveratrol in different plant parts of Morus species and related Genera by HPTLC

USDA-ARS?s Scientific Manuscript database

Four aromatic compounds; oxyresveratrol (1), mulberroside A (2), cudraflavone C (3) and kuwanone J (4) were isolated from the stems of Morus rubra L. The quantitative determination of oxyresveratrol from M. rubra L., M. alba L. and related genera by high performance thin layer chromatography (HPTLC)...

Effect of sample preparation on the discrimination of bacterial isolates cultured in liquid nutrient media using laser induced breakdown spectroscopy

USDA-ARS?s Scientific Manuscript database

Laser induced breakdown spectroscopy (LIBS) is used as the basis for discrimination between 2 genera of gram-negative bacteria and 2 genera of gram-positive bacteria representing pathogenic threats commonly found in poultry processing rinse waters. Because LIBS-based discrimination relies primarily ...

Studies on the Thermophilic Actinomycetes1

PubMed Central

Tendler, M. D.; Burkholder, P. R.

1961-01-01

A total of 1,000 isolates of thermophilic actinomycetes representing two genera, Streptomyces and Thermoactinomyces, were studied. Media for cultivation and for physiological studies were designed. Differences between the two genera are noted and taxonomic criteria for the genus Thermoactinomyces are suggested. The importance of the nutritional environment to the thermophilic habit is noted. PMID:13775873

Diversity analysis of diazotrophic bacteria associated with the roots of tea (Camellia sinensis (L.) O. Kuntze).

PubMed

Gulati, Arvind; Sood, Swati; Rahi, Praveen; Thakur, Rishu; Chauhan, Sunita; Chawla, Isha

2011-06-01

The diversity elucidation by amplified ribosomal DNA restriction analysis and 16S rDNA sequencing of 96 associative diazotrophs, isolated from the feeder roots of tea on enriched nitrogen-free semisolid media, revealed the predominance of Gram-positive over Gram-negative bacteria within the Kangra valley in Himachal Pradesh, India. The Gram-positive bacteria observed belong to two taxonomic groupings; Firmicutes, including the genera Bacillus and Paenibacillus; and Actinobacteria, represented by the genus Microbacterium. The Gram-negative bacteria included alpha-Proteobacteria genera Brevundimonas, Rhizobium, and Mesorhizobium; gamma-Proteobacteria genera Pseudomonas and Stenotrophomonas; and beta-Proteobacteria genera Azospira, Burkholderia, Delftia, Herbaspirillum and Ralstonia. The low level of similarity of two isolates, with the type strains Paenibacillus xinjiangensis and Mesorhizobium albiziae, suggests the possibility of raising species novum. The bacterial strains of different phylogenetic groups exhibited distinct carbon-source utilization patterns and fatty acid methyl ester profiles. The strains differed in their nitrogenase activities with relatively high activity seen in the Gramnegative strains exhibiting the highest similarity to Azospira oryzae, Delftia lacustris and Herbaspirillum huttiense.

Isolation and characterization of endophytic taxol-producing fungi from Taxus chinensis.

PubMed

Liu, Kaihui; Ding, Xiaowei; Deng, Baiwan; Chen, Wenqiang

2009-09-01

This study investigated the endophytic fungi diversity of Taxus chinensis and screened the taxol-producing fungi in the host. A total of 115 endophytic fungi isolates obtained from bark segments of T. chinensis were grouped into 23 genera based on the morphological traits and sequence analysis of the internal transcribed spacers (ITS1-5.8S-ITS2), indicating endophytic fungi in T. chinensis are diverse and abundant. Diaporthe, Phomopsis (anamorph of Diaporthe), Acremonium, and Pezicula were the dominant genera, whereas the remaining genera were infrequent groups. The 13 representative species of the distinct genera were capable of producing taxol verified by reverse-phase high performance liquid chromatography (HPLC). Among the taxol-producing fungi, the yield of taxol produced by the Metarhizium anisopliae, H-27 was 846.1 microg l(-1) in reformative potato dextrose liquid medium, and the fungal taxol was further validated by mass spectrometry (MS). The taxol-producing fungi (92.3%) were infrequent communities, suggesting that infrequent fungi associated with T. chinensis might be a fascinating reservoir of taxol-generating fungi.

Molecular and Phenotypic Characterization of Phialemonium and Lecythophora Isolates from Clinical Samples▿

PubMed Central

Perdomo, H.; Sutton, D. A.; García, D.; Fothergill, A. W.; Gené, J.; Cano, J.; Summerbell, R. C.; Rinaldi, M. G.; Guarro, J.

2011-01-01

Several members of the fungal genera Phialemonium and Lecythophora are occasional agents of severe human and animal infections. These species are difficult to identify, and relatively little is known about their frequency in the clinical setting. The objective of this study was to characterize morphologically and molecularly, on the basis of the analysis of large-subunit ribosomal DNA sequences, a set of 68 clinical isolates presumed to belong to these genera. A total of 59 isolates were determined to be Phialemonium species (n = 32) or a related Cephalotheca species (n = 6) or Lecythophora species (n = 20) or a related Coniochaeta species (n = 1). Nine isolates identified to be Acremonium spp. or Phaeoacremonium spp. were excluded from further study. The most common species were Phialemonium obovatum and Phialemonium curvatum, followed by Lecythophora hoffmannii, Cephalotheca foveolata, and Lecythophora mutabilis. PMID:21270235

[Characterization of air mycobiota in two repositories of the National Archives of the Republic of Cuba].

PubMed

Borrego Alonso, Sofía; Perdomo Amistad, Ivette

2014-01-01

The high relative humidity and temperatures in tropical countries create favorable conditions for development of fungi that are not only a risk to human health but they can also colonize documentary support. To study the concentration of the airborne fungi in two repositories of the National Archives of the Republic of Cuba, the mycobiota deposited on different photographic supports and maps preserved in these repositories, and to determine the taxonomic characterization of the fungi isolated. The air sampling was performed using a sedimentation method, and the supports (6 pictures and 7 maps) were analyzed using moistened sterile swabs. The Cladosporium genus was predominant, followed by Aspergillus and Penicillium genera. Filamentous fungi were isolated in all the photos and maps, and yeasts were only isolated from a photographic supports and a map. We identified several species of Aspergillus and Penicillium genera, but Aspergillus niger and Aspergillus flavus predominated. Candida and Rhodotorula were the yeast genera isolated. The fungal concentration of the air demonstrated that the environments were not contaminated. From the 26 species of filamentous fungi isolated only 5 were detected in the indoor air of the repositories and on one or more of the document supports analyzed (representing a 19.3%). This shows that there is a low ecological relationship between the fungi detected in the indoor air and those that were isolated from the supports studied. Copyright © 2012 Revista Iberoamericana de Micología. Published by Elsevier Espana. All rights reserved.

Isolation and Physiological Characterization of Psychrophilic Denitrifying Bacteria from Permanently Cold Arctic Fjord Sediments (Svalbard, Norway)

NASA Technical Reports Server (NTRS)

Canion, Andy; Prakash, Om; Green, Stefan J.; Jahnke, Linda; Kuypers, Marcel M. M.; Kostka, Joel E.

2013-01-01

A large proportion of reactive nitrogen loss from polar sediments is mediated by denitrification, but microorganisms mediating denitrification in polar environments remain poorly characterized. A combined approach of most-probable-number (MPN) enumeration, cultivation and physiological characterization was used to describe psychrophilic denitrifying bacterial communities in sediments of three Arctic fjords in Svalbard (Norway). A MPN assay showed the presence of 10(sup 3)-10(sup 6) cells of psychrophilic nitrate-respiring bacteria g(sup -1) of sediment. Fifteen strains within the Proteobacteria were isolated using a systematic enrichment approach with organic acids as electron donors and nitrate as an electron acceptor. Isolates belonged to five genera, including Shewanella, Pseudomonas, Psychromonas (Gammaproteobacteria), Arcobacter (Epsilonproteobacteria) and Herminiimonas (Betaproteobacteria). All isolates were denitrifiers, except Shewanella, which exhibited the capacity for dissimilatory nitrate reduction to ammonium (DNRA). Growth from 0 to 40 degC demonstrated that all genera except Shewanella were psychrophiles with optimal growth below 15 degC, and adaptation to low temperature was demonstrated as a shift from primarily C16:0 saturated fatty acids to C16:1 monounsaturated fatty acids at lower temperatures. This study provides the first targeted enrichment and characterization of psychrophilic denitrifying bacteria from polar sediments, and two genera, Arcobacter and Herminiimonas, are isolated for the first time from permanently cold marine sediments.

Devriesea agamarum causes dermatitis in bearded dragons (Pogona vitticeps).

PubMed

Hellebuyck, Tom; Martel, An; Chiers, Koen; Haesebrouck, Freddy; Pasmans, Frank

2009-03-02

Devriesea agamarum is frequently isolated from dermatitis in lizards, notably from cheilitis in spiny tailed lizards (genus Uromastyx). It was the aim of the present study to assess the role of this bacterium as a causative agent of dermatitis by fulfilling Koch's postulates. First, its association with diseased lizards was demonstrated. The bacterium was isolated from several, mainly desert dwelling squamate species showing symptoms of dermatitis and/or septicaemia. The affected lizards mainly belonged to the family of the Agamidae (genera Pogona, Uromastyx, Agama) and in one case to the Iguanidae (genus Crotaphytus). Secondly, the occurrence of D. agamarum in 66 clinically healthy bearded dragons, 21 clinically healthy Uromastyx species and 40 squamate eggshells was studied. The bacterium was isolated from the oral cavity of 10 bearded dragons but from none of the healthy Uromastyx species. Hence D. agamarum was found to be part of the oral microbiota in Pogona vitticeps. Finally, bearded dragons (P. vitticeps) were experimentally inoculated with D. agamarum by direct application of a bacterial suspension on intact and abraded skin. At the scarified skin of all inoculated lizards, dermatitis was induced from which D. agamarum was re-isolated. In conclusion, D. agamarum is a facultative pathogenic bacterium, able to cause dermatitis in agamid lizards when the integrity of the skin is breached.

Comparison of direct colony method versus extraction method for identification of gram-positive cocci by use of Bruker Biotyper matrix-assisted laser desorption ionization-time of flight mass spectrometry.

PubMed

Alatoom, Adnan A; Cunningham, Scott A; Ihde, Sherry M; Mandrekar, Jayawant; Patel, Robin

2011-08-01

We evaluated Bruker Biotyper (version 2.0) matrix-assisted laser desorption ionization-time of flight (MALDI-TOF) mass spectrometry (MS) for the identification of 305 clinical isolates of staphylococci, streptococci, and related genera by comparing direct colony testing with preparatory extraction. Isolates were previously identified by use of phenotypic testing and/or 16S rRNA gene sequencing. Manufacturer-specified score cutoffs for genus- and species-level identification were used. After excluding 7 isolates not present in the Biotyper library, the Biotyper correctly identified 284 (95%) and 207 (69%) isolates to the genus and species levels, respectively, using extraction. By using direct colony testing, the Biotyper identified 168 (56%) and 60 (20%) isolates to the genus and species levels, respectively. Overall, more isolates were identified to the genus and species levels with preparatory extraction than with direct colony testing (P < 0.0001). The analysis was repeated after dividing the isolates into two subgroups, staphylococci, streptococci, and enterococci (n = 217) and "related genera" (n = 81). For the former subgroup, the extraction method resulted in the identification of 213 (98%) and 171 (79%) isolates to the genus and species levels, respectively, whereas the direct colony method identified 136 (63%) and 56 (26%) isolates to the genus and species levels, respectively. In contrast, for the subgroup of related genera, the extraction method identified 71 (88%) and 36 (44%) isolates to the genus and species levels, respectively, while the direct colony method identified 32 (40%) and 4 (5%) isolates to the genus and species levels, respectively. For both subgroups, preparatory extraction was superior to direct colony testing for the identification of isolates to the genus and species levels (P < 0.0001). Preparatory extraction is needed for the identification of a substantial proportion of Gram-positive cocci using the Biotyper method according to manufacturer-specified score cutoffs.

Secondary metabolites: applications on cultural heritage.

PubMed

Sasso, S; Scrano, L; Bonomo, M G; Salzano, G; Bufo, S A

2013-01-01

Biological sciences and related bio-technology play a very important role in research projects concerning protection and preservation of cultural heritage for future generations. In this work secondary metabolites of Burkholderia gladioli pv. agaricicola (Bga) ICMP 11096 strain and crude extract of glycoalkaloids from Solanaceae plants, were tested against a panel of microorganisms isolated from calcarenite stones of two historical bridges located in Potenza and in Campomaggiore (Southern Italy). The isolated bacteria belong to Bacillus cereus and Arthrobacter agilis species, while fungi belong to Aspergillus, Penicillium, Coprinellus, Fusarium, Rhizoctonio and Stemphylium genera. Bga broth (unfiltered) and glycoalkaloids extracts were able to inhibit the growth of all bacterial isolates. Bga culture was active against fungal colonies, while Solanaceae extract exerted bio-activity against Fusarium and Rhizoctonia genera.

Taxonomic hierarchy of the phylum Firmicutes and novel Firmicutes species originated from various environments in Korea.

PubMed

Seong, Chi Nam; Kang, Joo Won; Lee, Ji Hee; Seo, So Yeon; Woo, Jung Jae; Park, Chul; Bae, Kyung Sook; Kim, Mi Sun

2018-01-01

This study assessed the taxonomic hierarchy of the phylum Firmicutes as well as elucidated the isolation and classification states of novel Firmicutes species isolated from Korean territory. The hierarchical classification system of the phylum Firmicutes has been developed since 1872 when the genus Bacillus was first reported and has been generally adopted since 2001. However, this taxonomic hierarchy is still being modified. Until Feb. 2017, the phylum Firmicutes consisted of seven classes (Bacilli, Clostridia, Erysipelotrichia, Limnochordia, Negativicutes, Thermolithobacteria, and Tissierellia), 13 orders, 45 families, and 421 genera. Firmicutes species isolated from various environments in Korea have been reported from 2000, and 187 species have been approved as of Feb. 2017. All Firmicutes species were affiliated with three classes (Bacilli, Clostridia, and Erysipelotrichia), four orders (Bacillales, Lactobacillales, Clostridiales, and Erysipelotrichales), 17 families, and 54 genera. A total of 173 species belong to the class Bacilli, of which 151 species were affiliated with the order Bacillales and the remaining 22 species with the order Lactobacillales. Twelve species belonging to the class Clostridia were affiliated within only one order, Clostridiales. The most abundant family was Bacillaceae (67 species), followed by the family Paenibacillaceae (56 species). Thirteen novel genera were created using isolates from the Korean environment. A number of Firmicutes species were isolated from natural environments in Korean territory. In addition, a considerable number of species were isolated from artificial resources such as fermented foods. Most Firmicutes species, belonging to the families Bacillaceae, Planococcaceae, and Staphylococcaceae, isolated from Korean fermented foods and solar salterns were halophilic or halotolerant. Firmicutes species were isolated from the whole territory of Korea, especially large numbers from Provinces Gyeonggi, Chungnam, and Daejeon.

Biosynthetic potential of actinomycetes in brown forest soil on the eastern coast of the aegean sea

NASA Astrophysics Data System (ADS)

Shirokikh, I. G.; Shirokikh, A. A.

2017-11-01

The taxonomic and functional structures of the actinomycetal complex in the litter and upper horizon of the brown forest soil was studied in a Pinus brutia var. pendulifolia forest on the eastern coast of the Aegean Sea. The complex of actinomycetes included representatives of the Streptomyces and Micromonospora genera and oligosporus forms. Streptomycetes predominated (73.8%) in the soil, and micromonospores (66.7%) were dominants in the litter. Thirty isolates of ten Streptomyces species from five series and three sections prevailed. In the upper soil horizon, species of the Helvolo-Flavus Helvolus section predominated (48%); the S. felleus species occurred most frequently. Among the isolated cultures, the S. globisporus and S. sindenensis species capable to produce antitumor antibiotics were found. The testing of the antimicrobial activity of the natural isolates showed that five strains inhibit the growth of pathogenic Fusarium sp., Alternaria sp., Acremonium sp., and Bipolaris sorokiniana fungi. When testing the effect of streptomycetes on the production of cellulases, a high-efficient strain belonging to the S. noboritoensis species was revealed. All the streptomycetes isolated from the brown forest soil produced auxins at the rate of 7.8 to 19.7 μg of indole acetic acid/mL of the liquid medium in the presence of 200 mg/L of tryptophan. Twelve isolates of streptomycetes were transferred to the collection of biotechnologically promising cultures for studying their properties.

Permissiveness of freshly isolated environmental strains of amoebae for growth of Legionella pneumophila.

PubMed

Dupuy, Mathieu; Binet, Marie; Bouteleux, Celine; Herbelin, Pascaline; Soreau, Sylvie; Héchard, Yann

2016-03-01

Legionella pneumophila is a pathogenic bacterium commonly found in water and responsible for severe pneumonia. Free-living amoebae are protozoa also found in water, which feed on bacteria by phagocytosis. Under favorable conditions, some L. pneumophila are able to resist phagocytic digestion and even multiply within amoebae. However, it is not clear whether L. pneumophila could infect at a same rate a large range of amoebae or if there is some selectivity towards specific amoebal genera or strains. Also, most studies have been performed using collection strains and not with freshly isolated strains. In our study, we assess the permissiveness of freshly isolated environmental strains of amoebae, belonging to three common genera (i.e. Acanthamoeba, Naegleria and Vermamoeba), for growth of L. pneumophila at three different temperatures. Our results indicated that all the tested strains of amoebae were permissive to L. pneumophila Lens and that there was no significant difference between the strains. Intracellular proliferation was more efficient at a temperature of 40°C. In conclusion, our work suggests that, under favorable conditions, virulent strains of L. pneumophila could equally infect a large number of isolates of common freshwater amoeba genera. © FEMS 2016. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Isolation and identification of culturable fungi from the genitals and semen of healthy giant pandas (Ailuropoda melanoleuca).

PubMed

Ma, Xiaoping; Li, Changcheng; Hou, Jiafa; Gu, Yu

2017-11-21

In order to better understand the possible role of fungi in giant panda reproduction and overall health, it is important to provide a baseline for the normal fungal composition in the reproductive system. Using morphology and internal transcribed spacer (ITS) sequence analysis, we systematically isolated and identified fungal species from the vagina, foreskin, and semen of 21 (11 males and 10 females) healthy giant pandas to understand the normal fungal flora of the genital tracts. A total of 76 fungal strains were obtained, representing 42 genera and 60 species. Among them 47 fungal strains were obtained from vaginal samples, 24 from foreskins, and 5 from semen samples. Several fungal strains were isolated from more than one sample. More fungal species were isolated from females from males. The predominant genera were Aspergillus, Trichosporon, and Penicillium, followed by Candida, Cladosporium, Sordariomycetes, and Diaporthe. The average number of strains in the female vagina was significantly higher than in the foreskin and semen of male. A total of 60 fungal species (belonging to 42 genera) were identified in the giant panda's genital tract. Some of the species were commonly shared in both males and females. These findings provide novel information on the fungal community in the reproductive tracts of giant pandas.

The Madeira Archipelago As a Significant Source of Marine-Derived Actinomycete Diversity with Anticancer and Antimicrobial Potential

PubMed Central

Prieto-Davó, Alejandra; Dias, Tiago; Gomes, Sofia E.; Rodrigues, Sara; Parera-Valadez, Yessica; Borralho, Pedro M.; Pereira, Florbela; Rodrigues, Cecilia M. P.; Santos-Sanches, Ilda; Gaudêncio, Susana P.

2016-01-01

Marine-derived actinomycetes have demonstrated an ability to produce novel compounds with medically relevant biological activity. Studying the diversity and biogeographical patterns of marine actinomycetes offers an opportunity to identify genera that are under environmental pressures, which may drive adaptations that yield specific biosynthetic capabilities. The present study describes research efforts to explore regions of the Atlantic Ocean, specifically around the Madeira Archipelago, where knowledge of the indigenous actinomycete diversity is scarce. A total of 400 actinomycetes were isolated, sequenced, and screened for antimicrobial and anticancer activities. The three most abundant genera identified were Streptomyces, Actinomadura, and Micromonospora. Phylogenetic analyses of the marine OTUs isolated indicated that the Madeira Archipelago is a new source of actinomycetes adapted to life in the ocean. Phylogenetic differences between offshore (>100 m from shore) and nearshore (< 100 m from shore) populations illustrates the importance of sampling offshore in order to isolate new and diverse bacterial strains. Novel phylotypes from chemically rich marine actinomycete groups like MAR4 and the genus Salinispora were isolated. Anticancer and antimicrobial assays identified Streptomyces, Micromonospora, and Salinispora as the most biologically active genera. This study illustrates the importance of bioprospecting efforts at unexplored regions of the ocean to recover bacterial strains with the potential to produce novel and interesting chemistry. PMID:27774089

Chemical releases of social behavior, II. source and specificity of the odor trail substances in four attine genera. (Hymenoptera: Formicidae)

Treesearch

Murray S. Blum; John C. Moser; A.D. Cordero

1964-01-01

The higher members of the tribe Attini characteristically lay persistent and extensive odor trails especially in many neotropical areas. Thus, in Acromyrmex and Atta, long columns of foraging workers are frequently present on the odor trails but in the less specialized attine genera, workers may forage either in files or singly. Weber (1958...

Fungal contamination assessment in Portuguese elderly care centers.

PubMed

Viegas, C; Almeida-Silva, M; Gomes, A Quintal; Wolterbeek, H T; Almeida, S M

2014-01-01

Individuals spend 80-90% of their day indoors and elderly subjects are likely to spend even a greater amount of time indoors. Thus, indoor air pollutants such as bioaerosols may exert a significant impact on this age group. The aim of this study was to characterize fungal contamination within Portuguese elderly care centers. Fungi were measured using conventional as well as molecular methods in bedrooms, living rooms, canteens, storage areas, and outdoors. Bioaerosols were evaluated before and after the microenvironments' occupancy in order to understand the role played by occupancy in fungal contamination. Fungal load results varied from 32 colony-forming units CFU m(-3) in bedrooms to 228 CFU m(-3) in storage areas. Penicillium sp. was the most frequently isolated (38.1%), followed by Aspergillus sp. (16.3%) and Chrysonilia sp. (4.2%). With respect to Aspergillus genus, three different fungal species in indoor air were detected, with A. candidus (62.5%) the most prevalent. On surfaces, 40 different fungal species were isolated and the most frequent was Penicillium sp. (22.2%), followed by Aspergillus sp. (17.3%). Real-time polymerase chain reaction did not detect the presence of A. fumigatus complex. Species from Penicillium and Aspergillus genera were the most abundant in air and surfaces. The species A. fumigatus was present in 12.5% of all indoor microenvironments assessed. The living room was the indoor microenvironment with lowest fungal concentration and the storage area was highest.

A Systematic Approach for Discovering Novel, Clinically Relevant Bacteria

PubMed Central

Simmon, Keith E.; Fisher, Mark A.

2012-01-01

Sequencing of the 16S rRNA gene (16S) is a reference method for bacterial identification. Its expanded use has led to increased recognition of novel bacterial species. In most clinical laboratories, novel species are infrequently encountered, and their pathogenic potential is often difficult to assess. We reviewed partial 16S sequences from >26,000 clinical isolates, analyzed during February 2006–June 2010, and identified 673 that have <99% sequence identity with valid reference sequences and are thus possibly novel species. Of these 673 isolates, 111 may represent novel genera (<95% identity). Isolates from 95 novel taxa were recovered from multiple patients, indicating possible clinical relevance. Most repeatedly encountered novel taxa belonged to the genera Nocardia (14 novel taxa, 42 isolates) and Actinomyces (12 novel taxa, 52 isolates). This systematic approach for recognition of novel species with potential diagnostic or therapeutic relevance provides a basis for epidemiologic surveys and improvement of sequence databases and may lead to identification of new clinical entities. PMID:22377371

A systematic approach for discovering novel, clinically relevant bacteria.

PubMed

Schlaberg, Robert; Simmon, Keith E; Fisher, Mark A

2012-03-01

Sequencing of the 16S rRNA gene (16S) is a reference method for bacterial identification. Its expanded use has led to increased recognition of novel bacterial species. In most clinical laboratories, novel species are infrequently encountered, and their pathogenic potential is often difficult to assess. We reviewed partial 16S sequences from >26,000 clinical isolates, analyzed during February 2006-June 2010, and identified 673 that have <99% sequence identity with valid reference sequences and are thus possibly novel species. Of these 673 isolates, 111 may represent novel genera (<95% identity). Isolates from 95 novel taxa were recovered from multiple patients, indicating possible clinical relevance. Most repeatedly encountered novel taxa belonged to the genera Nocardia (14 novel taxa, 42 isolates) and Actinomyces (12 novel taxa, 52 isolates). This systematic approach for recognition of novel species with potential diagnostic or therapeutic relevance provides a basis for epidemiologic surveys and improvement of sequence databases and may lead to identification of new clinical entities.

Leaf-inhabiting genera of the Gnomoniaceae, Diaporthales

PubMed Central

Sogonov, M.V.; Castlebury, L.A.; Rossman, A.Y.; Mejía, L.C.; White, J.F.

2008-01-01

The Gnomoniaceae are characterised by ascomata that are generally immersed, solitary, without a stroma, or aggregated with a rudimentary stroma, in herbaceous plant material especially in leaves, twigs or stems, but also in bark or wood. The ascomata are black, soft-textured, thin-walled, and pseudoparenchymatous with one or more central or eccentric necks. The asci usually have a distinct apical ring. The Gnomoniaceae includes species having ascospores that are small, mostly less than 25 μm long, although some are longer, and range in septation from non-septate to one-septate, rarely multi-septate. Molecular studies of the Gnomoniaceae suggest that the traditional classification of genera based on characteristics of the ascomata such as position of the neck and ascospores such as septation have resulted in genera that are not monophyletic. In this paper the concepts of the leaf-inhabiting genera in the Gnomoniaceae are reevaluated using multiple genes, specifically nrLSU, translation elongation factor 1-alpha (tef1-α), and RNA polymerase II second largest subunit (rpb2) for 64 isolates. ITS sequences were generated for 322 isolates. Six genera of leaf-inhabiting Gnomoniaceae are defined based on placement of their type species within the multigene phylogeny. The new monotypic genus Ambarignomonia is established for an unusual species, A. petiolorum. A key to 59 species of leaf-inhabiting Gnomoniaceae is presented and 22 species of Gnomoniaceae are described and illustrated. PMID:19287541

Biosynthetic Potential of Phylogenetically Unique Endophytic Actinomycetes from Tropical Plants▿ †

PubMed Central

Janso, Jeffrey E.; Carter, Guy T.

2010-01-01

The culturable diversity of endophytic actinomycetes associated with tropical, native plants is essentially unexplored. In this study, 123 endophytic actinomycetes were isolated from tropical plants collected from several locations in Papua New Guinea and Mborokua Island, Solomon Islands. Isolates were found to be prevalent in roots but uncommon in leaves. Initially, isolates were dereplicated to the strain level by ribotyping. Subsequent characterization of 105 unique strains by 16S rRNA gene sequence analysis revealed that 17 different genera were represented, and rare genera, such as Sphaerisporangium and Planotetraspora, which have never been previously reported to be endophytic, were quite prevalent. Phylogenetic analyses grouped many of the strains into clades distinct from known genera within Thermomonosporaceae and Micromonosporaceae, indicating that they may be unique genera. Bioactivity testing and liquid chromatography-mass spectrometry (LC-MS) profiling of crude fermentation extracts were performed on 91 strains. About 60% of the extracts exhibited bioactivity or displayed LC-MS profiles with spectra indicative of secondary metabolites. The biosynthetic potential of 29 nonproductive strains was further investigated by the detection of putative polyketide synthase (PKS) and nonribosomal peptide synthetase (NRPS) genes. Despite their lack of detectable secondary metabolite production in fermentation, most were positive for type I (66%) and type II (79%) PKS genes, and all were positive for NRPS genes. These results suggest that tropical plants from New Guinea and the adjacent archipelago are hosts to unique endophytic actinomycetes that possess significant biosynthetic potential. PMID:20472734

Phylogenetic diversity of Flavobacteria isolated from the North Sea on solid media.

PubMed

Hahnke, Richard L; Harder, Jens

2013-10-01

Flavobacteria are abundant in the North Sea, an epeiric sea on the continental shelf of Europe. However, this abundance has so far not been reflected by the number of strains in culture collections. In this study, Flavobacteria were isolated from pelagic and benthic samples, such as seawater, phytoplankton, sediment and its porewater, and from surfaces of animals and seaweeds on agar plates with a variety of carbon sources. Dilution cultivation with a new medium, incubation at low temperatures and with long incubation times, and colony screening by a Flavobacteria-Cytophagia-specific PCR detecting 16S rRNA gene sequences led to a collection of phylogenetically diverse strains. Two strains affiliated with Flammeovirgaceae and seven strains affiliated with Cyclobacteriaceae, whereas within the Flavobacteriaceae 20 isolated strains presumably represented seven novel candidate genera and 355 strains affiliated with 26 of 80 validly described marine Flavobacteriaceae genera, based on a genus boundary of 95.0% 16S rRNA gene sequence identity. The majority of strains (276) affiliated with 37 known species in 16 genera (based on a boundary of 98.7% 16S rRNA gene sequence identity), whereas 79 strains likely represented 42 novel species in 22 established Flavobacteriaceae genera. Pigmentation, iridescence, gliding motility, agar lysis, and flexirubin as a chemical marker supported the taxonomy at the species level. This study demonstrated the culturability on solid medium of phylogenetically diverse Flavobacteria originating from the North Sea. Copyright © 2013 Elsevier GmbH. All rights reserved.

Borreria and Spermacoce species (Rubiaceae): A review of their ethnomedicinal properties, chemical constituents, and biological activities

PubMed Central

Conserva, Lucia Maria; Ferreira, Jesu Costa

2012-01-01

Borreira and Spermacoce are genera of Rubiaceae widespread in tropical and subtropical America, Africa, Asia, and Europe. Based on its fruits morphology they are considered by many authors to be distinct genera and most others, however, prefer to combine the two taxa under the generic name Spermacoce. Whereas the discussion is still unclear, in this work they were considered as synonyms. Some species of these genera play an important role in traditional medicine in Africa, Asia, Europe, and South America. Some of these uses include the treatment of malaria, diarrheal and other digestive problems, skin diseases, fever, hemorrhage, urinary and respiratory infections, headache, inflammation of eye, and gums. To date, more than 60 compounds have been reported from Borreria and Spermacoce species including alkaloids, iridoids, flavonoids, terpenoids, and other compounds. Studies have confirmed that extracts from Borreria and Spermacoce species as well as their isolated compounds possess diverse biological activities, including anti-inflammatory, antitumor, antimicrobial, larvicidal, antioxidant, gastrointestinal, anti-ulcer, and hepatoprotective, with alkaloids and iridoids as the major active principles. This paper briefly reviews the ethnomedicinal uses, phytochemistry, and biological activities of some isolated compounds and extracts of both genera. PMID:22654404

Isolation and characterization of bioactive fungi from shark Carcharodon carcharias' gill with biopharmaceutical prospects

NASA Astrophysics Data System (ADS)

Zhang, Yi; Han, Jinyuan; Feng, Yan; Mu, Jun; Bao, Haiyan; Kulik, Andreas; Grond, Stephanie

2016-01-01

Until recently, little was known about the fungi found in shark gills and their biomedicinal potential. In this article, we described the isolation, bioactivity, diversity, and secondary metabolites of bioactive fungi from the gill of a shark ( Carcharodon carcharias). A total of 115 isolates were obtained and grown in 12 culture media. Fifty-eight of these isolates demonstrated significant activity in four antimicrobial, pesticidal, and cytotoxic bioassay models. Four randomly selected bioactive isolates inhibited human cancer cell proliferation during re-screening. These active isolates were segregated into 6 genera using the internal transcribed spacer-large subunit (ITS-LSU) rDNA-sequence BLAST comparison. Four genera, Penicillium, Aspergillus, Mucor, and Chaetomium were the dominant taxa. A phylogenic tree illustrated their intergenera and intragenera genetic diversity. HPLC-DAD-HRMS analysis and subsequent database searching revealed that nine representative strains produced diverse bioactive compound profiles. These results detail the broad range of bioactive fungi found in a shark's gills, revealing their biopharmaceutical potential. To the best of our knowledge, this is the first study characterizing shark gill fungi and their bioactivity.

Fungi inhabiting household environments in Riyadh, Saudi Arabia.

PubMed

Bokhary, H A; Parvez, S

1995-05-01

Fungi inhabiting household environments in the West, East and Central localities of Riyadh city were screened. The screened area included bedrooms, drawing rooms, living rooms, kitchens and bathrooms. The common genera of fungi isolated were Alternaria, Aspergillus, Cercospora, Chaetomium, Cladosporium, Curvularia, Drechslera, Embellisia, Fusarium, Mucor, Penicillium, Rhizopus, Scytalidium, Trichoderma, Torula and Ulocladium. Two uncommon genera Nodulosporium and Oidiodendron for Saudi Arabian mycoflora were also isolated. In all the localities, the highest number of fungal colonies per plate or per gram were found in the living rooms, followed by bedrooms. The number of colonies per plate or per gram was in general higher in densely populated than in less populated areas.

Study of Fungal Colonization of Wheat Kernels in Syria with a Focus on Fusarium Species

PubMed Central

Alkadri, Dima; Nipoti, Paola; Döll, Katharina; Karlovsky, Petr; Prodi, Antonio; Pisi, Annamaria

2013-01-01

Wheat is one of the main crops in Mediterranean countries, and its cultivation has an important role in the Syrian economy. In Syria, Fusarium head blight (FHB) has not been reported so far. Mycological analysis of 48 samples of wheat kernels collected from cultivation areas with different climatic conditions were performed in 2009 and 2010. Fungal isolates were identified at the genus level morphologically; Fusarium species were characterized morphologically and by species-specific PCR. The most frequent fungal genera found were Alternaria spp. and Cladosporium spp., with frequencies of 24.7% and 8.1%, respectively, while the frequency of Fusarium spp. was 1.5% of kernels. Most frequent Fusarium species were F. tricinctum (30% of all Fusarium isolates), F. culmorum (18%), F. equiseti (14%) and F. graminearum (13%). The mycotoxin production potential of selected Fusarium isolates was assessed by HPLC-MS analysis of rice cultures; chemotyping by PCR was carried out for comparison. All six F. graminearum strains tested produced small amounts (<3 mg/kg) of nivalenol (NIV). All ten F. culmorum strains tested produced large amounts of trichothecenes (>100 mg/kg); four strains produced NIV and six strains produced deoxynivalenol (DON) and 3-acetyl-deoxynivalenol (3Ac-DON). PCR chemotyping lead to an oversimplified picture, because all 3Ac-DON chemotype strains produced more DON than 3Ac-DON; furthermore, the strongest NIV producers produced significant amounts of DON. All tested strains of F. culmorum, F. graminearum, F. pseudograminearum (two strains) and most F. equiseti strains (five of six strains) produced zearalenone. Grains of durum wheat were more frequently colonized by Fusarium spp. than grains of soft wheat. Incidence of Fusarium spp. in irrigated fields was higher than in rainfed fields. The incidence of Fusarium strains producing mycotoxins raises concerns about the risk of Fusarium head blight to Syria and its consequences for public health. PMID:23493058

Revisions of Ruizodendron and Pseudephedranthus (Annonaceae) including a new species and an overview of most up-to-date revisions of Neotropical Annonaceae genera

PubMed Central

Erkens, Roy H.J.; Oosterhof, Jessica; Westra, Lubbert Y.T.; Maas, Paul J.M.

2017-01-01

Abstract We present revisions of the Neotropical genera Ruizodendron and Pseudephedranthus (Annonaceae). Ruizodendron includes a single species R. ovale. Pseudephedranthus now comprises two species, with the description of the new species P. enigmaticus sp. nov. extending the range of the genus beyond the Upper Rio Negro region of Brazil (Amazonas) and adjacent Venezuela (P. fragrans), to include Guyana, Suriname, and the Brazilian state of Pará. An overview is provided of current revisions of Neotropical Annonaceae genera that will aid in accessing proper species information for this frequently encountered tropical rain forest family. PMID:29158697

Microorganisms isolated from root canals presenting necrotic pulp and their drug susceptibility in vitro.

PubMed

Lana, M A; Ribeiro-Sobrinho, A P; Stehling, R; Garcia, G D; Silva, B K; Hamdan, J S; Nicoli, J R; Carvalho, M A; Farias, L de M

2001-04-01

The knowledge about causative agents involved in endodontic infections is increasing, especially due to the improvement of culture techniques for anaerobic bacteria, showing that these microorganisms are predominant in this pathology. In this study, 31 canals with pulp necrosis were microbiologically analyzed before and after manipulation. Obligate and facultative anaerobes, microaerophilic bacteria and yeasts were recovered from 24, 14, 5 and 2 clinical specimens, respectively. The most frequent genera were Prevotella, Fusobacterium, Lactobacillus, Streptococcus, Clostridium and Peptostreptococcus for bacteria and Candida and Saccharomyces for yeasts. Strong positive associations, using an odds ratio system, were found between Clostridium and Prevotella and between Peptostreptococcus and Fusobacterium. Even after the instrumentation and the use of Ca(OH)2, facultative anaerobes were detected in two root canals and yeasts in three. Microorganisms were isolated from seven canals at the end of the endodontic treatment: facultative anaerobes from five and yeasts from one. The microbiological evaluation of root canals with pulp necrosis suggests the presence of polymicrobial infections, mainly involving obligate anaerobes, and shows that the infection may persist after treatment.

A floral survey of cliff habitats along Bull Run at Manassas National Battlefield Park, Virginia, 2014

USGS Publications Warehouse

Stroh, Esther D.; Struckhoff, Matthew A.; Grabner, Keith W.

2015-08-06

Isolated patches of native vegetation in human-modified landscapes are important reservoirs of biological diversity because they may be the only places in which rare or native species can persist. Manassas National Battlefield Park, Virginia, is an island embedded in a matrix of intensively modified lands; it is becoming increasingly isolated due to growth of the greater Washington, D.C. area. A series of cliffs along Bull Run support an eastern white pine community disjunct from its more typical range in the Appalachian Mountains. Cliffs frequently support vegetation communities that differ from surrounding habitat. In this ecological context, the cliffs along Bull Run are islands of specialized habitat within an island of natural and semi-natural communities (the park), surrounded by a human-dominated landscape. A floral survey of these cliffs was a top priority identified by the National Park Service National Capital Region via the National Resource Preservation Program; in 2014, we completed a floral survey of 11 cliffs in the park. We recorded 282 species in 194 genera and 83 families, including 23 newly documented species for the park.

Diverse deep-sea fungi from the South China Sea and their antimicrobial activity.

PubMed

Zhang, Xiao-Yong; Zhang, Yun; Xu, Xin-Ya; Qi, Shu-Hua

2013-11-01

We investigated the diversity of fungal communities in nine different deep-sea sediment samples of the South China Sea by culture-dependent methods followed by analysis of fungal internal transcribed spacer (ITS) sequences. Although 14 out of 27 identified species were reported in a previous study, 13 species were isolated from sediments of deep-sea environments for the first report. Moreover, these ITS sequences of six isolates shared 84-92 % similarity with their closest matches in GenBank, which suggested that they might be novel phylotypes of genera Ajellomyces, Podosordaria, Torula, and Xylaria. The antimicrobial activities of these fungal isolates were explored using a double-layer technique. A relatively high proportion (56 %) of fungal isolates exhibited antimicrobial activity against at least one pathogenic bacterium or fungus among four marine pathogenic microbes (Micrococcus luteus, Pseudoaltermonas piscida, Aspergerillus versicolor, and A. sydowii). Out of these antimicrobial fungi, the genera Arthrinium, Aspergillus, and Penicillium exhibited antibacterial and antifungal activities, while genus Aureobasidium displayed only antibacterial activity, and genera Acremonium, Cladosporium, Geomyces, and Phaeosphaeriopsis displayed only antifungal activity. To our knowledge, this is the first report to investigate the diversity and antimicrobial activity of culturable deep-sea-derived fungi in the South China Sea. These results suggest that diverse deep-sea fungi from the South China Sea are a potential source for antibiotics' discovery and further increase the pool of fungi available for natural bioactive product screening.

Potential of Polycyclic Aromatic Hydrocarbon-Degrading Bacterial Isolates to Contribute to Soil Fertility

PubMed Central

Chirima, George Johannes

2016-01-01

Restoration of polycyclic aromatic hydrocarbon- (PAH-) polluted sites is presently a major challenge in agroforestry. Consequently, microorganisms with PAH-degradation ability and soil fertility improvement attributes are sought after in order to achieve sustainable remediation of polluted sites. This study isolated PAH-degrading bacteria from enriched cultures of spent automobile engine-oil polluted soil. Isolates' partial 16S rRNA genes were sequenced and taxonomically classified. Isolates were further screened for their soil fertility attributes such as phosphate solubilization, atmospheric nitrogen fixation, and indoleacetic acid (IAA) production. A total of 44 isolates were obtained and belong to the genera Acinetobacter, Arthrobacter, Bacillus, Flavobacterium, Microbacterium, Ochrobactrum, Pseudomonas, Pseudoxanthomonas, Rhodococcus, and Stenotrophomonas. Data analysed by principal component analysis showed the Bacillus and Ochrobactrum isolates displayed outstanding IAA production. Generalized linear modelling statistical approaches were applied to evaluate the contribution of the four most represented genera (Pseudomonas, Acinetobacter, Arthrobacter, and Rhodococcus) to soil fertility. The Pseudomonas isolates were the most promising in all three soil fertility enhancement traits evaluated and all isolates showed potential for one or more of the attributes evaluated. These findings demonstrate a clear potential of the isolates to participate in restorative bioremediation of polluted soil, which will enhance sustainable agricultural production and environmental protection. PMID:27774456

Complete Genome sequence of Burkholderia phymatum STM815T, a broad host range and efficient nitrogen-fixing symbiont of Mimosa species

PubMed Central

Moulin, Lionel; Klonowska, Agnieszka; Caroline, Bournaud; Booth, Kristina; Vriezen, Jan A.C.; Melkonian, Rémy; James, Euan K.; Young, J. Peter W.; Bena, Gilles; Hauser, Loren; Land, Miriam; Kyrpides, Nikos; Bruce, David; Chain, Patrick; Copeland, Alex; Pitluck, Sam; Woyke, Tanja; Lizotte-Waniewski, Michelle; Bristow, Jim; Riley, Margaret

2014-01-01

Burkholderia phymatum is a soil bacterium able to develop a nitrogen-fixing symbiosis with species of the legume genus Mimosa, and is frequently found associated specifically with Mimosa pudica. The type strain of the species, STM 815T, was isolated from a root nodule in French Guiana in 2000. The strain is an aerobic, motile, non-spore forming, Gram-negative rod, and is a highly competitive strain for nodulation compared to other Mimosa symbionts, as it also nodulates a broad range of other legume genera and species. The 8,676,562 bp genome is composed of two chromosomes (3,479,187 and 2,697,374 bp), a megaplasmid (1,904,893 bp) and a plasmid hosting the symbiotic functions (595,108 bp). PMID:25197461

Complete Genome sequence of Burkholderia phymatum STM815, a broad host range and efficient nitrogen-fixing symbiont of Mimosa species

DOE Office of Scientific and Technical Information (OSTI.GOV)

Moulin, Lionel; Klonowska, Agnieszka; Caroline, Bournaud

Burkholderia phymatum is a soil bacterium able to develop a nitrogen-fixing symbiosis with species of the legume genus Mimosa, and is frequently found associated specifically with Mimosa pudica. The type strain of the species, STM 815T, was isolated from a root nodule in French Guiana in 2000. The strain is an aerobic, motile, non-spore forming, Gram-negative rod, and is a highly competitive strain for nodulation compared to other Mimosa symbionts, as it also nodulates a broad range of other legume genera and species. The 8,676,562 bp genome is composed of two chromosomes (3,479,187 and 2,697,374 bp), a megaplasmid (1,904,893 bp)more » and a plasmid hosting the symbiotic functions (595,108 bp).« less

Exposure to airborne fungi during sorting of recyclable plastics in waste treatment facilities.

PubMed

Černá, Kristýna; Wittlingerová, Zdeňka; Zimová, Magdaléna; Janovský, Zdeněk

2017-02-28

In working environment of waste treatment facilities, employees are exposed to high concentrations of airborne microorganisms. Fungi constitute an essential part of them. This study aims at evaluating the diurnal variation in concentrations and species composition of the fungal contamination in 2 plastic waste sorting facilities in different seasons. Air samples from the 2 sorting facilities were collected through the membrane filters method on 4 different types of cultivation media. Isolated fungi were classified to genera or species by using a light microscopy. Overall, the highest concentrations of airborne fungi were recorded in summer (9.1×10³-9.0×10⁵ colony-forming units (CFU)/m₃), while the lowest ones in winter (2.7×10³-2.9×10⁵ CFU/m³). The concentration increased from the beginning of the work shift and reached a plateau after 6-7 h of the sorting. The most frequently isolated airborne fungi were those of the genera Penicillium and Aspergillus. The turnover of fungal species between seasons was relatively high as well as changes in the number of detected species, but potentially toxigenic and allergenic fungi were detected in both facilities during all seasons. Generally, high concentrations of airborne fungi were detected in the working environment of plastic waste sorting facilities, which raises the question of health risk taken by the employees. Based on our results, the use of protective equipment by employees is recommended and preventive measures should be introduced into the working environment of waste sorting facilities to reduce health risk for employees. Med Pr 2017;68(1):1-9. This work is available in Open Access model and licensed under a CC BY-NC 3.0 PL license.

An isolate of Haemophilus haemolyticus produces a bacteriocin-like substance that inhibits the growth of nontypeable Haemophilus influenzae.

PubMed

Latham, Roger D; Gell, David A; Fairbairn, Rory L; Lyons, A Bruce; Shukla, Shakti D; Cho, Kum Yin; Jones, David A; Harkness, Nick M; Tristram, Stephen G

2017-04-01

Nontypeable Haemophilus influenzae (NTHi) frequently colonises the upper respiratory tract and is an important cause of respiratory infections. Resistance to antibiotics is an emerging trend in NTHi and alternative prevention or treatment strategies are required. Haemophilus haemolyticus is a common commensal occupying the same niche as NTHi and, if able to produce substances that inhibit NTHi growth, may have a role as a probiotic. In this study, ammonium sulphate extracts from broth culture of 100 H. haemolyticus isolates were tested for the presence of substances inhibitory to NTHi using a well diffusion assay. One isolate produced a substance that consistently inhibited the growth of NTHi. The substance was inactivated by protease enzymes and had a molecular size of ca. 30 kDa as determined by size exclusion chromatography. When the substance was tested against bacteria from eight Gram-negative and three Gram-positive genera, only Haemophilus spp. were inhibited. Quantitative PCR testing showed the substance to be different to 'haemocin', the previously described bacteriocin of H. influenzae type b. These molecular characteristics, together with narrow-spectrum activity, suggest the substance may be a novel bacteriocin, and there is potential for this H. haemolyticus isolate to function as a probiotic for reduction of colonisation and subsequent infection with NTHi. Copyright © 2017 Elsevier B.V. and International Society of Chemotherapy. All rights reserved.

Alkaliphilic and halophilic hydrocarbon-utilizing bacteria from Kuwaiti coasts of the Arabian Gulf.

PubMed

Al-Awadhi, H; Sulaiman, Rasha H D; Mahmoud, Huda M; Radwan, S S

2007-11-01

Green animate materials from the intertidal zone of the Arabian Gulf coast accommodated more alkaliphilic and halophilic bacteria than inanimate materials. The alkaliphilic oil-utilizing bacteria, as identified by their 16S ribonucleic acid sequences, belonged to the following genera arranged in decreasing frequences: Marinobacter, Micrococcus, Dietzia, Bacillus, Oceanobacillus, and Citricoccus. The halophilic oil-utilizing bacteria belonged to the genera: Marinobacter, Georgenia, Microbacterium, Stappia, Bacillus, Isoptericola, and Cellulomonas. Most isolates could grow on a wide range of pure n-alkanes and aromatic compounds, as sole sources of carbon and energy. Quantitative gas liquid chromatographic analysis showed that individual isolates attenuated crude oil and representative pure hydrocarbons in culture. The optimum pH for most of the alkaliphilic genera was pH 10, and the optimum salinity for the halophiles ranged between 2.5 and 5% NaCl (w/v). It was concluded that as far as their microbial makeup is concerned, oily alkaline and saline intertidal areas of the Kuwaiti coasts have a self-cleaning potential.

Mycoflora and mycotoxin-producing fungi of air-dust particles from Egypt.

PubMed

Abdel-Hafez, S I; Shoreit, A A; Abdel-Hafez, A I; el Maghraby, O M

1986-01-01

Using the dilution-plate method, 27 genera and 64 species were collected from 20 air-dust samples on glucose - (24 genera and 57 species) and cellulose - (21 genera and 45 species) Czapek's agar at 28 degrees C. There are basic similarities between the mycoflora of air-dust on the two media and the most prevalent species were Aspergillus niger, A. flavus, A. ochraceus, A. terreus, A. versicolor, Penicillium chrysogenum, P. funiculosum, Alternaria alternata, Cladosporium herbarum, Fusarium oxysporum, Rhizopus stolonifer and Trichoderma viride. Chaetomium globosum, Stachybotrys chartarum, Humicola grisea and Arthrobotrys oligospora were common only on cellulose agar plates. Extracts of mycelium from 25 isolates were tested with brine schrimp (Artemia salina); of these 23 displayed varying degrees of toxicity. Thin layer chromatographic analysis of 12 isolates of Aspergillus flavus revealed that 4 strains were producing detectable aflatoxin. Zearalenone production was noted for 3 out of 5 strains of Fusarium oxysporum and 2 out of 5 strains of F. solani.

Phylogenetic impoverishment of Amazonian tree communities in an experimentally fragmented forest landscape.

PubMed

Santos, Bráulio A; Tabarelli, Marcelo; Melo, Felipe P L; Camargo, José L C; Andrade, Ana; Laurance, Susan G; Laurance, William F

2014-01-01

Amazonian rainforests sustain some of the richest tree communities on Earth, but their ecological and evolutionary responses to human threats remain poorly known. We used one of the largest experimental datasets currently available on tree dynamics in fragmented tropical forests and a recent phylogeny of angiosperms to test whether tree communities have lost phylogenetic diversity since their isolation about two decades previously. Our findings revealed an overall trend toward phylogenetic impoverishment across the experimentally fragmented landscape, irrespective of whether tree communities were in 1-ha, 10-ha, or 100-ha forest fragments, near forest edges, or in continuous forest. The magnitude of the phylogenetic diversity loss was low (<2% relative to before-fragmentation values) but widespread throughout the study landscape, occurring in 32 of 40 1-ha plots. Consistent with this loss in phylogenetic diversity, we observed a significant decrease of 50% in phylogenetic dispersion since forest isolation, irrespective of plot location. Analyses based on tree genera that have significantly increased (28 genera) or declined (31 genera) in abundance and basal area in the landscape revealed that increasing genera are more phylogenetically related than decreasing ones. Also, the loss of phylogenetic diversity was greater in tree communities where increasing genera proliferated and decreasing genera reduced their importance values, suggesting that this taxonomic replacement is partially underlying the phylogenetic impoverishment at the landscape scale. This finding has clear implications for the current debate about the role human-modified landscapes play in sustaining biodiversity persistence and key ecosystem services, such as carbon storage. Although the generalization of our findings to other fragmented tropical forests is uncertain, it could negatively affect ecosystem productivity and stability and have broader impacts on coevolved organisms.

Evolutionary asymmetry in the arbuscular mycorrhizal symbiosis: conservatism in fungal morphology does not predict host plant growth.

PubMed

Koch, Alexander M; Antunes, Pedro M; Maherali, Hafiz; Hart, Miranda M; Klironomos, John N

2017-05-01

Although arbuscular mycorrhizal (AM) fungi are obligate symbionts that can influence plant growth, the magnitude and direction of these effects are highly variable within fungal genera and even among isolates within species, as well as among plant taxa. To determine whether variability in AM fungal morphology and growth is correlated with AM fungal effects on plant growth, we established a common garden experiment with 56 AM fungal isolates comprising 17 genera and six families growing with three plant host species. Arbuscular mycorrhizal fungal morphology and growth was highly conserved among isolates of the same species and among species within a family. By contrast, plant growth response to fungal inoculation was highly variable, with the majority of variation occurring among different isolates of the same AM fungal species. Our findings show that host performance cannot be predicted from AM fungal morphology and growth traits. Divergent effects on plant growth among isolates within an AM fungal species may be caused by coevolution between co-occurring fungal and plant populations. © 2017 The Authors. New Phytologist © 2017 New Phytologist Trust.

Entomologic investigations of an epidemic of St. Louis encephalitis in Pine Bluff, Arkansas, 1991.

PubMed

Savage, H M; Smith, G C; Moore, C G; Mitchell, C J; Townsend, M; Marfin, A A

1993-07-01

An epidemic of St. Louis encephalitis (SLE) occurred in Jefferson County, Arkansas during July-August 1991. At least 26 human cases were involved, with 25 cases in the town of Pine Bluff. Twelve isolates of SLE virus were obtained from mosquitoes collected in Pine Bluff between August 13 and 24: 11 from pools of Culex pipiens quinquefasciatus, resulting in a minimum infection rate of 1.6 per 1,000 (n = 6,768) for this subspecies, and one isolate from a pool of 22 mosquitoes identified as Cx. (Culex) spp. Three of the SLE-positive pools, two from Cx. p. quinquefasciatus and one from Cx. (Cux.) spp., also yielded isolates of Flanders virus. Larval surveys resulted in the collection of seven species in four genera from 28 larva-positive habitats and the identification of one significant site of Cx. p. quinquefasciatus production. Ecologic assessments conducted at 12 randomly selected residences resulted in the identification of 17 larva-positive habitats, for an average mosquito-positive habitat rate of 1.4 per residence, and a Cx. p. quinquefasciatus larva-positive habitat rate of 0.6 per residence. Aedes albopictus and Cx. p. quinquefasciatus were the species most frequently encountered in larval surveys in residential neighborhoods.

[Morphological and biochemical features of fungi isolated from patients with renal failure].

PubMed

Drozdowska, Agata

2007-01-01

Patients with renal failure are more frequently at risk of fungal infections than the healthy individuals. The aim of the study was: (1) Evaluation of the prevalence of fungi in biological materials obtained from different ontocenoses from patients with end-stage and chronic renal failure undergoing haemodialysis and conservative treatment, respectively. (2) Species determining of isolated fungal strains and evaluation their morphological and biochemical features with regard to biotyping. (3) Examining the connection between intraspecies features of fungal strains isolated from different ontocenoses of the same patient. The study group comprised 136 persons, including 56 patients with end-stage renal failure dialysed for the mean period of 36.2 (+/- 1.62) months--all patients were on chronic haemodialysis therapy (4 hours sessions, 3 times per week), 50 patients with chronic renal failure undergoing conservative treatment and 30 persons with the negative history of any renal disease--control group. At the moment of the evaluation and collection of samples all patients were in good condition, none of the patients revealed symptoms suggesting possible fungal infection. Material for mycological examinations included washings from the oral cavity and samples of urine and faeces. In order to evaluate morphological and biochemical features of fungi the following methods were applied: (1) macrocultures in solid Sabouraud medium, (2) direct microscopic slides, (3) API 20 C AUX test and (4) API ZYM test (bioMérieux). Totally 385 samples for mycological examinations were collected from different ontocenoses, from which 161 fungal strains were isolated and classified to 17 species from 5 genera. Most strains belonged to the genus Candida 96.9% and the most frequently occurring species was C. albicans (60.3%). Other species from this genus composed 39.7%, among which in 11.8% of cases C. parapsilosis was determined, and the following were: C. guilliermondii and C. humicola--both species isolated in 5.59%, C. glabrata (4.35%), C. rugosa and C. tropicalis (both species were isolated in 2.48%). The remaining isolated fungal strains (3.11 +/- 1.37%) belonged to genera Cryptococcus, Geotrichum, Saccharomyces and Trichosporon. The prevalence of fungi in collected biological materials from chronic dialysed patients, treated conservatively and persons from control group was determined at the level of 96.4%, 64.0% and 63.3%, respectively. In all examined groups fungi were found in high percentage in the ontocenoses of oral cavity and gastrointestinal tract; in dialysed patients (40.7%), treated conservatively (34.4%) and in persons with negative history of any renal disease (42.1%). It should be expressed that in 9.37% of patients with chronic renal failure undergoing conservative treatment fungi were determined at the same time in materials obtained from three ontocenoses--oral cavity, gastrointestinal tract and urinary tract. The majority of C. albicans strains (34.0%) was described by the use of code AUX 2 576 174; code 2 566 174 was found in 23.4% of species. Strains with code AUX 2 576 174 in 96,9% were isolated from chronic haemodialysed patients whereas code 2 566 174 characterized strains (68.2%) obtained from patients treated conservatively. Examined fungal strains from genus Candida obtained from all persons revealed the activity of 10 to 17 enzymes in the API ZYM test. Strains of genus Candida albicans obtained from patients with chronic renal failure treated conservatively and undergoing haemodialysis in majority belonged to biotype A (58.8%) and D3 (40.4%), respectively.

Mycoflora and mycotoxin contamination of Roundup Ready soybean harvested in the Pampean Region, Argentina.

PubMed

Garrido, Carolina E; González, Héctor H L; Salas, María Paula; Resnik, Silvia L; Pacin, Ana M

2013-08-01

A total of 89 freshly harvested soybean seed samples (Roundup Ready [transgenic] soybean cultivars) from the 2010/2011 crop season were collected from five locations in the Northern Pampean Region II, Argentina. These samples were analyzed for internal mycoflora, toxin production of isolated fungi, and for a range of mycotoxins. Mycotoxin analysis of aflatoxins (AFs), zearalenone (ZEA), fumonisins (FBs) and ochratoxin A (OTA) was done by HPLC-FLD (high performance liquid chromatography with postcolumn fluorescence derivatization), alternariol and alternariol monomethyl ether with HPLC-UV (HPLC with UV detection), trichothecenes (deoxynivalenol, nivalenol, T-2 toxin, HT-2 toxin, fusarenon X, 3-acetyldeoxynivalenol and 15-acetyldeoxynivalenol were analyzed by GC-ECD (gas chromatography with electron capture detector). Fungal colonization was more frequently found for samples from América, Saladillo and Trenque Lauquen than for samples from General Villegas and Trenel; a total of 1,401 fungal isolates were obtained from the soybean seeds. The most commonly identified fungal genera were Alternaria, Sclerotinia, Chaetomium, Cladosporium, Aspergillus, Penicillium, Phomopsis and Fusarium. Alternaria alternata, A.tenuissima, Aspergillus flavus, Penicillium citrinum, Fusarium verticillioides and F.semitectum were the predominant toxigenic fungal species. Mycotoxin production was confirmed for several isolates of toxigenic species, including Aspergillus flavus, A. parasiticus, Alternaria alternata, A.tenuissima, Fusarium graminearum, F semitectum and F. verticillioides. In particular, the percentage of mycotoxigenic Alternaria alternata (100%), A.tenuissima (95%) and aflatoxigenic strains of A. flavus (57%) were remarkably high. Although none of the mycotoxins, AFs, ZEA, FBs, trichothecenes and OTA, were directly detected in samples of soybean seeds, the frequent presence of toxigenic fungal species indicates the risk of multiple mycotoxin contamination.

Diverse culturable bacterial communities with cellulolytic potential revealed from pristine habitat in Indian trans-Himalaya.

PubMed

Thakur, Vikas; Kumar, Vijay; Kumar, Sanjay; Singh, Dharam

2018-05-28

Pangi-Chamba Himalaya (PCH) region is very pristine, unique and virgin niche for bioresource exploration. In the current study, for the first time, the bacterial diversity of this region for potential cellulose degrader was investigated. A total of 454 pure bacterial isolates were obtained from diverse sites in PCH region and 111 isolates were further selected for 16S rDNA characterization based on ARDRA grouping. Identified bacteria belongs to twenty-eight genera representing four phyla namely Firmicutes, Proteobacteria, Actinobacteria and Bacteroidetes. Pseudomonas was most abundant genera followed by Bacillus, Geobacillus, Arthrobacter, Paenibacillus, and Flavobacterium. In addition, 6 putative novel bacteria (based on 16S rDNA sequence similarity) and thermophiles from non-thermogenic sites were also reported for the first time. Screening for cellulose degradation ability on carboxymethyl cellulose (CMC) plates had revealed 70.92% of cellulolytic bacteria. Current study reports diverse genera (Arthrobacter, Paenibacillus, Chryseobacterium, Pedobacter, Streptomyces, Agromyces, Flavobacterium, and Pseudomonas), high cellulose hydrolysis zone, and wide pH and temperature functional cellulolytic bacteria hitherto reported in the literature. Diverse bacterial genera with high cellulolytic activity in broad pH and temperature range provide opportunity to develop a bioprocess for efficient pretreatment of lignocellulosic biomass, which is currently being investigated.

Endophytic fungi associated with roots of date palm (Phoenix dactylifera) in coastal dunes.

PubMed

Mohamed Mahmoud, Fadila; Krimi, Zoulikha; Maciá-Vicente, Jose G; Brahim Errahmani, Mohamed; Lopez-Llorca, Luis V

Symbiotic interactions with fungal endophytes are argued to be responsible for the tolerance of plants to some stresses and for their adaptation to natural conditions. In this study we aimed to examine the endophytic fungal diversity associated with roots of date palms growing in coastal dune systems, and to screen this collection of endophytes for potential use as biocontrol agents, for antagonistic activity and mycoparasitism, and as producers of antifungal compounds with potential efficacy against root diseases of date palm. Roots of nine individual date palms growing in three coastal locations in the South-East of Spain (Guardamar, El Carabassí, and San Juan) were selected to isolate endophytic fungi. Isolates were identified on the basis of morphological and/or molecular characters. Five hundred and fifty two endophytic fungi were isolated and assigned to thirty morphological taxa or molecular operational taxonomic units. Most isolates belonged to Ascomycota, and the dominant order was Hypocreales. Fusarium and Clonostachys were the most frequently isolated genera and were present at all sampling sites. Comparisons of the endophytic diversity with previous studies, and their importance in the management of the date palm crops are discussed. This is the first study on the diversity of endophytic fungi associated with roots of date palm. The isolates obtained might constitute a source of biological control agents and biofertilizers for use in crops of this plant. Copyright © 2016 Asociación Española de Micología. Publicado por Elsevier España, S.L.U. All rights reserved.

Identification of aerobic Gram-positive bacilli by use of Vitek MS.

PubMed

Navas, Maria; Pincus, David H; Wilkey, Kathy; Sercia, Linda; LaSalvia, Margaret; Wilson, Deborah; Procop, Gary W; Richter, Sandra S

2014-04-01

The accuracy of Vitek MS mass spectrometric identifications was assessed for 206 clinically significant isolates of aerobic Gram-positive bacilli representing 20 genera and 38 species. The Vitek MS identifications were correct for 85% of the isolates (56.3% to the species level, 28.6% limited to the genus level), with misidentifications occurring for 7.3% of the isolates.

'Prevalence and antimicrobial susceptibility of Listeria monocytogenes and methicillin-resistant Staphylococcus aureus strains from raw meat and meat products in Zaria, Nigeria.

PubMed

Ndahi, M D; Kwaga, J K P; Bello, M; Kabir, J; Umoh, V J; Yakubu, S E; Nok, A J

2014-03-01

The bacterial genera Listeria and Staphylococcus have been frequently isolated from food products and are responsible for a number of animal and human diseases. The aim of the study was to simultaneously isolate and characterize L. monocytogenes and Staphylococcus species from 300 samples of raw meat and meat products, to determine the susceptibility of the organisms to commonly used antimicrobial agents and to determine the presence of haemolysin A (hyl) virulence gene in L. monocytogenes and staphylococcal cassette chromosome mecA (SCCmec) gene in the Staph. aureus isolates using PCR. Of the 85 Listeria isolates tested, 12 L. monocytogenes were identified and tested for their sensitivity to 14 antimicrobial agents. All the 12 isolates (100%) were resistant to nine antimicrobial agents, but however sensitive to gentamicin. Only one isolate was found to harbour the hylA gene. Twenty-nine isolates were confirmed as Staph. aureus by the Microbact 12S identification system and were all presumptively identified as methicillin-resistant Staph. aureus species using oxacillin-resistant Staph. aureus basal medium (ORSAB). The 29 Staph. aureus isolates were tested for their sensitivity to 16 antimicrobial agents, and 11 were resistant to methicillin. None of the 11 Staph. aureus isolates harboured the methicillin resistance, mecA gene. Listeria monocytogenes and Staphylococcus aureus are important agents of foodborne diseases. Occurrence of these infectious agents was established in meat and meat products in Zaria, Nigeria. Majority of isolates obtained from this study, displayed multidrug resistance to commonly used antimicrobial agents, including methicillin resistance among the Staph. aureus isolates. The potential virulence of L. monocytogenes found in ready-to-eat food was documented by the carriage of hly A gene by one of the isolates. A different mechanism of methicillin resistance or different homologue of mec A gene may be circulating among Nigerian isolates. © 2013 The Society for Applied Microbiology.

Surface microbial consortia from Livarot, a French smear-ripened cheese.

PubMed

Larpin-Laborde, Sandra; Imran, Muhammad; Bonaïti, Catherine; Bora, Nagamani; Gelsomino, Roberto; Goerges, Stefanie; Irlinger, Françoise; Goodfellow, Michael; Ward, Alan C; Vancanneyt, Marc; Swings, Jean; Scherer, Siegfried; Guéguen, Micheline; Desmasures, Nathalie

2011-08-01

The surface microflora (902 isolates) of Livarot cheeses from three dairies was investigated during ripening. Yeasts were mainly identified by Fourier transform infrared spectroscopy. Geotrichum candidum was the dominating yeast among 10 species. Bacteria were identified using Biotype 100 strips, dereplicated by repetitive extragenic palindromic PCR (rep-PCR); 156 representative strains were identified by either BOX-PCR or (GTG)(5)-PCR, and when appropriate by 16S rDNA sequencing and SDS-PAGE analysis. Gram-positive bacteria accounted for 65% of the isolates and were mainly assigned to the genera Arthrobacter , Brevibacterium , Corynebacterium , and Staphylococcus . New taxa related to the genera Agrococcus and Leucobacter were found. Yeast and Gram-positive bacteria strains deliberately added as smearing agents were sometimes undetected during ripening. Thirty-two percent of the isolates were Gram-negative bacteria, which showed a high level of diversity and mainly included members of the genera Alcaligenes , Hafnia , Proteus , Pseudomonas , and Psychrobacter . Whatever the milk used (pasteurized or unpasteurized), similar levels of biodiversity were observed in the three dairies, all of which had efficient cleaning procedures and good manufacturing practices. It appears that some of the Gram-negative bacteria identified should now be regarded as potentially useful in some cheese technologies. The assessment of their positive versus negative role should be objectively examined.

[Occurrence and number of bacteria from the Micrococcus, Kocuria, Nesterenkonia, Kytococcus and Dermacoccus genera on skin and mucous membranes in humans].

PubMed

Szczerba, Izabela

2003-01-01

The aim of work was to evaluate the frequency of occurrence of bacteria from genera of Micrococcus, Kocuria, Nesterenkonia, kytococcus and Dermatococcus on human skin and mucous membranes in healthy population. Among 150 investigated persons these bacteria were found in 122 (81.3%). The frequency of isolation was similar in both sex (82.4% in female and 79.7% in male). Most often the strains were isolated from oral cavity (48.7%), and from skin of palm and forearm (40.7% and 37.3%). Least frequency of occurrence was observed in vestibule of nose (26%). The predominant isolated strains were: M. luteus (26.2%), and N. halobia (21%) followed by K. varians (16.4%), M. lylae (12.2%), D. sedentarius (9.1%), K. kristinae (7.3%), K. nishinomiyaensis (7.3%), K. rosea (0.3%).

Diversity of lactic acid bacteria in sian-sianzih (fermented clams), a traditional fermented food in Taiwan.

PubMed

Chen, Yi-sheng; Wu, Hui-chung; Li, Ya-han; Leong, Kun-hon; Pua, Xiao-hui; Weng, Ming-kai; Yanagida, Fujitoshi

2012-01-30

Sian-sianzih (fermented clams) is a popular traditional fermented food in Taiwan. The lactic acid bacteria (LAB) microflora in sian-sianzih have not been studied in detail. In this study, LAB from sian-sianzih were isolated, characterized and identified. A total of 186 cultures of LAB were isolated from seven sian-sianzih samples and 29 cultures were isolated from its main raw substrate: clams. The identification results revealed up to 11 distinct bacterial species belonging to five genera in sian-sianzih, and three species belonging to two genera in clams. The most common bacterial genera in sian-sianzih were Lactobacillus and Weissella, followed by Leuconostoc, Pediococcus and Lactococcus. A regional similarity in LAB, with differences in diversity, was observed in the current study. On the other hand, Lactococcus lactis subsp. lactis was the most common species found in raw clam samples. The results also suggested that greater LAB diversity could be observed in wild clams than in cultured ones. Furthermore, antibacterial activities of the isolates were determined, and one Weisella hellenica strain showed inhibitory activity against the indicator strain Lactobacilluas sakei JCM 1157(T) . A sensory assessment of seven sian-sianzih samples was also performed and the results indicated that diversity of LAB has a great effect on its aroma and taste formation. The results demonstrate that various LAB species are distributed in sian-sianzih and have a great effect on the flavor of sian-sianzih. Copyright © 2011 Society of Chemical Industry.

Structural and functional diversity of rhizobacteria associated with Rauwolfia spp. across the Western Ghat regions of Karnataka, India.

PubMed

Prasanna Kumar, S P; Hariprasad, P; Brijesh Singh, S; Gowtham, H G; Niranjana, S R

2014-01-01

The present study carried out with denaturing gradient gel electrophoresis of DNA extracted from rhizosphere soils of Rauwolfia spp. collected from Western Ghat (WG) regions of Karnataka indicated that Pseudomonas sp. was prevalently found followed by Methylobacterium sp., Bacillus sp. and uncultured bacteria. A total of 200 rhizobacteria were isolated from 58 rhizosphere soil samples comprising of 15 different bacterial genera. The Shannon Weaver diversity index (H') and Simpson's diversity index (D) were found to be 2.57 and 0.91 for cultivable bacteria, respectively. The total species richness of cultivable rhizobacteria was high in Coorg district comprising 15 bacterial genera while in Mysore district, four bacterial genera were recorded. Rarefaction curve analysis also indicated the presence of higher species richness in samples of Shimoga and Coorg. All the rhizobacteria were screened for their multiple plant growth promotion and disease suppression traits. The results revealed that 70% of the isolates colonized tomato roots, 42% produced indole acetic acid, 55% solubilized phosphorus, while 43, 22, 27, 19, 40, 15 and 44% produced siderophore, salicylic acid, hydrogen cyanide, chitinase, phytase, cellulase and protease, respectively. Rhizobacterial isolates showing antagonistic activity against Fusarium oxysporum and Aspergillus flavus were 53 and 33%, respectively. Plant growth promotion studies revealed that most of the isolates increased percent germination with significantly higher vigour index as compared to untreated control. Most predominant rhizobacteria found in the rhizospheres of Rauwolfia spp. of WG regions are potential PGPR which can serve as biofertilizers and biopesticides.

Airborne microorganisms cultivable on naturally ventilated document repositories of the National Archive of Cuba.

PubMed

Borrego, Sofía; Perdomo, Ivette

2016-02-01

The quality of the indoor air can provide very useful information for the artwork conservation. The aim of the study was to evaluate the microbial concentration inside six document repositories of the National Archive of the Republic of Cuba in two months of 1 year. The repositories are large, high, and have a natural cross-ventilation system. The microbial sampling was done in July 2010 (summer or rainy month) and February 2011 (winter or dry month) using the SAS Super 100 biocollector at 100 L/min. An appropriate selective culture media were used to isolate fungi and bacteria. A high total microbial concentration on the north side of the building in two studied months was observed. The fungal concentrations were significantly higher in July 2010 in all repositories, while the bacterial concentrations were significantly higher mostly in February 2011 only in repositories located on the first and second floor of the building. Eight fungal genera in the indoor air of all environments were isolated. Regardless of the side of the analyzed building, Penicillium, Aspergillus, and Cladosporium were the predominant genera. Aspergillus flavus and Aspergillus niger were the species isolated in almost all of the analyzed repositories in the studied months. Gram-positive bacteria prevailed among bacterial groups isolated from indoor air repositories, and some percentages corresponded to the genera Bacillus and Streptomyces. In Cuba, the temperature and relative humidity are high during the whole year but the natural ventilation plays an important role in retarding microbial growth on materials.

Basfia succiniciproducens gen. nov., sp. nov., a new member of the family Pasteurellaceae isolated from bovine rumen.

PubMed

Kuhnert, Peter; Scholten, Edzard; Haefner, Stefan; Mayor, Désirée; Frey, Joachim

2010-01-01

Gram-negative, coccoid, non-motile bacteria that are catalase-, urease- and indole-negative, facultatively anaerobic and oxidase-positive were isolated from the bovine rumen using an improved selective medium for members of the Pasteurellaceae. All strains produced significant amounts of succinic acid under anaerobic conditions with glucose as substrate. Phenotypic characterization and multilocus sequence analysis (MLSA) using 16S rRNA, rpoB, infB and recN genes were performed on seven independent isolates. All four genes showed high sequence similarity to their counterparts in the genome sequence of the patent strain MBEL55E, but less than 95 % 16S rRNA gene sequence similarity to any other species of the Pasteurellaceae. Genetically these strains form a very homogeneous group in individual as well as combined phylogenetic trees, clearly separated from other genera of the family from which they can also be separated based on phenotypic markers. Genome relatedness as deduced from the recN gene showed high interspecies similarities, but again low similarity to any of the established genera of the family. No toxicity towards bovine, human or fish cells was observed and no RTX toxin genes were detected in members of the new taxon. Based on phylogenetic clustering in the MLSA analysis, the low genetic similarity to other genera and the phenotypic distinction, we suggest to classify these bovine rumen isolates as Basfia succiniciproducens gen. nov., sp. nov. The type strain is JF4016(T) (=DSM 22022(T) =CCUG 57335(T)).

Biodeterioration Risk Threatens the 3100 Year Old Staircase of Hallstatt (Austria): Possible Involvement of Halophilic Microorganisms.

PubMed

Piñar, Guadalupe; Dalnodar, Dennis; Voitl, Christian; Reschreiter, Hans; Sterflinger, Katja

2016-01-01

The prosperity of Hallstatt (Salzkammergut region, Austria) is based on the richness of salt in the surrounding mountains and salt mining, which is documented as far back as 1500 years B.C. Substantial archaeological evidence of Bronze and Iron Age salt mining has been discovered, with a wooden staircase (1108 B.C.) being one of the most impressive and well preserved finds. However, after its discovery, fungal mycelia have been observed on the surface of the staircase, most probably due to airborne contamination after its find. As a basis for the further preservation of this valuable object, the active micro-flora was examined to investigate the presence of potentially biodegradative microorganisms. Most of the strains isolated from the staircase showed to be halotolerant and halophilic microorganisms, due to the saline environment of the mine. Results derived from culture-dependent assays revealed a high fungal diversity, including both halotolerant and halophilic fungi, the most dominant strains being members of the genus Phialosimplex (synonym: Aspergillus). Additionally, some typical cellulose degraders, namely Stachybotrys sp. and Cladosporium sp. were detected. Numerous bacterial strains were isolated and identified as members of 12 different genera, most of them being moderately halophilic species. The most dominant isolates affiliated with species of the genera Halovibrio and Marinococcus. Halophilic archaea were also isolated and identified as species of the genera Halococcus and Halorubrum. Molecular analyses complemented the cultivation assays, enabling the identification of some uncultivable archaea of the genera Halolamina, Haloplanus and Halobacterium. Results derived from fungi and bacteria supported those obtained by cultivation methods, exhibiting the same dominant members in the communities. The results clearly showed the presence of some cellulose degraders that may become active if the requirements for growth and the environmental conditions turn suitable; therefore, these microorganisms must be regarded as a threat to the wood.

Rapid identification of Campylobacter, Arcobacter, and Helicobacter isolates by PCR-restriction fragment length polymorphism analysis of the 16S rRNA gene.

PubMed

Marshall, S M; Melito, P L; Woodward, D L; Johnson, W M; Rodgers, F G; Mulvey, M R

1999-12-01

A rapid two-step identification scheme based on PCR-restriction fragment length polymorphism (PCR-RFLP) analysis of the 16S rRNA gene was developed in order to differentiate isolates belonging to the Campylobacter, Arcobacter, and Helicobacter genera. For 158 isolates (26 reference cultures and 132 clinical isolates), specific RFLP patterns were obtained and species were successfully identified by this assay.

Detection, isolation, and characterization of acidophilic methanotrophs from Sphagnum mosses.

PubMed

Kip, Nardy; Ouyang, Wenjing; van Winden, Julia; Raghoebarsing, Ashna; van Niftrik, Laura; Pol, Arjan; Pan, Yao; Bodrossy, Levente; van Donselaar, Elly G; Reichart, Gert-Jan; Jetten, Mike S M; Damsté, Jaap S Sinninghe; Op den Camp, Huub J M

2011-08-15

Sphagnum peatlands are important ecosystems in the methane cycle. Methane-oxidizing bacteria in these ecosystems serve as a methane filter and limit methane emissions. Yet little is known about the diversity and identity of the methanotrophs present in and on Sphagnum mosses of peatlands, and only a few isolates are known. The methanotrophic community in Sphagnum mosses, originating from a Dutch peat bog, was investigated using a pmoA microarray. A high biodiversity of both gamma- and alphaproteobacterial methanotrophs was found. With Sphagnum mosses as the inoculum, alpha- and gammaproteobacterial acidophilic methanotrophs were isolated using established and newly designed media. The 16S rRNA, pmoA, pxmA, and mmoX gene sequences showed that the alphaproteobacterial isolates belonged to the Methylocystis and Methylosinus genera. The Methylosinus species isolated are the first acid-tolerant members of this genus. Of the acidophilic gammaproteobacterial strains isolated, strain M5 was affiliated with the Methylomonas genus, and the other strain, M200, may represent a novel genus, most closely related to the genera Methylosoma and Methylovulum. So far, no acidophilic or acid-tolerant methanotrophs in the Gammaproteobacteria class are known. All strains showed the typical features of either type I or II methanotrophs and are, to the best of our knowledge, the first isolated (acidophilic or acid-tolerant) methanotrophs from Sphagnum mosses.

[Diversity of endophytic fungi associated with Ferula sinkiangensis K. M. Shen].

PubMed

Sun, Li; Zhu, Jun; Li, Xiaojin; Shi, Shubing; Guo, Shunxing

2014-08-04

We studied the diversity of endophytic fungi associated with Ferula sinkiangensis K. M. Shen. Endophytic fungi from different years (1-2 years, 3-4 years and > 5 years) and different parts (root, stemand leaf) of Ferula sinkiangensis K. M. Shen were isolated by tissue expand method. Strains were classified by morphology and similarity of internal transcribed spacer (ITS) sequence by Clustal X method. Composition, diversity and preference of endophytic fungal community were analyzed by the isolation rate (IR), isolation frequency (IF), Shannon-Wiener biodiversity index (H'), Margalef Richness index (R). In total 140 endophytic fungi were isolated from F. sinkiangensis K. M. Shen and classified into 18 genera. Among the 140 isolates, Aureobasidium (25.7%), Alternaria (16.4%) and Phyllosticta (15.7%) were the dominant genera. The isolation results show that there were some notable differences between distribution and composition of the endophytic fungi isolated from different years and different parts of Ferula sinkiangensis K. M. Shen. Meanwhile, a certain degree of years and tissue preference were also obvious. The results obtained in this study will be helpful to exploit the endophytic fungal resources of Ferula sinkiangensis K. M. Shen, which can also provide a new way for the realization of the artificial breeding of Ferula sinkiangensis K. M. Shen.

The pathogen biology, identification and management of Rhizoctonia species with emphasis on isolates infecting turfgrasses

USDA-ARS?s Scientific Manuscript database

R. solani is an economically important soilborne basidiomycetous pathogen of worldwide distribution and it is known to attack at least 188 species of higher plants, including crops, vegetables, ornamentals, forest trees and turfgrasses. The pathogenic isolates may belong to multiple genera and speci...

Presence and distribution of yeasts in the reproductive tract in healthy female horses.

PubMed

Azarvandi, A; Khosravi, A R; Shokri, H; Talebkhan Garoussi, M; Gharahgouzlou, F; Vahedi, G; Sharifzadeh, A

2017-09-01

Yeasts are commensal organisms found in the reproductive and gastrointestinal tracts, and on the skin and other mucosa in mammals. The purpose of this study was to isolate and identify yeast flora in the caudal reproductive tract in healthy female horses. Longitudinal study. A total of 453 samples were collected using double-guarded swabs from the vestibule, clitoral fossa and vagina in 151 horses. All samples were cultured on Sabouraud 4% dextrose agar and incubated at 35°C for 7-10 days. Isolates were identified according to their morphological characteristics and biochemical profiles. Yeast colonies were isolated from 60 (39.7%) of the 151 horses. The isolated yeasts belonged to nine genera, and included Candida spp. (53.2%), Cryptococcus spp. (12.2%), Saccharomyces spp. (10.5%), Geotrichum spp. (8.0%), Rhodotorula spp. (7.1%), Malassezia spp. (3.7%), Trichosporon spp. (2.6%), Kluyveromyces spp. (2.6%) and Sporothrix spp. (0.2%). Candida krusei (43.1%) was the most frequent Candida species isolated. There was a significant difference in prevalence between C. krusei and other Candida species (P<0.05). The vestibule contained more yeast isolates (48.0%) than the vagina (18.3%). The isolation of yeast colonies from multiparous females (76.8%) was significantly higher than from maiden mares (P<0.05). The study was limited by the difficulty of distinguishing between normal flora and potential pathogens. Candida spp., in particular C. krusei, represent important flora resident in the caudal reproductive tract in healthy female horses. This is particularly important in contexts that require the initiation of empirical treatment prior to the completion of culture results. © 2016 EVJ Ltd.

First Preliminary Report on Isolation and Characterization of Novel Acinetobacter spp. in Casing Soil Used for Cultivation of Button Mushroom, Agaricus bisporus (Lange) Imbach

PubMed Central

Choudhary, D. K.

2011-01-01

Despite evaluation of large number of agroindustrial wastes for their use as casing material for Agaricus bisporus (Lange) Imbach cultivation, scant attention has been given to the importance of biological properties of casing materials. In the present study, an attempt was made to characterize the bacterial flora in casing layer, namely, Farm Yard Manure (FYM) and Spent Mushroom Substrate/spent compost (SMS/SC) (FYM+SC, 3 : 1) and FYM and Vermi Compost (VC) (FYM+VC, 3 : 1), employing partial 16S rDNA sequencing. Available data showed a significant variety of organisms that included Acinetobacter and Pseudomonas of the γ-proteobacteria, that were the most frequently encountered genera. This is the first preliminary report on the microbial diversity of casing soils and demonstrates the presence of Acinetobacter spp. that has not been previously described in casing material. PMID:22007222

Identification of Aerobic Gram-Positive Bacilli by Use of Vitek MS

PubMed Central

Navas, Maria; Pincus, David H.; Wilkey, Kathy; Sercia, Linda; LaSalvia, Margaret; Wilson, Deborah; Procop, Gary W.

2014-01-01

The accuracy of Vitek MS mass spectrometric identifications was assessed for 206 clinically significant isolates of aerobic Gram-positive bacilli representing 20 genera and 38 species. The Vitek MS identifications were correct for 85% of the isolates (56.3% to the species level, 28.6% limited to the genus level), with misidentifications occurring for 7.3% of the isolates. PMID:24501030

Bacterial isolates from the bryozoan Membranipora membranacea: influence of culture media on isolation and antimicrobial activity.

PubMed

Heindl, Herwig; Thiel, Vera; Wiese, Jutta; Imhoff, Johannes F

2012-03-01

From specimens of the bryozoan Membranipora membranacea collected in the Baltic Sea, bacteria were isolated on four different media, which significantly increased the diversity of the isolated groups. All isolates were classified according to 16S rRNA gene sequence analysis and tested for antimicrobial properties using a panel of five indicator strains and six different media. Each medium featured a unique set of isolated phylotypes, and a phylogenetically diverse collection of isolates was obtained. A total of 96 isolates were assigned to 49 phylotypes and 29 genera. Only one-third of the members of these genera had been isolated previously from comparable sources. The isolates were affiliated with Alpha- and Gammaproteobacteria, Bacilli, and Actinobacteria. A comparable large portion of up to 22 isolates, i.e., 15 phylotypes, probably represent new species. Likewise, 47 isolates (approximately 50%) displayed antibiotic activities, mostly against grampositive indicator strains. Of the active strains, 63.8 % had antibiotic traits only on one or two of the growth media, whereas only 12.7 % inhibited growth on five or all six media. The application of six different media for antimicrobial testing resulted in twice the number of positive hits as obtained with only a single medium. The use of different media for the isolation of bacteria as well as the variation of media considered suitable for the production of antibiotic substances significantly enhanced both the number of isolates obtained and the proportion of antibiotic active cultures. Thus the approach described herein offers an improved strategy in the search for new antibiotic compounds.

Symbiosis within Symbiosis: Evolving Nitrogen-Fixing Legume Symbionts.

PubMed

Remigi, Philippe; Zhu, Jun; Young, J Peter W; Masson-Boivin, Catherine

2016-01-01

Bacterial accessory genes are genomic symbionts with an evolutionary history and future that is different from that of their hosts. Packages of accessory genes move from strain to strain and confer important adaptations, such as interaction with eukaryotes. The ability to fix nitrogen with legumes is a remarkable example of a complex trait spread by horizontal transfer of a few key symbiotic genes, converting soil bacteria into legume symbionts. Rhizobia belong to hundreds of species restricted to a dozen genera of the Alphaproteobacteria and Betaproteobacteria, suggesting infrequent successful transfer between genera but frequent successful transfer within genera. Here we review the genetic and environmental conditions and selective forces that have shaped evolution of this complex symbiotic trait. Copyright © 2015 Elsevier Ltd. All rights reserved.

Isolation and identification of culturable bacteria, capable of heterotrophic growth, from rapid sand filters of drinking water treatment plants.

PubMed

Vandermaesen, Johanna; Lievens, Bart; Springael, Dirk

The microbial community in sand filters (SFs) of drinking water treatment plants (DWTPs) likely contributes to SF functionalities, such as organic carbon removal through heterotrophic metabolism. However, the dynamics and functionality of the SF microbiome and microbial communities in oligotrophic freshwater environments in general, are poorly understood. Therefore, the availability of bacterial strains from these oligotrophic environments is of great interest, but such organisms are currently underrepresented in culture collections. Focusing on heterotrophic carbon metabolism, bacteria were isolated from SFs using conventional media and media that contained SF extracts to mimic the SF environment. The majority of isolates belonged to Betaproteobacteria, more specifically to the families Comamonadaceae (genera Acidovorax, Curvibacter, Hydrogenophaga, Simplicispira, Paucibacter, Pelomonas, Piscinibacter and Rhodoferax) and Oxalobacteraceae (Undibacterium). Additionally, members of Alphaproteobacteria (Mesorhizobium), Gammaproteobacteria (Aeromonas and Perlucidibaca) and Actinobacteria (Rhodococcus and Brachybacterium) were isolated. Several of those genera have only rarely been described, but appear typical inhabitants of oligotrophic freshwater environments. In this regard, the Comamonadaceae isolates are of particular interest. Our study shows that bacteria representative of oligotrophic environments can be isolated using simple isolation procedures. The isolates provide a microbial framework for extending our knowledge of the taxonomy, physiology and functionality of oligotrophic freshwater microbiomes and their interactions with possible invaders. Copyright © 2017 Institut Pasteur. Published by Elsevier Masson SAS. All rights reserved.

Evaluating fungal populations by genera/species on wide body commercial passenger aircraft and in airport terminals.

PubMed

McKernan, Lauralynn Taylor; Burge, Harriet; Wallingford, Kenneth M; Hein, Misty J; Herrick, Robert

2007-04-01

Given the potential health effects of fungi and the amount of time aircrew and passengers spend inside aircraft, it is important to study fungal populations in the aircraft environment. Research objectives included documenting the genera/species of airborne culturable fungal concentrations and total spore concentrations on a twin-aisle wide body commercial passenger aircraft. Twelve flights between 4.5 and 6.5 h in duration on Boeing 767 (B-767) aircraft were evaluated. Two air cooling packs and 50% recirculation rate (i.e. 50:50 mix of outside air and filtered inside air) were utilized during flight operations. Passenger occupancy rates varied from 67 to 100%. N-6 impactors and total spore traps were used to collect sequential, triplicate air samples in the front and rear of coach class during six sampling intervals throughout each flight: boarding, mid-climb, early cruise, mid-cruise, late cruise and deplaning. Comparison air samples were also collected inside and outside the airport terminals at the origin and destination cities resulting in a total of 522 culturable and 517 total spore samples. A total of 45 surface wipe samples were collected using swabs onboard the aircraft and inside the airport terminals. A variety of taxa were observed in the culturable and total spore samples. A frequency analysis of the fungal data indicated that Cladosporium, Aspergillus and Penicillium were predominant genera in the culturable samples whereas Cladosporium, Basidiospores and Penicillium/Aspergillus were predominant in the total spore samples. Fungal populations observed inside the aircraft were comprised of similar genera, detected significantly less frequently and with lower mean concentrations than those observed in typical office buildings. Although sources internal to the aircraft could not be ruled out, our data demonstrate the importance of passenger activity as the source of the fungi observed on aircraft. Isolated fungal peak events occurred occasionally when concentrations of a particular genus or species rose sharply inside the cabin for a limited period. Overall, our research demonstrates that on the sampled flights the B-767 filtration system operated efficiently to remove fungal spores when two air cooling packs and 50% recirculation rate were utilized during flight operations.

Comparison of ubiquitous antibiotic-resistant Enterobacteriaceae populations isolated from wastewaters, surface waters and drinking waters.

PubMed

Figueira, Vânia; Serra, Elizabete A; Vaz-Moreira, Ivone; Brandão, Teresa R S; Manaia, Célia M

2012-03-01

This study aimed at assessing the role of ubiquitous (non-Escherichia coli) Enterobacteriaceae in the dissemination of antimicrobial resistance through the urban water cycle. Enterobacteriaceae isolated from a municipal wastewater treatment plant (111 isolates), urban water streams (33 isolates) and drinking water (123 isolates) were compared in terms of: (i) genera distribution, (ii) resistance to 12 antibiotics, and (iii) class 1 and class 2 integrons. The predominant bacterial genera were the same in the different types of water, although with a distinct pattern of species. The most prevalent resistance phenotypes were observed for amoxicillin, ticarcillin, cephalothin and sulphamethoxazole (24-59% in the three types of water). No resistance against ceftazidime or meropenem was observed. Resistance to cephalothin, amoxicillin and sulphamethoxazole was significantly more prevalent in drinking water, water streams and wastewater, respectively, than in the other types of water. It was possible to recognize antibiotic-resistance associations, namely for the pairs streptomycin-tetracycline (positive) and ticarcillin-cephalotin (negative). Class 1 and/or class 2 integrons with similar gene cassettes were detected in the three types of water. This study demonstrated that Enterobacteriaceae are important vehicles of antibiotic resistance, namely in drinking water.

Culturable diversity of halophilic bacteria in foreshore soils

PubMed Central

Irshad, Aarzoo; Ahmad, Irshad; Kim, Seung Bum

2014-01-01

Halophilic bacteria are commonly found in natural environments containing significant concentration of NaCl such as inland salt lakes and evaporated sea-shore pools, as well as environments such as curing brines, salted food products and saline soils. Dependence on salt is an important phenotypic characteristic of halophilic bacteria, which can be used in the polyphasic characterization of newly discovered microorganisms. In this study the diversity of halophilic bacteria in foreshore soils of Daecheon, Chungnam, and Saemangeum, Jeonbuk, was investigated. Two types of media, namely NA and R2A supplemented with 3%, 5%, 9%, 15%, 20% and 30% NaCl were used. More than 200 halophilic bacteria were isolated and BOX-PCR fingerprinting analysis was done for the typing of the isolates. The BLAST identification results showed that isolated strains were composed of 4 phyla, Firmicutes (60%), Proteobacteria (31%), Bacteriodetes (5%) and Actinobacteria (4%). Isolates were affiliated with 16 genera and 36 species. Bacillus was the dominant genus in the phylum Firmicutes, comprising 24% of the total isolates. Halomonas (12%) and Shewanella (12%) were also found as the main genera. These findings show that the foreshore soil of Daecheon Beach and Saemangeum Sea of Korea represents an untapped source of bacterial biodiversity. PMID:25242943

Culturable diversity of halophilic bacteria in foreshore soils.

PubMed

Irshad, Aarzoo; Ahmad, Irshad; Kim, Seung Bum

2014-01-01

Halophilic bacteria are commonly found in natural environments containing significant concentration of NaCl such as inland salt lakes and evaporated sea-shore pools, as well as environments such as curing brines, salted food products and saline soils. Dependence on salt is an important phenotypic characteristic of halophilic bacteria, which can be used in the polyphasic characterization of newly discovered microorganisms. In this study the diversity of halophilic bacteria in foreshore soils of Daecheon, Chungnam, and Saemangeum, Jeonbuk, was investigated. Two types of media, namely NA and R2A supplemented with 3%, 5%, 9%, 15%, 20% and 30% NaCl were used. More than 200 halophilic bacteria were isolated and BOX-PCR fingerprinting analysis was done for the typing of the isolates. The BLAST identification results showed that isolated strains were composed of 4 phyla, Firmicutes (60%), Proteobacteria (31%), Bacteriodetes (5%) and Actinobacteria (4%). Isolates were affiliated with 16 genera and 36 species. Bacillus was the dominant genus in the phylum Firmicutes, comprising 24% of the total isolates. Halomonas (12%) and Shewanella (12%) were also found as the main genera. These findings show that the foreshore soil of Daecheon Beach and Saemangeum Sea of Korea represents an untapped source of bacterial biodiversity.

A new species of Rhytidognathus (Carabidae, Migadopini) from Argentina

PubMed Central

Roig-Juñent, Sergio; Rouaux, Julia

2012-01-01

Abstract The Migadopini are a small tribe of Carabidae with 47 species that occur in South America, Australia, and New Zealand, in the sub-Antarctic areas. In South America, most of the genera inhabit areas related to sub-Antartic Nothofagus forest except two monogeneric genera, the Ecuadorian genus Aquilex Moret and the Pampean genus Rhytidognathus Chaudoir. These two genera are geographically isolated from the remaining five South American genera. New material of Rhytidognathus from the northeast of Buenos Aires province and from Entre Ríos province permits establishing that the previous records of Rhytidognathus ovalis (Dejean) for Argentina were erroneous and that it belongs to a new species. Based on external morphological characters and from male and female genitalia we describe Rhytidognathus platensis as a new species. In this contribution we provide illustrations, keys, habitat characteristics and some biogeographic considerations on the distribution of Rhytidognathus. PMID:23275755

A new species of Rhytidognathus (Carabidae, Migadopini) from Argentina.

PubMed

Roig-Juñent, Sergio; Rouaux, Julia

2012-01-01

The Migadopini are a small tribe of Carabidae with 47 species that occur in South America, Australia, and New Zealand, in the sub-Antarctic areas. In South America, most of the genera inhabit areas related to sub-Antartic Nothofagus forest except two monogeneric genera, the Ecuadorian genus Aquilex Moret and the Pampean genus Rhytidognathus Chaudoir. These two genera are geographically isolated from the remaining five South American genera. New material of Rhytidognathus from the northeast of Buenos Aires province and from Entre Ríos province permits establishing that the previous records of Rhytidognathus ovalis (Dejean) for Argentina were erroneous and that it belongs to a new species. Based on external morphological characters and from male and female genitalia we describe Rhytidognathus platensis as a new species. In this contribution we provide illustrations, keys, habitat characteristics and some biogeographic considerations on the distribution of Rhytidognathus.

Baobabopsis, a new genus of graminicolous downy mildews from tropical Australia, with an updated key to the genera of downy mildews.

PubMed

Thines, Marco; Telle, Sabine; Choi, Young-Joon; Tan, Yu Pei; Shivas, Roger G

2015-12-01

So far 19 genera of downy mildews have been described, of which seven are parasitic to grasses. Here, we introduce a new genus, Baobabopsis, to accommodate two distinctive downy mildews, B. donbarrettii sp. nov., collected on Perotis rara in northern Australia, and B. enneapogonis sp. nov., collected on Enneapogon spp. in western and central Australia. Baobabopsis donbarrettii produced both oospores and sporangiospores that are morphologically distinct from other downy mildews on grasses. Molecular phylogenetic analyses showed that the two species of Baobabopsis occupied an isolated position among the known genera of graminicolous downy mildews. The importance of the Poaceae for the evolution of downy mildews is highlighted by the observation that more than a third of the known genera of downy mildews occur on grasses, while more than 90 % of the known species of downy mildews infect eudicots.

General and specialized media routinely employed for primary isolation of bacterial pathogens of fishes

USGS Publications Warehouse

Starliper, C.E.

2008-01-01

There are a number of significant diseases among cultured and free-ranging freshwater fishes that have a bacterial etiology; these represent a variety of gram-negative and gram-positive genera. Confirmatory diagnosis of these diseases involves primary isolation of the causative bacterium on bacteriologic media. Frequently used "general" bacteriologic media simply provide the essential nutrients for growth. For most of the major pathogens, however, there are differential and/or selective media that facilitate primary recovery. Some specialized media are available as "ready-to-use" from suppliers, while others must be prepared. Differential media employ various types of indicator systems, such as pH indicators, that allow diagnosticians to observe assimilation of selected substrates. An advantage to the use of differential media for primary isolation is that they hasten bacterial characterization by yielding the appropriate positive or negative result for a particular substrate, often leading to a presumptive identification. Selective media also incorporate agent(s) that inhibit the growth of contaminants typically encountered with samples from aquatic environments. Media that incorporate differential and/or selective components are ideally based on characters that are unique to the targeted bacterium, and their use can reduce the time associated with diagnosis and facilitate early intervention in affected fish populations. In this review, the concepts of general and differential/selective bacteriologic media and their use and development for fish pathogens are discussed. The media routinely employed for primary isolation of the significant bacterial pathogens of fishes are presented. ?? Wildlife Disease Association 2008.

Survival of epiphytic bacteria from seed stored on the Long Duration Exposure Facility (LDEF)

NASA Technical Reports Server (NTRS)

Schuerger, Andrew C.; Norman, Bret L.; Angelo, Joseph A., Jr.

1991-01-01

This study was designed to determine the survival of microorganisms exposed to the relatively harsh conditions found in low Earth orbit (LEO). Seed of corn, sunflower, canteloupe, zucchini, bean, pea, and pumpkin cultivars were packaged in two 18 x 2.5 cm aluminum tubes; wall thickness for each tube was 1.33 mm. One seed tube was attacked to payload M0006, tray C-2; a second tube was stored at room temperature in a lab on Earth. Five lithium fluoride thermoluminescent dosimetry wafers (TLD-100 wafers) were placed in each aluminum tube. The total mean dosages for flight and ground-control TLD wafers were 210.0 and 0.9 rads, respectively. Seeds were washed for 2 hrs in a phosphate buffered saline solution. Bacteria were isolated by plating samples of the seed-washings onto dilute tryptic soy agar. Pure isolates of morphologically distinct bacteria were obtained by standard microbiological procedures. Bacteria were grouped according to colony-type and preliminary identification was completed using a fatty-acid analysis system. Bacillus spp. were the primary microoganisms that survived on seed during the experiment. Bacterial diversity and relative abundance were similar for the ground flight seed. Bacillus subtilus, B. pumilus, B. licheniformis, B. polymyxa, B. megaterium, and B. pabuli were isolated most frequently. Members of the genera Kurthia, Listeria, Micrococcus, and Arthrobacter were also isolated from flight and ground control seed. Results support the hypothesis that terrestrial microorganisms can survive long periods of time in the relatively harsh LEO environment.

Relationship between wood-inhabiting fungi and Reticulitermes spp

Treesearch

Grant T. Kirker; Terence Wagner; Susan Diehl

2012-01-01

Fungi from coarse woody debris samples containing or lacking termites were isolated, and identified from upland and bottomland hardwoods and pines in northeast Mississippi. Samples yielded 860 unique fungal isolates, with 59% identified to genus level. Four phyla, six classes, 10 orders, 14 families, and 50 genera were recovered. The fungal groups encountered by...

The contribution of endophytic bacteria to Albizia lebbeck-mediated phytoremediation of tannery effluent contaminated soil.

PubMed

Manikandan, Muthu; Kannan, Vijayaraghavan; Mendoza, Ordetta Hannah; Kanimozhi, Mahalingam; Chun, Sechul; Pašić, Lejla

2016-01-01

Toxicity of chromium often impairs the remediation capacity of plants used in phytoremediation of polluted soils. In this study, we have identified Albizia lebbeck as a prospective chromium hyperaccumulator and examined cultivable diversity of endophytes present in chromium-treated and control saplings. High numbers (22-100%) of endophytic bacteria, isolated from root, stem, and leaf tissues, could tolerate elevated (1-3 mM) concentrations of K2CrO7. 16S rRNA gene sequence-based phylogenetic analysis showed that the 118 isolates obtained comprised of 17 operational taxonomic units affiliated with the proteobacterial genera Rhizobium (18%), Marinomonas (1%), Pseudomonas (16%), and Xanthomonas (7%) but also with members of Firmicutes genera, such as Bacillus (35%) and Salinococcus (3%). The novel isolates belonging to Salinococcus and Bacillus could tolerate high K2CrO7 concentrations (3 mM) and also showed elevated activity of chromate reductase. In addition, majority (%) of the endophytic isolates also showed production of indole-3-acetic acid. Taken together, our results indicate that the innate endophytic bacterial community assists plants in reducing heavy metal toxicity.

Enrichment and identification of naphthalene-degrading bacteria from the Persian Gulf.

PubMed

Hassanshahian, Mehdi; Boroujeni, Negar Amini

2016-06-15

Naphthalene is a ubiquitous pollutant of the marine environment, and naphthalene biodegradation has been receiving constant scientific consideration. For cleanup of aromatic contaminated sites, bioremediation methods are considered as economical and safe approaches for the marine environment. The aims of this research are isolation and characterization of naphthalene-degrading bacteria from some marine samples of the Persian Gulf. Fifty four naphthalene-degrading bacteria were isolated from marine samples (sediment and seawater) that are enriched in ONR7a medium with naphthalene as the only carbon source. Some screening tests such as growth at high concentration of naphthalene, bioemulsifier production and surface hydrophobicity were done to select the best and prevalent strains for naphthalene degradation. Determination of the nucleotide sequence of the gene encoding for 16S rRNA shows that these isolated strains belong to these genera: Shewanella, Salegentibacter, Halomonas, Marinobacter, Oceanicola, Idiomarina and Thalassospira. These strains can degrade half of the percentage of naphthalene in 10days of incubation. This research is the first report on isolation of these genera from the Persian Gulf as naphthalene-degrader. Copyright © 2016 Elsevier Ltd. All rights reserved.

Moulds contaminants on Norwegian dry-cured meat products.

PubMed

Asefa, Dereje T; Gjerde, Ragnhild O; Sidhu, Maan S; Langsrud, Solveig; Kure, Cathrine F; Nesbakken, Truls; Skaar, Ida

2009-01-15

Dry-cured meat production has a long tradition in Norway. However, uncontrolled mould growth on the surface of the dry-cured meat products is causing significant quality problems. As some moulds are mycotoxigenic, their growth on the dry-cured meat products could also pose a serious health risk. Such quality problems and potential health risks can be better handled if the types of moulds growing on the products are known. In total, 161 samples were collected from the ripening and packaging stages of production with the aim of identifying moulds contaminating smoked and unsmoked Norwegian dry-cured meat products. Moulds were isolated either by transferring aerial mycelium of each visible mould colonies on the products or by directly plating pieces of meat on suitable agar media. The isolates were identified at a species level by a polyphasic approach. In total, 264 isolates belonging to 20 species and four fungal genera were identified. The genus Penicillium covered 88.3% of the total isolates. This genus contributed to the isolates of smoked and unsmoked products by 91% and 84% respectively. Penicillium nalgiovense was the dominant species isolated from both smoked and unsmoked products and covered 38% of the total isolates. Penicillium solitum and P. commune were the next most frequently isolated species with a contribution of 13% and 10% respectively. Species of Cladosporium and Eurotium contributed to the total isolates by 6% and 4.9% respectively. Smoking seems to affect the growth of these dominating species differently. An increase in the isolation frequency of P. nalgiovense accompanied by the reduction in the occurrence of P. solitum, P. commune and species of Cladosporium was observed on smoked products. The survey showed that the species of Penicillium are associated with Norwegian dry-cured meat products in general. Penicillium nalgiovense, the dominating mould species, is a potential producer of penicillin and its presence could represent a threat to allergic consumers.

[Selective-differential nutrient medium "Shewanella IRHLS agar" for isolation of Shewanella genus bacteria].

PubMed

Sivolodsky, E P

2015-01-01

Development of a selective-differential nutrient medium for isolation of Shewanella genus bacteria. 73 strains of Shewanella bacteria (S. algae--3, S. baltica--26, S. putrefaciens--44) and 80 strains of 22 other bacteria genera were used. Shewanella species were identified by methods and criteria proposed by Nozue H. et al., 1992; Khashe S. et al., 1998. Nutrient media "Shewanella IRHLS Agar" for shewanella isolation was developed. Medium selective factors: irgazan DP-300 (I). 0.14-0.2 g/l and rifampicin (R) 0.0005-0.001 g/l. Shevanella colonies were detected by the production of hydrogen sulfide (H), lipase presence (L), lack of sorbitol fermentation (S). The medium suppressed the growth of hydrogen sulfide producers (Salmonella, Proteus) and blocked hydrogen sulfide production by Citrobacter. Growth of Escherichia, Enterobacter, Klebsiella, Shigella, Staphylococcus, Bacillus was also suppressed, Analytical sensitivity of the medium was 1-2 CFU/ml for Shewanella and Stenotrophomonas, Aerombnas, Serratia genera bacteria. 72 strains of Shewanella were isolated from water of Neva river in this medium, 91.7 ± 3.2% of those produced H2S. 1 strain of S. algae was isolated from clinical material. The developed media allows to use it in a complex for Stenotrophomo- nas sp., Aeromonas sp., Serratia sp., Citrobactersp. and Shewanella bacteria isolation.

High frequency of silver resistance genes in invasive isolates of Enterobacter and Klebsiella species.

PubMed

Sütterlin, S; Dahlö, M; Tellgren-Roth, C; Schaal, W; Melhus, Å

2017-07-01

Silver-based products have been marketed as an alternative to antibiotics, and their consumption has increased. Bacteria may, however, develop resistance to silver. To study the presence of genes encoding silver resistance (silE, silP, silS) over time in three clinically important Enterobacteriaceae genera. Using polymerase chain reaction (PCR), 752 bloodstream isolates from the years 1990-2010 were investigated. Age, gender, and ward of patients were registered, and the susceptibility to antibiotics and silver nitrate was tested. Clonality and single nucleotide polymorphism were assessed with repetitive element sequence-based PCR, multi-locus sequence typing, and whole-genome sequencing. Genes encoding silver resistance were detected most frequently in Enterobacter spp. (48%), followed by Klebsiella spp. (41%) and Escherichia coli 4%. Phenotypical resistance to silver nitrate was found in Enterobacter (13%) and Klebsiella (3%) isolates. The lowest carriage rate of sil genes was observed in blood isolates from the neonatology ward (24%), and the highest in blood isolates from the oncology/haematology wards (66%). Presence of sil genes was observed in international high-risk clones. Sequences of the sil and pco clusters indicated that a single mutational event in the silS gene could have caused the phenotypic resistance. Despite a restricted consumption of silver-based products in Swedish health care, silver resistance genes are widely represented in clinical isolates of Enterobacter and Klebsiella species. To avoid further selection and spread of silver-resistant bacteria with a high potential for healthcare-associated infections, the use of silver-based products needs to be controlled and the silver resistance monitored. Copyright © 2017 The Healthcare Infection Society. Published by Elsevier Ltd. All rights reserved.

Phylogeny and taxonomic revision of the Planistromellaceae including its coelomycetous anamorphs: contributions towards a monograph of the genus Kellermania.

PubMed

Minnis, A M; Kennedy, A H; Grenier, D B; Palm, M E; Rossman, A Y

2012-12-01

The core species of the family Planistromellaceae are included in the teleomorphic genera Planistroma and Planistromella and the connected anamorphic, coelomycetous genera Alpakesa, Kellermania, and Piptarthron. These genera have been defined primarily on the basis of ascospore septation or number of conidial appendages. Due to a lack of DNA sequence data, phylogenetic placement of these genera within the Dothideomycetes, evaluation of monophyly, and questions about generic boundaries could not be adequately addressed in the past. Isolates of nearly all of the known species in these genera were studied genetically and morphologically. DNA sequence data were generated for the nSSU, ITS, nLSU, and RPB1 markers and analysed phylogenetically. These results placed the Planistromellaceae, herein recognised as a distinct family, in an unresolved position relative to other genera within the order Botryosphaeriales. Species representing the core genera of the Planistromellaceae formed a clade and evaluation of its topology revealed that previous morphology-based definitions of genera resulted in an artificial classification system. Alpakesa, Kellermania, Piptarthron, Planistroma, and Planistromella are herein recognised as belonging to the single genus Kellermania. The following new combinations are proposed: Kellermania crassispora, K. dasylirionis, K. macrospora, K. plurilocularis, and K. unilocularis. Five new species are described, namely K. con- fusa, K. dasylirionicola, K. micranthae, K. ramaleyae, and K. rostratae. Descriptions of species in vitro and a key to species known from culture are provided.

PRELIMINARY SURVEY OF ENTOMOPATHOGENIC NEMATODES IN UPPER NORTHERN THAILAND.

PubMed

Vitta, Apichat; Fukruksa, Chamaiporn; Yimthin, Thatcha; Deelue, Kitsakorn; Sarai, Chutima; Polseela, Raxsina; Thanwisai, Aunchalee

2017-01-01

Entomopathogenic nematodes (EPNs) of the genera Steinernema and Heterorhabditis are used as biocontrol agents for insect pests. Survey of indigenous EPNs provides not only the diversity aspects but also the contribution in pest management in local areas. The objective of this study was to survey EPNs in upper northern Thailand. Nine hundred seventy soil samples were obtained from 194 sites in upper northern region of Thailand; of these 60 (6.2%) had EPNs in 2 genera: Steinernema (32 isolates) and Heterorhabditis (28 isolates). Most EPNs were isolated from loam with a soil temperature of 24-38°C, a pH of 1.5-7.0 and a soil moisture content of 0.5-6.8%. Molecular identification based on sequencing of a partial region of an internal transcribed spacer was performed for Heterorhabditis and the 28S rDNA for Steinernema. A BLASTN search of known sequence EPNs revealed 24 isolates of S. websteri and one isolate of S. scarabaei were identified; closely related to S. websteri (accession no. JF503100) and S. scarabaei (accession no. AY172023). The Heterorhabditis species identified were: H. indica (11 isolates), H. gerrardi (2 isolates) and Heterorhabditis sp (8 isolates). Phylogenetic analysis revealed 11 isolates of Heterorhabditis were related to H. indica; 2 isolates were related to Heterorhabditis gerrardi and 8 isolates were closely related to Heterorhabditis sp SGmg3. The study results show the genetic diversity of EPNs and describe a new observation of S. scarabaei and H. gerrardi in Thailand. This finding is new and provides important information for further study on using native EPNs in biological control.

Detection, Isolation, and Characterization of Acidophilic Methanotrophs from Sphagnum Mosses ▿ †

PubMed Central

Kip, Nardy; Ouyang, Wenjing; van Winden, Julia; Raghoebarsing, Ashna; van Niftrik, Laura; Pol, Arjan; Pan, Yao; Bodrossy, Levente; van Donselaar, Elly G.; Reichart, Gert-Jan; Jetten, Mike S. M.; Sinninghe Damsté, Jaap S.; Op den Camp, Huub J. M.

2011-01-01

Sphagnum peatlands are important ecosystems in the methane cycle. Methane-oxidizing bacteria in these ecosystems serve as a methane filter and limit methane emissions. Yet little is known about the diversity and identity of the methanotrophs present in and on Sphagnum mosses of peatlands, and only a few isolates are known. The methanotrophic community in Sphagnum mosses, originating from a Dutch peat bog, was investigated using a pmoA microarray. A high biodiversity of both gamma- and alphaproteobacterial methanotrophs was found. With Sphagnum mosses as the inoculum, alpha- and gammaproteobacterial acidophilic methanotrophs were isolated using established and newly designed media. The 16S rRNA, pmoA, pxmA, and mmoX gene sequences showed that the alphaproteobacterial isolates belonged to the Methylocystis and Methylosinus genera. The Methylosinus species isolated are the first acid-tolerant members of this genus. Of the acidophilic gammaproteobacterial strains isolated, strain M5 was affiliated with the Methylomonas genus, and the other strain, M200, may represent a novel genus, most closely related to the genera Methylosoma and Methylovulum. So far, no acidophilic or acid-tolerant methanotrophs in the Gammaproteobacteria class are known. All strains showed the typical features of either type I or II methanotrophs and are, to the best of our knowledge, the first isolated (acidophilic or acid-tolerant) methanotrophs from Sphagnum mosses. PMID:21724892

Description of Groenewaldozyma gen. nov. for placement of Candida auringiensis, Candida salmanticensis and Candida tartarivorans.

PubMed

Kurtzman, Cletus P

2016-07-01

DNA sequence analyses have demonstrated that species of the polyphyletic anamorphic ascomycete genus Candida may be members of described teleomorphic genera, members of the Candida tropicalis clade upon which the genus Candida is circumscribed, or members of isolated clades that represent undescribed genera. From phylogenetic analysis of gene sequences from nuclear large subunit rRNA, mitochondrial small subunit rRNA and cytochrome oxidase II, Candida auringiensis (NRRL Y-17674(T), CBS 6913(T)), Candida salmanticensis (NRRL Y-17090(T), CBS 5121(T)), and Candida tartarivorans (NRRL Y-27291(T), CBS 7955(T)) were shown to be members of an isolated clade and are proposed for reclassification in the genus Groenewaldozyma gen. nov. (MycoBank MB 815817). Neighbouring taxa include species of the Wickerhamiella clade and Candida blankii.

PCR-based approach to SINE isolation: simple and complex SINEs.

PubMed

Borodulina, Olga R; Kramerov, Dmitri A

2005-04-11

Highly repeated copies of short interspersed elements (SINEs) occur in eukaryotic genomes. The distribution of each SINE family is usually restricted to some genera, families, or orders. SINEs have an RNA polymerase III internal promoter, which is composed of boxes A and B. Here we propose a method for isolation of novel SINE families based on genomic DNA PCR with oligonucleotide identical to box A as a primer. Cloning of the size-heterogeneous PCR-products and sequencing of their terminal regions allow determination of SINE structure. Using this approach, two novel SINE families, Rhin-1 and Das-1, from the genomes of great horseshoe bat (Rhinolophus ferrumequinum) and nine-banded armadillo (Dasypus novemcinctus), respectively, were isolated and studied. The distribution of Rhin-1 is restricted to two of six bat families tested. Copies of this SINE are characterized by frequent internal insertions and significant length (200-270 bp). Das-1 being only 90 bp in length is one of the shortest SINEs known. Most of Das-1 nucleotide sequences demonstrate significant similarity to alanine tRNA which appears to be an evolutionary progenitor of this SINE. Together with three other known SINEs (ID, Vic-1, and CYN), Das-1 constitutes a group of simple SINEs. Interestingly, three SINE families of this group are alanine tRNA-derived. Most probably, this tRNA gave rise to short and simple but successful SINEs several times during mammalian evolution.

Occurrence of Pasteuria spp. in Florida

PubMed Central

Hewlett, T. E.; Cox, R.; Dickson, D. W.; Dunn, R. A.

1994-01-01

Two years of data collected from the Florida Nematode Assay Laboratory of the Florida Cooperative Extension Service and 4 years of data from the Florida Department of Agriculture and Consumer Services, Division of Plant Industry, were compiled to find out the distribution of Pasteuria spp. on nematodes in Florida soils. Information recorded came from 335 samples and included nematode genera with Pasteuria endospores attached, host plants associated with the samples, and the origins of the samples. Pasteuria spp. were detected on 14 different plant-parasitic nematode genera in 41 Florida counties and associated with over 39 different plant species and in seven fallow fields. Pasteuria-infected nematodes were associated with a wide range of plant hosts, although frequency of associations with these hosts reflected the sample bias of the laboratories involved. Meloidogyne and Hoplolaimus spp. were the two nematode genera most frequently associated with Pasteuria. Pasteuria spp. were observed attached to members of these two genera in 176 and 59 soil samples, respectively. PMID:19279936

Diverse Bacteria with Lignin Degrading Potentials Isolated from Two Ranks of Coal

PubMed Central

Wang, Lu; Nie, Yong; Tang, Yue-Qin; Song, Xin-Min; Cao, Kun; Sun, Li-Zhu; Wang, Zhi-Jian; Wu, Xiao-Lei

2016-01-01

Taking natural coal as a “seed bank” of bacterial strains able to degrade lignin that is with molecular structure similar to coal components, we isolated 393 and 483 bacterial strains from a meager lean coal sample from Hancheng coalbed and a brown coal sample from Bayannaoer coalbed, respectively, by using different media. Statistical analysis showed that isolates were significantly more site-specific than medium-specific. Of the 876 strains belonging to 27 genera in Actinobacteria, Firmicutes, and Proteobacteria, 612 were positive for lignin degradation function, including 218 strains belonging to 35 species in Hancheng and 394 strains belonging to 19 species in Zhongqi. Among them, the dominant lignin-degrading strains were Thauera (Hancheng), Arthrobacter (Zhongqi) and Rhizobium (both). The genes encoding the laccases- or laccase-like multicopper oxidases, key enzymes in lignin production and degradation, were detected in three genera including Massila for the first time, which was in high expression by real time PCR (qRT-PCR) detection, confirming coal as a good seed bank. PMID:27667989

Novel squalene-producing thraustochytrids found in mangrove water.

PubMed

Otagiri, Masato; Khalid, Ammara; Moriya, Shigeharu; Osada, Hiroyuki; Takahashi, Shunji

2017-10-01

On extended screening of squalene-producing strains in Okinawa mangrove water, we identified 14 novel squalene-producing thraustochytrids from 172 unialgal clonal isolates. The novel thraustochytrids produced 13.9-7.54 mg squalene/g dry cell weight. Eight isolates were found to belong to potentially novel squalene-producing genera, forming a monophyletic cluster independent from any known thraustochytrids.

World Reference Center for Arboviruses.

DTIC Science & Technology

1981-02-01

CTF isolates including clones of the Florio strain. Representatives of the genera Rotavirus , cytoplasmic polyhedrosis virus group, and plant reovirus...group were supplied as purified virus preparations; and the virus strains respectively included a human rotavirus isolated from a fecal sample, Bom x...strain - CTF), Rotavirus (human rotavirus - HR), cytoplasmic polyhedrosis group ( Bombyx mori cytoplasmic polyhedrosis -CPV), and plant reovirus group

Nematophagous fungi from decomposing cattle faeces in Argentina.

PubMed

Saumell, Carlos Alfredo; Fernández, Alicia Silvina; Fusé, Luis Alberto; Rodríguez, Manuela; Sagüés, María Federica; Iglesias, Lucía Emilia

2015-01-01

Biological control of gastrointestinal nematodes of ruminants by use of nematophagous fungi would become part of any livestock parasite integral control system. Identifying autochthonous species that could then be selected for mass production is an important phase in the practical use of biological control. To search for nematophagous fungi with potential use as biological control agents against gastrointestinal nematodes in Argentina. Decomposing cattle faeces sampled in different locations were incubated in water agar 2% with Panagrellus sp. The developed nematophagous fungi were transferred to new water agar 2% plates and then to corn meal agar plates in order to carry out their identification. Fungal diversity and richness were also assessed. Seventeen species from nine genera of nematophagous fungi were found. Twelve species were nematode-trapping fungi and three species plus two fungi identified to genus level corresponded to endoparasitic fungi. Arthrobotrys conoides, Arthrobotrys oligospora, Duddingtonia flagrans, Monacrosporium doedycoides, Arthrobotrys robusta and Drechmeria coniospora were the most frequently isolated species overall in the whole study (6.6%, 5.7%, 5.7%, 5.7%, 4.7% and 4.7%, respectively) although other species were more frequently recorded at local levels such as Arthrobotrys pyriformis (18.8%). Only A. conoides has been previously isolated from ruminant faecal samples in Argentina. Five nematode-trapping fungal species are mentioned for the first time in the Americas D. flagrans and A. conoides, both identified in the present study, are among the most promising ones as biological control agents against gastrointestinal nematodes of ruminants. Copyright © 2013 Revista Iberoamericana de Micología. Published by Elsevier Espana. All rights reserved.

Causative agents of nosocomial mycoses.

PubMed

Tomsiková, A

2002-01-01

In the last few years mycoses have been caused by fungi formerly considered to be harmless for humans. They cause diseases of plants and insects; some of them are also used in the industry. They are now usually called "emerging fungi". We investigated this flora with respect to their potential to cause infections in hospitals. These fungi are present in the air, on medical objects and instrumentation, in the respiratory tract and on the hands of hospital staff; other sources have been identified in the use of iatrogenic methods. Mycotic diseases, their risk factors, their clinical pictures, and spectra of agents were analyzed in 1990-2000; the results were compared with data in the literature. Transplantations were the most frequent risk factors, fungemia and abscess the most frequent clinical picture and filamentous fungi (genera Absidia, Acremonium, Alternaria, Apophysomyces, Aspergillus, Bipolaris, Cladophialophora, Cunninghamella, Exserohilum, Fusarium, Chaetomium, Chrysosporium, Lecythophora, Ochroconis, Paecilomyces, Pythium, Rhizopus, Scedosporium, Scopulariopsis) were the most frequent agents of nosocomial infections. These filamentous fungi and also some yeasts (genera Candida, Cryptococcus, Trichosporon) bring about different clinical syndromes in both immunocompromised and immunocompetent patients.

16S rDNA analysis of periodontal plaque in chronic obstructive pulmonary disease and periodontitis patients.

PubMed

Wu, Xingwen; Chen, Jiazhen; Xu, Meng; Zhu, Danting; Wang, Xuyang; Chen, Yulin; Wu, Jing; Cui, Chenghao; Zhang, Wenhong; Yu, Liying

2017-01-01

This study investigated if chronic obstructive pulmonary disease (COPD) is correlated with periodontitis via periodontal microbiota and if certain bacteria affect periodontitis as well as COPD. Moreover, the study investigated whether suffering from COPD is associated with a decrease in the richness and diversity of periodontal microbiota. Subgingival plaque was obtained from 105 patients. Bacterial DNA was isolated from 55 COPD and 50 non-COPD participants (either with or without periodontitis). 16S rRNA gene metagenomic sequencing was used to characterize the microbiota and to determine taxonomic classification. In the non-periodontitis patients, suffering from COPD resulted in a decrease in bacteria richness and diversity in the periodontal microenvironment. An increase in the genera Dysgonomonas , Desulfobulbus , and Catonella and in four species ( Porphyromonas endodontalis , Dysgonomonas wimpennyi , Catonella morbi , and Prevotella intermedia ) in both COPD and periodontitis patients suggests that an increase in these periodontitis-associated microbiota may be related to COPD. Three genera ( Johnsonella , Campylobacter , and Oribacterium ) were associated with COPD but not with periodontitis. The decrease in the genera Arcanobacterium , Oribacterium , and Streptomyces in COPD patients implies that these genera may be health-associated genera, and the decrease in these genera may be related to disease. These data support the hypothesis that COPD is correlated with periodontitis via these significantly changed specific bacteria.

Indirect Manganese Removal by Stenotrophomonas sp. and Lysinibacillus sp. Isolated from Brazilian Mine Water.

PubMed

Barboza, Natália Rocha; Amorim, Soraya Sander; Santos, Pricila Almeida; Reis, Flávia Donária; Cordeiro, Mônica Mendes; Guerra-Sá, Renata; Leão, Versiane Albis

2015-01-01

Manganese is a contaminant in the wastewaters produced by Brazilian mining operations, and the removal of the metal is notoriously difficult because of the high stability of the Mn(II) ion in aqueous solutions. To explore a biological approach for removing excessive amounts of aqueous Mn(II), we investigated the potential of Mn(II) oxidation by both consortium and bacterial isolates from a Brazilian manganese mine. A bacterial consortium was able to remove 99.7% of the Mn(II). A phylogenetic analysis of isolates demonstrated that the predominant microorganisms were members of Stenotrophomonas, Bacillus, and Lysinibacillus genera. Mn(II) removal rates between 58.5% and 70.9% were observed for Bacillus sp. and Stenotrophomonas sp. while the Lysinibacillus isolate 13P removes 82.7%. The catalytic oxidation of Mn(II) mediated by multicopper oxidase was not properly detected; however, in all of the experiments, a significant increase in the pH of the culture medium was detected. No aggregates inside the cells grown for a week were found by electronic microscopy. Nevertheless, an energy-dispersive X-ray spectroscopy of the isolates revealed the presence of manganese in Stenotrophomonas sp. and Lysinibacillus sp. grown in K medium. These results suggest that members of Stenotrophomonas and Lysinibacillus genera were able to remove Mn(II) by a nonenzymatic pathway.

Molecular and phenetic characterization of the bacterial assemblage of Hot Lake, WA, an environment with high concentrations of magnesium sulphate, and its relevance to Mars

NASA Astrophysics Data System (ADS)

Kilmer, Brian R.; Eberl, Timothy C.; Cunderla, Brent; Chen, Fei; Clark, Benton C.; Schneegurt, Mark A.

2014-01-01

Hot Lake (Oroville, WA) is an athalassohaline epsomite lake that can have precipitating concentrations of MgSO4 salts, mainly epsomite. Little biotic study has been done on epsomite lakes and it was unclear whether microbes isolated from epsomite lakes and their margins would fall within recognized halotolerant genera, common soil genera or novel phyla. Our initial study cultivated and characterized epsotolerant bacteria from the lake and its margins. Approximately 100 aerobic heterotrophic microbial isolates were obtained by repetitive streak-plating in high-salt media including either 10% NaCl or 2 M MgSO4. The collected isolates were all bacteria, nearly evenly divided between Gram-positive and Gram-negative clades, the most abundant genera being Halomonas, Idiomarina, Marinobacter, Marinococcus, Nesterenkonia, Nocardiopsis and Planococcus. Bacillus, Corynebacterium, Exiguobacterium, Kocuria and Staphylococcus also were cultured. This initial study included culture-independent community analysis of direct DNA extracts of lake margin soil using PCR-based clone libraries and 16S rRNA gene phylogeny. Clones assigned to Gram-positive bacterial clades (70% of total clones) were dominated by sequences related to uncultured actinobacteria. There were abundant Deltaproteobacteria clones related to bacterial sulphur metabolisms and clones of Legionella and Coxiella. These epsomite lake microbial communities seem to be divided between bacteria primarily associated with hyperhaline environments rich in NaCl and salinotolerant relatives of common soil organisms. Archaea appear to be in low abundance and none were isolated, despite near-saturated salinities. Growth of microbes at very high concentrations of magnesium and other sulphates has relevance to planetary protection and life-detection missions to Mars, where scant liquid water may form as deliquescent brines and appear as eutectic liquids.

[Separation and identification of endophytic fungi from desert plant Cynanchum komarovii].

PubMed

Duan, Hai-Jing; Han, Ting; Wu, Xiu-Li; Li, Na; Chen, Jing; Qin, Lu-Ping

2013-02-01

The research aimed to investigate the entophytic fungal community of Cynanchum Komarrovii, including the biodiversity in different organs and the correlations with ecological environment. Endophytic fungi with patent bioactivity were also rapidly screened. PDA medium was used to isolate and purify the endophytic fungi from C. komarovii living in Shaanxi and Ningxia district, respectively. The strains were identified based on the morphological characteristics of the fungi and similarity of 5.8S gene and internal transcribed spacer (ITS) sequence. Pyriculaia oryzae model was applied to preliminarily screen the active fungi. Ninety-four strains of endophytic fungi were isolated and identified to 9 species, 13 genera, 9 families and 6 orders, among them, 47 strains were from the plants living in Ningxia. And then, 5 of them were isolated from roots, 14 from branches, and 28 from leaves. They were identified belonging to 8 species, 9 genera, 5 families and 4 orders. Additionally, 47 strains were from the plants living in Shaanxi. 16 were isolated from the roots, 18 from branches, 13 from leaves. They were identified belonging to 5 species, 8 genera, 6 families and 4 orders. By preliminary screening, 18 strains of endophytes completely inhibited the germination of conidium, which showed a potential bioactivity for these fungi. Both N4 and S17 strains had stronger growth inhibition effect. Endophytic fungi from desert plant C. komarovii have the feature of diversity. Different geographical environment and type of organizations lead to the significant difference on the quantity and the species composition. Most of fungi in Ningxia C. komarovii distribute in leaves. However, most of those in Shaanxi C. komarovii distribute in stems and leaves. It also indicated that endophytes from C. komarovii had a strong antifungal activity.

Diversity and enumeration of halophilic and alkaliphilic bacteria in Spanish-style green table-olive fermentations.

PubMed

Lucena-Padrós, Helena; Ruiz-Barba, José Luis

2016-02-01

The presence and enumeration of halophilic and alkaliphilic bacteria in Spanish-style table-olive fermentations was studied. Twenty 10-tonne fermenters at two large manufacturing companies in Spain, previously studied through both culture dependent and independent (PCR-DGGE) methodologies, were selected. Virtually all this microbiota was isolated during the initial fermentation stage. A total of 203 isolates were obtained and identified based on 16S rRNA gene sequences. They belonged to 13 bacterial species, included in 11 genera. It was noticeable the abundance of halophilic and alkaliphilic lactic acid bacteria (HALAB). These HALAB belonged to the three genera of this group: Alkalibacterium, Marinilactibacillus and Halolactibacillus. Ten bacterial species were isolated for the first time from table olive fermentations, including the genera Amphibacillus, Natronobacillus, Catenococcus and Streptohalobacillus. The isolates were genotyped through RAPD and clustered in a dendrogram where 65 distinct strains were identified. Biodiversity indexes found statistically significant differences between both patios regarding genotype richness, diversity and dominance. However, Jaccard similarity index suggested that the halophilic/alkaliphilic microbiota in both patios was more similar than the overall microbiota at the initial fermentation stage. Thus, up to 7 genotypes of 6 different species were shared, suggesting adaptation of some strains to this fermentation stage. Morisita-Horn similarity index indicated a high level of codominance of the same species in both patios. Halophilic and alkaliphilic bacteria, especially HALAB, appeared to be part of the characteristic microbiota at the initial stage of this table-olive fermentation, and they could contribute to the conditioning of the fermenting brines in readiness for growth of common lactic acid bacteria. Copyright © 2015 Elsevier Ltd. All rights reserved.

Diversity of Bacterial Communities on Four Frequently Used Surfaces in a Large Brazilian Teaching Hospital

PubMed Central

Pereira da Fonseca, Tairacan Augusto; Pessôa, Rodrigo; Felix, Alvina Clara; Sanabani, Sabri Saeed

2016-01-01

Frequently used hand-touch surfaces in hospital settings have been implicated as a vehicle of microbial transmission. In this study, we aimed to investigate the overall bacterial population on four frequently used surfaces using a culture-independent Illumina massively parallel sequencing approach of the 16S rRNA genes. Surface samples were collected from four sites, namely elevator buttons (EB), bank machine keyboard buttons (BMKB), restroom surfaces, and the employee biometric time clock system (EBTCS), in a large public and teaching hospital in São Paulo. Taxonomical composition revealed the abundance of Firmicutes phyla, followed by Actinobacteria and Proteobacteria, with a total of 926 bacterial families and 2832 bacterial genera. Moreover, our analysis revealed the presence of some potential pathogenic bacterial genera, including Salmonella enterica, Klebsiella pneumoniae, and Staphylococcus aureus. The presence of these pathogens in frequently used surfaces enhances the risk of exposure to any susceptible individuals. Some of the factors that may contribute to the richness of bacterial diversity on these surfaces are poor personal hygiene and ineffective routine schedules of cleaning, sanitizing, and disinfecting. Strict standards of infection control in hospitals and increased public education about hand hygiene are recommended to decrease the risk of transmission in hospitals among patients. PMID:26805866

FT-IR spectroscopy: A powerful tool for studying the inter- and intraspecific biodiversity of cultivable non-Saccharomyces yeasts isolated from grape must.

PubMed

Grangeteau, Cédric; Gerhards, Daniel; Terrat, Sebastien; Dequiedt, Samuel; Alexandre, Hervé; Guilloux-Benatier, Michèle; von Wallbrunn, Christian; Rousseaux, Sandrine

2016-02-01

The efficiency of the FT-IR technique for studying the inter- and intra biodiversity of cultivable non-Saccharomyces yeasts (NS) present in different must samples was examined. In first, the capacity of the technique FT-IR to study the global diversity of a given sample was compared to the pyrosequencing method, used as a reference technique. Seven different genera (Aureobasidium, Candida, Cryptococcus, Hanseniaspora, Issatchenkia, Metschnikowia and Pichia) were identified by FT-IR and also by pyrosequencing. Thirty-eight other genera were identified by pyrosequencing, but together they represented less than 6% of the average total population of 6 musts. Among the species identified, some of them present organoleptic potentials in winemaking, particularly Starmerella bacillaris (synonym Candidazemplinina). So in a second time, we evaluated the capacity of the FT-IR technique to discriminate the isolates of this species because few techniques were able to study intraspecific NS yeast biodiversity. The results obtained were validated by using a classic method as ITS sequencing. Biodiversity at strain level was high: 19 different strains were identified from 58 isolates. So, FT-IR spectroscopy seems to be an accurate and reliable method for identifying major genera present in the musts. The two biggest advantages of the FT-IR are the capacity to characterize intraspecific biodiversity of non-Saccharomyces yeasts and the possibility to discriminate a lot of strains. Copyright © 2015 Elsevier B.V. All rights reserved.

Genome Sequence of Aeribacillus pallidus Strain GS3372, an Endospore-Forming Bacterium Isolated in a Deep Geothermal Reservoir

PubMed Central

Filippidou, Sevasti; Jaussi, Marion; Junier, Thomas; Wunderlin, Tina; Jeanneret, Nicole; Regenspurg, Simona; Li, Po-E; Lo, Chien-Chi; McMurry, Kim; Gleasner, Cheryl D.; Vuyisich, Momchilo; Chain, Patrick S.

2015-01-01

The genome of strain GS3372 is the first publicly available strain of Aeribacillus pallidus. This endospore-forming thermophilic strain was isolated from a deep geothermal reservoir. The availability of this genome can contribute to the clarification of the taxonomy of the closely related Anoxybacillus, Geobacillus, and Aeribacillus genera. PMID:26316637

The Gastrointestinal Tract of the White-Throated Woodrat (Neotoma albigula) Harbors Distinct Consortia of Oxalate-Degrading Bacteria

PubMed Central

Kohl, Kevin D.; Dearing, M. Denise

2014-01-01

The microbiota inhabiting the mammalian gut is a functional organ that provides a number of services for the host. One factor that may regulate the composition and function of gut microbial communities is dietary toxins. Oxalate is a toxic plant secondary compound (PSC) produced in all major taxa of vascular plants and is consumed by a variety of animals. The mammalian herbivore Neotoma albigula is capable of consuming and degrading large quantities of dietary oxalate. We isolated and characterized oxalate-degrading bacteria from the gut contents of wild-caught animals and used high-throughput sequencing to determine the distribution of potential oxalate-degrading taxa along the gastrointestinal tract. Isolates spanned three genera: Lactobacillus, Clostridium, and Enterococcus. Over half of the isolates exhibited significant oxalate degradation in vitro, and all Lactobacillus isolates contained the oxc gene, one of the genes responsible for oxalate degradation. Although diverse potential oxalate-degrading genera were distributed throughout the gastrointestinal tract, they were most concentrated in the foregut, where dietary oxalate first enters the gastrointestinal tract. We hypothesize that unique environmental conditions present in each gut region provide diverse niches that select for particular functional taxa and communities. PMID:24362432

Antimicrobial Activity of Medicinal Plants Correlates with the Proportion of Antagonistic Endophytes

PubMed Central

Egamberdieva, Dilfuza; Wirth, Stephan; Behrendt, Undine; Ahmad, Parvaiz; Berg, Gabriele

2017-01-01

Medicinal plants are known to harbor potential endophytic microbes, due to their bioactive compounds. In a first study of ongoing research, endophytic bacteria were isolated from two medicinal plants, Hypericum perforatum and Ziziphora capitata with contrasting antimicrobial activities from the Chatkal Biosphere Reserve of Uzbekistan, and their plant-specific traits involved in biocontrol and plant growth promotion were evaluated. Plant extracts of H. perforatum exhibited a remarkable activity against bacterial and fungal pathogens, whereas extracts of Z. capitata did not exhibit any potential antimicrobial activity. Matrix-assisted laser desorption ionization (MALDI) time-of-flight (TOF) mass spectrometry (MS) was used to identify plant associated culturable endophytic bacteria. The isolated culturable endophytes associated with H. perforatum belong to eight genera (Arthrobacter, Achromobacter, Bacillus, Enterobacter, Erwinia, Pseudomonas, Pantoea, Serratia, and Stenotrophomonas). The endophytic isolates from Z. capitata also contain those genera except Arthrobacter, Serratia, and Stenotrophomonas. H. perforatum with antibacterial activity supported more bacteria with antagonistic activity, as compared to Z. capitata. The antagonistic isolates were able to control tomato root rot caused by Fusarium oxysporum and stimulated plant growth under greenhouse conditions and could thus be a cost-effective source for agro-based biological control agents. PMID:28232827

Diversity of Lactic Acid Bacteria Associated with Banana Fruits in Taiwan.

PubMed

Chen, Yi-Sheng; Liao, Yu-Jou; Lan, Yi-Shan; Wu, Hui-Chung; Yanagida, Fujitoshi

2017-04-01

Banana is a popular fruit worldwide. The lactic acid bacteria (LAB) microflora in banana fruits has not been studied in detail. A total of 164 LAB were isolated from banana fruits in Taiwan. These isolates were initially divided into nine groups (r1 to r9) using restriction fragment length polymorphism analysis and 16S ribosomal DNA sequencing. Isolates belonging to Lactobacillus plantarum group were further divided into three additional groups using multiplex PCR assay targeting the recA gene. The most common bacterial genera found in banana fruits were Lactobacillus and Weissella. The distribution of LAB indicated that, in most cases, neighboring regions shared common strains, but there were still some differences between regions. On the basis of phylogenetic analysis of 16S rRNA, rpoA, and pheS gene sequences, two strains included in the genera Lactobacillus were identified as potential novel species or subspecies. In addition, a total 36 isolates were found to have bacteriocin-producing abilities. These results suggest that various LAB are associated with banana fruits in Taiwan. This is the first report describing the distribution and varieties of LAB associated with banana fruits. In addition, one potential novel LAB species was also found in this study.

Characterization of butter spoiling yeasts and their inhibition by some spices.

PubMed

Sagdic, Osman; Ozturk, Ismet; Bayram, Okan; Kesmen, Zulal; Yilmaz, Mustafa Tahsin

2010-01-01

This study was designed to identify the yeasts in packaged and unpackaged butters and screen antiyeast activity of spices, including marjoram (Origanum majorana L.), summer savory (Satureja hortensis L.), and black cumin (Nigella sativa L.) against the most dominant yeast species in the packaged and unpackaged butters. Mean total yeast populations were 5.40 log CFU/g in unpackaged butter samples and 2.22 log CFU/g in packaged butter samples, indicating better hygienic quality of packaged samples. Forty-nine yeast species were isolated and identified from butter samples with the most prevalent isolates belonging to genera Candida-C. kefyr, C. zeylanoides, and C. lambica-and with moderate number of isolates belonging to genera Cryptococcus, Rhodotorula, Saccharomyces, and Zygosaccharomyces. Black cumin exhibited the highest antiyeast activity against C. zeylanoides and C. lambica species, even inhibited these species, while summer savory inhibited C. kefyr. The results of this study revealed clear antimicrobial potential of black cumin against the yeast species isolated from butters. Marjoram, summer savory, and black cumin could be used as natural antimicrobial agents against spoilage yeasts in food preservation, especially in butter. © 2010 Institute of Food Technologists®

The Mycobiota of Air Inside and Outside the Meju Fermentation Room and the Origin of Meju Fungi.

PubMed

Kim, Dae-Ho; Kim, Sun-Hwa; Kwon, Soon-Wo; Lee, Jong-Kyu; Hong, Seung-Beom

2015-09-01

The fungi on Meju are known to play an important role as degrader of macromolecule of soybeans. In order to elucidate the origin of fungi on traditional Meju, mycobiota of the air both inside and outside traditional Meju fermentation rooms was examined. From 11 samples of air collected from inside and outside of 7 Meju fermentation rooms, 37 genera and 90 species of fungi were identified. In outside air of the fermentation room, Cladosporium sp. and Cladosporium cladosporioides were the dominant species, followed by Cladosporium tenuissimum, Eurotium sp., Phoma sp., Sistotrema brinkmannii, Alternaria sp., Aspergillus fumigatus, Schizophyllum commune, and Penicillium glabrum. In inside air of the fermentation room, Cladosporium sp., Aspergillus oryzae, Penicillium chrysogenum, Asp. nidulans, Aspergillus sp., Cla. cladosporioides, Eurotium sp., Penicillium sp., Cla. tenuissimum, Asp. niger, Eur. herbariorum, Asp. sydowii, and Eur. repens were collected with high frequency. The concentrations of the genera Aspergillus, Eurotium, and Penicillium were significantly higher in inside air than outside air. From this result and those of previous reports, the origin of fungi present on Meju was inferred. Of the dominant fungal species present on Meju, Lichtheimia ramosa, Mucor circinelloides, Mucor racemosus, and Scopulariopsis brevicaulis are thought to be originated from outside air, because these species are not or are rarely isolated from rice straw and soybean; however, they were detected outside air of fermentation room and are species commonly found in indoor environments. However, Asp. oryzae, Pen. polonicum, Eur. repens, Pen. solitum, and Eur. chevalieri, which are frequently found on Meju, are common in rice straw and could be transferred from rice straw to Meju. The fungi grow and produce abundant spores during Meju fermentation, and after the spores accumulate in the air of fermentation room, they could influence mycobiota of Meju fermentation in the following year. This could explain why concentrations of the genera Aspergillus, Eurotium, and Penicillium are much higher inside than outside of the fermentation rooms.

Field investigations of bacterial contaminants and their effects on extended porcine semen.

PubMed

Althouse, G C; Kuster, C E; Clark, S G; Weisiger, R M

2000-03-15

Field investigations (n=23) were made over a 3-yr period at North American boar studs and farms in which the primary complaint was sperm agglutination in association with decreased sperm longevity of extended semen, and increased regular returns to estrus and/or vaginal discharges across parity. Microscopic examination of extended semen from these units revealed depressed gross motility (usually <30%), sperm agglutination, and sperm cell death occurring within 2 d of semen collection and processing regardless of the semen extender used. The extended semen exhibited a high number of induced acrosome abnormalities (>20%). Sample pH was acidic (5.7 to 6.4) in 93% of the submitted samples. Aerobic culture yielded a variety of bacteria from different genera. A single bacterial contaminant was obtained from 66% of the submitted samples (n=37 doses); 34% contained 2 or more different bacterial genera. The most frequently isolated contaminant bacteria from porcine extended semen were Alcaligenes xylosoxydans (n=3), Burkholderia cepacia (n=6), Enterobacter cloacae (n=6), Escherichia coli (n=6), Serratia marcescens (n=5), and Stenotrophomonas [Xanthomonas] maltophilia (n=6); these 6 bacteria accounted for 71% of all contaminated samples, and were spermicidal when re-inoculated and incubated in fresh, high quality extended semen. All contaminant bacteria were found to be resistant to the aminoglycoside gentamicin, a common preservative antibiotic used in commercial porcine semen extenders. Eleven genera were spermicidal in conjunction with an acidic environment, while 2 strains (E. coli, S. maltophilia) were spermicidal without this characteristic acidic environment. Bacteria originated from multiple sources at the stud/farm, and were of animal and nonanimal origin. A minimum contamination technique (MCT) protocol was developed to standardize hygiene and sanitation. This protocol focused on MCT's during boar preparation, semen collection, semen processing and laboratory sanitation. Implementation of the MCT, in addition to specific recommendations in stud management, resulted in the control of bacterial contamination in the extended semen.

The Mycobiota of Air Inside and Outside the Meju Fermentation Room and the Origin of Meju Fungi

PubMed Central

Kim, Dae-Ho; Kim, Sun-Hwa; Kwon, Soon-wo; Lee, Jong-Kyu

2015-01-01

The fungi on Meju are known to play an important role as degrader of macromolecule of soybeans. In order to elucidate the origin of fungi on traditional Meju, mycobiota of the air both inside and outside traditional Meju fermentation rooms was examined. From 11 samples of air collected from inside and outside of 7 Meju fermentation rooms, 37 genera and 90 species of fungi were identified. In outside air of the fermentation room, Cladosporium sp. and Cladosporium cladosporioides were the dominant species, followed by Cladosporium tenuissimum, Eurotium sp., Phoma sp., Sistotrema brinkmannii, Alternaria sp., Aspergillus fumigatus, Schizophyllum commune, and Penicillium glabrum. In inside air of the fermentation room, Cladosporium sp., Aspergillus oryzae, Penicillium chrysogenum, Asp. nidulans, Aspergillus sp., Cla. cladosporioides, Eurotium sp., Penicillium sp., Cla. tenuissimum, Asp. niger, Eur. herbariorum, Asp. sydowii, and Eur. repens were collected with high frequency. The concentrations of the genera Aspergillus, Eurotium, and Penicillium were significantly higher in inside air than outside air. From this result and those of previous reports, the origin of fungi present on Meju was inferred. Of the dominant fungal species present on Meju, Lichtheimia ramosa, Mucor circinelloides, Mucor racemosus, and Scopulariopsis brevicaulis are thought to be originated from outside air, because these species are not or are rarely isolated from rice straw and soybean; however, they were detected outside air of fermentation room and are species commonly found in indoor environments. However, Asp. oryzae, Pen. polonicum, Eur. repens, Pen. solitum, and Eur. chevalieri, which are frequently found on Meju, are common in rice straw and could be transferred from rice straw to Meju. The fungi grow and produce abundant spores during Meju fermentation, and after the spores accumulate in the air of fermentation room, they could influence mycobiota of Meju fermentation in the following year. This could explain why concentrations of the genera Aspergillus, Eurotium, and Penicillium are much higher inside than outside of the fermentation rooms. PMID:26539041

Identification of pink-pigmented bacteria isolated from environmental water samples and their biofilm formation abilities.

PubMed

Furuhata, Katsunori; Kato, Yuko; Goto, Keiichi; Saitou, Keiko; Sugiyama, Jun-Ichi; Hara, Motonobu; Fukuyama, Masahumi

2008-06-01

Sixty-seven strains of pink-pigmented bacteria, which were isolated from environmental water samples collected nationwide, were identified by partial 16S rDNA sequence analysis. In addition, the biofilm formation ability of the isolates was experimentally investigated. We could identify only 2 strains at the species level: Pedobacter roseus HS-38 and Runella slithyformis HS-77. The results showed that of the strains tested, 22 strains (32.8%) were Pedobacter spp., which was most frequently identified, followed by 19 strains (28.4%) of Arcicella spp., 16 strains (23.9%) of Deinococcus spp., 5 strains (7.5%) of Roseomonas spp., 4 strains (6.0%) of Flectobacillus spp. and 1 strain (1.5%) of Runella sp. Most isolates showed low similarity values to previously known species, and they were found to be novel species. At a result, it was difficult to identify environmental water-derived pink-pigmented bacteria at the species level. On the other hand, when we measured the absorbance by the crystal violet staining to examine the quantities of biofilm formation of these strains, fifty-five (82.0%) of the 67 isolates formed biofilm. The absorbance of Deinococcus sp. HS-75 was the highest (3.56). When comparing the absorbance values among the genera, Roseomonas spp. showed the highest absorbance (mean:1.62), followed by Deinococcus spp. (mean: 1.03), and Arcicella spp. (mean: 1.01). Strains of Flectobacillus spp. (mean: 0.48) and Pedobacter spp. (mean: 0.42) showed lower absorbance values. As above, it was shown that, at the species level, the pink-pigmented bacteria in the water in the Japanese environment had various levels of ability to form biofilm.

Pestalotiopsis and allied genera from Camellia, with description of 11 new species from China.

PubMed

Liu, Fang; Hou, Lingwei; Raza, Mubashar; Cai, Lei

2017-04-13

A total of 124 Pestalotiopsis-like isolates associated with symptomatic and asymptomatic tissues of Camellia sinensis and other Camellia spp. from eight provinces in China were investigated. Based on single- and multi-locus (ITS, TEF, TUB2) phylogenies, as well as morphological characters, host associations and geographical distributions, they were classified into at least 19 species in three genera, i.e. Neopestalotiopsis, Pestalotiopsis and Pseudopestalotiopsis. Eight novel species in Pestalotiopsis and three novel species in Pseudopestalotiopsis were described. Our data suggested that the currently widely used loci in Pestalotiopsis-like genera do not consistently provide stable and sufficient resolution tree topologies, especially for Neopestalotiopsis. Moreover, the number, branch pattern and length of the conidial basal appendages were revealed to be phylogenetically informative characters in Pestalotiopsis.

Screening of different sample types associated with sheep and cattle for the presence of nematophagous fungi in China.

PubMed

Cai, Kui-Zheng; Liu, Jun-Lin; Liu, Wei; Wang, Bo-Bo; Xu, Qiang; Sun, Long-Jie; Chen, Ming-Yue; Zhao, Ming-Wang; Wu, Jia-Yan; Li, Xiao-Shan; Yang, Jing; Wei, Shuan; Chen, Chun-Rong; Ma, Zhong-Ren; Xu, Chun-Lan; Wang, Feng; Hu, Qian-Lin; Fang, Wen-Xiu; Zheng, Tian-Hui; Wang, Yue-Ying; Zhu, Wen-Long; Li, Dan; Li, Qing; Zhang, Chao; Cai, Bing; Wang, Fan; Yang, Zai-Yun; Liu, Yan-Qiu

2016-03-01

A total of 1502 samples, including feces of sheep (793) and cattle (348), pasture soil (118), dung compost (147) and barn soil (96), were examined between October 2012 and August 2014 to discover potential strains of nematophagous fungi for the biological control of livestock-parasitic nematodes. These samples were collected from 87 sites located in 48 counties of 20 provinces (autonomous regions/municipalities) of China. Fungi were identified down to a species level. Four hundred and seventy-seven isolates, which were distributed in 8 genera and 28 taxa, were identified as nematophagous fungi. Nematode-trapping fungi included 17 species and one unidentified species of Arthrobotrys, two of Dactylella, Drechslerella dactyloides, and Duddingtonia flagrans. Five identified species and two unidentified species of endoparasitic fungi were isolated. The predominant species from all regions were Arthrobotrys oligospora, followed by Arthrobotrys musiformis, Arthrobotrys (Monacrosporium) thaumasiun, and Arthrobotrys (Monacrosporium) microscaphoides. Species with adhesive networks were the most frequently isolated. Among the endoparasitic fungi, Podocrella harposporifera (Harposporium anguillulae) was the most common species, followed by Harposporium lilliputanum and Harposporium arcuatum. Based on Shannon diversity index, the diversity levels of nematophagous fungi were relatively higher in samples associated with cattle, barn soil, and subtropical monsoon climate zone. Three species isolated from this study, namely, Duddingtonia flagrans, Arthrobotrys salina (Monacrosporium salinum), and Arthrobotrys oligospora var. sarmatica, are newly recorded in China, and 20 species (including one unidentified species) are newly recorded in sheep and cattle barn soils worldwide. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

[Isolation and physiological characteristics of endophytic actinobacteria from medicinal plants].

PubMed

Du, Huijing; Su, Jing; Yu, Liyan; Zhang, Yuqin

2013-01-04

To isolate, incubate and characterize cultivable endophytic antinobacteria from medicinal plants, and analyze the diversity of the endophytic antinobacteria, then explore the novel microbial resources. Ten media were used to isolate endophytic antinobacteria from 37 fresh medicinal plant tissue samples. The optimal cultivation conditions for endophytic antinobacteria were determined by comparison. Based on the morphology of the colonies and cells of the new isolates, we chose 174 isolates to analyze their 16S rRNA gene sequences and the diversity of the medicinal plant endophytic antinobacteria. The physiological characteristics of 27 representative strains were studied using Biolog GEN III MicroPlates, API 50CH and API ZYM kits. In total 940 endophytics affiliated to 47 genera of 30 families were isolated, among which more than 600 actinobacteria belonged to 34 genera and 7 unknown taxa. Good growth of the endophytic antinobacteria on PYG (peptone-yeast-glycerol) medium with pH 7.2 at 28-32 degrees C was observed. Physiological characteristics differences of these isolates related to their phylogenetic relationships. Greater differences were shown among the strains from the same host plants than those from differ,ent plants grown in the same area. There are great diverse endophytic actinobacteria inside the medicinal plants. No direct relationship of the endophytic actinobacteria from medicinal plants with the host plants in the sole carbon source utilization, fermentation of carbon sources to produce acid and the enzyme activities was found, while it seemed that the physiological characteristics of the isolates related to the geographical distribution of their host.

Evaluation of fungal growth on cellulose-containing and inorganic ceiling tile.

PubMed

Karunasena, E; Markham, N; Brasel, T; Cooley, J D; Straus, D C

2001-01-01

Buildings with poor indoor air quality (IAQ) frequently have many areas with surface fungal contamination. Studies have demonstrated that certain fungal genera (e.g., Cladosporium, Penicillium, and Stachybotrys) are able to grow on building materials such as wallpaper, drywall, and ceiling tiles, particularly after water damage has occurred. Due to the increasing awareness of sick building syndrome (SBS), it has become essential to identify building materials that prevent the interior growth of fungi. The objective of this study was to identify building materials that would not support the growth of certain fungal genera, regardless of whether an external food source was made available. The growth of three fungal genera (Cladosporium, Penicillium, and Stachybotrys) was evaluated on cellulose-containing ceiling tile (CCT) and inorganic ceiling tile (ICT). Both types of ceiling tile were exposed to environmental conditions which can occur inside a building. Our results show that ICT did not support the growth of these three fungal genera while CCT did. Our data demonstrate that ICT could serve as an ideal replacement for CCT.

16S rDNA analysis of periodontal plaque in chronic obstructive pulmonary disease and periodontitis patients

PubMed Central

Wu, Xingwen; Chen, Jiazhen; Xu, Meng; Zhu, Danting; Wang, Xuyang; Chen, Yulin; Wu, Jing; Cui, Chenghao; Zhang, Wenhong; Yu, Liying

2017-01-01

ABSTRACT This study investigated if chronic obstructive pulmonary disease (COPD) is correlated with periodontitis via periodontal microbiota and if certain bacteria affect periodontitis as well as COPD. Moreover, the study investigated whether suffering from COPD is associated with a decrease in the richness and diversity of periodontal microbiota. Subgingival plaque was obtained from 105 patients. Bacterial DNA was isolated from 55 COPD and 50 non-COPD participants (either with or without periodontitis). 16S rRNA gene metagenomic sequencing was used to characterize the microbiota and to determine taxonomic classification. In the non-periodontitis patients, suffering from COPD resulted in a decrease in bacteria richness and diversity in the periodontal microenvironment. An increase in the genera Dysgonomonas, Desulfobulbus, and Catonella and in four species (Porphyromonas endodontalis, Dysgonomonas wimpennyi, Catonella morbi, and Prevotella intermedia) in both COPD and periodontitis patients suggests that an increase in these periodontitis-associated microbiota may be related to COPD. Three genera (Johnsonella, Campylobacter, and Oribacterium) were associated with COPD but not with periodontitis. The decrease in the genera Arcanobacterium, Oribacterium, and Streptomyces in COPD patients implies that these genera may be health-associated genera, and the decrease in these genera may be related to disease. These data support the hypothesis that COPD is correlated with periodontitis via these significantly changed specific bacteria. PMID:28748030

Genome Sequence of Aeribacillus pallidus Strain GS3372, an Endospore-Forming Bacterium Isolated in a Deep Geothermal Reservoir.

PubMed

Filippidou, Sevasti; Jaussi, Marion; Junier, Thomas; Wunderlin, Tina; Jeanneret, Nicole; Regenspurg, Simona; Li, Po-E; Lo, Chien-Chi; Johnson, Shannon; McMurry, Kim; Gleasner, Cheryl D; Vuyisich, Momchilo; Chain, Patrick S; Junier, Pilar

2015-08-27

The genome of strain GS3372 is the first publicly available strain of Aeribacillus pallidus. This endospore-forming thermophilic strain was isolated from a deep geothermal reservoir. The availability of this genome can contribute to the clarification of the taxonomy of the closely related Anoxybacillus, Geobacillus, and Aeribacillus genera. Copyright © 2015 Filippidou et al.

[Occurrence of bacteria in the mouth from genera of Micrococcus, Kocuria, Nesterenkonia, Kytococcus and Dermacoccus].

PubMed

Szczerba, Izabela; Krzemiński, Zbigniew

2002-01-01

The aim of the study was to assess the prevalence of different bacteria in the oral cavity. The bacteria were present in the oral cavities of 73 (48.7%) of 150 individuals. Nesterenkonia halobia, the most frequently isolated species, was found in 20 (27%) individuals, Micrococcus luteus in 16 (22%), Kocuria kristinae in 12 (16%), Kocuria varians in 10 (14%), Dermacoccus sedentarius in 9 (12%), Micrococcus lylae in 8 (11%), and Kytococcus nishinomiyaensis in 3 (4%). Mean counts of these microorganisms were relatively low and amounted in log10 CFU/ml saliva for M. luteus 1.87 +/- 0.52, for M. lylae 2.03 +/- 0.39, for N. halobia 2.14 +/- 0.56, for K. kristinae 2.20 +/- 0.69, for K. varians 2.19 +/- 0.67, for K. nishinomiyaensis 1.72 +/- 0.39, and for D. sedentarius 2.27 +/- 0.55. The factor limiting the population sizes of these microorganisms was most probably the antagonistic activity of the bacteria living in oral cavity.

Revised taxonomy and nomenclature of rodent Pasteurellaceae: Implications for monitoring.

PubMed

Boot, R; Nicklas, W; Christensen, H

2018-01-01

Pasteurellosis is a well-recognized disease with similar pathology in all laboratory rodent species. Pasteurella pneumotropica is the most frequently mentioned member of the Pasteurellaceae isolated from mice and rats. Numerous other Pasteurellaceae taxa have been obtained from mice, rats, and other rodent species. Recently, rodent Pasteurellaceae have been submitted to comprehensive genetic and phenotypic (polyphasic) taxonomic studies. As a result they are now classed within six validly published new genera, namely Cricetibacter, Mesocricetibacter, Mannheimia, Muribacter, Necropsobacter, and Rodentibacter. All previously used names such as P. pneumotropica have become obsolete. The new classification forms a firm basis for the correct phenotypic identification of Pasteurellaceae from laboratory animals and for the selection of strains for pathogenicity studies. Consequences of taxonomic changes notably involve molecular methods used for the detection of Pasteurellaceae infection in laboratory animal colonies. Testing may be done using primer sets that detect all Pasteurellaceae taxa or sets developed to detect host-specific members of the family.

Research on marine actinobacteria in India.

PubMed

Sivakumar, K; Sahu, Maloy Kumar; Thangaradjou, T; Kannan, L

2007-09-01

Marine actinobacteriology is one of the major emerging areas of research in tropics. Marine actinobacteria occur on the sediments and in water and also other biomass (mangrove) and substrates (animal). These organisms are gaining importance not only for their taxonomic and ecological perspectives, but also for their unique metabolites and enzymes. Many earlier studies on these organisms were confined only to the temperate regions. In tropical environment, investigations on them have gained importance only in the last two decades. So far, from the Indian peninsula, 41 species of actinobacteria belonging to 8 genera have been recorded. The genus, Streptomyces of marine origin has been more frequently recorded. Of 9 maritime states of India, only 4 have been extensively covered for the study of marine actinobacteria. Most of the studies conducted pertain to isolation, identification and maintenance of these organisms in different culture media. Further, attention has been focused on studying their antagonistic properties against different pathogens. Their biotechnological potentials are yet to be fully explored.

Diversity of cultured photosynthetic flagellates in the North East Pacific and Arctic Oceans in summer

NASA Astrophysics Data System (ADS)

Balzano, S.; Gourvil, P.; Siano, R.; Chanoine, M.; Marie, D.; Lessard, S.; Sarno, D.; Vaulot, D.

2012-06-01

During the MALINA cruise (summer 2009) an extensive effort was undertaken to isolate phytoplankton strains from the North East (NE) Pacific Ocean, the Bering Strait, and the Beaufort Sea. Strains were isolated by flow cytometry sorting (FCS) and pipetting before or after phytoplankton enrichment of seawater samples. Strains were isolated both onboard and back in the laboratory and cultured at 4 °C under light/dark conditions. Overall, we isolated and characterised by light microscopy and 18S rRNA gene sequencing 104 strains of photosynthetic flagellates which grouped into 21 genotypes (defined by 99.5% 18S rRNA gene sequence similarity) mainly affiliated to Chlorophyta and Heterokontophyta. The taxon most frequently isolated was an Arctic ecotype of the green algal genus Micromonas (Arctic Micromonas) which was almost the only phytoplankter recovered within picoplankton (≤ 2 μm) size range. Strains of Arctic Micromonas as well as three unidentified strains related to the same genus were identified in further details by sequencing the Internal Transcribed Spacer (ITS) region of the rRNA operon. The MALINA Micromonas strains share identical 18S rRNA and ITS sequences suggesting high genetic homogeneity within Arctic Micromonas. The unidentified strains form a genotype likely belonging to a new genus within the family Mamiellaceae to which Micromonas belongs. Other green algae genotypes from the genera Nephroselmis, Chlamydomonas, Pyramimonas were also isolated whereas Heterokontophyta included Pelagophyceae, Dictyochophyceae and Chrysophyceae. Dictyochophyceae included Pedinellales which could not be identified to the genus level whereas Chrysophyceae comprised Dinobryon faculiferum. Moreover, we isolated Rhodomonas sp. as well as a few Haptophyta and dinoflagellates. We identified the dinoflagellate Woloszynskia cincta by Scanning Electron Microscopy (SEM) and 28S rRNA gene sequencing. Our morphological analyses show that this species possess the diagnostic features of the genus Biecheleria, and the 28S rRNA gene topology corroborates this affiliation. We thus propose the transfer of W. cincta to the genus Biecheleria and its recombination as Biecheleria cincta.

Diversity of cultured photosynthetic flagellates in the northeast Pacific and Arctic Oceans in summer

NASA Astrophysics Data System (ADS)

Balzano, S.; Gourvil, P.; Siano, R.; Chanoine, M.; Marie, D.; Lessard, S.; Sarno, D.; Vaulot, D.

2012-11-01

During the MALINA cruise (summer 2009), an extensive effort was undertaken to isolate phytoplankton strains from the northeast (NE) Pacific Ocean, the Bering Strait, the Chukchi Sea, and the Beaufort Sea. In order to characterise the main photosynthetic microorganisms occurring in the Arctic during the summer season, strains were isolated by flow cytometry sorting (FCS) and single cell pipetting before or after phytoplankton enrichment of seawater samples. Strains were isolated both onboard and back in the laboratory and cultured at 4 °C under light/dark conditions. Overall, we isolated and characterised by light microscopy and 18 S rRNA gene sequencing 104 strains of photosynthetic flagellates which grouped into 21 genotypes (defined by 99.5% 18 S rRNA gene sequence similarity), mainly affiliated to Chlorophyta and Heterokontophyta. The taxon most frequently isolated was an Arctic ecotype of the green algal genus Micromonas (Arctic Micromonas), which was nearly the only phytoplankter recovered within the picoplankton (< 2 μm) size range. Strains of Arctic Micromonas as well as other strains from the same class (Mamiellophyceae) were identified in further detail by sequencing the internal transcribed spacer (ITS) region of the rRNA operon. The MALINA Micromonas strains share identical 18 S rRNA and ITS sequences suggesting high genetic homogeneity within Arctic Micromonas. Three other Mamiellophyceae strains likely belong to a new genus. Other green algae from the genera Nephroselmis, Chlamydomonas, and Pyramimonas were also isolated, whereas Heterokontophyta included some unidentified Pelagophyceae, Dictyochophyceae (Pedinellales), and Chrysophyceae (Dinobryon faculiferum). Moreover, we isolated some Cryptophyceae (Rhodomonas sp.) as well as a few Prymnesiophyceae and dinoflagellates. We identified the dinoflagellate Woloszynskia cincta by scanning electron microscopy (SEM) and 28 S rRNA gene sequencing. Our morphological analyses show that this species possess the diagnostic features of the genus Biecheleria, and the 28 S rRNA gene topology corroborates this affiliation. We thus propose the transfer of W. cincta to the genus Biecheleria and its recombination as Biecheleria cincta.

Isolation and characterization of halophilic bacteria and archaea from salt ponds in Hangu Saltworks, Tianjin, China

NASA Astrophysics Data System (ADS)

Deng, Yuangao; Xu, Gaochao; Sui, Liying

2015-07-01

A total of 26 isolates were obtained from solar salt ponds of different salinities (100, 150, 200, and 250) in Hangu Saltworks Co. Ltd., Tianjin, China. Phylogenetic analysis of 16S rRNA gene sequences indicated that five bacteria genera Halomonas, Salinicoccus, Oceanobacillus, Gracibacillus, and Salimicrobium and one archaea genera Halorubrum were present. The genus Halomonas was predominant with eight strains distributed in a salinity range of 100-200, followed by Halorubrum with six strains in salinity 250. Based on the genus and original sampling salinity, eight bacterial and two archaeal isolates were selected for further morphological, physiological, and biochemical characterization. All of the bacterial strains were moderately halophilic with the optimal salinity for growth being either 50 or 100, while two archaeal strains were extremely halophilic with an optimal growth salinity of 200. Additionally, we put forth strain SM.200-5 as a new candidate Salimicrobium species based on the phylogenic analysis of the 16S rRNA gene sequence and its biochemical characteristics when compared with known related species.

Antibiotic susceptibility patterns and resistance genes of starter cultures and probiotic bacteria used in food.

PubMed

Kastner, Sabine; Perreten, Vincent; Bleuler, Helen; Hugenschmidt, Gabriel; Lacroix, Christophe; Meile, Leo

2006-03-01

A survey of starter and probiotic cultures was carried out to determine the current antibiotic resistance situation in microbial food additives in Switzerland. Two hundred isolates from 90 different sources were typed by molecular and other methods to belong to the genera Lactobacillus (74 samples), Staphylococcus (33 samples), Bifidobacterium (6 samples), Pediococcus (5 samples), or were categorized as lactococci or streptococci (82 samples). They were screened for phenotypic resistances to 20 antibiotics by the disk diffusion method. Twenty-seven isolates exhibiting resistances that are not an intrinsic feature of the respective genera were further analyzed by microarray hybridization as a tool to trace back phenotypic resistances to specific genetic determinants. Their presence was finally verified by PCR amplification or Southern hybridization. These studies resulted in the detection of the tetracycline resistance gene tet(K) in 5 Staphylococcus isolates used as meat starter cultures, the tetracycline resistance gene tet(W) in the probiotic cultures Bifidobacterium lactis DSM 10140 and Lactobacillus reuteri SD 2112 (residing on a plasmid), and the lincosamide resistance gene lnu(A) (formerly linA) in L. reuteri SD 2112.

Secrets of soil survival revealed by the genome sequence of Arthrobacter aurescens TC1.

PubMed

Mongodin, Emmanuel F; Shapir, Nir; Daugherty, Sean C; DeBoy, Robert T; Emerson, Joanne B; Shvartzbeyn, Alla; Radune, Diana; Vamathevan, Jessica; Riggs, Florenta; Grinberg, Viktoria; Khouri, Hoda; Wackett, Lawrence P; Nelson, Karen E; Sadowsky, Michael J

2006-12-01

Arthrobacter sp. strains are among the most frequently isolated, indigenous, aerobic bacterial genera found in soils. Member of the genus are metabolically and ecologically diverse and have the ability to survive in environmentally harsh conditions for extended periods of time. The genome of Arthrobacter aurescens strain TC1, which was originally isolated from soil at an atrazine spill site, is composed of a single 4,597,686 basepair (bp) circular chromosome and two circular plasmids, pTC1 and pTC2, which are 408,237 bp and 300,725 bp, respectively. Over 66% of the 4,702 open reading frames (ORFs) present in the TC1 genome could be assigned a putative function, and 13.2% (623 genes) appear to be unique to this bacterium, suggesting niche specialization. The genome of TC1 is most similar to that of Tropheryma, Leifsonia, Streptomyces, and Corynebacterium glutamicum, and analyses suggest that A. aurescens TC1 has expanded its metabolic abilities by relying on the duplication of catabolic genes and by funneling metabolic intermediates generated by plasmid-borne genes to chromosomally encoded pathways. The data presented here suggest that Arthrobacter's environmental prevalence may be due to its ability to survive under stressful conditions induced by starvation, ionizing radiation, oxygen radicals, and toxic chemicals.

Oral associated bacterial infection in horses: studies on the normal anaerobic flora from the pharyngeal tonsillar surface and its association with lower respiratory tract and paraoral infections.

PubMed

Bailey, G D; Love, D N

1991-02-15

Two hundred and seventy bacterial isolates were obtained from the pharyngeal tonsillar surface of 12 normal horses and 98 obligatory anaerobic bacteria were characterised. Of these, 57 isolates belonging to 7 genera (Peptostreptococcus (1); Eubacterium (9); Clostridium (6); Veillonella (6); Megasphera (1); Bacteroides (28); Fusobacterium (6)) were identified, and 16 of these were identified to species level (P. anaerobius (1); E. fossor (9); C. villosum (1); B. fragilis (1); B. tectum (2); B. heparinolyticus (2)). Three hundred and twenty isolates were obtained from 23 samples from horses with lower respiratory tract (LRT) or paraoral (PO) bacterial infections. Of the 143 bacteria selected for detailed characterisation, obligate anaerobes accounted for 100 isolates, facultative anaerobes for 42 isolates and obligate aerobes for one isolate. Phenotypic characterisation separated 99 of the isolates into 14 genera. Among the obligately anaerobic species, Gram-positive cocci including P. anaerobius comprised 25% of isolates, E. fossor 11% and other Gram-positive rods (excluding Clostridium sp.) 18% of isolates. The Gram-negative rods comprised B. fragilis 5%, B. heparinolyticus 5%, asaccharolytic pigmented Bacteroides 3% and other Bacteroides 13%, while a so-far unnamed species of Fusobacterium (7%), and Gram-negative corroding rods (3%) were isolated. Among the facultatively anaerobic isolates, S. equi subsp. zooepidemicus accounted for 31% of isolates, followed by Pasteurella spp. 19%, Escherichia coli 17%, Actinomyces spp. 9%, Streptococcus spp. 9%. Incidental facultative isolates were Enterococcus spp. 2%, Enterobacter cloaceae 2%, Actinobacillus spp. 2% and Gram-negative corroding rods 5%. On the basis of the similarities (as determined by DNA hybridization data and/or phenotypic characteristics) of some of the bacterial species (e.g. E. fossor and B. heparinolyticus) isolated from both the normal pharyngeal tonsillar surfaces and LRT and PO diseases of horses, it is considered that the most likely source of bacteria involved in these disease processes is flora from the oral cavity.

Niakha virus: A novel member of the family Rhabdoviridae isolated from phlebotomine sandflies in Senegal

PubMed Central

Vasilakis, Nikos; Widen, Steven; Mayer, Sandra V.; Seymour, Robert; Wood, Thomas G.; Popov, Vsevolov; Guzman, Hilda; da Rosa, Amelia P.A. Travassos; Ghedin, Elodie; Holmes, Edward C.; Walker, Peter J.; Tesh, Robert B.

2013-01-01

Members of the family Rhabdoviridae have been assigned to eight genera but many remain unassigned. Rhabdoviruses have a remarkably diverse host range that includes terrestrial and marine animals, invertebrates and plants. Transmission of some rhabdoviruses often requires an arthropod vector, such as mosquitoes, midges, sandflies, ticks, aphids and leafhoppers, in which they replicate. Herein we characterize Niakha virus (NIAV), a previously uncharacterized rhabdovirus isolated from phebotomine sandflies in Senegal. Analysis of the 11,124 nt genome sequence indicates that it encodes the five common rhabdovirus proteins with alternative ORFs in the M, G and L genes. Phylogenetic analysis of the L protein indicate that NIAV’s closest relative is Oak Vale rhabdovirus, although in this analysis NIAV is still so phylogenetically distinct that it might be classified as distinct from the eight currently recognized Rhabdoviridae genera. This observation highlights the vast, and yet not fully recognized diversity, of this family. PMID:23773405

Microbial quality and molecular identification of cultivable microorganisms isolated from an urban drinking water distribution system (Limassol, Cyprus).

PubMed

Botsaris, George; Kanetis, Loukas; Slaný, Michal; Parpouna, Christiana; Makris, Konstantinos C

2015-12-01

Microorganisms can survive and multiply in aged urban drinking water distribution systems, leading to potential health risks. The objective of this work was to investigate the microbial quality of tap water and molecularly identify its predominant cultivable microorganisms. Tap water samples collected from 24 different households scattered in the urban area of Limassol, Cyprus, were microbiologically tested following standard protocols for coliforms, E. coli, Pseudomonas spp., Enterococcus spp., and total viable count at 22 and 37 °C. Molecular identification was performed on isolated predominant single colonies using 16SrRNA sequencing. Approximately 85% of the household water samples were contaminated with one or more microorganisms belonging to the genera of Pseudomonas, Corynebacterium, Agrobacterium, Staphylococcus, Bacillus, Delftia, Acinetobacter, Enterococcus, Enterobacter, and Aeromonas. However, all samples tested were free from E. coli. This is the first report in Cyprus molecularly confirming specific genera of relevant microbial communities in tap water.

Russian Kefir Grains Microbial Composition and Its Changes during Production Process.

PubMed

Kotova, I B; Cherdyntseva, T A; Netrusov, A I

2016-01-01

By combining DGGE-PCR method, classical microbiological analysis and light- and electron microscopic observations, it was found that the composition of microbial communities of central Russia regions kefir grains, starter and kefir drink include bacteria of the genera Lactobacillus, Leuconostoc and Lactococcus, and yeast anamorphs of the genera Saccharomyces, Kazachstania and Gibellulopsis. Fifteen prokaryotic and four eukaryotic pure cultures of microorganisms were isolated and identified from kefir grains. It has been shown that members of the genus Lactobacillus prevailed in kefir grains, whereas strains Leuconostoc pseudomesenteroides and Lactococcus lactis dominated in the final product - kefir drink. Yeasts contained in kefir grains in small amounts have reached a significant number of cells in the process of development of this dairy product. The possibility of reverse cell aggregation has been attempted in a mixed cultivation of all isolated pure cultures, but full formation kefir grains is not yet observed after 1.5 years of observation and reinoculations.

Contributions to the herpetofauna of the Albertine Rift: Two new species of chameleon (Sauria: Chamaeleonidae) from an isolated montane forest, south eastern Democratic Republic of Congo.

PubMed

Tilbury, Colin R; Tolley, Krystal A

2015-01-13

Two new species of chameleons from the genera Rhampholeon and Kinyongia are described from an isolated montane forest remnant situated toward the southern end of the Albertine Rift bordering Lake Tanganyika. The closest known localities of species from these genera are 200km and 400km to the north respectively, separated by large intervening tracts of lowland savannah and Brachystegia (Miombo) woodland - habitats not normally inhabited by species of these genera. Rhampholeon hattinghi sp. nov. and Kinyongia mulyai sp. nov. bear superficial resemblances to previously described species (Rh. boulengeri Steindachner and K. adolfifriderici  (Sternfeld)). Rhampholeon hattinghi sp. nov. has a relatively smooth supra-orbital ridge, deep axillary but absent inguinal mite pockets, prominent white spots on the base of the tail and a uniquely derived hemipenal morphology with billowing parasulcal evaginations. Like K. adolfifriderici, Kinyongia mulyai sp. nov. is devoid of a rostral appendage but differs in having a longer and narrower head, a higher upper labial scale count and by the absence of a dorsal crest in the male. To place these new chameleons within the context of their respective genera, Bayesian and maximum likelihood phylogenetic analyses were carried out utilising two mitochondrial (ND2 and 16S) and one nuclear marker (RAG1).  Both chameleons were found to have morphological features that distinguish them from other congeners. Based on phylogenetic analysis they are clearly separate evolutionary lineages and are described as new species. 

Radioisotopic, Culture-Based, and Oligonucleotide Microchip Analyses of Thermophilic Microbial Communities in a Continental High-Temperature Petroleum Reservoir†

PubMed Central

Bonch-Osmolovskaya, Elizaveta A.; Miroshnichenko, Margarita L.; Lebedinsky, Alexander V.; Chernyh, Nikolai A.; Nazina, Tamara N.; Ivoilov, Valery S.; Belyaev, Sergey S.; Boulygina, Eugenia S.; Lysov, Yury P.; Perov, Alexander N.; Mirzabekov , Andrei D.; Hippe, Hans; Stackebrandt, Erko; L'Haridon, Stéphane; Jeanthon, Christian

2003-01-01

Activity measurements by radioisotopic methods and cultural and molecular approaches were used in parallel to investigate the microbial biodiversity and its physiological potential in formation waters of the Samotlor high-temperature oil reservoir (Western Siberia, Russia). Sulfate reduction with rates not exceeding 20 nmol of H2S liter−1 day−1 occurred at 60 and 80°C. In upper horizons (AB, A, and B), methanogenesis (lithotrophic and/or acetoclastic) was detected only in wells in which sulfate reduction did not occur. In some of the wells from deeper (J) horizons, high-temperature sulfate reduction and methanogenesis occurred simultaneously, the rate of lithotrophic methanogenesis exceeding 80 nmol of CH4 liter−1 day−1. Enrichment cultures indicated the presence of diverse physiological groups representing aerobic and anaerobic thermophiles and hyperthermophiles; fermentative organotrophs were predominant. Phylogenetic analyses of 15 isolates identified representatives of the genera Thermotoga, Thermoanaerobacter, Geobacillus, Petrotoga, Thermosipho, and Thermococcus, the latter four being represented by new species. Except for Thermosipho, the isolates were members of genera recovered earlier from similar habitats. DNA obtained from three samples was hybridized with a set of oligonucleotide probes targeting selected microbial groups encompassing key genera of thermophilic bacteria and archaea. Oligonucleotide microchip analyses confirmed the cultural data but also revealed the presence of several groups of microorganisms that escaped cultivation, among them representatives of the Aquificales/Desulfurobacterium-Thermovibrio cluster and of the genera Desulfurococcus and Thermus, up to now unknown in this habitat. The unexpected presence of these organisms suggests that their distribution may be much wider than suspected. PMID:14532074

Bacteria on smartphone touchscreens in a German university setting and evaluation of two popular cleaning methods using commercially available cleaning products.

PubMed

Egert, Markus; Späth, Kerstin; Weik, Karoline; Kunzelmann, Heike; Horn, Christian; Kohl, Matthias; Blessing, Frithjof

2015-03-01

Smartphone touchscreens are known as pathogen carriers in clinical environments. However, despite a rapidly growing number of smartphone users worldwide, little is known about bacterial contamination of smartphone touchscreens in non-clinical settings. Such data are needed to better understand the hygienic relevance of these increasingly popular items. Here, 60 touchscreens of smartphones provided by randomly chosen students of a German university were sampled by directly touching them with contact agar plates. The average bacterial load of uncleaned touchscreens was 1.37 ± 0.33 CFU/cm(2). Touchscreens wiped with commercially available microfiber cloths or alcohol-impregnated lens wipes contained significantly less bacteria than uncleaned touchscreens, i.e., 0.22 ± 0.10 CFU/cm(2) and 0.06 ± 0.02 CFU/cm(2), respectively. Bacteria isolated from cleaned and uncleaned touchscreens were identified by means of MALDI Biotyping. Out of 111 bacterial isolates, 56 isolates (50 %) were identified to genus level and 27 (24 %) to species level. The vast majority of the identified bacteria were typical human skin, mouth, lung, and intestinal commensals, mostly affiliated with the genera Staphylococcus and Micrococcus. Five out of 10 identified species were opportunistic pathogens. In conclusion, the touchscreens investigated here showed low bacterial loads and a species spectrum that is typical for frequently touched surfaces in domestic and public environments, the general health risk of which is still under debate.

Genera of euophryine jumping spiders (Araneae: Salticidae), with a combined molecular-morphological phylogeny.

PubMed

Zhang, Junxia; Maddison, Wayne P

2015-03-27

Morphological traits of euophryine jumping spiders were studied to clarify generic limits in the Euophryinae and to permit phylogenetic classification of genera lacking molecular data. One hundred and eight genera are recognized within the subfamily. Euophryine generic groups and the delimitation of some genera are reviewed in detail. In order to explore the effect of adding formal morphological data to previous molecular phylogenetic studies, and to find morphological synapomorphies, eighty-two morphological characters were scored for 203 euophryine species and seven outgroup species. The morphological dataset does not perform as well as the molecular dataset (genes 28S, Actin 5C; 16S-ND1, COI) in resolving the phylogeny of Euophryinae, probably because of frequent convergence and reversal. The formal morphological data were mapped on the phylogeny in order to seek synapomorphies, in hopes of extending the phylogeny to include taxa for which molecular data are not available. Because of homoplasy, few globally-applicable morphological synapomorphies for euophryine clades were found. However, synapomorphies that are unique locally in subclades still help to delimit euophryine generic groups and genera. The following synonyms of euophryine genera are proposed: Maeotella with Anasaitis; Dinattus with Corythalia; Paradecta with Compsodecta; Cobanus, Chloridusa and Wallaba with Sidusa; Tariona with Mopiopia; Nebridia with Amphidraus; Asaphobelis and Siloca with Coryphasia; Ocnotelus with Semnolius; Palpelius with Pristobaeus; Junxattus with Laufeia; Donoessus with Colyttus; Nicylla, Pselcis and Thianitara with Thiania. The new genus Saphrys is erected for misplaced species from southern South America.

Characterization of Micrococcus strains isolated from indoor air.

PubMed

Kooken, Jennifer M; Fox, Karen F; Fox, Alvin

2012-02-01

The characterization of microbes, such as opportunists and pathogens (e.g., methicillin resistant Staphylococcus aureus [MRSA]), in indoor air is important for understanding disease transmission from person-to-person. Common genera found in the human skin microbiome include Micrococcus and Staphylococcus, but there only a limited number of tests to differentiate these genera and/or species. Both genera are believed to be released into indoor air from the shedding of human skin and are morphologically difficult to distinguish. In the current work, after the extraction of proteins from micrococci and the separation of these proteins on one dimensional electrophoretic gels, tryptic peptides were analyzed by MALDI TOF MS and the mass profiles compared with those of a reference strain (ATCC 4698). The results confirmed that all strains were consistent in identity with Micrococcus luteus. Copyright © 2011 Elsevier Ltd. All rights reserved.

Characterization of Micrococcus strains isolated from indoor air

PubMed Central

Kooken, Jennifer M.; Fox, Karen F.; Fox, Alvin

2014-01-01

The characterization of microbes, such as of opportunists and pathogens (e.g. methicillin resistant Staphylococcus aureus [MRSA]), in indoor air is important for understanding disease transmission from person-to-person. Common genera found in the human skin microbiome include Micrococcus and Staphylococcus, but there only a limited number of tests to differentiate these genera and/or species. Both genera are believed to be released into indoor air from the shedding of human skin and are morphologically difficult to distinguish. In the current work, after the extraction of proteins from micrococci and the separation of these proteins on one dimensional electrophoretic gels, tryptic peptides were analyzed by MALDI TOF MS and the mass profiles compared with those of a reference strain (ATCC 4698). The results confirmed that all strains were consistent in identity with Micrococcus luteus. PMID:21963944

Identification and characterization of the dominant lactic acid bacteria isolated from traditional fermented milk in Mongolia.

PubMed

Sun, Z H; Liu, W J; Zhang, J C; Yu, J; Gao, W; Jiri, M; Menghe, B; Sun, T S; Zhang, H P

2010-05-01

Five samples of Airag and 20 of Tarag (both in Mongolia) were collected from scattered households. One hundred strains of lactic acid bacteria (LAB) were isolated and identified from these samples according to phenotypic characterization and 16S rRNA gene sequence analysis. Eighty-five isolates belonged to the genus Lactobacillus, 15 being classified as coccoid LAB. All isolates belonged to 5 genera and 11 to different species and subspecies. Lactobacillus (Lb.) helveticus was predominant population in Airag samples, Lb. fermentum and Lb. helveticus were the major LAB microflora in Tarag.

Arcopilus aureus, a Resveratrol-Producing Endophyte from Vitis vinifera.

PubMed

Dwibedi, Vagish; Saxena, Sanjai

2018-04-14

Resveratrol is extensively being used as a therapeutic moiety, as well as a pharmacophore for development of new drugs due to its multifarious beneficial effects. The objective of the present study was to isolate and screen the resveratrol-producing endophytic fungi from different varieties of Vitis vinifera. A total of 53 endophytic fungi belonging to different fungal genera were isolated from the stem and leaf tissues of Vitis vinifera (merlot, wild, pinot noir, Shiraz, muscat) from different grape-producing locations of India. Only 29 endophytic fungal isolates exhibited a positive test for phenolics by phytochemical methods. The resveratrol obtained after ethyl acetate extraction was confirmed using standard molecule on thin layer chromatography (TLC) with a retention factor (R f ) of 0.69. The purified and standard resveratrol were visualized under UV light as a violet-colored spot. In HPLC analysis of the ethyl acetate extract of culture broth of 11 endophytic isolates, the highest resveratrol content was found in #12VVLPM (89.1 μg/ml) followed by #18VVLPM (37.3 μg/ml) and 193VVSTPM (25.2 μg/ml) exhibiting a retention time of 3.36 min which corresponded to the standard resveratrol. The resveratrol-producing isolates belong to seven genera viz. Aspergillus, Botryosphaeria, Penicillium, Fusarium, Alternaria, Arcopilus, and Lasiodiplodia, and using morphological and molecular methods, #12VVLPM was identified as Arcopilus aureus.

COAGGREGATION OCCURS AMONGST BACTERIA WITHIN AND BETWEEN DOMESTIC SHOWERHEAD BIOFILMS

PubMed Central

Vornhagen, Jay; Stevens, Michael; McCormick, David; Dowd, Scot E.; Eisenberg, Joseph N.S.; Boles, Blaise R.; Rickard, Alexander H.

2014-01-01

Showerheads support the development multi-species biofilms that can be unsightly, produce malodor, and may harbor pathogens. The outer surface spray plates of many showerheads support visible biofilms that likely contain a mixture of bacteria from freshwater and potentially from human users. Coaggregation, a mechanism by which genetically distinct bacteria specifically recognize one another, may contribute to the retention and enrichment of different species within these biofilms. The aim of this work was to identify the bacterial composition of outer spray plate biofilms of three domestic shower heads and to determine the inter- and intra-biofilm coaggregation ability of each culturable isolate. The bacterial composition of the three biofilms was determined by using bacterial tag-encoded FLX amplicon pyrosequencing (bTEFAP) and by culturing on R2A medium. An average of 31 genera per biofilm were identified using bTEFAP and a total of 30 isolates were cultured. Even though the microbial diversity of each showerhead biofilm differed, every cultured isolate was able to coaggregate with at least one other isolate from the same or different showerhead biofilm. Promiscuous coaggregating isolates belonged to the genera Brevundimonas, Micrococcus, and Lysobacter. This work suggests that coaggregation may be a common feature of showerhead biofilms. Characterization of the mechanisms mediating coaggregation, and the inter-species interactions they facilitate, may allow for novel strategies to inhibit biofilm development. PMID:23194413

Indirect Manganese Removal by Stenotrophomonas sp. and Lysinibacillus sp. Isolated from Brazilian Mine Water

PubMed Central

Barboza, Natália Rocha; Amorim, Soraya Sander; Santos, Pricila Almeida; Reis, Flávia Donária; Cordeiro, Mônica Mendes; Guerra-Sá, Renata; Leão, Versiane Albis

2015-01-01

Manganese is a contaminant in the wastewaters produced by Brazilian mining operations, and the removal of the metal is notoriously difficult because of the high stability of the Mn(II) ion in aqueous solutions. To explore a biological approach for removing excessive amounts of aqueous Mn(II), we investigated the potential of Mn(II) oxidation by both consortium and bacterial isolates from a Brazilian manganese mine. A bacterial consortium was able to remove 99.7% of the Mn(II). A phylogenetic analysis of isolates demonstrated that the predominant microorganisms were members of Stenotrophomonas, Bacillus, and Lysinibacillus genera. Mn(II) removal rates between 58.5% and 70.9% were observed for Bacillus sp. and Stenotrophomonas sp. while the Lysinibacillus isolate 13P removes 82.7%. The catalytic oxidation of Mn(II) mediated by multicopper oxidase was not properly detected; however, in all of the experiments, a significant increase in the pH of the culture medium was detected. No aggregates inside the cells grown for a week were found by electronic microscopy. Nevertheless, an energy-dispersive X-ray spectroscopy of the isolates revealed the presence of manganese in Stenotrophomonas sp. and Lysinibacillus sp. grown in K medium. These results suggest that members of Stenotrophomonas and Lysinibacillus genera were able to remove Mn(II) by a nonenzymatic pathway. PMID:26697496

Adaptation of cyanobacteria to the sulfide-rich microenvironment of black band disease of coral.

PubMed

Myers, Jamie L; Richardson, Laurie L

2009-02-01

Black band disease (BBD) is a cyanobacteria-dominated microbial mat that migrates across living coral colonies lysing coral tissue and leaving behind exposed coral skeleton. The mat is sulfide-rich due to the presence of sulfate-reducing bacteria, integral members of the BBD microbial community, and the sulfide they produce is lethal to corals. The effect of sulfide, normally toxic to cyanobacteria, on the photosynthetic capabilities of five BBD cyanobacterial isolates of the genera Geitlerinema (3), Leptolyngbya (1), and Oscillatoria (1) and six non-BBD cyanobacteria of the genera Leptolyngbya (3), Pseudanabaena (2), and Phormidium (1) was examined. Photosynthetic experiments were performed by measuring the photoincorporation of [(14)C] NaHCO(3) under the following conditions: (1) aerobic (no sulfide), (2) anaerobic with 0.5 mM sulfide, and (3) anaerobic with 0.5 mM sulfide and 10 microM 3-(3',4'-dichlorophenyl)-1,1-dimethylurea (DCMU). All five BBD cyanobacterial isolates tolerated sulfide by conducting sulfide-resistant oxygenic photosynthesis. Five of the non-BBD cyanobacterial isolates did not tolerate sulfide, although one Pseudanabaena isolate continued to photosynthesize in the presence of sulfide at a considerably reduced rate. None of the isolates conducted anoxygenic photosynthesis with sulfide as an electron donor. This is the first report on the physiology of a culture of Oscillatoria sp. found globally in BBD.

Hydrogenobacter subterraneus sp. nov., an extremely thermophilic, heterotrophic bacterium unable to grow on hydrogen gas, from deep subsurface geothermal water.

PubMed

Takai, K; Komatsu, T; Horikoshi, K

2001-07-01

A novel extreme thermophile was isolated from a water sample derived from a deep subsurface geothermal water pool at a depth of 1500 m in the Hacchoubaru geothermal plant in Oita Prefecture, Japan. The cells were found to be straight rods, each being motile by means of a polar flagellum. Growth was observed at temperatures between 60 and 85 degrees C (optimum 78 degrees C; 120 min doubling time) and between pH 5.5 and pH 9.0 (optimum 7.5). The isolate was a strictly aerobic heterotroph capable of utilizing a number of substrates such as yeast extract, peptone, tryptone, various carbohydrates, sugars, amino acids and organic acids. Elemental sulfur, thiosulfate, sulfide or cysteine-hydrochloride was required as an electron donor for growth. Hydrogen gas did not support growth. The G+C content of the genomic DNA was 44.7 mol%. Phylogenetic analysis based on 16S rDNA sequences and DNA-DNA hybridization analysis indicated that the isolate was closely related to members of the hydrogen-oxidizing, autotrophic and thermophilic genera Hydrogenobacter and Calderobacterium. However this isolate was differentiated from the previously described species of these genera on the basis of the physiological and molecular properties of the new isolate. The name Hydrogenobacter subterraneus sp. nov. is proposed; the type strain is HGP1T (= JCM 10560T = IFO 16485T).

Isolation and characterization of antagonistic fungi against potato scab pathogens from potato field soils.

PubMed

Tagawa, Masahiro; Tamaki, Hideyuki; Manome, Akira; Koyama, Osamu; Kamagata, Yoichi

2010-04-01

Potato scab is a serious plant disease caused by several Streptomyces sp., and effective control methods remain unavailable. Although antagonistic bacteria and phages against potato scab pathogens have been reported, to the best of our knowledge, there is no information about fungi that are antagonistic to the pathogens. The aim of this study was to isolate fungal antagonists, characterize their phylogenetic positions, determine their antagonistic activities against potato scab pathogens, and highlight their potential use as control agents under lower pH conditions. Fifteen fungal stains isolated from potato field soils were found to have antagonistic activity against three well-known potato scab pathogens: Streptomyces scabiei, Streptomyces acidiscabiei, and Streptomyces turgidiscabiei. These 15 fungal strains were phylogenetically classified into at least six orders and nine genera based on 18S rRNA gene sequencing analysis. These fungal isolates were related to members of the genera Penicillium, Eupenicillium, Chaetomium, Fusarium, Cladosporium, Mortierella, Kionochaeta, Pseudogymnoascus, and Lecythophora. The antagonistic activities of most of the fungal isolates were highly strengthened under the lower pH conditions, suggesting the advantage of combining their use with a traditional method such as soil acidification. This is the first report to demonstrate that phylogenetically diverse fungi show antagonistic activity against major potato scab pathogens. These fungal strains could be used as potential agents to control potato scab disease.

Fungi Associated with the Hemlock Woolly Adelgid, Adelges tsugae, and Assessment of Entomopathogenic Isolates for Management

PubMed Central

Reid, W.R.; Parker, B.L.; Gouli, S.Y.; Skinner, M.; Gouli, V.V.; Teillon, H.B.

2010-01-01

Fungi associated with the hemlock wooly adelgid, Adelges tsugae Annand (Hemiptera: Adelgidae), were collected throughout the eastern USA and southern China. Twenty fungal genera were identified, as were 79 entomopathogenic isolates, including: Lecanicillium lecanii (Zimmermann) (Hypocreales: Insertae sedis), Isaria farinosa (Holm: Fries.) (Cordycipitaceae), Beauveria bassiana (Balasamo) (Hyphomycetes), and Fusarium spp (Nectriaceae). The remaining fungal genera associated with insect cadavers were similar for both the USA and China collections, although the abundance of Acremonium (Hypocreaceae) was greater in China. The entomopathogenic isolates were assayed for efficacy against Myzus persicae (Sulzer) (Homoptera: Aphididae) and yielded mortality ranging from 3 to 92%. Ten isolates demonstrating the highest efficacy were further assessed for efficacy against field-collected A. tsugae under laboratory conditions. Overall, two B. bassiana, one L. lecanii, and a strain of Metarhizium anisopliae (Metchnikoff) (Hypocreales: Clavicipitaceae), demonstrated significantly higher efficacy against A. tsugae than the others. Isolates were further evaluated for conidial production, germination rate and colony growth at four temperatures representative of field conditions. All isolates were determined to be mesophiles with optimal temperature between 25–30° C. In general, conidial production increased with temperature, though two I. farinosa produced significantly more conidia at cooler temperatures. When efficacy values were compared with conidial production and temperature tolerances, Agricultural Research Service Collection of Entomopathogenic Fungi (ARSEF) 1080, 5170, and 5798 had characteristics comparable to the industrial B. bassiana strain GHA. PMID:20672977

Termite nests as an abundant source of cultivable actinobacteria for biotechnological purposes.

PubMed

Sujada, Nikhom; Sungthong, Rungroch; Lumyong, Saisamorn

2014-01-01

A total of 118 actinobacterial isolates were collected from the three types of termite nests (mound, carton, and subterranean nests) to evaluate their potential as a source of bioactive actinobacteria with antimicrobial activity. The highest number (67 isolates) and generic abundance (7 known genera) of actinobacterial isolates were obtained from carton nests. Streptomyces was the dominant genus in each type of termite nest. In the non-Streptomyces group, Nocardia was the dominant genus detected in mound and carton nests, while Pseudonocardia was the dominant genus in subterranean nests. A discovery trend of novel species (<99% similarity in the 16S rRNA gene sequence) was also observed in the termite nests examined. Each type of termite nest housed >20% of bioactive actinobacteria that could inhibit the growth of at least one test organism, while 12 isolates, belonging to the genera Streptomyces, Amycolatopsis, Pseudonocardia, Micromonospora and Nocardia, exhibited distinct antimicrobial activities. Streptomyces sp. CMU-NKS-3 was the most distinct bioactive isolate. It was closely related to S. padanus MITKK-103T, which was confirmed by 99% similarities in their 16S rRNA gene sequences. The highest level of extracellular antimicrobial substances was produced by the isolate CMU-NKS-3, which was grown in potato dextrose broth and exhibited a wide range (6.10×10(-4)-1.25 mg mL(-1)) of minimum inhibitory concentrations against diverse pathogens. We concluded that termite nests are an abundant source of bioactive strains of cultivable actinobacteria for future biotechnological needs.

Description of new genera and species of marine cyanobacteria from the Portuguese Atlantic coast.

PubMed

Brito, Ângela; Ramos, Vitor; Mota, Rita; Lima, Steeve; Santos, Arlete; Vieira, Jorge; Vieira, Cristina P; Kaštovský, Jan; Vasconcelos, Vitor M; Tamagnini, Paula

2017-06-01

Aiming at increasing the knowledge on marine cyanobacteria from temperate regions, we previously isolated and characterized 60 strains from the Portuguese foreshore and evaluate their potential to produce secondary metabolites. About 15% of the obtained 16S rRNA gene sequences showed less than 97% similarity to sequences in the databases revealing novel biodiversity. Herein, seven of these strains were extensively characterized and their classification was re-evaluated. The present study led to the proposal of five new taxa, three genera (Geminobacterium, Lusitaniella, and Calenema) and two species (Hyella patelloides and Jaaginema litorale). Geminobacterium atlanticum LEGE 07459 is a chroococcalean that shares morphological characteristics with other unicellular cyanobacterial genera but has a distinct phylogenetic position and particular ultrastructural features. The description of the Pleurocapsales Hyella patelloides LEGE 07179 includes novel molecular data for members of this genus. The filamentous isolates of Lusitaniella coriacea - LEGE 07167, 07157 and 06111 - constitute a very distinct lineage, and seem to be ubiquitous on the Portuguese coast. Jaaginema litorale LEGE 07176 has distinct characteristics compared to their marine counterparts, and our analysis indicates that this genus is polyphyletic. The Synechococcales Calenema singularis possess wider trichomes than Leptolyngbya, and its phylogenetic position reinforces the establishment of this new genus. Copyright © 2017 Elsevier Inc. All rights reserved.

[Yeast microbiota in artisanal cheeses from Corrientes, Argentina].

PubMed

Cardozo, Marina C; Fusco, Ángel J V; Carrasco, Marta S

The artisanal cheese from Corrientes (from the Spanish acronym QAC-Queso Artesanal de Corrientes/Artisanal Cheese from Corrientes) is a soft cheese elaborated with raw cow milk and an artisanal coagulant agent. Lactic bacteria contitute the main flora of this cheese although yeasts are also present in high quantities as secondary microbiota and might play a relevant role in cheese ripening. The aim of this work was to evaluate yeast occurrence during QAC elaboration and ripening, and the effect of seasonal variation. Yeasts were isolated and purified from raw materials and cheese at different ripening stagesl elaborated during the different seasons. Yeast sample counts were in the order of 10 3 - 10 7 UFC/ml o UFC/g. Ninety yeast strains were classified: 9 from milk, 28 from the coagulant agent, 10 from curd and 43 from cheese. Candida predominated in milk samples while other yeast genera had low incidence. Candida also predominated in the coagulant agent samples, followed by genera Myxozyma and Debaryomyces. The isolates obtained from cheese belonged to the same genera predominating in the coagulant agent, and showed the same order of prevalence. Copyright © 2017 Asociación Argentina de Microbiología. Publicado por Elsevier España, S.L.U. All rights reserved.

Diversity of Bacillus-like bacterial community in the sediments of the Bamenwan mangrove wetland in Hainan, China.

PubMed

Liu, Min; Cui, Ying; Chen, Yuqing; Lin, Xiangzhi; Huang, Huiqin; Bao, Shixiang

2017-03-01

Members of the genus Bacillus and related spore-forming genera are ubiquitous. However, Bacillus-like species isolated from marine sediments have attracted less interest than their terrestrial relatives. Here, we investigated the diversity of Bacillus-like bacterial communities in the sediments of the Bamenwan mangrove wetland in Hainan, China, using culture-dependent and culture-independent methods, and present the first report on this subject. We also discovered some potential novel species from the sediment samples. Four families, Bacillaceae (58%), Paenibacillaceae (22%), Alicyclobacillaceae (15%), and Planococcaceae (5%), and 9 genera, Bacillus (42%), Paenibacillus (16%), Halobacillus (13%), Alicyclobacillus (11%), Rummeliibacillus (5%), Cohnella (5%), Tumebacillus (4%), Pontibacillus (3%), and Aneurinibacillus (2%), were identified by pyrosequencing. In contrast, only 4 genera, Bacillus (57%), Paenibacillus (23%), Halobacillus (14%), and Virgibacillus (6%), were detected by the culture-dependent method. In the 16S rDNA sequencing analysis, the isolates HB12036 and HB12037 were closest to Bacillus okuhidensis Kh10-101 T and Paenibacillus xylanilyticus XIL14 T with similarities of 94.8% and 95.9%, respectively, indicating that these were novel species. Bacillus sp. HB12035 and HB12040 exhibited antimicrobial activity against Staphylococcus aureus ATCC 25923, and Bacillus sp. HB12033 exhibited antimicrobial activity against Ustilago scitaminea Syd.

Heterocyte-forming cyanobacteria from Brazilian saline-alkaline lakes.

PubMed

Genuário, Diego Bonaldo; Andreote, Ana Paula Dini; Vaz, Marcelo Gomes Marçal Vieira; Fiore, Marli Fátima

2017-04-01

Studies investigating the diversity of cyanobacteria from tropical environments are scarce, especially those devoted to the isolation and molecular characterization of the isolated strains. Among the Brazilian biomes, Pantanal has mainly been examined through microscopic observation of environmental samples, resulting in lists of morphotypes without any genetic information. Recently, two studies were conducted evaluating the morphologic and genetic diversity of cultured non-heterocytous cyanobacteria in this biome, which resulted in the separation and description of two novel genera. In order to complement the diversity of cultured cyanobacteria from saline-alkaline lakes in Pantanal, the present study is dedicated to the examination of cultured nitrogen-fixing heterocytous cyanobacteria from this extreme and underexplored environment. A total of fourteen cyanobacterial strains were isolated. According to morphological examination they belong to the order Nostocales and to the subsections IV.I and IV.II, according to the International Code of Nomenclature for Algae, Fungi and Plants and the Bergey's Manual of Systematic Bacteriology, respectively. Phylogenetic evaluation of their 16S rRNA gene sequences resulted in the formation of five clusters. Among them, one is clearly related to the genus Anabaenopsis whilst the remaining clusters may represent new genetic lineages. These novel sequences aid in the delimitation of problematic groups, especially those containing sequences belonging to mixed genera. The application of both morphologic and phylogenetic studies has proven to be an important tool in resolving problematic groups in cyanobacteria systematics. This strategy is essential in order to detect novel cyanobacteria genera from other tropical environments. Copyright © 2016 Elsevier Inc. All rights reserved.

Bacterial succession during curing process of a skate (Dipturus batis) and isolation of novel strains.

PubMed

Reynisson, E; Thornór Marteinsson, V; Jónsdóttir, R; Magnússon, S H; Hreggvidsson, G O

2012-08-01

To study the succession of cultivated and uncultivated microbes during the traditional curing process of skate. The microbial diversity was evaluated by sequencing 16Sr RNA clone libraries and cultivation in variety of media from skate samples taken periodically during a 9-day curing process. A pH shift was observed (pH 6·64-9·27) with increasing trimethylamine (2·6 up to 75·6 mg N per 100 g) and total volatile nitrogen (TVN) (from 58·5 to 705·8 mg N per 100 g) but with relatively slow bacterial growth. Uncured skate was dominated by Oceanisphaera and Pseudoalteromonas genera but was substituted after curing by Photobacterium and Aliivibrio in the flesh and Pseudomonas on the skin. Almost 50% of the clone library is derived from putative undiscovered species. Cultivation and enrichment strategies resulted in isolation of putatively new species belonging to the genera Idiomarina, Rheinheimera, Oceanisphaera, Providencia and Pseudomonas. The most abundant genera able to hydrolyse urea to ammonia were Oceanisphaera, Psychrobacter, Pseudoalteromonas and isolates within the Pseudomonas genus. The curing process of skate is controlled and achieved by a dynamic bacterial community where the key players belong to Oceanisphaera, Pseudoalteromonas, Photobacterium, Aliivibrio and Pseudomonas. For the first time, the bacterial population developments in the curing process of skate are presented and demonstrate a reservoir of many yet undiscovered bacterial species. No Claim to Norwegian Government works Journal of Applied Microbiology © 2012 The Society for Applied Microbiology.

Identification of subsurface microorganisms at Yucca Mountain; Third quarterly report, January 1, 1994--March 31, 1994

DOE Office of Scientific and Technical Information (OSTI.GOV)

Stetzenbach, L.D.

1994-05-01

Bacteria isolated from ground water samples taken from 31 springs during 1993 were collected and processed according to procedures described in earlier reports. These procedures required aseptic collection of surface water samples in sterile screw-capped containers, transportation to the HRC microbiology laboratory, and culture by spread plating onto R2A medium. The isolates were further processed for identification using a gas chromatographic analysis of fatty acid methyl esters (FAME) extracted from cell membranes. This work generated a presumptive identification of 113 bacterial species distributed among 45 genera using a database obtained from Microbial ID, Inc., Newark, Delaware (MIDI). A preliminary examinationmore » of the FAME data was accomplished using cluster analysis and principal component analysis software obtained from MIDI. Typically, bacterial strains that cluster at less than 10 Euclidian distance units have fatty acid patterns consistent among members of the same species. Thus an organism obtained from one source can be recognized if it is isolated again from the same or any other source. This makes it possible to track the distribution of organisms and monitor environmental conditions or fluid transport mechanisms. Microorganisms are seldom found as monocultures in natural environments. They are more likely to be closely associated with other genera with complementary metabolic requirements. An understanding of the indigenous microorganism population is useful in understanding subtle changes in the environment. However, classification of environmental organisms using traditional methods is not ideal because differentiation of species with small variations or genera with very similar taxonomic characteristics is beyond the capabilities of traditional microbiological methods.« less

Antimicrobial susceptibility of clinical isolates of Actinomyces and related genera reveals an unusual clindamycin resistance among Actinomyces urogenitalis strains.

PubMed

Barberis, Claudia; Budia, Mabel; Palombarani, Susana; Rodriguez, Carlos Hernán; Ramírez, María Soledad; Arias, Barbara; Bonofiglio, Laura; Famiglietti, Angela; Mollerach, Marta; Almuzara, Marisa; Vay, Carlos

2017-03-01

Patterns of antimicrobial susceptibility in Actinomyces and related genera are very limited in the literature. Data of predominant susceptibility profiles could contribute to the establishment of an accurate empirical treatment. A total of 113 isolates from clinical samples were included in this study. Each isolate was identified using phenotypic methods and MALDI-TOF/MS. When discrepancies were observed, 16S rRNA gene sequencing was performed. The minimum inhibitory concentrations (MICs) of nine antimicrobial agents (penicillin, ceftriaxone, linezolid, tetracycline, clindamycin, erythromycin, ciprofloxacin, levofloxacin and vancomycin) were tested against the species Actinotignum schaalii (n=23), Actinomyces turicensis (n=18), Actinomyces europaeus (n=13), Actinomyces naeslundii/Actinomyces viscosus group (n=12), Actinomyces urogenitalis (n=11), Actinomyces radingae (n=11), Actinomyces neuii (n=9), Actinomyces odontolyticus (n=8), Bifidobacterium scardovii (n=3), Actinomyces graevenitzii (n=2), Alloscardovia omnicolens (n=2) and Varibaculum cambriense (n=1). All of the isolates were susceptible to penicillin, ceftriaxone, vancomycin and linezolid. Almost all of the A. urogenitalis isolates (8/11) were resistant to clindamycin and showed susceptibility to erythromycin, suggesting an L-phenotype, however no determinants of clindamycin resistance (lnu and lsa genes) were detected by PCR. High MIC values to quinolones were observed in 54/113 isolates (47.8%). All of the A. urogenitalis isolates were highly resistant to ciprofloxacin and levofloxacin. These data highlight the importance of ongoing surveillance to provide relevant information for empirical management of infections caused by these organisms. Copyright © 2017 International Society for Chemotherapy of Infection and Cancer. Published by Elsevier Ltd. All rights reserved.

Human exposure to airborne fungi from genera used as biocontrol agents in plant production.

PubMed

Madsen, Anne Mette; Hansen, Vinni Mona; Meyling, Nicolai Vitt; Eilenberg, Jørgen

2007-01-01

The fungi Trichoderma harzianum, T. polysporum, T. viride, Paeciliomyces fumosoroseus, P. lilacinus, Verticillium/lecanicillium lecanii, Ulocladium oudemansii, U. atrum and Beauveria bassiana are used or considered to be used for biocontrol of pests and plant diseases. Human exposure to these fungi in environments where they may naturally occur or are used as biocontrol agents has not been directly investigated to date. This review aims to provide an overview of the current knowledge of human exposure to fungi from the relevant genera. The subject of fungal taxonomy due to the rapid development of this issue is also discussed. B. bassiana, V. lecanii, T. harzianum, T. polysporum, P. lilacinus and U. oudemansii were infrequently present in the air and thus people in general seem to be seldom exposed to these fungi. However, when V. lecanii was present, high concentrations were measured. Fungi from the genera Trichoderma, Paecilomyces and Ulocladium were rarely identified to the species level and sometimes high concentrations were reported. T. viride and U. atrum were detected frequently in different environments and sometimes with a high frequency of presence in samples. Thus, people seem to be frequently exposed to these fungi. Sequence data have led to recent revisions of fungal taxonomy, and in future studies it is important to specify the taxonomy used for identification, thus making comparisons possible.

Spectrofluorimetric study of the interaction of the mycotoxin citrinin with gold nanoparticles

USDA-ARS?s Scientific Manuscript database

Citrinin is a nephrotoxic secondary metabolite produced by certain fungal species from the Aspergillus, Penicillium, and Monascus genera. Citrinin producing species occasionally contaminate grains, and may pose food safety risks. Analysis of this mycotoxin is frequently carried out by liquid chromat...

IDENTIFICATION OF MICROCYSTIN TOXINS FROM A STRAIN OF MICROCYSTIS AERUGINOSA

EPA Science Inventory

Microcystin toxins are cyclic heptapeptides produced by several genera and species of cyanobacteria that are responsible for the "green scum" frequently observed on eutrophic surface waters. These toxins, which are a million times more toxic than cyanide ion, have caused deaths o...

Bioprospection of cold-adapted yeasts with biotechnological potential from Antarctica.

PubMed

Martorell, María Martha; Ruberto, Lucas Adolfo Mauro; Fernández, Pablo Marcelo; Castellanos de Figueroa, Lucía Inés; Mac Cormack, Walter Patricio

2017-06-01

The aim of this study was to investigate the ability to produce extracellular hydrolytic enzymes at low temperature of yeasts isolated from 25 de Mayo island, Antarctica, and to identify those exhibiting one or more of the evaluated enzymatic activities. A total of 105 yeast isolates were obtained from different samples and 66 were identified. They belonged to 12 basidiomycetous and four ascomycetous genera. Most of the isolates were ascribed to the genera Cryptococcus, Mrakia, Cystobasidium, Rhodotorula, Gueomyces, Phenoliferia, Leucosporidium, and Pichia. Results from enzymes production at low temperatures revealed that the Antarctic environment contains metabolically diverse cultivable yeasts, which represent potential tools for biotechnological applications. While most the isolates proved to produce 2-4 of the investigated exoenzymes, two of them evidenced the six evaluated enzymatic activities: Pichia caribbica and Guehomyces pullulans, which were characterized as psycrotolerant and psycrophilic, respectively. In addition, P. caribbica could assimilate several n-alkanes and diesel fuel. The enzyme production profile and hydrocarbons assimilation capacity, combined with its high level of biomass production and the extended exponential growth phase make P. caribbica a promising tool for cold environments biotechnological purposes in the field of cold-enzymes production and oil spills bioremediation as well. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Identification of Opportunistic Pathogenic Bacteria in Drinking Water Samples of Different Rural Health Centers and Their Clinical Impacts on Humans

PubMed Central

Pindi, Pavan Kumar; Raghuveer Yadav, P.; Shiva Shanker, A.

2013-01-01

International drinking water quality monitoring programs have been established in order to prevent or to reduce the risk of contracting water-related infections. A survey was performed on groundwater-derived drinking water from 13 different hospitals in the Mahabubnagar District. A total of 55 bacterial strains were isolated which belonged to both gram-positive and gram-negative bacteria. All the taxa were identified based on the 16S rRNA gene sequence analysis based on which they are phylogenetically close to 27 different taxa. Many of the strains are closely related to their phylogenetic neighbors and exhibit from 98.4 to 100% sequence similarity at the 16S rRNA gene sequence level. The most common group was similar to Acinetobacter junii (21.8%) and Acinetobacter calcoaceticus (10.9%) which were shared by 7 and 5 water samples, respectively. Out of 55 isolates, only 3 isolates belonged to coliform group which are Citrobacter freundii and Pantoea anthophila. More than half (52.7%, 29 strains) of the phylogenetic neighbors which belonged to 12 groups were reported to be pathogenic and isolated from clinical specimens. Out of 27 representative taxa are affiliated have eight representative genera in drinking water except for those affiliated with the genera Exiguobacterium, Delftia, Kocuria, and Lysinibacillus. PMID:23862144

Diversity of halophilic archaea from six hypersaline environments in Turkey.

PubMed

Ozcan, Birgul; Ozcengiz, Gulay; Coleri, Arzu; Cokmus, Cumhur

2007-06-01

The diversity of archaeal strains from six hypersaline environments in Turkey was analyzed by comparing their phenotypic characteristics and 16S rDNA sequences. Thirty-three isolates were characterized in terms of their phenotypic properties including morphological and biochemical characteristics, susceptibility to different antibiotics, and total lipid and plasmid contents, and finally compared by 16S rDNA gene sequences. The results showed that all isolates belong to the family Halobacteriaceae. Phylogenetic analyses using approximately 1,388 bp comparisions of 16S rDNA sequences demonstrated that all isolates clustered closely to species belonging to 9 genera, namely Halorubrum (8 isolates), Natrinema (5 isolates), Haloarcula (4 isolates), Natronococcus (4 isolates), Natrialba (4 isolates), Haloferax (3 isolates), Haloterrigena (3 isolates), Halalkalicoccus (1 isolate), and Halomicrobium (1 isolate). The results revealed a high diversity among the isolated halophilic strains and indicated that some of these strains constitute new taxa of extremely halophilic archaea.

Identification of Enterobacteriaceae by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry using the VITEK MS system.

PubMed

Richter, S S; Sercia, L; Branda, J A; Burnham, C-A D; Bythrow, M; Ferraro, M J; Garner, O B; Ginocchio, C C; Jennemann, R; Lewinski, M A; Manji, R; Mochon, A B; Rychert, J A; Westblade, L F; Procop, G W

2013-12-01

This multicenter study evaluated the accuracy of matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) mass spectrometry identifications from the VITEK MS system (bioMérieux, Marcy l'Etoile, France) for Enterobacteriaceae typically encountered in the clinical laboratory. Enterobacteriaceae isolates (n = 965) representing 17 genera and 40 species were analyzed on the VITEK MS system (database v2.0), in accordance with the manufacturer's instructions. Colony growth (≤72 h) was applied directly to the target slide. Matrix solution (α-cyano-4-hydroxycinnamic acid) was added and allowed to dry before mass spectrometry analysis. On the basis of the confidence level, the VITEK MS system provided a species, genus only, or no identification for each isolate. The accuracy of the mass spectrometric identification was compared to 16S rRNA gene sequencing performed at MIDI Labs (Newark, DE). Supplemental phenotypic testing was performed at bioMérieux when necessary. The VITEK MS result agreed with the reference method identification for 96.7% of the 965 isolates tested, with 83.8% correct to the species level and 12.8% limited to a genus-level identification. There was no identification for 1.7% of the isolates. The VITEK MS system misidentified 7 isolates (0.7 %) as different genera. Three Pantoea agglomerans isolates were misidentified as Enterobacter spp. and single isolates of Enterobacter cancerogenus, Escherichia hermannii, Hafnia alvei, and Raoultella ornithinolytica were misidentified as Klebsiella oxytoca, Citrobacter koseri, Obesumbacterium proteus, and Enterobacter aerogenes, respectively. Eight isolates (0.8 %) were misidentified as a different species in the correct genus. The VITEK MS system provides reliable mass spectrometric identifications for Enterobacteriaceae.

Yeast diversity and dynamics in the production processes of Norwegian dry-cured meat products.

PubMed

Asefa, Dereje T; Møretrø, Trond; Gjerde, Ragnhild O; Langsrud, Solveig; Kure, Cathrine F; Sidhu, Maan S; Nesbakken, Truls; Skaar, Ida

2009-07-31

This study investigate the diversity and dynamics of yeasts in the production processes of one unsmoked and two smoked dry-cured meat products of a Norwegian dry-cured meat production facility. A longitudinal observational study was performed to collect 642 samples from the meat, production materials, room installations and indoor and outdoor air of the production facility. Nutrient rich agar media were used to isolate the yeasts. Morphologically different isolates were re-cultivated in their pure culture forms. Both classical and molecular methods were employed for species identification. Totally, 401 yeast isolates belonging to 10 species of the following six genera were identified: Debaryomyces, Candida, Rhodotorula, Rhodosporidium, Cryptococcus and Sporidiobolus. Debaryomyces hansenii and Candida zeylanoides were dominant and contributed by 63.0% and 26.4% respectively to the total isolates recovered from both smoked and unsmoked products. The yeast diversity was higher at the pre-salting production processes with C. zeylanoides being the dominant. Later at the post-salting stages, D. hansenii occurred frequently. Laboratory studies showed that D. hansenii was more tolerant to sodium chloride and nitrite than C. zeylanoides. Smoking seems to have a killing or a temporary growth inhibiting effect on yeasts that extend to the start of the drying process. Yeasts were isolated only from 31.1% of the environmental samples. They belonged to six different species of which five of them were isolated from the meat samples too. Debaryomyces hansenii and Rhodotorula glutinis were dominant with a 62.6% and 22.0% contribution respectively. As none of the air samples contained D. hansenii, the production materials and room installations used in the production processes were believed to be the sources of contamination. The dominance of D. hansenii late in the production process replacing C. zeylanoides should be considered as a positive change both for the quality and safety of the products, as C. zeylanoides has been documented as an emerging pathogen.

Isolation of endosymbionts from Ipomoea carnea and Swainsona canescens that produce swainsonine

USDA-ARS?s Scientific Manuscript database

Fungi including Metarhizium anisopliae (Clavicipitaceae), Rhizoctonia leguminicola (Ceratobasidiaceae), and Undifilum (Pleosporaceae), an endophyte found in the plant genera Astragalus and Oxytropis (Fabaceae) have been reported to be responsible for the production of swainsonine. Based upon the ass...

Microbial cycling of isoprene, the most abundantly produced biological volatile organic compound on Earth.

PubMed

McGenity, Terry J; Crombie, Andrew T; Murrell, J Colin

2018-04-01

Isoprene (2-methyl-1,3-butadiene), the most abundantly produced biogenic volatile organic compound (BVOC) on Earth, is highly reactive and can have diverse and often detrimental atmospheric effects, which impact on climate and health. Most isoprene is produced by terrestrial plants, but (micro)algal production is important in aquatic environments, and the relative bacterial contribution remains unknown. Soils are a sink for isoprene, and bacteria that can use isoprene as a carbon and energy source have been cultivated and also identified using cultivation-independent methods from soils, leaves and coastal/marine environments. Bacteria belonging to the Actinobacteria are most frequently isolated and identified, and Proteobacteria have also been shown to degrade isoprene. In the freshwater-sediment isolate, Rhodococcus strain AD45, initial oxidation of isoprene to 1,2-epoxy-isoprene is catalyzed by a multicomponent isoprene monooxygenase encoded by the genes isoABCDEF. The resultant epoxide is converted to a glutathione conjugate by a glutathione S-transferase encoded by isoI, and further degraded by enzymes encoded by isoGHJ. Genome sequence analysis of actinobacterial isolates belonging to the genera Rhodococcus, Mycobacterium and Gordonia has revealed that isoABCDEF and isoGHIJ are linked in an operon, either on a plasmid or the chromosome. In Rhodococcus strain AD45 both isoprene and epoxy-isoprene induce a high level of transcription of 22 contiguous genes, including isoABCDEF and isoGHIJ. Sequence analysis of the isoA gene, encoding the large subunit of the oxygenase component of isoprene monooxygenase, from isolates has facilitated the development of PCR primers that are proving valuable in investigating the ecology of uncultivated isoprene-degrading bacteria.

Conjunctival bacterial and fungal flora in clinically normal sheep.

PubMed

Bonelli, Francesca; Barsotti, Giovanni; Attili, Anna Rita; Mugnaini, Linda; Cuteri, Vincenzo; Preziuso, Silvia; Corazza, Michele; Preziuso, Giovanna; Sgorbini, Micaela

2014-01-01

The aim was to identify conjunctival bacterial and fungal flora in clinically normal sheep. Prospective study. Tuscany. 100 eyes from 50 adult Massese female sheep were examined. The sheep included in the study were considered free of anterior ophthalmic abnormalities. Bacteria were identified by morphological assessment, Gram staining, biochemical tests. Identification of filamentous fungi was achieved at the genus level, and Aspergillus species were identified based on keys provided by other authors. Yeast colonies were highlighted, but not identified. Positive cultures were obtained from 100/100 eyes for bacteria, and from 86/100 eyes for fungi. A total of 14 types of bacteria and 5 types of fungi were isolated. Yeasts were isolated from 13/100 eyes. The most frequent fungal isolates were saprophytic fungi. Conjunctival bacterial and fungal flora of clinically normal eyes were reported in sheep. The positivity obtained for conjunctival bacteria was higher compared to findings in the literature by other authors in the same species (100 per cent v 40 per cent), while our results were in line with a recent work performed on mouflons (Ovis Musimon) with a 100 per cent positivity for bacterial conjunctival fornix. In our survey, Gram-positive species were prevalent, as reported by other authors in different species. Few data are available in the literature regarding conjunctival fungal flora in healthy small ruminants. The prevalence of conjunctival fungal flora in this study was higher than findings reported in mouflons (86 per cent v 45 per cent). Differences in fungal prevalence may be due to different methods of managing herds, though further studies are required to verify this hypothesis. The similarities in bacterial and fungal isolates between sheep and mouflons suggest a genera pattern of conjunctival colonisation by bacteria and fungi.

Isolation frequency of Candida present on the surfaces of mobile phones and handsx.

PubMed

Kordecka, Anna; Krajewska-Kułak, Elżbieta; Łukaszuk, Cecylia; Kraszyńska, Bogumiła; Kułak, Wojciech

2016-06-01

It is known that mobile phones may play a role in microorganism transmission. The aim of this study was to analyze the relationship between the number of Candida genera/species isolated from samples collected from the surfaces of mobile phones and the hands of the staff as well as the preferred health-related behavior. The mycological evaluation included 175 mobile telephones and the hands of staff members at the University Hospital in Białystok, Poland. We used the Count-Tact(TM) applicator, with CandiSelect (Bio-Rad). Self-administered questionnaire was used to gather data on mobile phones disinfection practices. Assessment of the preferred health-related behavior was based on The Multidemensional Health Locus of Control Scale (MHLC). Out of 175 mobile phones, 131 (74.9 %) were colonized. Candida glabrata, C. albicans and C.krusei were isolated more frequently from the hand as well as phone surface. The mean number of Candida colonies was higher in samples collected from hand surfaces than mobile phone surfaces. No significant correlation was found between the preferred health-related behavior and the frequency of washing hands, the way of using a mobile phone, the number of colonies or the isolation frequency for the fungi collected from the surface of the phones and hands of their owners. Only 19.4 % of the participants cleaned the surface of their phones. The prevalence of mobile phone contamination by Candida is high in the University Hospital in Białystok, Poland. Candida albicans, C. glabrata, and C. krusei were the dominant species in the samples collected from mobile phones and hands. These results pose the need to develop guidelines for mobile phone disinfection.

Temperature and host preferences drive the diversification of Saccharomyces and other yeasts: a survey and the discovery of eight new yeast species.

PubMed

Sylvester, Kayla; Wang, Qi-Ming; James, Brielle; Mendez, Russell; Hulfachor, Amanda Beth; Hittinger, Chris Todd

2015-05-01

Compared to its status as an experimental model system and importance to industry, the ecology and genetic diversity of the genus Saccharomyces has received less attention. To investigate systematically the biogeography, community members and habitat of these important yeasts, we isolated and identified nearly 600 yeast strains using sugar-rich enrichment protocols. Isolates were highly diverse and contained representatives of more than 80 species from over 30 genera, including eight novel species that we describe here: Kwoniella betulae f.a. (yHKS285(T) = NRRL Y-63732(T) = CBS 13896(T)), Kwoniella newhampshirensis f.a. (yHKS256(T) = NRRL Y-63731(T) = CBS 13917(T)), Cryptococcus wisconsinensis (yHKS301(T) = NRRL Y-63733(T) = CBS 13895(T)), Cryptococcus tahquamenonensis (yHAB242(T) = NRRL Y-63730(T) = CBS 13897(T)), Kodamaea meredithiae f.a. (yHAB239(T) = NRRL Y-63729(T) = CBS 13899(T)), Blastobotrys buckinghamii (yHAB196(T) = NRRL Y-63727(T) = CBS 13900(T)), Candida sungouii (yHBJ21(T) = NRRL Y-63726(T) = CBS 13907(T)) and Cyberlindnera culbertsonii f.a. (yHAB218(T) = NRRL Y-63728(T) = CBS 13898(T)), spp. nov. Saccharomyces paradoxus was one of the most frequently isolated species and was represented by three genetically distinct lineages in Wisconsin alone. We found a statistically significant association between Quercus (oak) samples and the isolation of S. paradoxus, as well as several novel associations. Variation in temperature preference was widespread across taxonomic ranks and evolutionary timescales. This survey highlights the genetic and taxonomic diversity of yeasts and suggests that host and temperature preferences are major ecological factors. © FEMS 2015. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Actinobacteria Isolated from an Underground Lake and Moonmilk Speleothem from the Biggest Conglomeratic Karstic Cave in Siberia as Sources of Novel Biologically Active Compounds

PubMed Central

Tokovenko, Bogdan T.; Protasov, Eugeniy S.; Gamaiunov, Stanislav V.; Rebets, Yuriy V.; Luzhetskyy, Andriy N.; Timofeyev, Maxim A.

2016-01-01

Actinobacteria isolated from unstudied ecosystems are one of the most interesting and promising sources of novel biologically active compounds. Cave ecosystems are unusual and rarely studied. Here, we report the isolation and characterization of ten new actinobacteria strains isolated from an ancient underground lake and moonmilk speleothem from the biggest conglomeratic karstic cave in Siberia with a focus on the biological activity of the obtained strains and the metabolite dereplication of one active strain. Streptomyces genera isolates from moonmilk speleothem demonstrated antibacterial and antifungal activities. Some of the strains were able to inhibit the growth of pathogenic Candida albicans. PMID:26901168

Actinomycetes from Eucalyptus and their biological activities for controlling Eucalyptus leaf and shoot blight.

PubMed

Himaman, Winanda; Thamchaipenet, Arinthip; Pathom-Aree, Wasu; Duangmal, Kannika

2016-01-01

In Thailand, Eucalyptus plantations rapidly expand across the country. Leaf and shoot blight caused by Cryptosporiopsis eucalypti, Cylindrocladium sp. and Teratosphaeria destructans is a serious disease in Eucalyptus plantations. In this study, a total of 477 actinomycete strains were successfully isolated from roots and rhizosphere soil of Eucalyptus. Four hundred and thirty nine isolates were classified as streptomycetes and 38 isolates were non-streptomycetes. Among these isolates, 272 (57.0%), 118 (24.7%) and 241 (50.5%) isolates were antagonistic to Cryptosporiopsis eucalypti, Cylindrocladium sp. and Teratosphaeria destructans, respectively. All isolates were tested for their abilities to produce siderophores, indole acetic acid (IAA) and solubilise phosphate. Most isolates (464, 97.3%) produced siderophores. The majority of isolates (345, 72.3%) solubilised phosphate. In addition, almost half of these isolates (237, 49.7%) produced indole acetic acid. Strain EUSKR2S82 which showed the strongest inhibitory effect against all tested fungi with plant growth promoting ability was selected to test with Eucalyptus. This strain could colonize plant roots and increase Eucalyptus roots length. In a detached leaves bioassay, the disease severity of EUSKR2S82-inoculated Eucalyptus leaves was only 30% compared to 95% in the control treatment. The 16S rRNA gene sequence analysis revealed that the strain EUSKR2S82 was related to Streptomyces ramulosus NRRL-B 2714(T) (99.44% similarity). Identification of non-streptomycete isolates using 16S rRNA gene sequences classified them into 9 genera: Actinoallomurus, Actinomadura, Amycolatopsis, Cryptosporangium, Microbispora, Micromonospora, Nocardia, Nonomuraea and Pseudonocardia. It is evident that Eucalyptus tree harbored several genera of actinomycetes. The selected isolate, EUSKR2S82 showed potential as a candidate for biocontrol agent of leaf and shoot blight of Eucalyptus and to promote growth. Copyright © 2016 Elsevier GmbH. All rights reserved.

Diversity of Bacteria Carried by Pinewood Nematode in USA and Phylogenetic Comparison with Isolates from Other Countries

PubMed Central

Proença, Diogo Neves; Fonseca, Luís; Powers, Thomas O.; Abrantes, Isabel M. O.; Morais, Paula V.

2014-01-01

Pine wilt disease (PWD) is native to North America and has spread to Asia and Europe. Lately, mutualistic relationship has been suggested between the pinewood nematode (PWN), Bursaphelenchus xylophilus the causal nematode agent of PWD, and bacteria. In countries where PWN occurs, nematodes from diseased trees were reported to carry bacteria from several genera. However no data exists for the United States. The objective of this study was to evaluate the diversity of the bacterial community carried by B. xylophilus, isolated from different Pinus spp. with PWD in Nebraska, United States. The bacteria carried by PWN belonged to Gammaproteobacteria (79.9%), Betaproteobacteria (11.7%), Bacilli (5.0%), Alphaproteobacteria (1.7%) and Flavobacteriia (1.7%). Strains from the genera Chryseobacterium and Pigmentiphaga were found associated with the nematode for the first time. These results were compared to results from similar studies conducted from other countries of three continents in order to assess the diversity of bacteria with associated with PWN. The isolates from the United States, Portugal and China belonged to 25 different genera and only strains from the genus Pseudomonas were found in nematodes from all countries. The strains from China were closely related to P. fluorescens and the strains isolated from Portugal and USA were phylogenetically related to P. mohnii and P. lutea. Nematodes from the different countries are associated with bacteria of different species, not supporting a relationship between PWN with a particular bacterial species. Moreover, the diversity of the bacteria carried by the pinewood nematode seems to be related to the geographic area and the Pinus species. The roles these bacteria play within the pine trees or when associated with the nematodes, might be independent of the presence of the nematode in the tree and only related on the bacteria's relationship with the tree. PMID:25127255

Differential Response of Coral Assemblages to Thermal Stress Underscores the Complexity in Predicting Bleaching Susceptibility.

PubMed

Chou, Loke Ming; Toh, Tai Chong; Toh, Kok Ben; Ng, Chin Soon Lionel; Cabaitan, Patrick; Tun, Karenne; Goh, Eugene; Afiq-Rosli, Lutfi; Taira, Daisuke; Du, Rosa Celia Poquita; Loke, Hai Xin; Khalis, Aizat; Li, Jinghan; Song, Tiancheng

2016-01-01

Coral bleaching events have been predicted to occur more frequently in the coming decades with global warming. The susceptibility of corals to bleaching during thermal stress episodes is dependent on many factors and an understanding of these underlying drivers is crucial for conservation management. In 2013, a mild bleaching episode ensued in response to elevated sea temperature on the sediment-burdened reefs in Singapore. Surveys of seven sites highlighted variable bleaching susceptibility among coral genera-Pachyseris and Podabacia were the most impacted (31% of colonies of both genera bleached). The most susceptible genera such as Acropora and Pocillopora, which were expected to bleach, did not. Susceptibility varied between less than 6% and more than 11% of the corals bleached, at four and three sites respectively. Analysis of four of the most bleached genera revealed that a statistical model that included a combination of the factors (genus, colony size and site) provided a better explanation of the observed bleaching patterns than any single factor alone. This underscored the complexity in predicting the coral susceptibility to future thermal stress events and the importance of monitoring coral bleaching episodes to facilitate more effective management of coral reefs under climate change.

Diversity and Spatiotemporal Distribution of Larval Odonate Assemblages in Temperate Neotropical Farm Ponds

PubMed Central

Pires, Mateus Marques; Kotzian, Carla Bender; Spies, Marcia Regina

2014-01-01

Abstract Farm ponds help maintain diversity in altered landscapes. However, studies on the features that drive this type of property in the Neotropics are still lacking, especially for the insect fauna. We analyzed the spatial and temporal distribution of odonate larval assemblages in farm ponds. Odonates were sampled monthly at four farm ponds from March 2008 to February 2009 in a temperate montane region of southern Brazil. A small number of genera were frequent and accounted for most of the dominant fauna. The dominant genera composition differed among ponds. Local spatial drivers such as area, hydroperiod, and margin vegetation structure likely explain these results more than spatial predictors due to the small size of the study area. Circular analysis detected seasonal effect on assemblage abundance but not on richness. Seasonality in abundance was related to the life cycles of a few dominant genera. This result was explained by temperature and not rainfall due to the temperate climate of the region studied. The persistence of dominant genera and the sparse occurrence of many taxa over time probably led to a lack in a seasonal pattern in assemblage richness. PMID:25527585

Synergistic plant-microbe interactions between endophytic bacterial communities and the medicinal plant Glycyrrhiza uralensis F.

PubMed

Li, Li; Mohamad, Osama Abdalla Abdelshafy; Ma, Jinbiao; Friel, Ariel D; Su, Yangui; Wang, Yun; Musa, Zulpiya; Liu, Yonghong; Hedlund, Brian P; Li, Wenjun

2018-03-07

Little is known about the composition, diversity, and geographical distribution of bacterial communities associated with medicinal plants in arid lands. To address this, a collection of 116 endophytic bacteria were isolated from wild populations of the herb Glycyrrhiza uralensis Fisch (licorice) in Xinyuan, Gongliu, and Tekesi of Xinjiang Province, China, and identified based on their 16S rRNA gene sequences. The endophytes were highly diverse, including 20 genera and 35 species. The number of distinct bacterial genera obtained from root tissues was higher (n = 14) compared to stem (n = 9) and leaf (n = 6) tissue. Geographically, the diversity of culturable endophytic genera was higher at the Tekesi (n = 14) and Xinyuan (n = 12) sites than the Gongliu site (n = 4), reflecting the extremely low organic carbon content, high salinity, and low nutrient status of Gongliu soils. The endophytic bacteria exhibited a number of plant growth-promoting activities ex situ, including diazotrophy, phosphate and potassium solubilization, siderophore production, auxin synthesis, and production of hydrolytic enzymes. Twelve endophytes were selected based on their ex situ plant growth-promoting activities for growth chamber assays to test for their ability to promote growth of G. uralensis F. and Triticum aestivum (wheat) plants. Several strains belonging to the genera Bacillus (n = 6) and Achromobacter (n = 1) stimulated total biomass production in both G. uralensis and T. aestivum under low-nutrient conditions. This work is the first report on the isolation and characterization of endophytes associated with G. uralensis F. in arid lands. The results demonstrate the broad diversity of endophytes associated with wild licorice and suggest that some Bacillus strains may be promising candidates for biofertilizers to promote enhanced survival and growth of licorice and other valuable crops in arid environments.

16S Ribosomal DNA Characterization of Nitrogen-Fixing Bacteria Isolated from Banana (Musa spp.) and Pineapple (Ananas comosus (L.) Merril)

PubMed Central

Magalhães Cruz, Leonardo; Maltempi de Souza, Emanuel; Weber, Olmar Baler; Baldani, José Ivo; Döbereiner, Johanna; de Oliveira Pedrosa, Fábio

2001-01-01

Nitrogen-fixing bacteria isolated from banana (Musa spp.) and pineapple (Ananas comosus (L.) Merril) were characterized by amplified 16S ribosomal DNA restriction analysis and 16S rRNA sequence analysis. Herbaspirillum seropedicae, Herbaspirillum rubrisubalbicans, Burkholderia brasilensis, and Burkholderia tropicalis were identified. Eight other types were placed in close proximity to these genera and other alpha and beta Proteobacteria. PMID:11319127

Experimental Proteus mirabilis Burn Surface Infection

DTIC Science & Technology

1982-02-01

Reprinted from the Achie of Surgery ECTE February 1982, Volume 117 Copyright 19 2. American Medical Association MAY 2 8 1982 V0A Experimental Proteus ... mirabilis Burn Surface Infection Albert T. McManus, PhD; Charles G. McLeod, Jr, DVM; Arthur D. Mason, Jr, MD * We established a human burn Isolate of... Proteus mirabills as have examined human burn isolates from the genera an experimental pathogen. Infliction of a nonfatal scald injury Enterobacter

A Phylogeny of the Family Poritidae (Cnidaria, Scleractinia) Based on Molecular and Morphological Analyses

PubMed Central

Kitano, Yuko F.; Benzoni, Francesca; Arrigoni, Roberto; Shirayama, Yoshihisa; Wallace, Carden C.; Fukami, Hironobu

2014-01-01

The family Poritidae formerly included 6 genera: Alveopora, Goniopora, Machadoporites, Porites, Poritipora, and Stylaraea. Morphologically, the genera can be differentiated based on the number of tentacles, the number of septa and their arrangement, the length of the polyp column, and the diameter of the corallites. However, the phylogenetic relationships within and between the genera are unknown or contentious. On the one hand, Alveopora has been transferred to the Acroporidae recently because it was shown to be more closely related to this family than to the Poritidae by previous molecular studies. On the other hand, Goniopora is morphologically similar to 2 recently described genera, Machadoporites and Poritipora, particularly with regard to the number of septa (approximately 24), but they have not yet been investigated at the molecular level. In this study, we analyzed 93 samples from all 5 poritid genera and Alveopora using 2 genetic markers (the barcoding region of the mitochondrial COI and the ITS region of the nuclear rDNA) to investigate their phylogenetic relationships and to revise their taxonomy. The reconstructed molecular trees confirmed that Alveopora is genetically distant from all poritid genera but closely related to the family Acroporidae, whereas the other genera are genetically closely related. The molecular trees also revealed that Machadoporites and Poritipora were indistinguishable from Goniopora. However, Goniopora stutchburyi was genetically isolated from the other congeneric species and formed a sister group to Goniopora together with Porites and Stylaraea, thus suggesting that 24 septa could be an ancestral feature in the Poritidae. Based on these data, we move G. stutchburyi into a new genus, Bernardpora gen. nov., whereas Machadoporites and Poritipora are merged with Goniopora. PMID:24871224

Microbial Diversity of Emalahleni Mine Water in South Africa and Tolerance Ability of the Predominant Organism to Vanadium and Nickel

PubMed Central

Kamika, Ilunga; Momba, Maggie N. B.

2014-01-01

The present study aims firstly at determining the microbial diversity of mine-water collected in Emalahleni, South Africa and secondly isolating and characterizing the most dominant bacterial species found in the mine water in terms of its resistance to both V5+ and Ni2+ in a modified wastewater liquid media. The results revealed a microbial diversity of 17 orders, 27 families and 33 genera were found in the mine-water samples with Marinobacteria (47.02%) and Anabaena (17.66%) being the most abundant genera. Considering their abundance in the mine-water samples, a species of the Marinobacter genera was isolated, identified, and characterised for metal tolerance and removal ability. The MWI-1 isolate (Marinobacter sp. MWI-1 [AB793286]) was found to be closely related to Marinobacter goseongensis at 97% of similarity. The isolate was exposed to various concentrations of Ni2+ and V5+ in wastewater liquid media and its tolerance to metals was also assessed. The MWI-1 isolate could tolerate V5+ and Ni2+ separately at concentrations (in terms of MIC) up to 13.41±0.56 mM and 5.39±0.5 mM at pH 7, whereas at pH 3, the tolerance limit decrease to 11.45±0.57 mM and 2.67±0.1 mM, respectively. The removal of V5+ and Ni2+ in liquid media was noted to gradually decrease with a gradual increase of the test metals. A significant difference (p<0.05) between V5+ and Ni2+ removal was noted. Marinobacter sp. MWI-1 achieved the maximum permissible limit of 0.1 mg-V5+/L prescribed by UN-FAO at 100 mg/L, while at 200 mg/L only V5+ was removed at approximately 95% and Ni2+ at 47%. This study suggests that mine-water indigenous microorganisms are the best solution for the remediation of polluted mine water. PMID:24465951

The biology, identification and management of Rhizoctonia pathogens

USDA-ARS?s Scientific Manuscript database

Rhizoctonia solani is an economically important soilborne pathogen causing economic losses to crops, vegetables, ornamentals, forest trees and turfgrasses. The pathogenic isolates may belong to diverse genera and species and are variously responsible for pre- or post-emergence damping off of seedlin...

[Multicenter Prospective Observational Study of Fungal Keratitis--Identification and Susceptibility Test of Fungi].

PubMed

Sunada, Atsuko; Asari, Seishi; Inoue, Yoshitsugu; Ohashi, Yuichi; Suzuki, Takashi; Shimomura, Yoshikazu; Fukuda, Masahiko; Sotozono, Chie; Hatano, Hiroshi; Eguchi, Hiroshi; Araki-Sasaki, Kaoru; Hoshi, Saichi; Yaguchi, Takashi; Makimura, Koichi; Yokokura, Shunji; Mochizuki, Kiyofumi; Monden, Yu; Nejima, Ryohei

2016-01-01

To investigate the causative fungi of fungal keratitis in Japan and their drug susceptibility. Identification and antifungal susceptibility test for 8 drugs (micafungin, amphotericin B, flucytosine, fluconazole, itraconazole, voriconazole, miconazole and pimaricin) were performed using isolated fungi from patients with fungal keratitis treated at 27 facilities in Japan between November 1, 2011 and October 31, 2013. Fungal strains were detected in 72 (50.7%) out of 142 samples. The major isolates were Fusarium spp. (18), Candida parapsilosis (12), C. albicans (11) and Alternaria spp. (6), in all, fungi of 31 species were identified by gene analysis. In the yeast-like fungi, susceptibility rates were evident for more than 80% in voriconazole, pimaricin, flucytosine, micafungin, amphotericin B and fluconazole. In filamentous fungi, the susceptibility rate was less than 50% except for PMR (90%). Fusarium spp., which were susceptible to amphotericin B and pimaricin, showed lower susceptibility rates compared with other genera. Although various genera and species of fungi cause fungal keratitis, the obtained drug susceptibility data in this study demonstrates the different susceptibility patterns among the major isolates (Fusarium spp., C. parapsilosis, C. albicans and other groups). This is important evidence useful for fungal keratitis treatment.

Termite Nests as an Abundant Source of Cultivable Actinobacteria for Biotechnological Purposes

PubMed Central

Sujada, Nikhom; Sungthong, Rungroch; Lumyong, Saisamorn

2014-01-01

A total of 118 actinobacterial isolates were collected from the three types of termite nests (mound, carton, and subterranean nests) to evaluate their potential as a source of bioactive actinobacteria with antimicrobial activity. The highest number (67 isolates) and generic abundance (7 known genera) of actinobacterial isolates were obtained from carton nests. Streptomyces was the dominant genus in each type of termite nest. In the non-Streptomyces group, Nocardia was the dominant genus detected in mound and carton nests, while Pseudonocardia was the dominant genus in subterranean nests. A discovery trend of novel species (<99% similarity in the 16S rRNA gene sequence) was also observed in the termite nests examined. Each type of termite nest housed >20% of bioactive actinobacteria that could inhibit the growth of at least one test organism, while 12 isolates, belonging to the genera Streptomyces, Amycolatopsis, Pseudonocardia, Micromonospora and Nocardia, exhibited distinct antimicrobial activities. Streptomyces sp. CMU-NKS-3 was the most distinct bioactive isolate. It was closely related to S. padanus MITKK-103T, which was confirmed by 99% similarities in their 16S rRNA gene sequences. The highest level of extracellular antimicrobial substances was produced by the isolate CMU-NKS-3, which was grown in potato dextrose broth and exhibited a wide range (6.10×10−4–1.25 mg mL−1) of minimum inhibitory concentrations against diverse pathogens. We concluded that termite nests are an abundant source of bioactive strains of cultivable actinobacteria for future biotechnological needs. PMID:24909709

Genetic Analysis of Phytophthora nicotianae Populations from Different Hosts Using Microsatellite Markers.

PubMed

Biasi, Antonio; Martin, Frank N; Cacciola, Santa O; di San Lio, Gaetano Magnano; Grünwald, Niklaus J; Schena, Leonardo

2016-09-01

In all, 231 isolates of Phytophthora nicotianae representing 14 populations from different host genera, including agricultural crops (Citrus, Nicotiana, and Lycopersicon), potted ornamental species in nurseries (Lavandula, Convolvulus, Myrtus, Correa, and Ruta), and other plant genera were characterized using simple-sequence repeat markers. In total, 99 multilocus genotypes (MLG) were identified, revealing a strong association between genetic grouping and host of recovery, with most MLG being associated with a single host genus. Significant differences in the structure of populations were revealed but clonality prevailed in all populations. Isolates from Citrus were found to be genetically related regardless of their geographic origin and were characterized by high genetic uniformity and high inbreeding coefficients. Higher variability was observed for other populations and a significant geographical structuring was determined for isolates from Nicotiana. Detected differences were related to the propagation and cultivation systems of different crops. Isolates obtained from Citrus spp. are more likely to be distributed worldwide with infected plant material whereas Nicotiana and Lycopersicon spp. are propagated by seed, which would not contribute to the spread of the pathogen and result in a greater chance for geographic isolation of lineages. With regard to ornamental species in nurseries, the high genetic variation is likely the result of the admixture of diverse pathogen genotypes through the trade of infected plant material from various geographic origins, the presence of several hosts in the same nursery, and genetic recombination through sexual reproduction of this heterothallic species.

Molecular characterization of the endophytic fungal community associated with Eichhornia azurea (Kunth) and Eichhornia crassipes (Mart.) (Pontederiaceae) native to the Upper Paraná River floodplain, Brazil.

PubMed

Almeida, T T; Orlandelli, R C; Azevedo, J L; Pamphile, J A

2015-05-11

Endophytic fungi live in the interior of healthy plants without causing them any damage. These fungi are of biotechnological interest; they may be used in the biological control of pests and plant diseases, and in the pharmaceutical industry. The aquatic macrophytes Eichhornia azurea (Kunth) and Eichhornia crassipes (Mart.) belong to the Pontederiaceae family. The first is a fixed-floating species and the second is a free-floating species that is known for its phytoremediation potential. The fungal endophytes associated with the leaves of E. azurea and E. crassipes, native to the Upper Paraná River floodplain, Brazil, were isolated. The sequencing of the ITS1-5.8S-ITS2 region of ribosomal DNA was performed and the nucleotide sequences obtained were compared with those available in the GenBank database for the molecular identification of the isolates. The construction of phylogenetic trees was performed using the MEGA5 software. The results showed that high colonization frequencies were obtained from the 610 foliar fragments sampled from each plant: 87.86% for E. azurea and 88.85% for E. crassipes. At the genus level, it was possible to identify 19 fungal endophytes belonging to the genera Alternaria, Bipolaris, Cercospora, Diaporthe, Gibberella, Pestalotiopsis, Plectosphaerella, Phoma, and Saccharicola. Two other endophytes were identified at the species level (Microsphaeropsis arundinis). Genera Bipolaris, Cercospora, Microsphaeropsis, and Phoma were found as endophytes in the two macrophytes and the other genera were host-specific, being isolated from only one macrophyte, proving that there is a small difference in the endophytic diversity of the two Eichhornia species analyzed.

Multicenter Evaluation of the Vitek MS v3.0 System for the Identification of Filamentous Fungi.

PubMed

Rychert, Jenna; Slechta, E Sue; Barker, Adam P; Miranda, Edwin; Babady, N Esther; Tang, Yi-Wei; Gibas, Connie; Wiederhold, Nathan; Sutton, DeAnna; Hanson, Kimberly E

2018-02-01

Invasive fungal infections are an important cause of morbidity and mortality affecting primarily immunocompromised patients. While fungal identification to the species level is critical to providing appropriate therapy, it can be slow and laborious and often relies on subjective morphological criteria. The use of matrix-assisted laser desorption ionization-time of flight (MALDI-TOF) mass spectrometry has the potential to speed up and improve the accuracy of identification. In this multicenter study, we evaluated the accuracy of the Vitek MS v3.0 system in identifying 1,601 clinical mold isolates compared to identification by DNA sequence analysis and supported by morphological and phenotypic testing. Among the 1,519 isolates representing organisms in the v3.0 database, 91% ( n = 1,387) were correctly identified to the species level. An additional 27 isolates (2%) were correctly identified to the genus level. Fifteen isolates were incorrectly identified, due to either a single incorrect identification ( n = 13) or multiple identifications from different genera ( n = 2). In those cases, when a single identification was provided that was not correct, the misidentification was within the same genus. The Vitek MS v3.0 was unable to identify 91 (6%) isolates, despite repeat testing. These isolates were distributed among all the genera. When considering all isolates tested, even those that were not represented in the database, the Vitek MS v3.0 provided a single correct identification 98% of the time. These findings demonstrate that the Vitek MS v3.0 system is highly accurate for the identification of common molds encountered in the clinical mycology laboratory. Copyright © 2018 American Society for Microbiology.

Microbial diversity in Los Azufres geothermal field (Michoacán, Mexico) and isolation of representative sulfate and sulfur reducers.

PubMed

Brito, Elcia M S; Villegas-Negrete, Norberto; Sotelo-González, Irene A; Caretta, César A; Goñi-Urriza, Marisol; Gassie, Claire; Hakil, Florence; Colin, Yannick; Duran, Robert; Gutiérrez-Corona, Felix; Piñón-Castillo, Hilda A; Cuevas-Rodríguez, Germán; Malm, Olaf; Torres, João P M; Fahy, Anne; Reyna-López, Georgina E; Guyoneaud, Rémy

2014-03-01

Los Azufres spa consists of a hydrothermal spring system in the Mexican Volcanic Axis. Five samples (two microbial mats, two mud pools and one cenote water), characterized by high acidity (pH between 1 and 3) and temperatures varying from 27 to 87 °C, were investigated for their microbial diversity by Terminal-Restriction Fragment Length Polymorphism (T-RFLP) and 16S rRNA gene library analyses. These data are the first to describe microbial diversity from Los Azufres geothermal belt. The data obtained from both approaches suggested a low bacterial diversity in all five samples. Despite their proximity, the sampling points differed by their physico-chemical conditions (mainly temperature and matrix type) and thus exhibited different dominant bacterial populations: anoxygenic phototrophs related to the genus Rhodobacter in the biomats, colorless sulfur oxidizers Acidithiobacillus sp. in the warm mud and water samples, and Lyzobacter sp.-related populations in the hot mud sample (87 °C). Molecular data also allowed the detection of sulfate and sulfur reducers related to Thermodesulfobium and Desulfurella genera. Several strains affiliated to both genera were enriched or isolated from the mesophilic mud sample. A feature common to all samples was the dominance of bacteria involved in sulfur and iron biogeochemical cycles (Rhodobacter, Acidithiobacillus, Thiomonas, Desulfurella and Thermodesulfobium genera).

Characterization of aerosolized bacteria and fungi from desert dust events in Mali, West Africa

USGS Publications Warehouse

Kellogg, C.A.; Griffin, Dale W.; Garrison, V.H.; Peak, K.K.; Royall, N.; Smith, R.R.; Shinn, E.A.

2004-01-01

Millions of metric tons of African desert dust blow across the Atlantic Ocean each year, blanketing the Caribbean and southeastern United States. Previous work in the Caribbean has shown that atmospheric samples collected during dust events contain living microbes, including plant and opportunistic human pathogens. To better understand the potential downwind public health and ecosystem effects of the dust microbes, it is important to characterize the source population. We describe 19 genera of bacteria and 3 genera of fungi isolated from air samples collected in Mali, a known source region for dust storms, and over which large dust storms travel.

Genus IX. Kutzneria Stackebrandt, Kroppenstedt, Jahnke, Kemmerling and Gurtler 1994, 267vp

USDA-ARS?s Scientific Manuscript database

The physiology, systematics and ecology of the species that currently composes the actinobacterial genus Kutzneria is presented. The phylogenetic position of the species within this genus relative to the other genera within the suborder Pseudonocardineae is discussed. Methods for isolation, preser...

Genetic characterization, molecular epidemiology, and phylogenetic relationships of insect-specific viruses in the taxon Negevirus

PubMed Central

Nunes, Marcio R.T.; Contreras-Gutierrez, María Angélica; Guzman, Hilda; Martins, Livia C.; Barbirato, Mayla Feitoza; Savit, Chelsea; Balta, Victoria; Uribe, Sandra; Vivero, Rafael; Suaza, Juan David; Oliveira, Hamilton; Nunes Neto, Joaquin P.; Carvalho, Valeria L.; da Silva, Sandro Patroca; Cardoso, Jedson F.; de Oliveira, Rodrigo Santo; da Silva Lemos, Poliana; Wood, Thomas G.; Widen, Steven G.; Vasconcelos, Pedro F.C.; Fish, Durland; Vasilakis, Nikos; Tesh, Robert B.

2017-01-01

The recently described taxon Negevirus is comprised of a diverse group of insect-specific viruses isolated from mosquitoes and phlebotomine sandflies. In this study, a comprehensive genetic characterization, molecular, epidemiological and evolutionary analyses were conducted on nearly full-length sequences of 91 new negevirus isolates obtained in Brazil, Colombia, Peru, Panama, USA and Nepal. We demonstrated that these arthropod restricted viruses are clustered in two major phylogenetic groups with origins related to three plant virus genera (Cilevirus, Higrevirus and Blunevirus). Molecular analyses demonstrated that specific host correlations are not present with most negeviruses; instead, high genetic variability, wide host-range, and cross-species transmission were noted. The data presented here also revealed the existence of five novel insect-specific viruses falling into two arthropod-restrictive virus taxa, previously proposed as distinct genera, designated Nelorpivirus and Sandewavirus. Our results provide a better understanding of the molecular epidemiology, evolution, taxonomy and stability of this group of insect-restricted viruses. PMID:28193550

Genetic characterization, molecular epidemiology, and phylogenetic relationships of insect-specific viruses in the taxon Negevirus.

PubMed

Nunes, Marcio R T; Contreras-Gutierrez, María Angélica; Guzman, Hilda; Martins, Livia C; Barbirato, Mayla Feitoza; Savit, Chelsea; Balta, Victoria; Uribe, Sandra; Vivero, Rafael; Suaza, Juan David; Oliveira, Hamilton; Nunes Neto, Joaquin P; Carvalho, Valeria L; da Silva, Sandro Patroca; Cardoso, Jedson F; de Oliveira, Rodrigo Santo; da Silva Lemos, Poliana; Wood, Thomas G; Widen, Steven G; Vasconcelos, Pedro F C; Fish, Durland; Vasilakis, Nikos; Tesh, Robert B

2017-04-01

The recently described taxon Negevirus is comprised of a diverse group of insect-specific viruses isolated from mosquitoes and phlebotomine sandflies. In this study, a comprehensive genetic characterization, molecular, epidemiological and evolutionary analyses were conducted on nearly full-length sequences of 91 new negevirus isolates obtained in Brazil, Colombia, Peru, Panama, USA and Nepal. We demonstrated that these arthropod restricted viruses are clustered in two major phylogenetic groups with origins related to three plant virus genera (Cilevirus, Higrevirus and Blunevirus). Molecular analyses demonstrated that specific host correlations are not present with most negeviruses; instead, high genetic variability, wide host-range, and cross-species transmission were noted. The data presented here also revealed the existence of five novel insect-specific viruses falling into two arthropod-restrictive virus taxa, previously proposed as distinct genera, designated Nelorpivirus and Sandewavirus. Our results provide a better understanding of the molecular epidemiology, evolution, taxonomy and stability of this group of insect-restricted viruses. Copyright © 2017 Elsevier Inc. All rights reserved.

Niakha virus: a novel member of the family Rhabdoviridae isolated from phlebotomine sandflies in Senegal.

PubMed

Vasilakis, Nikos; Widen, Steven; Mayer, Sandra V; Seymour, Robert; Wood, Thomas G; Popov, Vsevolov; Guzman, Hilda; Travassos da Rosa, Amelia P A; Ghedin, Elodie; Holmes, Edward C; Walker, Peter J; Tesh, Robert B

2013-09-01

Members of the family Rhabdoviridae have been assigned to eight genera but many remain unassigned. Rhabdoviruses have a remarkably diverse host range that includes terrestrial and marine animals, invertebrates and plants. Transmission of some rhabdoviruses often requires an arthropod vector, such as mosquitoes, midges, sandflies, ticks, aphids and leafhoppers, in which they replicate. Herein we characterize Niakha virus (NIAV), a previously uncharacterized rhabdovirus isolated from phebotomine sandflies in Senegal. Analysis of the 11,124 nt genome sequence indicates that it encodes the five common rhabdovirus proteins with alternative ORFs in the M, G and L genes. Phylogenetic analysis of the L protein indicate that NIAV's closest relative is Oak Vale rhabdovirus, although in this analysis NIAV is still so phylogenetically distinct that it might be classified as distinct from the eight currently recognized Rhabdoviridae genera. This observation highlights the vast, and yet not fully recognized diversity, of this family. Copyright © 2013 Elsevier Inc. All rights reserved.

Distribution of mosquitoes and mosquito-borne arboviruses in Yunnan Province near the China-Myanmar-Laos border.

PubMed

Wang, Jinglin; Zhang, Hailin; Sun, Xiaohong; Fu, Shihong; Wang, Huanqin; Feng, Yun; Wang, Huanyu; Tang, Qing; Liang, Guo-Dong

2011-05-01

Economic development and increased tourism in the southern region of Yunnan Province in China, adjacent to several countries in Southeast Asia, has increased the likelihood of import and export of vectors and vector-borne diseases. We report the results of surveillance of mosquitoes and mosquito-borne arboviruses along the border of China-Myanmar-Laos in 2005 and 2006, and information associating several arboviruses with infections and possibly disease in local human populations. Seventeen mosquito species representing four genera were obtained, and 14 strains of mosquito-borne viruses representing six viruses in five genera were isolated from Culex tritaeniorhynchus. In addition, IgM against Japanese encephalitis virus, Sindbis virus, Yunnan orbivirus and novel Banna virus was detected in acute-phase serum samples obtained from hospitalized patients with fever and encephalitis near the areas where the viruses were isolated. This investigation suggests that Japanese encephalitis virus, Sindbis virus, and lesser-known arboviruses circulate and may be infecting humans in the China-Myanmar-Laos border region.

Prevalence and Antimicrobial Resistance of Thermophilic Campylobacter spp. from Cattle Farms in Washington State

PubMed Central

Bae, Wonki; Kaya, Katherine N.; Hancock, Dale D.; Call, Douglas R.; Park, Yong Ho; Besser, Thomas E.

2005-01-01

The prevalence of thermophilic Campylobacter spp. was investigated in cattle on Washington State farms. A total of 350 thermophilic Campylobacter isolates were isolated from 686 cattle sampled on 15 farms (eight dairies, two calf rearer farms, two feedlots, and three beef cow-calf ranches). Isolate species were identified with a combination of phenotypic tests, hipO colony blot hybridization, and multiplex lpxA PCR. Breakpoint resistance to four antimicrobials (ciprofloxacin, nalidixic acid, erythromycin, and doxycycline) was determined by agar dilution. Campylobacter jejuni was the most frequent species isolated (34.1%), followed by Campylobacter coli (7.7%) and other thermophilic campylobacters (1.5%). The most frequently detected resistance was to doxycycline (42.3% of 350 isolates). Isolates from calf rearer facilities were more frequently doxycycline resistant than isolates from other farm types. C. jejuni was most frequently susceptible to all four of the antimicrobial drugs studied (58.8% of 272 isolates). C. coli isolates were more frequently resistant than C. jejuni, including resistance to quinolone antimicrobials (89.3% of isolates obtained from calves on calf rearer farms) and to erythromycin (72.2% of isolates obtained from feedlot cattle). Multiple drug resistance was more frequent in C. coli (51.5%) than in C. jejuni (5.1%). The results of this study demonstrate that C. jejuni is widely distributed among Washington cattle farms, while C. coli is more narrowly distributed but significantly more resistant. PMID:15640184

Diversity of endophytic fungi and screening of fungal paclitaxel producer from Anglojap yew, Taxus x media

PubMed Central

2013-01-01

Background Endophytic fungi represent underexplored resource of novel lead compounds and have a capacity to produce diverse class of plant secondary metabolites. Here we investigated endophytic fungi diversity and screening of paclitaxel-producing fungi from Taxus x media. Results Eighty-one endophytic fungi isolated from T. media were grouped into 8 genera based on the morphological and molecular identification. Guignardia and Colletotrichum were the dominant genera, whereas the remaining genera were infrequent groups. The genera Glomerella and Gibberella were first reported in Taxus. Three representative species of the distinct genera gave positive hits by molecular marker screening and were capable of producing taxol which were validated by HPLC-MS. Among these 3 taxol-producing fungi, the highest yield of taxol was 720 ng/l by Guignardia mangiferae HAA11 compared with those of Fusarium proliferatum HBA29 (240 ng/l) and Colletotrichum gloeosporioides TA67 (120 ng/l). This is the first report of taxol producer from Guignardia. Moreover, the lower similarities of ts and bapt between microbial and plant origin suggested that fungal taxol biosynthetic cluster might be repeatedly invented during evolution, nor horizontal gene transfer from Taxus species. Conclusions Taxol-producing endophytic fungi could be a fascinating reservoir to generate taxol-related drug lead and to elucidate the remained 5 unknown genes or the potential regulation mechanism in the taxol biosynthesis pathway. PMID:23537181

Characterization of juvenile maritime pine (Pinus pinaster Ait.) ectomycorrhizal fungal community using morphotyping, direct sequencing and fruitbodies sampling.

PubMed

Pestaña Nieto, Montserrat; Santolamazza Carbone, Serena

2009-02-01

Using ectomycorrhizal root tip morphotyping (anatomical and morphological identification), molecular analysis (internal transcribed spacer region amplification and sequencing), and fruitbody sampling, we assessed diversity and composition of the ectomycorrhizal fungal community colonizing juvenile Pinus pinaster Ait. under natural conditions in NW Spain. Overall, we found 15 Basidiomycetes and two Ascomycetes. Members of the family Thelephoraceae represented up to 59.4% of the samples. The most frequent species was Tomentella sublilacina followed by Thelephora terrestris, Russula drimeia, Suillus bovinus, and Paxillus involutus, while the less frequent were Pseudotomentella tristis, Lactarius subdulcis, Russula ochroleuca, and Entoloma conferendum. From October 2007 to June 2008, we sampled 208 sporocarps belonging to seven genera and nine species: Thelephora terrestris, Paxillus involutus, Suillus bovinus, Xerocomus badius, Scleroderma verrucosum, Amanita gemmata, A. rubescens, Amanita sp., and Russula sp. The species belonging to the genus Amanita, X. badius and S. verrucosum were not found on root samples. By comparing our results with a bibliographic review of papers published from 1922 to 2006, we found five genera and six species which have not been previously reported in symbiosis with P. pinaster. This is the first time that the diversity of the ectomycorrhizal fungal community associated with P. pinaster was investigated using molecular techniques. Considering that only 38% of the genera found by sequencing were found as fruitbodies, we conclude that integrating morphotyping and sporocarps surveys with molecular analysis of ectomycorrhizas is important to documenting the ectomycorrhizal fungus community.

Survey of Microbial Diversity in Flood Areas during Thailand 2011 Flood Crisis Using High-Throughput Tagged Amplicon Pyrosequencing.

PubMed

Mhuantong, Wuttichai; Wongwilaiwalin, Sarunyou; Laothanachareon, Thanaporn; Eurwilaichitr, Lily; Tangphatsornruang, Sithichoke; Boonchayaanant, Benjaporn; Limpiyakorn, Tawan; Pattaragulwanit, Kobchai; Punmatharith, Thantip; McEvoy, John; Khan, Eakalak; Rachakornkij, Manaskorn; Champreda, Verawat

2015-01-01

The Thailand flood crisis in 2011 was one of the largest recorded floods in modern history, causing enormous damage to the economy and ecological habitats of the country. In this study, bacterial and fungal diversity in sediments and waters collected from ten flood areas in Bangkok and its suburbs, covering residential and agricultural areas, were analyzed using high-throughput 454 pyrosequencing of 16S rRNA gene and internal transcribed spacer sequences. Analysis of microbial community showed differences in taxa distribution in water and sediment with variations in the diversity of saprophytic microbes and sulfate/nitrate reducers among sampling locations, suggesting differences in microbial activity in the habitats. Overall, Proteobacteria represented a major bacterial group in waters, while this group co-existed with Firmicutes, Bacteroidetes, and Actinobacteria in sediments. Anaeromyxobacter, Steroidobacter, and Geobacter were the dominant bacterial genera in sediments, while Sulfuricurvum, Thiovirga, and Hydrogenophaga predominated in waters. For fungi in sediments, Ascomycota, Glomeromycota, and Basidiomycota, particularly in genera Philipsia, Rozella, and Acaulospora, were most frequently detected. Chytridiomycota and Ascomycota were the major fungal phyla, and Rhizophlyctis and Mortierella were the most frequently detected fungal genera in water. Diversity of sulfate-reducing bacteria, related to odor problems, was further investigated using analysis of the dsrB gene which indicated the presence of sulfate-reducing bacteria of families Desulfobacteraceae, Desulfobulbaceae, Syntrobacteraceae, and Desulfoarculaceae in the flood sediments. The work provides an insight into the diversity and function of microbes related to biological processes in flood areas.

Complete Genome Sequence of a New Ruminococcaceae Bacterium Isolated from Anaerobic Biomass Hydrolysis.

PubMed

Hahnke, Sarah; Abendroth, Christian; Langer, Thomas; Codoñer, Francisco M; Ramm, Patrice; Porcar, Manuel; Luschnig, Olaf; Klocke, Michael

2018-04-05

A new Ruminococcaceae bacterium, strain HV4-5-B5C, participating in the anaerobic digestion of grass, was isolated from a mesophilic two-stage laboratory-scale leach bed biogas system. The draft annotated genome sequence presented in this study and 16S rRNA gene sequence analysis indicated the affiliation of HV4-5-B5C with the family Ruminococcaceae outside recently described genera. Copyright © 2018 Hahnke et al.

Bioactive Secondary Metabolites from a Thai Collection of Soil and Marine-Derived Fungi of the Genera Neosartorya and Aspergillus.

PubMed

Zin, War War May; Prompanya, Chadaporn; Buttachon, Suradet; Kijjoa, Anake

2016-01-01

Fungi are microorganisms which can produce interesting secondary metabolites with structural diversity. Although terrestrial fungi have been extensively investigated for their bioactive secondary metabolites such as antibiotics, marine-derived fungi have only recently attracted attention of Natural Products chemists. Our group has been working on the secondary metabolites produced by the cultures of the fungi of the genera Neosartorya and Aspergillus, collected from soil and marine environments from the tropical region for the purpose of finding new leads for anticancer and antibacterial drugs. This review covers only the secondary metabolites of four soil and six marine-derived species of Neosarorya as well as a new species of marine-derived Aspergillus, investigated by our group. In total, we have isolated fifty three secondary metabolites which can be categorized as polyketides (two), isocoumarins (six), terpenoids (two), meroterpenes (fourteen), alkaloids (twenty eight) and cyclic peptide (one). The anticancer and antibacterial activities of these fungal metabolites are also discussed. Among fifty three secondary metabolites isolated, only the alkaloid eurochevalierine and the cadinene sesquiterpene, isolated from the soil fungus N. pseudofisheri, showed relevant in vitro cytostatic activity against glioblastoma (U373) and non-small cell lung cancer (A549) cell lines while the meroditerpene aszonapyrone A exhibited strong antibacterial activity against multidrug-resistant Gram-positive bacteria and also strong antibiofilm activity in these isolates.

Gram-positive anaerobic cocci--commensals and opportunistic pathogens.

PubMed

Murphy, Elizabeth Carmel; Frick, Inga-Maria

2013-07-01

Among the Gram-positive anaerobic bacteria associated with clinical infections, the Gram-positive anaerobic cocci (GPAC) are the most prominent and account for approximately 25-30% of all isolated anaerobic bacteria from clinical specimens. Still, routine culture and identification of these slowly growing anaerobes to the species level has been limited in the diagnostic laboratory, mainly due to the requirement of prolonged incubation times and time-consuming phenotypic identification. In addition, GPAC are mostly isolated from polymicrobial infections with known pathogens and therefore their relevance has often been overlooked. However, through improvements in diagnostic and in particular molecular techniques, the isolation and identification of individual genera and species of GPAC associated with specific infections have been enhanced. Furthermore, the taxonomy of GPAC has undergone considerable changes over the years, mainly due to the development of molecular identification methods. Existing species have been renamed and novel species have been added, resulting in changes of the nomenclature. As the abundance and significance of GPAC in clinical infections grow, knowledge of virulence factors and antibiotic resistance patterns of different species becomes more important. The present review describes recent advances of GPAC and what is known of the biology and pathogenic effects of Anaerococcus, Finegoldia, Parvimonas, Peptoniphilus and Peptostreptococcus, the most important GPAC genera isolated from human infections. © 2012 Federation of European Microbiological Societies. Published by Blackwell Publishing Ltd. All rights reserved.

Diversity of yeasts associated with the sea surface microlayer and underlying water along the northern coast of Taiwan.

PubMed

Chang, Chin-Feng; Lee, Ching-Fu; Lin, Kao-Yung; Liu, Shiu-Mei

2016-01-01

Yeast communities inhabiting the sea surface microlayer (SSML) on the northern coast of Taiwan were examined using a cultivation method and compared with those inhabiting the underlying water (UW) at a 50-cm depth. Culturable yeasts were recovered from the SSML and UW samples collected in the morning during 4 field campaigns, and 420 strains were isolated. The 420 isolates were grouped into 43 species using a polyphasic molecular approach, including sequence analysis of the 26S rDNA D1/D2 domain and 5.8S-ITS region. From the SSML samples, 12 genera and 39 species, including 7 new species of Cryptococcus sp. (1), Candida spp. (4), and Rhodotorula spp. (2), were isolated. From the UW samples, 10 genera and 21 species, including one new species of Rhodotorula sp. (1), were isolated. Rhodotorula mucilaginosa was the most abundant species present in the yeast community in SSML (37.6%) and UW (21.6%) samples. Basidiomycetous yeasts (63.6%) and pigmented yeasts (64.5%) comprised the major yeast population. The yeast community in the SSML had a higher species number and abundance than the UW. Moreover, although the majority of yeast community species were from the SSML, individual species distribution in the SSML was unequal. Copyright © 2015 Institut Pasteur. Published by Elsevier Masson SAS. All rights reserved.

Lactobacilli and bifidobacteria in human breast milk: influence of antibiotherapy and other host and clinical factors.

PubMed

Soto, Ana; Martín, Virginia; Jiménez, Esther; Mader, Isabelle; Rodríguez, Juan M; Fernández, Leonides

2014-07-01

The objective of this work was to study the lactobacilli and bifidobacteria population in human milk of healthy women, and to investigate the influence that several factors (including antibioteraphy during pregnancy and lactation, country and date of birth, delivery mode, or infant age) may exert on such population. A total of 160 women living in Germany or Austria provided the breast milk samples. Initially, 66 samples were randomly selected and cultured on MRS-Cys agar plates. Then, the presence of DNA from the genera Lactobacillus and Bifidobacterium, and from most of the Lactobacillus and Bifidobacterium species that were isolated, was assessed by qualitative polymerase chain reaction (PCR) using genus- and species-specific primers. Lactobacilli and bifidobacteria could be isolated from the milk of 27 (40.91%) and 7 (10.61%), respectively, of the 66 cultured samples. On the contrary, Lactobacillus and Bifidobacterium sequences were detected by PCR in 108 (67.50%) and 41 (25.62%), respectively, of the 160 samples analyzed. The Lactobacillus species most frequently isolated and detected was L salivarius (35.00%), followed by L fermentum (25.00%) and L gasseri (21.88%), whereas B breve (13.75%) was the bifidobacterial species most commonly recovered and whose DNA was most regularly found. The number of lactobacilli- or bifidobacteria-positive samples was significantly lower in women who had received antibiotherapy during pregnancy or lactation. Our results suggest that either the presence of lactobacilli and/or bifidobacteria or their DNA may constitute good markers of a healthy human milk microbiota that has not been altered by the use of antibiotics.

Microbial Ecology of Activated Sludge

PubMed Central

Dias, F. F.; Bhat, J. V.

1964-01-01

Over 300 bacterial strains were isolated from seven samples of activated sludge by plating on sewage agar. Gram-negative bacteria of the genera Zoogloea and Comamonas predominated. Many isolates (51%) showed sudanophilic inclusions of poly-β-hydroxybutyric acid, whereas 34% accumulated iodophilic material on media containing starch. A large number required either vitamins or amino acids, or both, for growth. None of the isolates tested for their ability to bring about changes in autoclaved sewage produced an effluent comparable in quality to the activated sludge control, although the Zoogloea did produce activated sludgelike flocs. A study of 150 bacterial strains isolated from raw sewage revealed that they differed from the sludge isolates in several respects. Coliforms, which constitute nearly a quarter of the sewage isolates, were rarely encountered in sludge. PMID:14215970

[Pyothorax in 26 cats: clinical signs, laboratory results and therapy (2000-2007)].

PubMed

Ottenjann, Mareike; Lübke-Becker, Antina; Linzmann, Helge; Brunnberg, Leo; Kohn, Barbara

2008-01-01

Common historical findings in 26 cats with pyothorax were dyspnea (85%), lethargy (65%), and anorexia (62%), common clinical findings were dyspnea (89%), tachypnea (73%), fever (39%), and hypothermia (27%). Frequent laboratory abnormalities were leukocytosis (68%) with a left shift (100%), anemia (65%), hypoalbuminemia (91%), hyperglobulinemia (86%), hyperbilirubinemia (60%) as well as azotemia (52%). The thoracic effusion was purulent in all cats, the thoracic fluid evaluation (n = 19) met the criteria for an inflammatory exudate (protein 32-63 g/l, median 44; cell count 54.4-390 x 10(9)/l, median 100). Cytological analysis revealed bacteria in 21 of 24 cats. From 16 cats 13 different genera were isolated, 5 cultures were without bacterial growth. In 12.5% of the cats a single population of bacteria was identified, and in 87.5% a mixture of 2-4 different bacterial species were cultured. Obligate anaerobic bacteria were the most common isolates (70%) followed by facultative anaerob (22.5%) and aerob growing (7.5%) bacteria. Bacterial culture most often yielded Fusobacteria spp., Prevotella spp., Pasteurella spp., Porphyromonas spp. and Bacteroides spp. Three cats were euthanized at the day of presentation. A thoracic lavage was performed in 22 cats; mechanical complications with the chest tubes occured in 4 cats. Thoracotomy was performed in 2 cats. Of the 23 treated cats 17 survived (74%).

[Culturable psychrotolerant methanotrophic bacteria in landfill cover soil].

PubMed

Kallistova, A Iu; Montonen, L; Jurgens, G; Munster, U; Kevbrina, M V; Nozhevnikova, A N

2014-01-01

Methanotrophs closely related to psychrotolerant members of the genera Methylobacter and Methylocella were identified in cultures enriched at 10@C from landfill cover soil samples collected in the period from April to November. Mesophilic methanotrophs of the genera Methylobacter and Methylosinus were found in cultures enriched at 20 degrees C from the same cover soil samples. A thermotolerant methanotroph related to Methylocaldum gracile was identified in the culture enriched at 40 degrees C from a sample collected in May (the temperature of the cover soil was 11.5-12.5 degrees C). In addition to methanotrophs, methylobacteria of the genera Methylotenera and Methylovorus and members of the genera Verrucomicrobium, Pseudomonas, Pseudoxanthomonas, Dokdonella, Candidatus Protochlamydia, and Thiorhodospira were also identified in the enrichment cultures. A methanotroph closely related to the psychrotolerant species Methylobacter tundripaludum (98% sequence identity of 16S r-RNA genes with the type strain SV96(T)) was isolated in pure culture. The introduction of a mixture of the methanotrophic enrichments, grown at 15 degrees C, into the landfill cover soil resulted in a decrease in methane emission from the landfill surface in autumn (October, November). The inoculum used was demonstrated to contain methanotrophs closely related to Methylobacter tundripaludum SV96.

Revision of Ephydrini Zetterstedt (Diptera: Ephydridae) from the Americas south of the United States.

PubMed

Mathis, Wayne N; Marinoni, Luciane

2016-05-27

The Neotropical genera and species of the tribe Ephydrini are revised and include nine genera and 33 species. Of the nine genera, Setacera Cresson, Cirrula Cresson, Dimecoenia Cresson, Paracoenia Cresson and Ephydra Fallén are mostly temperate in distribution, primarily in the Northern Hemisphere. The other four genera, which are exclusively Neotropical, include two, Austrocoenia and Notiocoenia, that were treated previously in the tribe Scatellini, and two recently described genera: Paraephydra (type species: Paraephydra freitasi (Oliveira)) and Neoephydra (type species: Neoephydra araucaria Mathis). New species described herein are: Neoephydra neotropica (Chile), N. dasycephala (Argentina and Peru), N. mallonota (Argentina, Bolivia, and Chile), N. shewelli (Argentina, Bolivia, and Chile), N. inca (Argentina, Bolivia, Peru), N. penai (Chile) and N. trichina (Argentina and Chile). New synonyms are (cited in their original combinations): Ephydra densepilosa Hendel = E. ciligena Rondani, Dimecoenia grumanni Oliveira = E. ciligena Rondani, D. coltaensis Cresson = D. zurcheri Hendel, D. carrerai Oliveira = D. zurcheri Hendel, D. lopesi = E. ciligena Rondani, D. travassosi Mello and Oliveira = E. prionoptera Thomson. A neotype is designated for E. caesia Wulp, and the following lectotype designations have also been made to better stabilize nomenclature (here cited in their original combination): Ephydra chilensis Macquart, Ephydra densepilosa Hendel, Ephydra pravoneura Hendel, Ephydra prionoptera Thomson, and Dimecoenia zurcheri Hendel. Dimecoenia venteli Oliveira is listed as a species inquirenda, as the type series includes only female specimens that we cannot presently recognize. Although the genera and subgenera are fairly easily distinguished, the included species are frequently difficult to separate, and we have generally relied on characters of the male terminalia to determine a species identity. Illustrations of male terminalia and distribution maps are included for each species and keys to all taxa have been provided.

Sequence Analysis of Raspberry latent virus Suggests a New Genus of Dicot Infecting Reoviruses

USDA-ARS?s Scientific Manuscript database

Currently, there are three assigned genera of plant reoviruses: Phytoreovirus, Fijivirus and Oryzavirus. With only two exceptions, all plant reoviruses infect monocotyledonous plants. The recent characterization of Raspberry latent virus (RpLV) isolated from red raspberry plants in northern Washingt...

ASSESSMENT OF ISOLATED WETLAND CONDITION IN FLORIDA USING EPIPHYTIC DIATOMS AT GENUS, SPECIES, AND SUBSPECIES TAXONOMIC RESOLUTION

EPA Science Inventory

Diatoms are useful indicators of aquatic conditions, and metrics based on published autecological indicator values have been developed utilizing their sensitivities to various ambient physical and chemical conditions. The autecological values often differ within genera, and indee...

Proteomic analysis of a mutant of Trichoderma arundinaceum impaired in the trichothecene biosynthesis reveals a systemic function of these compounds in the fungal physiology

USDA-ARS?s Scientific Manuscript database

Trichothecenes are sesquiterpene mycotoxins produced by several fungal genera including Fusarium, Trichothecium, Myrothecium, Stachybotrys, and Trichoderma. These toxins have attracted great attention because they are frequent contaminants of food and animal feed, and can be easily absorbed by anim...

Filamentous fungi associated with natural infection of noble rot on withered grapes.

PubMed

Lorenzini, M; Simonato, B; Favati, F; Bernardi, P; Sbarbati, A; Zapparoli, G

2018-05-02

The effects of noble rot infection of grapes on the characteristics of different types of wine, including Italian passito wine, are well known. Nevertheless, there is still little information on filamentous fungi associated with noble-rotten grapes. In this study, withered Garganega grapes for passito wine production, naturally infected by noble rot, were analyzed and compared to sound grapes. Skin morphology and fungal population on berry surfaces were analyzed. Scanning electron microscopy analysis revealed microcracks, germination conidia and branched hyphae on noble-rotten berries. Penicillium, Aureobasidium and Cladosporium were the most frequent genera present. Analysis of single berries displayed higher heterogeneity of epiphytic fungi in those infected by noble-rot than in sound berries. Penicillium adametzoides, Cladosporium cladospoirioides and Coniochaeta polymorpha were recovered. These, to the best of our knowledge, had never been previously isolated from withered grapes and, for C. polymorpha, from grapevine. This study provided novel data on noble rot mycobiota and suggests that fungi that co-habit with B. cinerea could have an important role on grape and wine quality. Copyright © 2018 Elsevier B.V. All rights reserved.

Mycotoxigenic potentials of the genera: Aspergillus, Fusarium and Penicillium isolated from houseflies (Musca domestica L.).

PubMed

Phoku, J Z; Barnard, T G; Potgieter, N; Dutton, M F

2017-04-01

A study on the potential of houseflies (Musca domestica L.) to spread fungal spores in Gauteng Province, South Africa proved that houseflies are vectors for fungal spores. Therefore, there is a need to determine the toxigenic potentials and to identify the mycotoxins produced by fungal isolates derived from this study. In total 377 potentially toxigenic isolates of Aspergillus (186), Fusarium (85) and Penicillium (106) species (spp.) were isolated. These isolates were further tested for their ability to produce aflatoxins (AFs) [aflatoxin B 1 , B 2 , G 1 and G 2 ], deoxynivalenol (DON), fumonisin B 1 (FB 1 ) ochratoxin A (OTA), and zearalenone (ZEA) by high-performance liquid chromatography (HPLC) respectively. Strains of A. flavus and A. parasiticus belonging to the genera of Aspergillus were found to be the main producers of AFB 1 , AFB 2 , AFG 1 , and AFG 2 , while A. carbonarius, A. niger and A. ochraceus produced OTA. Fumonisin B 1 was produced by F. verticillioides and F. proliferatum with concentrations ranging from 20 to 1834μg/kg and 79 to 262μg/kg respectively. Deoxynivalenol produced mainly by F. culmorum (2-6μg/kg), F. graminearum (1-4μg/kg), F. poae (1-3μg/kg), and F. sporotrichioides (2-3μg/kg) species was the least detected toxin in this study. The high mycotoxins levels produced in isolates from houseflies in this study are regarded as unsafe, especially when international legislated tolerance levels for mycotoxins are considered. Thus, possible human exposure to mycotoxins may pose concerns with respect to human health and demands constant and consistent investigation. Copyright © 2017 Elsevier B.V. All rights reserved.

The relationship between gorgonian coral (Cnidaria: Gorgonacea) diseases and African dust storms

USGS Publications Warehouse

Weir-Brush, J. R.; Garrison, V.H.; Smith, G.W.; Shinn, E.A.

2004-01-01

The number of reports of coral diseases has increased throughout the world in the last 20 years. Aspergillosis, which primarily affects Gorgonia ventalina and G. flabellum, is one of the few diseases to be characterized. This disease is caused by Aspergillus sydowii, a terrestrial fungus with a worldwide distribution. Upon infection, colonies may lose tissue, and ultimately, mortality may occur if the infection is not sequestered. The spores of A. sydowii are <5 ??m, small enough to be easily picked up by winds and dispersed over great distances. Aspergillosis is prevalent in the Caribbean, and it appears that this primarily terrestrial fungus has adapted to a marine environment. It has been proposed that dust storms originating in Africa may be one way in which potential coral pathogens are distributed and deposited into the marine environments of the Caribbean. To test the hypothesis that African dust storms transport and deposit pathogens, we collected air samples from both dust storms and periods of nondust in St. John, U.S. Virgin Islands. Because we focused on fungal pathogens and used A. sydowii as a model, we isolated and cultured fungi on various types of media. Fungi including Aspergillus spp. were isolated from air samples taken from dust events and non-dust events. Twenty-three separate cultures and seven genera were isolated from dust event samples whereas eight cultures from five genera were isolated from non-dust air samples. Three isolates from the Virgin Islands dust event samples morphologically identified as Aspergillus spp. produced signs of aspergillosis in seafans, and the original pathogens were re-isolated from those diseased seafans fulfilling Koch's Postulates. This research supports the hypothesis that African dust storms transport across the Atlantic Ocean and deposit potential coral pathogens in the Caribbean.

Bacteria associated with larvae and adults of the Asian longhorned beetle (Coleoptera: Cerambycidae)

Treesearch

John D. Podgwaite; Vincent D' Amico; Roger T. Zerillo; Heidi Schoenfeldt

2013-01-01

Bacteria representing several genera were isolated from integument and alimentary tracts of live Asian longhorned beetle, Anaplophora glabripennis (Motschulsky), larvae and adults. Insects examined were from infested tree branches collected from sites in New York and Illinois. Staphylococcus sciuri (Kloos) was the most common...

Attempt to develop live attenuated bacterial vaccines by selecting resistance to gossypol, proflavine hemisulfate, novobiocin, or ciprofloxacin

USDA-ARS?s Scientific Manuscript database

In an attempt to develop attenuated bacteria as potential live vaccines, four chemicals (gossypol, proflavine hemisulfate, novobiocin, and ciprofloxacin) were used to modify the following four genera of bacteria through chemical-resistance strategy: 1) Aeromonas hydrophila (9 isolates); 2) Edwardsie...

Attempt to develop live attenuated bacterial vaccines by selecting resistance to gossypol, proflavine hemisulfate, novobiocin, or ciprofloxacin

USDA-ARS?s Scientific Manuscript database

In an attempt to develop attenuated bacteria as potential live vaccines, four chemicals (gossypol, proflavine hemisulfate, novobiocin, and ciprofloxacin) were used to modify the following four genera of bacteria through chemical-resistance strategy: (1) Aeromonas hydrophila (9 isolates); (2) Edwards...

Diversity and bioprospection of fungal community present in oligotrophic soil of continental Antarctica

USDA-ARS?s Scientific Manuscript database

The diversity of fungal communities from different substrates in Antarctica were studied and their capability to produce bioactive compounds. A one hundred and one fungal isolates were identified by molecular analysis in 35 different fungal taxa from 20 genera. Pseudogymnoascus sp. 3, Pseudogymnoasc...

Fungi associated with rocks of the Atacama Desert: taxonomy, distribution, diversity, ecology and bioprospection for bioactive compounds

USDA-ARS?s Scientific Manuscript database

This study assessed the diversity of fungi living in rocks from different altitudes in the Atacama Desert, Chile. Eighty-one fungal isolates obtained were identified as 21 species of 12 genera from Ascomycota using molecular techniques. Cladosporium halotolerans, Penicillium chrysogenum and Penicill...

Diversity, metal resistance and uranium sequestration abilities of bacteria from uranium ore deposit in deep earth stratum.

PubMed

Islam, Ekramul; Sar, Pinaki

2016-05-01

Metal resistance and uranium (U) sequestration abilities of bacteria residing in subsurface U ore was investigated using 122 pure culture strains isolated through enrichment. The cumulative frequencies of isolates resistant to each metal tested were as follows: As(V), 74%; Zn, 58%; Ni, 53%; Cd, 47%; Cr(VI), 41%; Co, 40%; Cu, 20%; and Hg, 4%. 16S rRNA gene analysis revealed that isolated bacteria belonged to 14 genera with abundance of Arthrobacter, Microbacterium, Acinetobacter and Stenotrophomonas. Cobalt did not interfere with the growth of most of the bacterial isolates belonging to different groups while U allowed growth of four different genera of which Stenotrophomonas and Microbacterium showed high U tolerance. Interestingly, tolerance to Ni, Zn, Cu, and Hg was observed only in Microbacterium, Arthrobacter, Paenibacillus¸ and Acinetobacter, respectively. However, Microbacterium was found to be dominant when isolated from other five different metal enrichments including U. Uranium removal study showed that 84% of the test bacteria could remove more than 50mgUg(-1) dry weight from 80 or 160mgL(-1) U within 48h. In general, Microbacterium, Arthrobacter and Acinetobacter could remove a higher amount of U. High resolution transmission electron microscopy (HRTEM) study of U exposed cells revealed that accumulated U sequestered mostly around the cell periphery. The study highlights that indigenous U ore deposit bacteria have the potential to interact with U, and thus could be applied for bioremediation of U contaminated sites or wastes. Copyright © 2016 Elsevier Inc. All rights reserved.

Bioclimatic niches are conserved and unrelated to pollination syndromes in Antillean Gesneriaceae

PubMed Central

Faure, Julie; Ginzbarg, Steven; Clark, John; Joly, Simon

2017-01-01

The study of the evolution of abiotic niches can be informative regarding the speciation drivers in a given group. Yet, two factors that could potentially affect niche evolution have seldom been addressed concomitantly, which are biotic interactions and geographical isolation. In this study, we used as a model group the Antillean plant genera Gesneria and Rhytidophyllum (Gesneriaceae) to evaluate the effect of pollinators and geographical isolation on the bioclimatic niche. These genera possess species characterized by interspecific geographical isolation in different islands and are pollinated by different pollinators. Some species are pollinated by hummingbirds, other by bats, while some are more generalists and are pollinated by pollinators from both functional groups. After describing the bioclimatic niches of plant species, we measured niche overlap for species pairs and we fitted Brownian motion and Ornstein–Uhlenbeck (OU) evolution models with multiple evolutionary regimes to test for an effect of pollination strategy or geographical isolation on bioclimatic niche evolution of these plants. The analysis of niche overlap between plant species, which could not be corrected for phylogenetic relationships, showed that it was significantly influenced by pollination mode and island distribution. By contrast, the best fitting evolutionary model on niche optima and tolerance was always an OU model with a unique selective regime, suggesting that neither pollination strategy nor island isolation had an important effect on bioclimatic niches at a macroevolutionary scale. Instead, we conclude that bioclimatic niches of Antillean Gesneriaceae evolved under phylogenetic conservatism and hypothesize that this macroevolutionary pattern could result from adaptation to temporally variable climates in the Antilles. PMID:29291050

Ecological and physiological studies on soil fungi at Western region, libya.

PubMed

El-Said, A H M; Saleem, A

2008-03-01

Sixty three species and 5 varieties belonging to 30 fungal genera were collected from 75 soil samples. Cultivated (29 genera and 58 species + 5 var.), desert (22 and 35 + 2 var.) and saline soil (21 and 41 + 1 var.) fungi were recovered on glucose-, cellulose- and 50% sucrose-Czapek's agar at 28℃. The most common genera were Alternaria, Aspergillus, Emericella, Fusarium, Mycosphaerella, Nectria and Penicillium. The most prevalent species from the three types of soils on the three types of media were Alternaria alternata, Aspergillus flavus, A. fumigatus, A. niger, A. terreus, Emericella nidulans, Fusarium oxysporum, Mycosphaerella tassiana, Nectria haematococca and Penicillium chrysogenum. Chaetomium globosum was in the top of fungi in producing endo-β-1,4-glucanases among the 42 tested isolates obtained from soils on cellulose-Czapek's agar. Maximum production of this enzyme by C. globosum obtained after 6 days of incubation at 30℃ with culture medium containing maltose as a carbon source and ammonium nitrate as a nitrogen source and pH initially adjusted to 6.

Characterization of bacterial strains isolated from a beef-processing plant following cleaning and disinfection - Influence of isolated strains on biofilm formation by Sakaï and EDL 933 E. coli O157:H7.

PubMed

Marouani-Gadri, Nesrine; Augier, Gladys; Carpentier, Brigitte

2009-07-31

The objective of this study was to investigate the effects on Escherichia coli O157:H7 biofilm formation of bacteria isolated from meat site surfaces following cleaning and disinfection. We first isolated and identified, to the genus level, strains of the latter organisms. Samples were obtained by swabbing the surfaces of equipment or floors over areas ranging from 315 to 3200 cm(2) in a slaughter hall, a meat cutting room and a meat boning room of a meat-processing plant. The number of bacteria recovered from these surfaces ranged from <1 to> 10(5) CFU/cm(2). In the slaughter hall, stainless steel was in one case one of the most contaminated materials and in other cases one of the less contaminated. The same observation was made for conveyor belts made of polyvinyl chloride in the boning room. Dominant genera in the meat plant were Staphylococcus and Bacillus which were both 34% of the isolates from the slaughter hall and 14 and 4% respectively of the isolates from the cutting room. Randomly selected isolates of each of the genera recovered from the slaughter hall were cultured with E. coli O157:H7 in meat exudate at 15 degrees C to form dual-organism biofilms on polyurethane. In all cases but one, the isolates increased the numbers of attached E. coli O157:H7. The effects ranged from 0.37 to 1.11 for EDL 933 strain and from 0.19 to 1.38 log (CFU/cm(2)) for Sakaï strain. This is the first time that a resident microbiota of a meat-processing plant has been shown to have a favourable effect on E. coli O157:H7 colonization of a solid surface, which is of great interest from a food safety standpoint.

Study on mycoflora of poultry feed ingredients and finished feed in Iran

PubMed Central

Ghaemmaghami, Seyed Soheil; Modirsaneii, Mehrdad; Khosravi, Ali Reza; Razzaghi-Abyaneh, Mehdi

2016-01-01

Background and Objectives: Unhygienic poultry feedstuffs can lead to nutrient losses and detrimental effect on poultry production and public health. In the present study, mycobiota and colony-forming units per gram in ingredients and finish poultry feed was evaluated with special reference to potentially mycotoxigenic fungi. Materials and Methods: Eighty five samples of corn, soybean meal and poultry finished feed were collected from nine poultry feed factories located in three provinces i.e. Tehran, Alborz and Qom in Iran from October 2014 to January 2015. Samples were cultured on Sabouraud dextrose agar (SDA), Aspergillus flavus and parasiticus agar (AFPA) and dichloran rosebengal chloramphenicol agar (DRBC) and incubated at 28 °C for 7–10 days. Purified fungal colonies were identified by a combination of macro- and microscopic morphological criteria. For determining the rate of fungal contamination, samples were cultured on SDA and colony forming units (CFUs) were calculated. Results: A total of 384 fungal isolates belonging to 7 genera of filamentous fungi and yeasts were obtained from corn (124 isolates), soybean meal (92 isolates), and feed before (72 isolates), and after pelleting (96 isolates). The most prominent fungal isolate in corn, soybean meal and feed before pelleting (feed as mash form) was Fusarium but in feed after pelleting was Aspergillus. Among 5 Aspergillus species isolated, potentially aflatoxigenic A. flavus isolates was predominant in corn (46.6%), soybean meal (72.7%) and poultry finished feed (75%). CFUs results indicated that 9/22 corn samples (40.9%), none of 22 soybean meal samples, 19/41 finished feed (46.3%) were contaminated higher than the standard limit. Conclusions: Our results indicated that corn, soybean meal and finished feed of poultry feed mill are contaminated with various fungal genera by different levels sometimes higher that the standard limits. Contamination with potentially mycotoxigenic fungi especially Aspergillus species may be considered as a human public health hazard. PMID:27092224

Microbial background flora in small-scale cheese production facilities does not inhibit growth and surface attachment of Listeria monocytogenes.

PubMed

Schirmer, B C T; Heir, E; Møretrø, T; Skaar, I; Langsrud, S

2013-10-01

The background microbiota of 5 Norwegian small-scale cheese production sites was examined and the effect of the isolated strains on the growth and survival of Listeria monocytogenes was investigated. Samples were taken from the air, food contact surfaces (storage surfaces, cheese molds, and brine) and noncontact surfaces (floor, drains, and doors) and all isolates were identified by sequencing and morphology (mold). A total of 1,314 isolates were identified and found to belong to 55 bacterial genera, 1 species of yeast, and 6 species of mold. Lactococcus spp. (all of which were Lactococcus lactis), Staphylococcus spp., Microbacterium spp., and Psychrobacter sp. were isolated from all 5 sites and Rhodococcus spp. and Chryseobacterium spp. from 4 sites. Thirty-two genera were only found in 1 out of 5 facilities each. Great variations were observed in the microbial background flora both between the 5 producers, and also within the various production sites. The greatest diversity of bacteria was found in drains and on rubber seals of doors. The flora on cheese storage shelves and in salt brines was less varied. A total of 62 bacterial isolates and 1 yeast isolate were tested for antilisterial activity in an overlay assay and a spot-on-lawn assay, but none showed significant inhibitory effects. Listeria monocytogenes was also co-cultured on ceramic tiles with bacteria dominating in the cheese production plants: Lactococcus lactis, Pseudomonas putida, Staphylococcus equorum, Rhodococcus spp., or Psychrobacter spp. None of the tested isolates altered the survival of L. monocytogenes on ceramic tiles. The conclusion of the study was that no common background flora exists in cheese production environments. None of the tested isolates inhibited the growth of L. monocytogenes. Hence, this study does not support the hypothesis that the natural background flora in cheese production environments inhibits the growth or survival of L. monocytogenes. Copyright © 2013 American Dairy Science Association. Published by Elsevier Inc. All rights reserved.

Study on mycoflora of poultry feed ingredients and finished feed in Iran.

PubMed

Ghaemmaghami, Seyed Soheil; Modirsaneii, Mehrdad; Khosravi, Ali Reza; Razzaghi-Abyaneh, Mehdi

2016-02-01

Unhygienic poultry feedstuffs can lead to nutrient losses and detrimental effect on poultry production and public health. In the present study, mycobiota and colony-forming units per gram in ingredients and finish poultry feed was evaluated with special reference to potentially mycotoxigenic fungi. Eighty five samples of corn, soybean meal and poultry finished feed were collected from nine poultry feed factories located in three provinces i.e. Tehran, Alborz and Qom in Iran from October 2014 to January 2015. Samples were cultured on Sabouraud dextrose agar (SDA), Aspergillus flavus and parasiticus agar (AFPA) and dichloran rosebengal chloramphenicol agar (DRBC) and incubated at 28 °C for 7-10 days. Purified fungal colonies were identified by a combination of macro- and microscopic morphological criteria. For determining the rate of fungal contamination, samples were cultured on SDA and colony forming units (CFUs) were calculated. A total of 384 fungal isolates belonging to 7 genera of filamentous fungi and yeasts were obtained from corn (124 isolates), soybean meal (92 isolates), and feed before (72 isolates), and after pelleting (96 isolates). The most prominent fungal isolate in corn, soybean meal and feed before pelleting (feed as mash form) was Fusarium but in feed after pelleting was Aspergillus. Among 5 Aspergillus species isolated, potentially aflatoxigenic A. flavus isolates was predominant in corn (46.6%), soybean meal (72.7%) and poultry finished feed (75%). CFUs results indicated that 9/22 corn samples (40.9%), none of 22 soybean meal samples, 19/41 finished feed (46.3%) were contaminated higher than the standard limit. Our results indicated that corn, soybean meal and finished feed of poultry feed mill are contaminated with various fungal genera by different levels sometimes higher that the standard limits. Contamination with potentially mycotoxigenic fungi especially Aspergillus species may be considered as a human public health hazard.

Phylogenetic diversity and biological activity of culturable Actinobacteria isolated from freshwater fish gut microbiota.

PubMed

Jami, Mansooreh; Ghanbari, Mahdi; Kneifel, Wolfgang; Domig, Konrad J

2015-06-01

The diversity of Actinobacteria isolated from the gut microbiota of two freshwater fish species namely Schizothorax zarudnyi and Schizocypris altidorsalis was investigated employing classical cultivation techniques, repetitive sequence-based PCR (rep-PCR), partial and full 16S rDNA sequencing followed by phylogenetic analysis. A total of 277 isolates were cultured by applying three different agar media. Based on rep-PCR profile analysis a subset of 33 strains was selected for further phylogenetic investigations, antimicrobial activity testing and diversity analysis of secondary-metabolite biosynthetic genes. The identification based on 16S rRNA gene sequencing revealed that the isolates belong to eight genera distributed among six families. At the family level, 72% of the 277 isolates belong to the family Streptomycetaceae. Among the non-streptomycetes group, the most dominant group could be allocated to the family of Pseudonocardiaceae followed by the members of Micromonosporaceae. Phylogenetic analysis clearly showed that many of the isolates in the genera Streptomyces, Saccharomonospora, Micromonospora, Nocardiopsis, Arthrobacter, Kocuria, Microbacterium and Agromyces formed a single and distinct cluster with the type strains. Notably, there is no report so far about the occurrence of these Actinobacteria in the microbiota of freshwater fish. Of the 33 isolates, all the strains exhibited antibacterial activity against a set of tested human and fish pathogenic bacteria. Then, to study their associated potential capacity to synthesize diverse bioactive natural products, diversity of genes associated with secondary-metabolite biosynthesis including PKS I, PKS II, NRPS, the enzyme PhzE of the phenazine pathways, the enzyme dTGD of 6-deoxyhexoses glycosylation pathway, the enzyme Halo of halogenation pathway and the enzyme CYP in polyene polyketide biosynthesis were investigated among the isolates. All the strains possess at least two types of the investigated biosynthetic genes, one-fourth of them harbours more than four. This study demonstrates the significant diversity of Actinobacteria in the fish gut microbiota and it's potential to produce biologically active compounds. Copyright © 2015 Elsevier GmbH. All rights reserved.

Characterisation of the genomes of four putative vesiculoviruses: tench rhabdovirus, grass carp rhabdovirus, perch rhabdovirus and eel rhabdovirus European X.

PubMed

Stone, David M; Kerr, Rose C; Hughes, Margaret; Radford, Alan D; Darby, Alistair C

2013-11-01

The complete coding sequences were determined for four putative vesiculoviruses isolated from fish. Sequence alignment and phylogenetic analysis based on the predicted amino acid sequences of the five main proteins assigned tench rhabdovirus and grass carp rhabdovirus together with spring viraemia of carp and pike fry rhabdovirus to a lineage that was distinct from the mammalian vesiculoviruses. Perch rhabdovirus, eel virus European X, lake trout rhabdovirus 903/87 and sea trout virus were placed in a second lineage that was also distinct from the recognised genera in the family Rhabdoviridae. Establishment of two new rhabdovirus genera, "Perhabdovirus" and "Sprivivirus", is discussed.

Coexistence of Burkholderia, Cupriavidus, and Rhizobium sp. nodule bacteria on two Mimosa spp. in Costa Rica.

PubMed

Barrett, Craig F; Parker, Matthew A

2006-02-01

rRNA gene sequencing and PCR assays indicated that 215 isolates of root nodule bacteria from two Mimosa species at three sites in Costa Rica belonged to the genera Burkholderia, Cupriavidus, and Rhizobium. This is the first report of Cupriavidus sp. nodule symbionts for Mimosa populations within their native geographic range in the neotropics. Burkholderia spp. predominated among samples from Mimosa pigra (86% of isolates), while there was a more even distribution of Cupriavidus, Burkholderia, and Rhizobium spp. on Mimosa pudica (38, 37, and 25% of isolates, respectively). All Cupriavidus and Burkholderia genotypes tested formed root nodules and fixed nitrogen on both M. pigra and M. pudica, and sequencing of rRNA genes in strains reisolated from nodules verified identity with inoculant strains. Inoculation tests further indicated that both Cupriavidus and Burkholderia spp. resulted in significantly higher plant growth and nodule nitrogenase activity (as measured by acetylene reduction assays) relative to plant performance with strains of Rhizobium. Given the prevalence of Burkholderia and Cupriavidus spp. on these Mimosa legumes and the widespread distribution of these plants both within and outside the neotropics, it is likely that both beta-proteobacterial genera are more ubiquitous as root nodule symbionts than previously believed.

Coexistence of Burkholderia, Cupriavidus, and Rhizobium sp. Nodule Bacteria on two Mimosa spp. in Costa Rica

PubMed Central

Barrett, Craig F.; Parker, Matthew A.

2006-01-01

rRNA gene sequencing and PCR assays indicated that 215 isolates of root nodule bacteria from two Mimosa species at three sites in Costa Rica belonged to the genera Burkholderia, Cupriavidus, and Rhizobium. This is the first report of Cupriavidus sp. nodule symbionts for Mimosa populations within their native geographic range in the neotropics. Burkholderia spp. predominated among samples from Mimosa pigra (86% of isolates), while there was a more even distribution of Cupriavidus, Burkholderia, and Rhizobium spp. on Mimosa pudica (38, 37, and 25% of isolates, respectively). All Cupriavidus and Burkholderia genotypes tested formed root nodules and fixed nitrogen on both M. pigra and M. pudica, and sequencing of rRNA genes in strains reisolated from nodules verified identity with inoculant strains. Inoculation tests further indicated that both Cupriavidus and Burkholderia spp. resulted in significantly higher plant growth and nodule nitrogenase activity (as measured by acetylene reduction assays) relative to plant performance with strains of Rhizobium. Given the prevalence of Burkholderia and Cupriavidus spp. on these Mimosa legumes and the widespread distribution of these plants both within and outside the neotropics, it is likely that both β-proteobacterial genera are more ubiquitous as root nodule symbionts than previously believed. PMID:16461667

Isolation, taxonomic analysis, and phenotypic characterization of bacterial endophytes present in alfalfa (Medicago sativa) seeds.

PubMed

López, José Luis; Alvarez, Florencia; Príncipe, Analía; Salas, María Eugenia; Lozano, Mauricio Javier; Draghi, Walter Omar; Jofré, Edgardo; Lagares, Antonio

2018-02-10

A growing body of evidence has reinforced the central role of microbiomes in the life of sound multicellular eukaryotes, thus more properly described as true holobionts. Though soil was considered a main source of plant microbiomes, seeds have been shown to be endophytically colonized by microorganisms thus representing natural carriers of a selected microbial inoculum to the young seedlings. In this work we have investigated the type of culturable endophytic bacteria that are carried within surface-sterilized alfalfa seeds. MALDI-TOF analysis revealed the presence of bacteria that belonged to 40 separate genera, distributed within four taxa (Proteobacteria, Actinobacteria, Firmicutes, and Bacteroidetes). Nonsymbiotic members of the Rhizobiaceae family were also found. The evaluation of nine different in-vitro biochemical activities demonstrated isolates with complex combinations of traits that, upon a Principal-Component-Analysis, could be classified into four phenotypic groups. That isolates from nearly half of the genera identified had been able to colonize alfalfa plants grown under axenic conditions was remarkable. Further analyses should be addressed to investigating the colonization mechanisms of the alfalfa seeds, the evolutionary significance of the alfalfa-seed endophytes, and also how after germination the seed microbiome competes with spermospheric and rhizospheric soil bacteria to colonize newly emerging seedlings. Copyright © 2018 Elsevier B.V. All rights reserved.

A Model to Explain Plant Growth Promotion Traits: A Multivariate Analysis of 2,211 Bacterial Isolates

PubMed Central

da Costa, Pedro Beschoren; Granada, Camille E.; Ambrosini, Adriana; Moreira, Fernanda; de Souza, Rocheli; dos Passos, João Frederico M.; Arruda, Letícia; Passaglia, Luciane M. P.

2014-01-01

Plant growth-promoting bacteria can greatly assist sustainable farming by improving plant health and biomass while reducing fertilizer use. The plant-microorganism-environment interaction is an open and complex system, and despite the active research in the area, patterns in root ecology are elusive. Here, we simultaneously analyzed the plant growth-promoting bacteria datasets from seven independent studies that shared a methodology for bioprospection and phenotype screening. The soil richness of the isolate's origin was classified by a Principal Component Analysis. A Categorical Principal Component Analysis was used to classify the soil richness according to isolate's indolic compound production, siderophores production and phosphate solubilization abilities, and bacterial genera composition. Multiple patterns and relationships were found and verified with nonparametric hypothesis testing. Including niche colonization in the analysis, we proposed a model to explain the expression of bacterial plant growth-promoting traits according to the soil nutritional status. Our model shows that plants favor interaction with growth hormone producers under rich nutrient conditions but favor nutrient solubilizers under poor conditions. We also performed several comparisons among the different genera, highlighting interesting ecological interactions and limitations. Our model could be used to direct plant growth-promoting bacteria bioprospection and metagenomic sampling. PMID:25542031

Sea salts as a potential source of food spoilage fungi.

PubMed

Biango-Daniels, Megan N; Hodge, Kathie T

2018-02-01

Production of sea salt begins with evaporation of sea water in shallow pools called salterns, and ends with the harvest and packing of salts. This process provides many opportunities for fungal contamination. This study aimed to determine whether finished salts contain viable fungi that have the potential to cause spoilage when sea salt is used as a food ingredient by isolating fungi on a medium that simulated salted food with a lowered water activity (0.95 a w ). The viable filamentous fungi from seven commercial salts were quantified and identified by DNA sequencing, and the fungal communities in different salts were compared. Every sea salt tested contained viable fungi, in concentrations ranging from 0.07 to 1.71 colony-forming units per gram of salt. In total, 85 fungi were isolated representing seven genera. One or more species of the most abundant genera, Aspergillus, Cladosporium, and Penicillium was found in every salt. Many species found in this study have been previously isolated from low water activity environments, including salterns and foods. We conclude that sea salts contain many fungi that have potential to cause food spoilage as well as some that may be mycotoxigenic. Copyright © 2017 The Authors. Published by Elsevier Ltd.. All rights reserved.

Antimicrobial biosynthetic potential and genetic diversity of endophytic actinomycetes associated with medicinal plants.

PubMed

Gohain, Anwesha; Gogoi, Animesh; Debnath, Rajal; Yadav, Archana; Singh, Bhim P; Gupta, Vijai K; Sharma, Rajeev; Saikia, Ratul

2015-10-01

Endophytic actinomycetes are one of the primary groups that share symbiotic relationships with medicinal plants and are key reservoir of biologically active compounds. In this study, six selective medicinal plants were targeted for the first time for endophytic actinomycetes isolation from Gibbon Wild Life Sanctuary, Assam, India, during winter and summer and 76 isolates were obtained. The isolates were found to be prevalent in roots followed by stem and leaves. 16S rRNA gene sequence analysis revealed 16 genera, including rare genera, Verrucosispora, Isoptericola and Kytococcus, which have never been previously reported as endophytic. The genus Streptomyces (66%) was dominant in both seasons. Shannon's diversity index showed that Azadirachta indica (1.49), Rauwolfia serpentina (1.43) and Emblica officinalis (1.24) were relatively good habitat for endophytic actinomycetes. Antimicrobial strains showed prevalence of polyketide synthase (PKS) type-II (85%) followed by PKS type-I (14%) encoded in the genomes. Expression studies showed 12-fold upregulation of PKSII gene in seventh day of incubation for Streptomyces antibioticus (EAAG90). Our results emphasize that the actinomycetes assemblages within plant tissue exhibited biosynthetic systems encoding for important biologically active compounds. © FEMS 2015. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Viability, diversity and composition of the bacterial community in a high Arctic permafrost soil from Spitsbergen, Northern Norway.

PubMed

Hansen, Aviaja A; Herbert, Rodney A; Mikkelsen, Karina; Jensen, Lars Liengård; Kristoffersen, Tommy; Tiedje, James M; Lomstein, Bente Aa; Finster, Kai W

2007-11-01

The viable and non-viable fractions of the bacterial community in a 2347-year-old permafrost soil from Spitsbergen were subjected to a comprehensive investigation using culture-independent and culture-dependent methods. LIVE/DEAD BacLight staining revealed that 26% of the total number of bacterial cells were viable. Quantitatively, aerobic microcolonies, aerobic colony-forming units and culturable anaerobic bacteria comprised a minor fraction of the total number of viable bacteria, which underlines the necessity for alternative cultivation approaches in bacterial cryobiology. Sulfate reduction was detected at temperatures between -2 degrees C and 29 degrees C while methanogenesis was not detected. Bacterial diversity was high with 162 operational taxonomic units observed from 800 16S rDNA clone sequences. The 158 pure cultures isolated from the permafrost soil affiliated with 29 different bacterial genera, the majority of which have not previously been isolated from permafrost habitats. Most of the strains isolated were affiliated to the genera Cellulomonas and Arthrobacter and several of the pure cultures were closely related to bacteria reported from other cryohabitats. Characterization of viable bacterial communities in permafrost soils is important as it will enable identification of functionally important groups together with the as yet undescribed adaptations that bacteria have evolved for surviving subzero temperatures for millennia.

[Keratinophilic fungi in soils of parks of Corrientes city, Argentina].

PubMed

Sarmiento, María Mercedes; Mangiaterra, Magdalena; Bojanich, María Viviana; Basualdo, Juan Ángel; Giusiano, Gustavo

2016-01-01

The soil is a natural reservoir of keratinophilic fungi, which are a small but important group of filamentous fungi, some of which typically develop on keratinized tissues of living animals. There are numerous species of saprophytic fungi with recognized keratinophilic abilities, and several studies have been undertaken in order to link their presence to possible human disease. To know the biota of geophilic fungi in general and of keratinophilic fungi particularly in soils from two public parks. Soil samples from two public parks of Corrientes city, Argentina, were studied during two seasons, using the hook technique and serial dilutions for fungal isolation. Using the hook technique, 170 isolates were classified into 17 genera and 21 species, among which it is worth mentioning the presence of Microsporum canis. Shannon index for keratinophilic fungi in autumn was 2.27, and 1.92 in spring. By means of the serial dilutions technique, 278 fungi isolated were identified into 33 genera and 71 species. Shannon index in autumn was 3.9, and 3.5 in spring. The soils studied have particularly favorable conditions for the survival of pathogens and opportunistic geophilic fungi for humans and animals. Copyright © 2014 Asociación Española de Micología. Published by Elsevier Espana. All rights reserved.

Culture-dependent and culture-independent diversity of Actinobacteria associated with the marine sponge Hymeniacidon perleve from the South China Sea.

PubMed

Sun, Wei; Dai, Shikun; Jiang, Shumei; Wang, Guanghua; Liu, Guohui; Wu, Houbo; Li, Xiang

2010-06-01

In this report, the diversity of Actinobacteria associated with the marine sponge Hymeniacidon perleve collected from a remote island of the South China Sea was investigated employing classical cultivation and characterization, 16S rDNA library construction, 16S rDNA-restriction fragment length polymorphism (rDNA-RFLP) and phylogenetic analysis. A total of 184 strains were isolated using seven different media and 24 isolates were selected according to their morphological characteristics for phylogenetic analysis on the basis of their 16S rRNA gene sequences. Results showed that the 24 isolates were assigned to six genera including Salinispora, Gordonia, Mycobacterium, Nocardia, Rhodococcus and Streptomyces. This is the first report that Salinispora is present in a marine sponge from the South China Sea. Subsequently, 26 rDNA clones were selected from 191 clones in an Actinobacteria-specific 16S rDNA library of the H. perleve sample, using the RFLP technique for sequencing and phylogenetic analysis. In total, 26 phylotypes were clustered in eight known genera of Actinobacteria including Mycobacterium, Amycolatopsis, Arthrobacter, Brevibacterium, Microlunatus, Nocardioides, Pseudonocardia and Streptomyces. This study contributes to our understanding of actinobacterial diversity in the marine sponge H. perleve from the South China Sea.

Amphibian Symbiotic Bacteria Do Not Show a Universal Ability To Inhibit Growth of the Global Panzootic Lineage of Batrachochytrium dendrobatidis.

PubMed

Antwis, Rachael E; Preziosi, Richard F; Harrison, Xavier A; Garner, Trenton W J

2015-06-01

Microbiomes associated with multicellular organisms influence the disease susceptibility of hosts. The potential exists for such bacteria to protect wildlife from infectious diseases, particularly in the case of the globally distributed and highly virulent fungal pathogen Batrachochytrium dendrobatidis of the global panzootic lineage (B. dendrobatidis GPL), responsible for mass extinctions and population declines of amphibians. B. dendrobatidis GPL exhibits wide genotypic and virulence variation, and the ability of candidate probiotics to restrict growth across B. dendrobatidis isolates has not previously been considered. Here we show that only a small proportion of candidate probiotics exhibited broad-spectrum inhibition across B. dendrobatidis GPL isolates. Moreover, some bacterial genera showed significantly greater inhibition than others, but overall, genus and species were not particularly reliable predictors of inhibitory capabilities. These findings indicate that bacterial consortia are likely to offer a more stable and effective approach to probiotics, particularly if related bacteria are selected from genera with greater antimicrobial capabilities. Together these results highlight a complex interaction between pathogens and host-associated symbiotic bacteria that will require consideration in the development of bacterial probiotics for wildlife conservation. Future efforts to construct protective microbiomes should incorporate bacteria that exhibit broad-spectrum inhibition of B. dendrobatidis GPL isolates. Copyright © 2015, American Society for Microbiology. All Rights Reserved.

Construction of a dairy microbial genome catalog opens new perspectives for the metagenomic analysis of dairy fermented products.

PubMed

Almeida, Mathieu; Hébert, Agnès; Abraham, Anne-Laure; Rasmussen, Simon; Monnet, Christophe; Pons, Nicolas; Delbès, Céline; Loux, Valentin; Batto, Jean-Michel; Leonard, Pierre; Kennedy, Sean; Ehrlich, Stanislas Dusko; Pop, Mihai; Montel, Marie-Christine; Irlinger, Françoise; Renault, Pierre

2014-12-13

Microbial communities of traditional cheeses are complex and insufficiently characterized. The origin, safety and functional role in cheese making of these microbial communities are still not well understood. Metagenomic analysis of these communities by high throughput shotgun sequencing is a promising approach to characterize their genomic and functional profiles. Such analyses, however, critically depend on the availability of appropriate reference genome databases against which the sequencing reads can be aligned. We built a reference genome catalog suitable for short read metagenomic analysis using a low-cost sequencing strategy. We selected 142 bacteria isolated from dairy products belonging to 137 different species and 67 genera, and succeeded to reconstruct the draft genome of 117 of them at a standard or high quality level, including isolates from the genera Kluyvera, Luteococcus and Marinilactibacillus, still missing from public database. To demonstrate the potential of this catalog, we analysed the microbial composition of the surface of two smear cheeses and one blue-veined cheese, and showed that a significant part of the microbiota of these traditional cheeses was composed of microorganisms newly sequenced in our study. Our study provides data, which combined with publicly available genome references, represents the most expansive catalog to date of cheese-associated bacteria. Using this extended dairy catalog, we revealed the presence in traditional cheese of dominant microorganisms not deliberately inoculated, mainly Gram-negative genera such as Pseudoalteromonas haloplanktis or Psychrobacter immobilis, that may contribute to the characteristics of cheese produced through traditional methods.

Microbial Community Succession During Lactate Amendment of Chromium Contaminated Groundwater Reveals a Predominance of Pelosinus spp.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Mosher, Jennifer J; Phelps, Tommy Joe; Drake, Meghan M

2012-01-01

Microbial community structure and metabolism in contaminated ecosystems are potentially controlled not only by the different populations within the community, but a myriad of dynamic physicochemical parameters as well. The goal of the current work was to determine the impact of organic acid enrichment, in this case lactate, on the succession of the native microbial community from a contaminated groundwater aquifer. Triplicate anaerobic, continuous-flow glass reactors were inoculated with Hanford 100-H groundwater and incubated for 95 days to obtain a stable, enriched community. The microbial community experienced a shift in the population dynamics over time to eventually form a communitymore » with far less diversity than the original. The final community was dominated by Pelosinus spp. and to a lesser degree, Acetobacterium spp. with small amounts of other bacteria and archaea including methanogens. The resultant diversity was far decreased from 63 genera within 12 phyla to 11 bacterial genera (from three phyla) and 2 archaeal genera (from one phylum). Isolation efforts were successful in attaining new species of Pelosinus and known members of Methanosarcina barkerii along with several sulfate- and Fe(III)- reducing consortia members. The continuous-flow reactors allowed for testing physiochemical factors with microbial community dynamics on a smaller, replicable, scale while also facilitating the isolation of several previously uncultured community members. These lab-scale simulations will presumably allow for a deeper understanding of the community metabolism with specific carbon amendments that can inform future in situ efforts.« less

Molecules and beyond: Assessing the distinctness of the Great Lakes wolf

Treesearch

Michael K. Schwartz; John A. Vucetich

2009-01-01

The dog family, Canidae, is a widely distributed group of species that have evolved and radiated relatively recently into 16 genera and 36 recognized species (Nowak 1999). Specific taxonomic designations for some canid taxa can be unclear due to frequent interspecific hybridization among species in both historical and contemporary times, and our imperfect...

Microorganisms as Analytical Indicators. Experimental Methods and Techniques,

DTIC Science & Technology

1980-01-01

Representa- tives of the genera Bacillus, Micrococcus, Escherichia, Pseudomonas, Aspergillus , and Penicillium are most frequently encountered...necessary for synthesis of prodigiosin, and magnesium is required for synthesis of bacteriochlorophylls. A change in the color of aspergillus spores...mesentericus niger and Bac. subtilis niger as a function of the concentration of phosphonium salts in the nutrient medium. The degree of

Phenrica littoralis a potential candidate for the biological control of alligator weed, Alternanthera philoxeroides: redscription of the adult, first description of immature stages and biological notes

USDA-ARS?s Scientific Manuscript database

Flea beetles of aliligator weed, Alternanthera philoxeroides (Martius) Grisebach (Amaranthaceae), were collected in Argentina, Uruguay, Paraguay and Brazil. Species in the genera Disonycha Chevrolat, Agasicles Jacoby Systena Chevrolat and Phenrica Bechyne were frequently found on this weed. Phenric...

Next-Generation Sequencing of Elite Berry Germplasm and Data Analysis Using a Bioinformatics Pipeline for Virus Detection and Discovery

USDA-ARS?s Scientific Manuscript database

Berry crops (members of the genera Fragaria, Ribes, Rubus, Sambucus and Vaccinium) are known hosts for more than 70 viruses and new ones are identified frequently. In modern berry cultivars, viruses tend to be asymptomatic in single infections and symptoms only develop after plants accumulate multip...

Actinomycetes in Karstic caves of northern Spain (Altamira and Tito Bustillo).

PubMed

Groth, I; Vettermann, R; Schuetze, B; Schumann, P; Saiz-Jimenez, C

1999-05-01

A variety of isolation procedures were carried out to study the involvement of bacteria in the colonisation and biodeterioration of Spanish caves with paleolithic rock art (Altamira and Tito Bustillo). The applied techniques mainly aimed to isolate heterotrophic bacteria such as streptomycetes, nocardioform and coryneform actinomycetes, and other gram-positive and gram-negative bacteria. The results demonstrated that actinomycetes were the most abundant gram-positive bacteria in the caves. Actinomycetes revealed a great taxonomic diversity with the predominant isolates belonging to the genus Streptomyces. Members of the genera Nocardia, Rhodococcus, Nocardioides, Amycolatopsis, Saccharothrix, Brevibacterium, Microbacterium, and coccoid actinomycetes (family Micrococcaceae) were also found.

Survey of Microbial Diversity in Flood Areas during Thailand 2011 Flood Crisis Using High-Throughput Tagged Amplicon Pyrosequencing

PubMed Central

Mhuantong, Wuttichai; Wongwilaiwalin, Sarunyou; Laothanachareon, Thanaporn; Eurwilaichitr, Lily; Tangphatsornruang, Sithichoke; Boonchayaanant, Benjaporn; Limpiyakorn, Tawan; Pattaragulwanit, Kobchai; Punmatharith, Thantip; McEvoy, John; Khan, Eakalak; Rachakornkij, Manaskorn; Champreda, Verawat

2015-01-01

The Thailand flood crisis in 2011 was one of the largest recorded floods in modern history, causing enormous damage to the economy and ecological habitats of the country. In this study, bacterial and fungal diversity in sediments and waters collected from ten flood areas in Bangkok and its suburbs, covering residential and agricultural areas, were analyzed using high-throughput 454 pyrosequencing of 16S rRNA gene and internal transcribed spacer sequences. Analysis of microbial community showed differences in taxa distribution in water and sediment with variations in the diversity of saprophytic microbes and sulfate/nitrate reducers among sampling locations, suggesting differences in microbial activity in the habitats. Overall, Proteobacteria represented a major bacterial group in waters, while this group co-existed with Firmicutes, Bacteroidetes, and Actinobacteria in sediments. Anaeromyxobacter, Steroidobacter, and Geobacter were the dominant bacterial genera in sediments, while Sulfuricurvum, Thiovirga, and Hydrogenophaga predominated in waters. For fungi in sediments, Ascomycota, Glomeromycota, and Basidiomycota, particularly in genera Philipsia, Rozella, and Acaulospora, were most frequently detected. Chytridiomycota and Ascomycota were the major fungal phyla, and Rhizophlyctis and Mortierella were the most frequently detected fungal genera in water. Diversity of sulfate-reducing bacteria, related to odor problems, was further investigated using analysis of the dsrB gene which indicated the presence of sulfate-reducing bacteria of families Desulfobacteraceae, Desulfobulbaceae, Syntrobacteraceae, and Desulfoarculaceae in the flood sediments. The work provides an insight into the diversity and function of microbes related to biological processes in flood areas. PMID:26020967

[Diversity and enzyme-producing activity of culturable halophilic bacteria in Daishan Saltern of East China].

PubMed

Yang, Dan-Dan; Li, Qian; Huang, Jing-Jing; Chen, Min

2012-11-01

Soil and saline water samples were collected from the Daishan Saltern of East China, and the halophilic bacteria were isolated and cultured by using selective media, aimed to investigate the diversity and enzyme-producing activity of culturable halophilic bacteria in saltern environment. A total of 181 strains were isolated by culture-dependent method. Specific primers were used to amplify the 16S rRNA gene of bacteria and archaea. The operation taxonomy units (OTUs) were determined by ARDRA method, and the representative strain of each OTU was sequenced. The phylogenetic position of all the isolated strains was determined by 16S rRNA sequencing. The results showed that the isolated 181 strains displayed 21 operational taxonomic units (OTUs), of which, 12 OTUs belonged to halophilic bacteria, and the others belonged to halophilic archaea. Phylogenetic analysis indicated that there were 7 genera presented among the halophilic bacteria group, and 4 genera presented among the halophilic archaea group. The dominant halophilic strains were of Halomonas and Haloarcula, with 46.8% in halophilic bacteria and 49.1% in halophilic archaea group, respectively. Enzyme-producing analysis indicated that most strains displayed enzyme-producing activity, including the activities of producing amylase, proteinase and lipase, and the dominant strains capable of enzyme-producing were of Haloarcula. Our results showed that in the environment of Daishan Saltern, there existed a higher diversity of halophilic bacteria, being a source sink for screening enzyme-producing bacterial strains.

Polyphenolic substrates and dyes degradation by yeasts from 25 de Mayo/King George Island (Antarctica).

PubMed

Rovati, José I; Pajot, Hipólito F; Ruberto, Lucas; Mac Cormack, Walter; Figueroa, Lucía I C

2013-11-01

Antarctica offers a range of extreme climatic conditions, such as low temperatures, high solar radiation and low nutrient availability, and constitutes one of the harshest environments on Earth. Despite that, it has been successfully colonized by ’cold-loving’ fungi, which play a key role in decomposition cycles in cold ecosystems. However, knowledge about the ecological role of yeasts in nutrient or organic matter recycling/mineralization remains highly fragmentary. The aim of this work was to study the yeast microbiota in samples collected on 25 de Mayo/King George Island regarding the scope of their ability to degrade polyphenolic substrates such as lignin and azo dyes. Sixty-one yeast isolates were obtained from 37 samples, including soil, rocks, wood and bones. Molecular analyses based on rDNA sequences revealed that 35 yeasts could be identified at the species level and could be classified in the genera Leucosporidiella, Rhodotorula, Cryptococcus, Bullera and Candida. Cryptococcus victoriae was by far the most ubiquitous species. In total, 33% of the yeast isolates examined showed significant activity for dye decolorization, 25% for laccase activity and 38% for ligninolytic activity. Eleven yeasts did not show positive activity in any of the assays performed and no isolates showed positive activity across all tested substrates. A high diversity of yeasts were isolated in this work, possibly including undescribed species and conspicuous Antarctic yeasts, most of them belonging to oligotrophic, slow-growing and metabolically diverse basidiomycetous genera.

Nature, nomenclature and taxonomy of obligate methanol utilizing strains.

PubMed

Cercel, M

1999-01-01

In a screening program, a number of different bacterial strains with the ability to utilize methanol as a sole carbon and energy source were isolated and described. They are well known methanol utilizing genera Pseudomonas, Klebsiella, Micrococcus, Methylomonas or, on the contrary, the new, unknown genera and species of methylotrophic bacteria. In the last category, Acinetobacter and Alcaligenes are the new reported genera of organisms able to use methanol as a sole carbon and energy source. The present paper reports the very complex physiological and biochemical modifications when very versatile bacteria such as Pseudomonas aeruginosa and Acinetobacter calcoaceticus are cultured on methanol and when the obligate methylotrophic state is compared with the facultative methylotrophic state of the same bacterial strain. Based on experiments and comparisons with literature data, it seems that Methylomonas methanica is the obligate methylotrophic state of Pseudomonas aeruginosa and that Acinetobacter calcoaceticus is the facultative methylotrophic state of Methylococcus capsulatus, an obligate methylotroph. The relationship of the obligate to the facultative and of the facultative to the obligate methylotrophy were established. These new methylotrophic genera and species, the profound physiological and biochemical modifications as well as the new data concerning nature, nomenclature and taxonomy of methanol utilizing bateria were reported for the first time in 1983.

The Composition of Human Milk and Infant Faecal Microbiota Over the First Three Months of Life: A Pilot Study

PubMed Central

Murphy, Kiera; Curley, David; O’Callaghan, Tom F.; O’Shea, Carol-Anne; Dempsey, Eugene M.; O’Toole, Paul W.; Ross, R. Paul; Ryan, C. Anthony; Stanton, Catherine

2017-01-01

Human milk contains a diverse array of bioactives and is also a source of bacteria for the developing infant gut. The aim of this study was to characterize the bacterial communities in human milk and infant faeces over the first 3 months of life, in 10 mother-infant pairs. The presence of viable Bifidobacterium and Lactobacillus in human milk was also evaluated. MiSeq sequencing revealed a large diversity of the human milk microbiota, identifying over 207 bacterial genera in milk samples. The phyla Proteobacteria and Firmicutes and the genera Pseudomonas, Staphylococcus and Streptococcus were the predominant bacterial groups. A core of 12 genera represented 81% of the microbiota relative abundance in milk samples at week 1, 3 and 6, decreasing to 73% at week 12. Genera shared between infant faeces and human milk samples accounted for 70–88% of the total relative abundance in infant faecal samples, supporting the hypothesis of vertical transfer of bacteria from milk to the infant gut. In addition, identical strains of Bifidobacterium breve and Lactobacillus plantarum were isolated from the milk and faeces of one mother-infant pair. Vertical transfer of bacteria via breastfeeding may contribute to the initial establishment of the microbiota in the developing infant intestine. PMID:28094284

Molecular phylogeny of the Cladophoraceae (Cladophorales, Ulvophyceae), with the resurrection of Acrocladus Nägeli and Willeella Børgesen, and the description of Lurbica gen. nov. and Pseudorhizoclonium gen. nov.

PubMed

Boedeker, Christian; Leliaert, Frederik; Zuccarello, Giuseppe C

2016-12-01

The taxonomy of the Cladophoraceae, a large family of filamentous green algae, has been problematic for a long time due to morphological simplicity, parallel evolution, phenotypic plasticity, and unknown distribution ranges. Partial large subunit (LSU) rDNA sequences were generated for 362 isolates, and the analyses of a concatenated dataset consisting of unique LSU and small subunit (SSU) rDNA sequences of 95 specimens greatly clarified the phylogeny of the Cladophoraceae. The phylogenetic reconstructions showed that the three currently accepted genera Chaetomorpha, Cladophora, and Rhizoclonium are polyphyletic. The backbone of the phylogeny is robust and the relationships of the main lineages were inferred with high support, only the phylogenetic position of both Chaetomorpha melagonium and Cladophora rupestris could not be inferred unambiguously. There have been at least three independent switches between branched and unbranched morphologies within the Cladophoraceae. Freshwater environments have been colonized twice independently, namely by the freshwater Cladophora species as well as by several lineages of the Rhizoclonium riparium clade. In an effort to establish monophyletic genera, the genera Acrocladus and Willeella are resurrected and two new genera are described: Pseudorhizoclonium and Lurbica. © 2016 Phycological Society of America.

Exploring Bioactive Properties of Marine Cyanobacteria Isolated from the Portuguese Coast: High Potential as a Source of Anticancer Compounds

PubMed Central

Costa, Margarida; Garcia, Mónica; Costa-Rodrigues, João; Costa, Maria Sofia; Ribeiro, Maria João; Fernandes, Maria Helena; Barros, Piedade; Barreiro, Aldo; Vasconcelos, Vitor; Martins, Rosário

2013-01-01

The oceans remain a major source of natural compounds with potential in pharmacology. In particular, during the last few decades, marine cyanobacteria have been in focus as producers of interesting bioactive compounds, especially for the treatment of cancer. In this study, the anticancer potential of extracts from twenty eight marine cyanobacteria strains, belonging to the underexplored picoplanktonic genera, Cyanobium, Synechocystis and Synechococcus, and the filamentous genera, Nodosilinea, Leptolyngbya, Pseudanabaena and Romeria, were assessed in eight human tumor cell lines. First, a crude extract was obtained by dichloromethane:methanol extraction, and from it, three fractions were separated in a Si column chromatography. The crude extract and fractions were tested in eight human cancer cell lines for cell viability/toxicity, accessed with the 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyl tetrazolium bromide (MTT) and lactic dehydrogenase release (LDH) assays. Eight point nine percent of the strains revealed strong cytotoxicity; 17.8% showed moderate cytotoxicity, and 14.3% assays showed low toxicity. The results obtained revealed that the studied genera of marine cyanobacteria are a promising source of novel compounds with potential anticancer activity and highlight the interest in also exploring the smaller filamentous and picoplanktonic genera of cyanobacteria. PMID:24384871

Two new genera of songbirds represent endemic radiations from the Shola Sky Islands of the Western Ghats, India.

PubMed

Robin, V V; Vishnudas, C K; Gupta, Pooja; Rheindt, Frank E; Hooper, Daniel M; Ramakrishnan, Uma; Reddy, Sushma

2017-01-23

A long-standing view of Indian biodiversity is that while rich in species, there are few endemics or in-situ radiations within the subcontinent. One exception is the Western Ghats biodiversity hotspot, an isolated mountain range with many endemic species. Understanding the origins of the montane-restricted species is crucial to illuminate both taxonomic and environmental history. With evidence from genetic, morphometric, song, and plumage data, we show that two songbird lineages endemic to the Western Ghats montane forest each have diversified into multiple distinct species. Historically labeled as single species of widespread Asian genera, these two lineages are highly divergent and do not group with the taxa in which they were previously classified but rather are distinct early divergences in larger Asian clades of flycatchers and babblers. Here we designated two new genera, the Western Ghats shortwings as Sholicola and the laughingthrushes as Montecincla, and evaluated species-limits to reflect distinct units by revising six previously named taxa and describing one novel species. Divergence dating showed that both these montane groups split from their Himalayan relatives during the Miocene, which is coincident with a shift towards arid conditions that fragmented the previously contiguous humid forest across peninsular India and isolated these lineages in the Western Ghats. Furthermore, these two genera showed congruent patterns of diversification across the Western Ghats Sky Islands, coincident with other climatic changes. Our study reveals the existence of two independent endemic radiations in the high montane Western Ghats or Shola Sky Islands with coincident divergence times, highlighting the role of climate in the diversification of these ancient lineages. The endemic and highly divergent nature of these previously unrecognized species underscores the dearth of knowledge about the biogeography of the Asian tropics, even for comparatively well-known groups such as birds. The substantial increase in the diversity of this region underscores the need for more rigorous systematic analysis to inform biodiversity studies and conservation efforts.

Selective constraints, molecular recombination structure and phylogenetic reconstruction of isometric plant RNA viruses of the families Luteoviridae and Tymoviridae.

PubMed

Boulila, Moncef

2011-02-01

In an effort to enhance the knowledge on molecular evolution of currently the known members of the families Luteoviridae and Tymoviridae, in-depth molecular investigations in the entire genome of 147 accessions retrieved from the international databases, were carried out. Two algorithms (RECCO and RDP version 3.31β) adapted to the mosaic structure of viruses were utilized. The recombination frequency along the sequences was dissected and demonstrated that the three virus genera of the family Luteoviridae comprise numerous members subjected to recombination. It has pointed out that the major viruses swapped a few but long genomic segments. In addition, in Barley yellow dwarf virus, heredity material might be exchanged between two different serotypes. Even more, putative recombination events occurred between two different genera. Based on Fisher's Exact Test of Neutrality, positive selection acting on protein expression was detected only in the poleroviruses Cereal yellow dwarf virus, Potato leafroll virus and Wheat yellow dwarf virus. In contrast, several components of the family Tymoviridae were highly recombinant. Genomic portion exchange arose in many positions consisting of short fragments. Furthermore, no positive selection was detected. The evolutionary history showed, in the Luteoviridae, that all screened isolates split into three clusters corresponding to the three virus genera forming this family. Moreover, in the serotype PAV of Barley yellow dwarf virus, two major clades corresponding to PAV-USA and PAV-China, were delineated. Similarly, in the Tymoviridae, all analyzed isolates fell into four groups corresponding to the three virus genera composing this family along with the unclassified Tymoviridae. Inferred phylogenies reshuffled the existing classification and showed that Wheat yellow dwarf virus-RPV was genetically closely related to Cereal yellow dwarf virus and the unclassified Tymoviridae Grapevine syrah virus-1 constituted an integral part of the genus Marafivirus. Copyright © 2010 Elsevier Masson SAS. All rights reserved.

Diverse Gene Cassettes in Class 1 Integrons of Facultative Oligotrophic Bacteria of River Mahananda, West Bengal, India

PubMed Central

Chakraborty, Ranadhir; Kumar, Arvind; Bhowal, Suparna Saha; Mandal, Amit Kumar; Tiwary, Bipransh Kumar; Mukherjee, Shriparna

2013-01-01

Background In this study a large random collection (n = 2188) of facultative oligotrophic bacteria, from 90 water samples gathered in three consecutive years (2007–2009) from three different sampling sites of River Mahananda in Siliguri, West Bengal, India, were investigated for the presence of class 1 integrons and sequences of the amplification products. Methodology/Principal Findings Replica plating method was employed for determining the antibiotic resistance profile of the randomly assorted facultative oligotrophic isolates. Genomic DNA from each isolate was analyzed by PCR for the presence of class 1 integron. Amplicons were cloned and sequenced. Numerical taxonomy and 16S rRNA gene sequence analyses were done to ascertain putative genera of the class 1 integron bearing isolates. Out of 2188 isolates, 1667 (76.19%) were antibiotic-resistant comprising of both single-antibiotic resistance (SAR) and multiple-antibiotic resistant (MAR), and 521 (23.81%) were sensitive to all twelve different antibiotics used in this study. Ninety out of 2188 isolates produced amplicon(s) of varying sizes from 0.15 to 3.45 KB. Chi-square (χ2) test revealed that the possession of class 1 integron in sensitive, SAR and MAR is not equally probable at the 1% level of significance. Diverse antibiotic-resistance gene cassettes, aadA1, aadA2, aadA4, aadA5, dfrA1, dfrA5, dfrA7, dfrA12, dfrA16, dfrA17, dfrA28, dfrA30, dfr-IIe, blaIMP-9, aacA4, Ac-6′-Ib, oxa1, oxa10 and arr2 were detected in 64 isolates. The novel cassettes encoding proteins unrelated to any known antibiotic resistance gene function were identified in 26 isolates. Antibiotic-sensitive isolates have a greater propensity to carry gene cassettes unrelated to known antibiotic-resistance genes. The integron-positive isolates under the class Betaproteobacteria comprised of only two genera, Comamonas and Acidovorax of family Comamonadaceae, while isolates under class Gammaproteobacteria fell under the families, Moraxellaceae, Pseudomonadaceae, Aeromonadaceae and Enterobacteriaceae. Conclusions Oligotrophic bacteria are good sources of novel genes as well as potential reservoirs of antibiotic resistance gene casettes. PMID:23951238

DIFFERENTIATION OF AEROMONAS ISOLATES OBTAINED FROM DRINKING WATER DISTRIBUTION SYSTEM USING MATRIX-ASSISTED LASER DESCRIPTION/IONIZATION-MASS SPECTROMETRY (MALDI-MS)

EPA Science Inventory

The genus Aeromonas is one of several medically significant genera that have gained prominence due to their evolving taxonomy and controversial role in human diseases. In this study, matrix-assisted laser desorption/ionization-mass spectrometry (MALDI-MS) was used to analyze the...

Dregs of our forgotten ancestors: fermentative microorganisms in the prehistory of Europe, the steppes and Indo-Iranian Asia, and their contemporary use in traditional and probiotic beverages

USDA-ARS?s Scientific Manuscript database

Fermentative microorganisms in the yeast genera Debaryomyces, Hyphopichia, Kluyveromyces, Lachancea, Saccharomyces, and Wickerhamomyces (and in the bacterial genus Lactobacillus) have been isolated from a variety of fermented beverages. These same microorganisms were very likely unknowingly utilized...

Occurrence, structure, and function of the nitrogen-fixing microsymbiont Frankia from nodules of Arizona alder [Abstract

Treesearch

J. O. Dawson; G. J. Gottfried; D. Hahn

2005-01-01

Actinorhizal plants are nodulated by the symbiotic, nitrogen-fixing actinomycete Frankia. The genus Alnus in the family Betulaceae is one of the 25 genera in 8 families of angiospermous plants that are actinorhizal. Arizona alder (Alnus oblongifolia Torr.) occurs in isolated populations associated with the...

Gene Mapping and Phylogenetic Analysis of the Complete Genome from 30 Single-Stranded RNA Male-Specific Coliphages (Family Leviviridae)

EPA Science Inventory

Male-specific ssRNA (FRNA) coliphages belong to the family Leviviridae. Two genera subdivided into four genogroups (Levivirus, genogroups I and II and Allolevivirus, genogroups III and IV) comprise the lower taxonomic levels. Strains isolated from several continents have been p...

Use of bile-esculin agar for rapid differentiation of Enterobacteriaceae.

PubMed Central

Lindell, S S; Quinn, P

1975-01-01

Bile-esculin agar has been used for several years for the presumptive identification of group D streptococci. All members of the Enterobacteriaceae family will also grow on this medium, but only certain ones can hydrolyze esculin to 6,7-dihydroxycoumarin, which reacts with iron to produce a characteristic blackening of the medium. One thousand and six cultures from clinical specimens representing 20 genera were isolated and identified. Heavy inocula from fresh pure culture isolates on heart infusion agar were placed on bile-esculin agar slants and incubated at 35 C. The slants were examined at 4 h and again at 18 h for esculin hydrolysis. Shigella, Salmonella, Arizona, Proteus mirabilis, Proteus morganii, Providencia alcalifaciens, and Providencia stuartii all produced negative results. Klebsiella pneumoniae, Enterobacter aerogenes, Serratia marcescens, and Serratia rubidaea produced a positive reaction in 4 h. The other remaining eight genera exhibited varying results. The use of this medium in conjunction with triple sugar iron-lysine iron agar has been of great value in differentiating the Klebsiella-Enterobacter-Serratia group from other Enterobacteriaceae. PMID:1176613

Nucleotide Sequence Database Comparison for Routine Dermatophyte Identification by Internal Transcribed Spacer 2 Genetic Region DNA Barcoding.

PubMed

Normand, A C; Packeu, A; Cassagne, C; Hendrickx, M; Ranque, S; Piarroux, R

2018-05-01

Conventional dermatophyte identification is based on morphological features. However, recent studies have proposed to use the nucleotide sequences of the rRNA internal transcribed spacer (ITS) region as an identification barcode of all fungi, including dermatophytes. Several nucleotide databases are available to compare sequences and thus identify isolates; however, these databases often contain mislabeled sequences that impair sequence-based identification. We evaluated five of these databases on a clinical isolate panel. We selected 292 clinical dermatophyte strains that were prospectively subjected to an ITS2 nucleotide sequence analysis. Sequences were analyzed against the databases, and the results were compared to clusters obtained via DNA alignment of sequence segments. The DNA tree served as the identification standard throughout the study. According to the ITS2 sequence identification, the majority of strains (255/292) belonged to the genus Trichophyton , mainly T. rubrum complex ( n = 184), T. interdigitale ( n = 40), T. tonsurans ( n = 26), and T. benhamiae ( n = 5). Other genera included Microsporum (e.g., M. canis [ n = 21], M. audouinii [ n = 10], Nannizzia gypsea [ n = 3], and Epidermophyton [ n = 3]). Species-level identification of T. rubrum complex isolates was an issue. Overall, ITS DNA sequencing is a reliable tool to identify dermatophyte species given that a comprehensive and correctly labeled database is consulted. Since many inaccurate identification results exist in the DNA databases used for this study, reference databases must be verified frequently and amended in line with the current revisions of fungal taxonomy. Before describing a new species or adding a new DNA reference to the available databases, its position in the phylogenetic tree must be verified. Copyright © 2018 American Society for Microbiology.

Bacterial Contamination of Boar Semen and its Relationship to Sperm Quality Preserved in Commercial Extender Containing Gentamicin Sulfate.

PubMed

Gączarzewicz, D; Udała, J; Piasecka, M; Błaszczyk, B; Stankiewicz, T

2016-09-01

This study was designed to determine the degree and type of bacterial contamination in boar semen (79 ejaculates from Large White and Landrace boars) and its consequences for sperm quality during storage (27 extended semen samples, 16°C for five days) under practical conditions of artificial insemination (AI). The results revealed the presence of aerobic bacteria in 99% of the ejaculates (from 80 to 370 ×106 colony-forming units/mL). Most of the ejaculates contained two or three bacterial contaminants, while the Staphylococcus, Streptococcus, and Pseudomonas bacterial genera were most frequently isolated. Also detected were Enterobacter spp., Bacillus spp., Proteus spp., Escherichia coli, P. fluorescens, and P. aeruginosa. In general, the growth of certain bacterial types isolated prior to semen processing (Enterobacter spp., E. coli, P. fluorescens, and P. aeruginosa) was not discovered on different days of storage, but fluctuations (with a tendency towards increases) were found in the frequencies of Bacillus spp., Pseudomonas spp., and Staphylococcus spp. isolates up to the end of storage. Semen preserved for five days exhibited decreases in sperm motility and increases in the average number of total aerobic bacteria; this was associated with sperm agglutination, plasma membrane disruption, and acrosome damage. We inferred that, due to the different degrees and types of bacterial contaminants in the boar ejaculates, the inhibitory activity of some antimicrobial agents used in swine extenders (such as gentamicin sulfate) may be limited. Because such agents can contribute to the overgrowth of certain aerobic bacteria and a reduction in the quality of stored semen, procedures with high standards of hygiene and microbiological control should be used when processing boar semen.

Lactobacilli and Bifidobacteria in Human Breast Milk: Influence of Antibiotherapy and Other Host and Clinical Factors

PubMed Central

Soto, Ana; Martín, Virginia; Jiménez, Esther; Mader, Isabelle; Rodríguez, Juan M.; Fernández, Leonides

2014-01-01

ABSTRACT Objective: The objective of this work was to study the lactobacilli and bifidobacteria population in human milk of healthy women, and to investigate the influence that several factors (including antibioteraphy during pregnancy and lactation, country and date of birth, delivery mode, or infant age) may exert on such population. Methods: A total of 160 women living in Germany or Austria provided the breast milk samples. Initially, 66 samples were randomly selected and cultured on MRS-Cys agar plates. Then, the presence of DNA from the genera Lactobacillus and Bifidobacterium, and from most of the Lactobacillus and Bifidobacterium species that were isolated, was assessed by qualitative polymerase chain reaction (PCR) using genus- and species-specific primers. Results: Lactobacilli and bifidobacteria could be isolated from the milk of 27 (40.91%) and 7 (10.61%), respectively, of the 66 cultured samples. On the contrary, Lactobacillus and Bifidobacterium sequences were detected by PCR in 108 (67.50%) and 41 (25.62%), respectively, of the 160 samples analyzed. The Lactobacillus species most frequently isolated and detected was L salivarius (35.00%), followed by L fermentum (25.00%) and L gasseri (21.88%), whereas B breve (13.75%) was the bifidobacterial species most commonly recovered and whose DNA was most regularly found. The number of lactobacilli- or bifidobacteria-positive samples was significantly lower in women who had received antibiotherapy during pregnancy or lactation. Conclusions: Our results suggest that either the presence of lactobacilli and/or bifidobacteria or their DNA may constitute good markers of a healthy human milk microbiota that has not been altered by the use of antibiotics. PMID:24590211

Viruses Inhibit CO2 Fixation in the Most Abundant Phototrophs on Earth.

PubMed

Puxty, Richard J; Millard, Andrew D; Evans, David J; Scanlan, David J

2016-06-20

Marine picocyanobacteria of the genera Prochlorococcus and Synechococcus are the most numerous photosynthetic organisms on our planet [1, 2]. With a global population size of 3.6 × 10(27) [3], they are responsible for approximately 10% of global primary production [3, 4]. Viruses that infect Prochlorococcus and Synechococcus (cyanophages) can be readily isolated from ocean waters [5-7] and frequently outnumber their cyanobacterial hosts [8]. Ultimately, cyanophage-induced lysis of infected cells results in the release of fixed carbon into the dissolved organic matter pool [9]. What is less well known is the functioning of photosynthesis during the relatively long latent periods of many cyanophages [10, 11]. Remarkably, the genomes of many cyanophage isolates contain genes involved in photosynthetic electron transport (PET) [12-18] as well as central carbon metabolism [14, 15, 19, 20], suggesting that cyanophages may play an active role in photosynthesis. However, cyanophage-encoded gene products are hypothesized to maintain or even supplement PET for energy generation while sacrificing wasteful CO2 fixation during infection [17, 18, 20]. Yet this paradigm has not been rigorously tested. Here, we measured the ability of viral-infected Synechococcus cells to fix CO2 as well as maintain PET. We compared two cyanophage isolates that share different complements of PET and central carbon metabolism genes. We demonstrate cyanophage-dependent inhibition of CO2 fixation early in the infection cycle. In contrast, PET is maintained throughout infection. Our data suggest a generalized strategy among marine cyanophages to redirect photosynthesis to support phage development, which has important implications for estimates of global primary production. Copyright © 2016 The Author(s). Published by Elsevier Ltd.. All rights reserved.

Evolutionary history of a vanishing radiation: isolation-dependent persistence and diversification in Pacific Island partulid tree snails.

PubMed

Lee, Taehwan; Li, Jingchun; Churchill, Celia K C; Foighil, Diarmaid Ó

2014-09-24

Partulid tree snails are endemic to Pacific high islands and have experienced extraordinary rates of extinction in recent decades. Although they collectively range across a 10,000 km swath of Oceania, half of the family's total species diversity is endemic to a single Eastern Pacific hot spot archipelago (the Society Islands) and all three partulid genera display highly distinctive distributions. Our goal was to investigate broad scale (range wide) and fine scale (within-Society Islands) molecular phylogenetic relationships of the two widespread genera, Partula and Samoana. What can such data tell us regarding the genesis of such divergent generic distribution patterns, and nominal species diversity levels across Oceania? Museum, captive (zoo) and contemporary field specimens enabled us to genotype 54 of the ~120 recognized species, including many extinct or extirpated taxa, from 14 archipelagoes. The genera Partula and Samoana are products of very distinct diversification processes. Originating at the western edge of the familial range, the derived genus Samoana is a relatively recent arrival in the far eastern archipelagoes (Society, Austral, Marquesas) where it exhibits a stepping-stone phylogenetic pattern and has proven adept at both intra-and inter- archipelago colonization. The pronounced east-west geographic disjunction exhibited by the genus Partula stems from a much older long-distance dispersal event and its high taxonomic diversity in the Society Islands is a product of a long history of within-archipelago diversification. The central importance of isolation for partulid lineage persistence and diversification is evident in time-calibrated phylogenetic trees that show that remote archipelagoes least impacted by continental biotas bear the oldest clades and/or the most speciose radiations. In contemporary Oceania, that isolation is being progressively undermined and these tree snails are now directly exposed to introduced continental predators throughout the family's range. Persistence of partulids in the wild will require proactive exclusion of alien predators in at least some designated refuge islands.

Assay for Aflatoxin Production by the Genera Aspergillus and Penicillium1

PubMed Central

Mislivec, Philip B.; Hunter, J. H.; Tuite, John

1968-01-01

A total of 260 isolates, including 43 species of Penicillium and 7 species of Aspergillus, were screened for their ability to produce aflatoxin on rice. Chloroform extracts were analyzed by thin-layer chromatography. None of the isolates produced aflatoxin. Certain species of Penicillium produced fluorescent substances that either were similar in RF or were of similar color to B and G aflatoxins. These substances were subsequently proved not to be aflatoxin by two-dimensional chromatography, by reaction with iodine fumes, or by both methods. PMID:5664121

Genetic diversity and host specificity varies across three genera of blood parasites in ducks of the Pacific Americas Flyway

USGS Publications Warehouse

Reeves, Andrew B.; Smith, Matthew M.; Meixell, Brandt W.; Fleskes, Joseph P.; Ramey, Andrew M.

2015-01-01

Birds of the order Anseriformes, commonly referred to as waterfowl, are frequently infected by Haemosporidia of the genera Haemoproteus, Plasmodium, and Leucocytozoon via dipteran vectors. We analyzed nucleotide sequences of the Cytochrome b (Cytb) gene from parasites of these genera detected in six species of ducks from Alaska and California, USA to characterize the genetic diversity of Haemosporidia infecting waterfowl at two ends of the Pacific Americas Flyway. In addition, parasite Cytb sequences were compared to those available on a public database to investigate specificity of genetic lineages to hosts of the order Anseriformes. Haplotype and nucleotide diversity of Haemoproteus Cytb sequences was lower than was detected for Plasmodium and Leucocytozoon parasites. Although waterfowl are presumed to be infected by only a single species of Leucocytozoon, L. simondi, diversity indices were highest for haplotypes from this genus and sequences formed five distinct clades separated by genetic distances of 4.9%–7.6%, suggesting potential cryptic speciation. All Haemoproteus andLeucocytozoon haplotypes derived from waterfowl samples formed monophyletic clades in phylogenetic analyses and were unique to the order Anseriformes with few exceptions. In contrast, waterfowl-origin Plasmodium haplotypes were identical or closely related to lineages found in other avian orders. Our results suggest a more generalist strategy for Plasmodiumparasites infecting North American waterfowl as compared to those of the generaHaemoproteus and Leucocytozoon.

Genetic Diversity and Host Specificity Varies across Three Genera of Blood Parasites in Ducks of the Pacific Americas Flyway

PubMed Central

Reeves, Andrew B.; Smith, Mathew M.; Meixell, Brandt W.; Fleskes, Joseph P; Ramey, Andrew M.

2015-01-01

Birds of the order Anseriformes, commonly referred to as waterfowl, are frequently infected by Haemosporidia of the genera Haemoproteus, Plasmodium, and Leucocytozoon via dipteran vectors. We analyzed nucleotide sequences of the Cytochrome b (Cytb) gene from parasites of these genera detected in six species of ducks from Alaska and California, USA to characterize the genetic diversity of Haemosporidia infecting waterfowl at two ends of the Pacific Americas Flyway. In addition, parasite Cytb sequences were compared to those available on a public database to investigate specificity of genetic lineages to hosts of the order Anseriformes. Haplotype and nucleotide diversity of Haemoproteus Cytb sequences was lower than was detected for Plasmodium and Leucocytozoon parasites. Although waterfowl are presumed to be infected by only a single species of Leucocytozoon, L. simondi, diversity indices were highest for haplotypes from this genus and sequences formed five distinct clades separated by genetic distances of 4.9%–7.6%, suggesting potential cryptic speciation. All Haemoproteus and Leucocytozoon haplotypes derived from waterfowl samples formed monophyletic clades in phylogenetic analyses and were unique to the order Anseriformes with few exceptions. In contrast, waterfowl-origin Plasmodium haplotypes were identical or closely related to lineages found in other avian orders. Our results suggest a more generalist strategy for Plasmodium parasites infecting North American waterfowl as compared to those of the genera Haemoproteus and Leucocytozoon. PMID:25710468

Phylogenetic Diversity and Antifungal Activity of Endophytic Fungi Associated with Tephrosia purpurea

PubMed Central

Luo, Ze-Ping; Lin, Hai-Yan; Ding, Wen-Bing; He, Hua-Liang

2015-01-01

Sixty-one endophytic fungus strains with different colony morphologies were isolated from the leaves, stems and roots of Tephrosia purpurea with colonization rates of 66.95%, 37.50%, and 26.92%, respectively. Based on internal transcribed spacer sequence analysis, 61 isolates were classified into 16 genera belonging to 3 classes under the phylum Ascomycota. Of the 61 isolates, 6 (9.84%) exhibited antifungal activity against one or more indicator plant pathogenic fungi according to the dual culture test. Isolate TPL25 had the broadest antifungal spectrum of activity, and isolate TPL35 was active against 5 plant pathogenic fungi. Furthermore, culture filtrates of TPL25 and TPL35 exhibited greater than 80% growth inhibition against Sclerotinia sclerotiorum. We conclude that the endophytic fungal strains TPL25 and TPL35 are promising sources of bioactive compounds. PMID:26839503

Characterization of fungi isolated from the equipment used in the International Space Station or Space Shuttle.

PubMed

Satoh, Kazuo; Yamazaki, Takashi; Nakayama, Takako; Umeda, Yoshiko; Alshahni, Mohamed Mahdi; Makimura, Miho; Makimura, Koichi

2016-05-01

As a part of a series of studies regarding the microbial biota in manned space environments, fungi were isolated from six pieces of equipment recovered from the Japanese Experimental Module "KIBO" of the International Space Station and from a space shuttle. Thirty-seven strains of fungi were isolated, identified and investigated with regard to morphological phenotypes and antifungal susceptibilities. The variety of fungi isolated in this study was similar to that of several previous reports. The dominant species belonged to the genera Penicillium, Aspergillus and Cladosporium, which are potential causative agents of allergy and opportunistic infections. The morphological phenotypes and antifungal susceptibilities of the strains isolated from space environments were not significantly different from those of reference strains on Earth. © 2016 The Societies and John Wiley & Sons Australia, Ltd.

Fate of antibiotic resistant cultivable heterotrophic bacteria and antibiotic resistance genes in wastewater treatment processes.

PubMed

Zhang, Songhe; Han, Bing; Gu, Ju; Wang, Chao; Wang, Peifang; Ma, Yanyan; Cao, Jiashun; He, Zhenli

2015-09-01

Antibiotic resistant bacteria (ARB) and antibiotic resistance genes (ARGs) are emerging contaminants of environmental concern. Heterotrophic bacteria in activated sludge have an important role in wastewater treatment plants (WWTPs). However, the fate of cultivable heterotrophic ARB and ARGs in WWPTs process remains unclear. In the present study, we investigated the antibiotic-resistant phenotypes of cultivable heterotrophic bacteria from influent and effluent water of three WWTPs and analysed thirteen ARGs in ARB and in activated sludge from anoxic, anaerobic and aerobic compartments. From each influent or effluent sample of the three plants, 200 isolates were randomly tested for susceptibility to 12 antibiotics. In these samples, between 5% and 64% isolates showed resistance to >9 antibiotics and the proportion of >9-drug-resistant bacteria was lower in isolates from effluent than from influent. Eighteen genera were identified in 188 isolates from influent (n=94) and effluent (n=94) of one WWTP. Six genera (Aeromonas, Bacillus, Lysinibacillus, Microbacterium, Providencia, and Staphylococcus) were detected in both influent and effluent samples. Gram-negative and -positive isolates dominated in influent and effluent, respectively. The 13 tetracycline-, sulphonamide-, streptomycin- and β-lactam-resistance genes were detected at a higher frequency in ARB from influent than from effluent, except for sulA and CTX-M, while in general, the abundances of ARGs in activated sludge from two of the three plants were higher in aerobic compartments than in anoxic ones, indicating abundant ARGs exit in the excess sledges and/or in uncultivable bacteria. These findings may be useful for elucidating the effect of WWTP on ARB and ARGs. Copyright © 2015 Elsevier Ltd. All rights reserved.

Cyanotoxins from Black Band Disease of Corals and from Other Coral Reef Environments

PubMed Central

Sekar, Raju; Richardson, Laurie L.

2012-01-01

Many cyanobacteria produce cyanotoxins, which has been well documented from freshwater environments but not investigated to the same extent in marine environments. Cyanobacteria are an obligate component of the polymicrobial disease of corals known as black band disease (BBD). Cyanotoxins were previously shown to be present in field samples of BBD and in a limited number of BBD cyanobacterial cultures. These toxins were suggested as one of the mechanisms contributing to BBD-associated coral tissue lysis and death. In this work, we tested nine cyanobacterial isolates from BBD and additionally nine isolated from non-BBD marine sources for their ability to produce toxins. The presence of toxins was determined using cell extracts of laboratory grown cyanobacterial cultures using ELISA and the PP2A assay. Based on these tests, it was shown that cyanobacterial toxins belonging to the microcystin/nodularin group were produced by cyanobacteria originating from both BBD and non-BBD sources. Several environmental factors that can be encountered in the highly dynamic microenvironment of BBD were tested for their effect on both cyanobacterial growth yield and rate of toxin production using two of the BBD isolates of the genera Leptolyngbya and Geitlerinema. While toxin production was the highest under mixotrophic conditions (light and glucose) for the Leptolyngbya isolate, it was highest under photoautotrophic conditions for the Geitlerinema isolate. Our results show that toxin production among marine cyanobacteria is more widespread than previously documented, and we present data showing three marine cyanobacterial genera (Phormidium, Pseudanabaena, and Spirulina) are newly identified as cyanotoxin producers. We also show that cyanotoxin production by BBD cyanobacteria can be affected by environmental factors that are present in the microenvironment associated with this coral disease. PMID:19554362

Identification of bacteria in drinking and purified water during the monitoring of a typical water purification system

PubMed Central

Penna, Vessoni Thereza Christina; Martins, Silva Alzira Maria; Mazzola, Priscila Gava

2002-01-01

Background A typical purification system that provides purified water which meets ionic and organic chemical standards, must be protected from microbial proliferation to minimize cross-contamination for use in cleaning and preparations in pharmaceutical industries and in health environments. Methodology Samples of water were taken directly from the public distribution water tank at twelve different stages of a typical purification system were analyzed for the identification of isolated bacteria. Two miniature kits were used: (i) identification system (api 20 NE, Bio-Mérieux) for non-enteric and non-fermenting gram-negative rods; and (ii) identification system (BBL crystal, Becton and Dickson) for enteric and non-fermenting gram-negative rods. The efficiency of the chemical sanitizers used in the stages of the system, over the isolated and identified bacteria in the sampling water, was evaluated by the minimum inhibitory concentration (MIC) method. Results The 78 isolated colonies were identified as the following bacteria genera: Pseudomonas, Flavobacterium and Acinetobacter. According to the miniature kits used in the identification, there was a prevalence of isolation of P. aeruginosa 32.05%, P. picketti (Ralstonia picketti) 23.08%, P. vesiculares 12.82%,P. diminuta 11.54%, F. aureum 6.42%, P. fluorescens 5.13%, A. lwoffi 2.56%, P. putida 2.56%, P. alcaligenes 1.28%, P. paucimobilis 1.28%, and F. multivorum 1.28%. Conclusions We found that research was required for the identification of gram-negative non-fermenting bacteria, which were isolated from drinking water and water purification systems, since Pseudomonas genera represents opportunistic pathogens which disperse and adhere easily to surfaces, forming a biofilm which interferes with the cleaning and disinfection procedures in hospital and industrial environments. PMID:12182763

Cyanotoxins from black band disease of corals and from other coral reef environments.

PubMed

Gantar, Miroslav; Sekar, Raju; Richardson, Laurie L

2009-11-01

Many cyanobacteria produce cyanotoxins, which has been well documented from freshwater environments but not investigated to the same extent in marine environments. Cyanobacteria are an obligate component of the polymicrobial disease of corals known as black band disease (BBD). Cyanotoxins were previously shown to be present in field samples of BBD and in a limited number of BBD cyanobacterial cultures. These toxins were suggested as one of the mechanisms contributing to BBD-associated coral tissue lysis and death. In this work, we tested nine cyanobacterial isolates from BBD and additionally nine isolated from non-BBD marine sources for their ability to produce toxins. The presence of toxins was determined using cell extracts of laboratory grown cyanobacterial cultures using ELISA and the PP2A assay. Based on these tests, it was shown that cyanobacterial toxins belonging to the microcystin/nodularin group were produced by cyanobacteria originating from both BBD and non-BBD sources. Several environmental factors that can be encountered in the highly dynamic microenvironment of BBD were tested for their effect on both cyanobacterial growth yield and rate of toxin production using two of the BBD isolates of the genera Leptolyngbya and Geitlerinema. While toxin production was the highest under mixotrophic conditions (light and glucose) for the Leptolyngbya isolate, it was highest under photoautotrophic conditions for the Geitlerinema isolate. Our results show that toxin production among marine cyanobacteria is more widespread than previously documented, and we present data showing three marine cyanobacterial genera (Phormidium, Pseudanabaena, and Spirulina) are newly identified as cyanotoxin producers. We also show that cyanotoxin production by BBD cyanobacteria can be affected by environmental factors that are present in the microenvironment associated with this coral disease.

Braconid (Hymenoptera, Braconidae) parasitoids of bark beetles in upland spruce stands of the Czech Republic

Treesearch

Aural Lozan; Jiri Zeleny

2003-01-01

Several species of bark beetles occur frequently in the upland spruce forests of the Czech Republic; some of them are serious pests that may cause vast destruction of forest stands. In the last decade, a complex of several species from the genera Ips, Pityogenes and Polygraphus contributed to large-scale devastation of thousand...

Cutaneous HPV and skin cancer.

PubMed

Accardi, Rosita; Gheit, Tarik

2014-12-01

Papillomaviruses (HPVs) are small non-enveloped icosahedral viruses that infect the keratinocytes of skin and mucosa. The cutaneous HPV types are represented mainly by the beta and gamma genera, which are widely present in the skin of normal individuals. More than 40 beta-HPV types and 50 gamma-HPV types have been isolated, and these numbers are continuously growing. The main cause of non-melanoma skin cancer is exposure to ultraviolet radiation (UVR). However, cutaneous HPVs that belong to the beta genus may act as a co-carcinogen with UVR. The association between beta-HPVs and skin cancer was first reported in patients with epidermodysplasia verruciformis (EV), who frequently develop cutaneous squamous cell carcinoma (SCC) on sun-exposed areas. Isolation of HPVs from the lesions suggested that HPVs might act as a co-carcinogen with UVR in EV patients. Beta-HPVs may also play a role in cutaneous SCC in immunocompromised non-EV and in immunocompetent individuals. Several studies have reported an association of viral DNA and/or antibodies to beta HPV types with SCC. Interestingly, HPV prevalence and viral load decrease during skin carcinogenesis, being significantly higher in actinic keratosis than in SCC, suggesting that the virus may play a role in the early stages of tumour development (the "hit-and-run" hypothesis). Concordantly, in vivo and in vitro studies have shown that E6 and E7 from certain cutaneous HPV types display transforming activities, further confirming their potential role in carcinogenesis. Copyright © 2014 Elsevier Masson SAS. All rights reserved.

Species diversity of culturable endophytic fungi from Brazilian mangrove forests.

PubMed

de Souza Sebastianes, Fernanda Luiza; Romão-Dumaresq, Aline Silva; Lacava, Paulo Teixeira; Harakava, Ricardo; Azevedo, João Lúcio; de Melo, Itamar Soares; Pizzirani-Kleiner, Aline Aparecida

2013-08-01

This study aimed to perform a comparative analysis of the diversity of endophytic fungal communities isolated from the leaves and branches of Rhizophora mangle, Avicennia schaueriana and Laguncularia racemosa trees inhabiting two mangroves in the state of São Paulo, Brazil [Cananeia and Bertioga (oil spill-affected and unaffected)] in the summer and winter. Three hundred and forty-three fungi were identified by sequencing the ITS1-5.8S-ITS2 region of rDNA. Differences were observed in the frequencies of fungi isolated from the leaves and branches of these three different plant species sampled from the Bertioga oil spill-affected and the oil-unaffected mangrove sites in the summer and winter; these differences indicate a potential impact on fungal diversity in the study area due to the oil spill. The molecular identification of the fungi showed that the fungal community associated with these mangroves is composed of at least 34 different genera, the most frequent of which were Diaporthe, Colletotrichum, Fusarium, Trichoderma and Xylaria. The Shannon and the Chao1 indices [H'(95 %) = 4.00, H'(97 %) = 4.22, Chao1(95 %) = 204 and Chao1(97 %) = 603] indicated that the mangrove fungal community possesses a vast diversity and richness of endophytic fungi. The data generated in this study revealed a large reservoir of fungal genetic diversity inhabiting these Brazilian mangrove forests and highlighted substantial differences between the fungal communities associated with distinct plant tissues, plant species, impacted sites and sampling seasons.

Diversity and bioprospecting of fungal communities associated with endemic and cold-adapted macroalgae in Antarctica

PubMed Central

Godinho, Valéria M; Furbino, Laura E; Santiago, Iara F; Pellizzari, Franciane M; Yokoya, Nair S; Pupo, Diclá; Alves, Tânia MA; S Junior, Policarpo A; Romanha, Alvaro J; Zani, Carlos L; Cantrell, Charles L; Rosa, Carlos A; Rosa, Luiz H

2013-01-01

We surveyed the distribution and diversity of fungi associated with eight macroalgae from Antarctica and their capability to produce bioactive compounds. The collections yielded 148 fungal isolates, which were identified using molecular methods as belonging to 21 genera and 50 taxa. The most frequent taxa were Geomyces species (sp.), Penicillium sp. and Metschnikowia australis. Seven fungal isolates associated with the endemic Antarctic macroalgae Monostroma hariotii (Chlorophyte) displayed high internal transcribed spacer sequences similarities with the psychrophilic pathogenic fungus Geomyces destructans. Thirty-three fungal singletons (66%) were identified, representing rare components of the fungal communities. The fungal communities displayed high diversity, richness and dominance indices; however, rarefaction curves indicated that not all of the fungal diversity present was recovered. Penicillium sp. UFMGCB 6034 and Penicillium sp. UFMGCB 6120, recovered from the endemic species Palmaria decipiens (Rhodophyte) and M. hariotii, respectively, yielded extracts with high and selective antifungal and/or trypanocidal activities, in which a preliminary spectral analysis using proton nuclear magnetic resonance spectroscopy indicated the presence of highly functionalised aromatic compounds. These results suggest that the endemic and cold-adapted macroalgae of Antarctica shelter a rich, diversity and complex fungal communities consisting of a few dominant indigenous or mesophilic cold-adapted species, and a large number of rare and/or endemic taxa, which may provide an interesting model of algal–fungal interactions under extreme conditions as well as a potential source of bioactive compounds. PMID:23702515

A molecular phylogeny of the nightjars (Aves: Caprimulgidae) suggests extensive conservation of primitive morphological traits across multiple lineages.

PubMed

Larsen, Carl; Speed, Michael; Harvey, Nicholas; Noyes, Harry A

2007-03-01

We report a molecular re-assessment of the classification of the nightjars which draws conclusions that are strongly at odds with the traditional, morphology-based classifications. We used maximum likelihood and Bayesian methods to compare the cytochrome b gene for 14 species from seven of the 15 genera of the Caprimulgidae and partial cytochrome b sequence data was available for a further seven species including three further genera. We found that within the Caprimulgidae there were four geographically isolated clades with bootstrap support greater than 70%. One of these clades contained just Chordeiles species, the remaining three clades each contained a mixture of genera including Caprimulgus sp. A clade of exclusively South American nightjars included the genera Caprimulgus, Uropsalis, Eleopthreptus and Hydropsalis. A clade of African and Eurasian birds included Caprimulgus and Macrodipteryx. Phalaenoptilus nuttallii and Caprimulgus vociferous formed a clade of North American birds. Two ecological factors appear to make morphological classification potentially misleading: first, the apparent retention of primitive anti-predator and foraging-related traits across genetically divergent groups; second, rapid divergence in other traits, especially those related to mating, which generate high levels of morphological divergence between species that are genetically very similar. The cytochrome b data suggests that the genus Caprimulgus is not monophyletic and is restricted to Africa and Eurasia and that Caprimulgus species from outside this area have been misclassified as a consequence of retention of primitive adaptations for crepuscular/nocturnal living. Some other genera also appear to have little support from the cytochrome b data.

Extended-spectrum β-lactamase producing Enterobacteriaceae in bulk tank milk from German dairy farms.

PubMed

Odenthal, Sabrina; Akineden, Ömer; Usleber, Ewald

2016-12-05

Although the dairy farm environment is a known source of extended-spectrum β-lactamase (ESBL)-producing bacteria, surveillance data on ESBL in the milk production chain are still scarce. This study aimed at estimating the dimensions of the problem for public health and animal welfare by surveying ESBL-producing Enterobacteriaceae in raw bulk tank milk in Germany. Samples from 866 dairy farms, comprising about 1% of the total number of dairy farms in Germany, were first screened for presence of cefotaxime-resistant bacteria by selective enrichment. Suspect colonies were identified phenotypically and further characterized by biochemical and molecular methods, including analysis of resistance genes and clonal diversity in ESBL-producing isolates. Bulk tank milk from 82 (9.5%) farms yielded Enterobacteriaceae with confirmed ESBL-production. The most frequent ESBL-producing species was Escherichia coli (75.6%), followed by Citrobacter spp. (9.6%), Enterobacter cloacae (6.1%), and Klebsiella oxytoca (3.7%), a few isolates belonged to other species within the genera Hafnia, Raoutella and Serratia. The majority of isolates (95.1%) harbored the β-lactamase blaCTX-M gene, which has gained increased importance among ESBL-producing strains worldwide; the CTX-M group 1 was found to be the dominating (88.4%) phylogenetic group. All ESBL-positive Escherichia coli isolates were clonally heterogeneous, as determined by pulsed-field gel electrophoresis. The results from this survey demonstrate that ESBL-producing bacteria are distributed widely in the dairy farm environment in Germany. Therefore, raw milk is a potential source of exposure for the consumer, which is of increasing importance considering the trend of farmer-to-consumer direct marketing. Furthermore, dairy farm staff have an increased likelihood of exposure to ESBL-producing bacteria. Finally, ESBL-producing bacteria may also be transferred via waste milk to calves, thus further spreading antibiotic resistance in the farm environment. Copyright © 2016 Elsevier B.V. All rights reserved.

Alkaloids and Phenolic Compounds from Sida rhombifolia L. (Malvaceae) and Vasorelaxant Activity of Two Indoquinoline Alkaloids.

PubMed

Chaves, Otemberg Souza; Teles, Yanna Carolina Ferreira; Monteiro, Matheus Morais de Oliveira; Mendes Junior, Leônidas das Graças; Agra, Maria de Fátima; Braga, Valdir de Andrade; Silva, Tânia Maria Sarmento; Souza, Maria de Fátima Vanderlei de

2017-01-06

The follow-up of phytochemical and pharmacological studies of Sida rhombifolia L. (Malvaceae) aims to strengthen the chemosystematics and pharmacology of Sida genera and support the ethnopharmacological use of this species as hypotensive herb. The present work reports phytoconstituents isolated and identified from aerial parts of S. rhombifolia by using chromatographic and spectroscopic methods. The study led to the isolation of scopoletin ( 1 ), scoporone ( 2 ), ethoxy-ferulate ( 3 ), kaempferol ( 4 ), kaempferol-3- O -β-d-glycosyl-6''-α-d-rhamnose ( 5 ), quindolinone ( 6 ), 11-methoxy-quindoline ( 7 ), quindoline ( 8 ), and the cryptolepine salt ( 9 ). The alkaloids quindolinone ( 6 ) and cryptolepine salt ( 9 ) showed vasorelaxant activity in rodent isolated mesenteric arteries.

Brefeldin A, a cytotoxin produced by Paecilomyces sp. and Aspergillus clavatus isolated from Taxus mairei and Torreya grandis.

PubMed

Wang, Jianfeng; Huang, Yaojian; Fang, Meijuan; Zhang, Yongjie; Zheng, Zhonghui; Zhao, Yufen; Su, Wenjin

2002-09-06

Paecilomyces sp. and Aspergillus clavatus, which were isolated from Taxus mairei and Torreya grandis from southeast China, produced toxic metabolites when grown in liquid culture. Nuclear magnetic resonance techniques, infrared spectrometry, electrospray ionization mass spectroscopy and X-ray analysis identified brefeldin A, a bioactive metabolite produced by a number of fungal species belonging to the genera Alternaria, Ascochyta, Penicillium, Curvularia, Cercospora and Phyllosticta. This is the first report of the isolation of the cytotoxin from Paecilomyces sp. and A. clavatus. The relevance of brefeldin A to the association between these fungi and their host plants is discussed. Copyright 2002 Federation of European Microbiological Societies

Polar and antioxidant fraction of Plumbago europaea L., a spontaneous plant of Sardinia.

PubMed

Serrilli, A M; Sanfilippo, V; Ballero, M; Sanna, C; Poli, F; Scartezzini, P; Serafini, M; Bianco, A

2010-04-01

Secondary metabolite isolation and analysis of Plumbago europaea L. (Plumbaginaceae) is the aim of this work, which is included in a project of our groups on spontaneous and endemic Sardinian species. Plumbago europaea is the only specie of the genera that grows wild in Italy. Metabolites from leaves and roots of this specie were compared. Moreover, at present, literature on the phytochemical characterisation of P. europaea is poor. Plumbagin was isolated in both of the samples analysed, confirming its nature in the Plumbaginaceae family as chemotaxonomic marker of the Plumbaginae tribe. In this work, hydroplumbagin-4-O-glucoside and myricetin-3-O-rhamnoside are isolated for the first time in the genus.

Molecular and phenotypic characterization of endophytic bacteria isolated from sulla nodules.

PubMed

Beghalem, Hamida; Aliliche, Khadidja; Chriki, Ali; Landoulsi, Ahmed

2017-10-01

In the current study, bacterial diversity was investigated in root nodules of Sulla pallida and Sulla capitata. The isolates were analyzed on the basis of their phenotypic and molecular characteristics. The phylogenetic analysis based on 16S rRNA and housekeeping genes (recA and atpD) showed that the isolated bacteria related to Sinorhizobium, Neorhizobium, Phyllobacterium, Arthrobacter, Variovorax and Pseudomonas genera. This is the first report of Neorhizobium genus associated with Hedysarum genus. Phenotypically, all strains tolerate the elevated temperature of 40 °C, and salt stress at a concentration of 2%. In addition, the isolates failed to induce nodulation on their original host; and the symbiotic genes could not be amplified, suggesting that these strains are endophytic bacteria. Copyright © 2017 Elsevier Ltd. All rights reserved.

Occurrence of keratinophilic fungi on Indian birds.

PubMed

Dixit, A K; Kushwaha, R K

1991-01-01

Keratinophilic fungi were isolated from feathers of most common Indian birds, viz. domestic chicken (Gallus domesticus), domestic pigeon (Columba livia), house sparrow (Passer domesticus), house crow (Corvus splendens), duck (Anas sp.), rose-ringed parakeet (Psittacula krameri). Out of 87 birds, 58 yielded 4 keratinophilic fungal genera representing 13 fungal species and one sterile mycelium. The isolated fungi were cultured on Sabouraud's dextrose agar at 28 +/- 2 degrees C. Chrysosporium species were isolated on most of the birds. Chrysosporium lucknowense and Chrysosporium tropicum were the most common fungal species associated with these Indian birds. Maximum occurrence of fungi (47%) was recorded on domestic chickens and the least number of keratinophilic fungi was isolated from the domestic pigeon and duck. The average number of fungi per bird was found to be the 0.44.

Profile of microflora of the posterior intestine of Chinook salmon before, during, and after administration of rations with and without erythromycin

USGS Publications Warehouse

Moffitt, C.M.; Mobin, S.M.A.

2006-01-01

We describe the resident heterotrophic aerobic microflora of the salmonid posterior intestine before, during, and after the administration of rations with erythromycin in a hatchery raceway environment. We compare the profiles of medicated Chinook salmon Oncorhynchus tshawytscha with those of control fish that were not fed erythromycin. The combined counts of bacteria and yeasts per gram of fish intestine originating from four upstream raceways ranged from 3.0 ?? 102 to 9.6 ?? 105 colony-forming units (CFU) over the study period. Yeasts were commonly identified in the gut, and abundances ranged from 0% to more than 80% of the CFU. Erythromycin therapy decreased the total microbial population and altered the bacterial diversity in the gut during treatment. The intestinal microbial populations in fish medicated with erythromycin increased rapidly after treatment ceased, and by 25 d after treatment the CFU were similar in samples from both medicated and control fish populations. Of 325 isolates from fish selected for biochemical profiles, we identified a total of eight gram-positive and eight gram-negative genera. Bacillus spp. were common throughout sampling and were identified in samples of fish feed. Erythromycin-resistant, gram-positive bacteria were observed throughout the sampling in medicated and control fish. We identified seven gram-positive and two gram-negative genera in 74 selected isolates from control and erythromycin feeds. Our studies suggest that the aerobic microflora of the posterior intestine varies over time, and it is likely that few resistant genera of concern to human health are present.

Phylogeny of culturable cyanobacteria from Brazilian mangroves.

PubMed

Silva, Caroline Souza Pamplona; Genuário, Diego Bonaldo; Vaz, Marcelo Gomes Marçal Vieira; Fiore, Marli Fátima

2014-03-01

The cyanobacterial community from Brazilian mangrove ecosystems was examined using a culture-dependent method. Fifty cyanobacterial strains were isolated from soil, water and periphytic samples collected from Cardoso Island and Bertioga mangroves using specific cyanobacterial culture media. Unicellular, homocytous and heterocytous morphotypes were recovered, representing five orders, seven families and eight genera (Synechococcus, Cyanobium, Cyanobacterium, Chlorogloea, Leptolyngbya, Phormidium, Nostoc and Microchaete). All of these novel mangrove strains had their 16S rRNA gene sequenced and BLAST analysis revealed sequence identities ranging from 92.5 to 99.7% when they were compared with other strains available in GenBank. The results showed a high variability of the 16S rRNA gene sequences among the genotypes that was not associated with the morphologies observed. Phylogenetic analyses showed several branches formed exclusively by some of these novel 16S rRNA gene sequences. BLAST and phylogeny analyses allowed for the identification of Nodosilinea and Oxynema strains, genera already known to exhibit poor morphological diacritic traits. In addition, several Nostoc and Leptolyngbya morphotypes of the mangrove strains may represent new generic entities, as they were distantly affiliated with true genera clades. The presence of non-ribosomal peptide synthetase, polyketide synthase, microcystin and saxitoxin genes were detected in 20.5%, 100%, 37.5% and 33.3%, respectively, of the 44 tested isolates. A total of 134 organic extracts obtained from 44 strains were tested against microorganisms, and 26% of the extracts showed some antimicrobial activity. This is the first polyphasic study of cultured cyanobacteria from Brazilian mangrove ecosystems using morphological, genetic and biological approaches. Copyright © 2014 Elsevier GmbH. All rights reserved.

Phenol degradation and heavy metal tolerance of Antarctic yeasts.

PubMed

Fernández, Pablo Marcelo; Martorell, María Martha; Blaser, Mariana G; Ruberto, Lucas Adolfo Mauro; de Figueroa, Lucía Inés Castellanos; Mac Cormack, Walter Patricio

2017-05-01

In cold environments, biodegradation of organic pollutants and heavy metal bio-conversion requires the activity of cold-adapted or cold-tolerant microorganisms. In this work, the ability to utilize phenol, methanol and n-hexadecane as C source, the tolerance to different heavy metals and growth from 5 to 30 °C were evaluated in cold-adapted yeasts isolated from Antarctica. Fifty-nine percent of the yeasts were classified as psychrotolerant as they could grow in all the range of temperature tested, while the other 41% were classified as psychrophilic as they only grew below 25 °C. In the assimilation tests, 32, 78, and 13% of the yeasts could utilize phenol, n-hexadecane, and methanol as C source, respectively, but only 6% could assimilate the three C sources evaluated. In relation to heavy metals ions, 55, 68, and 80% were tolerant to 1 mM of Cr(VI), Cd(II), and Cu(II), respectively. Approximately a half of the isolates tolerated all of them. Most of the selected yeasts belong to genera previously reported as common for Antarctic soils, but several other genera were also isolated, which contribute to the knowledge of this cold environment mycodiversity. The tolerance to heavy metals of the phenol-degrading cold-adapted yeasts illustrated that the strains could be valuable as inoculant for cold wastewater treatment in extremely cold environments.

Integument Mycobiota of Wild European Hedgehogs (Erinaceus europaeus) from Catalonia, Spain.

PubMed

Molina-López, R A; Adelantado, C; Arosemena, E L; Obón, E; Darwich, L; Calvo, M A

2012-01-01

There are some reports about the risk of manipulating wild hedgehogs since they can be reservoirs of potential zoonotic agents like dermatophytes. The aim of this study was to describe the integument mycobiota, with special attention to dermatophytes of wild European hedgehogs. Samples from spines and fur were cultured separately in Sabouraud dextrose agar (SDA) with antibiotic and dermatophyte test medium (DTM) plates. Nineteen different fungal genera were isolated from 91 cultures of 102 hedgehogs. The most prevalent genera were Cladosporium (79.1%), Penicillium (74.7%), Alternaria (64.8%), and Rhizopus (63.7%). A lower prevalence of Aspergillus (P = 0,035; χ (2) = 8,633) and Arthrinium (P = 0,043; χ (2) = 8,173) was isolated during the spring time and higher frequencies of Fusarium (P = 0,015; χ (2) = 10,533) during the autumn. The prevalence of Acremonium was significantly higher in young animals (70%, 26/37) than in adults (30%, 11/37) (P = 0,019; χ (2) = 5,915). Moreover, the majority of the saprophytic species that grew at the SDA culture were also detected at the DTM. Finally, no cases of ringworm were diagnosed and no dermatophytes spp. were isolated. Concluding, this study provides the first description of fungal mycobiota of the integument of wild European hedgehogs in Spain, showing a large number of saprophytic species and the absence of dermatophytes.

Integument Mycobiota of Wild European Hedgehogs (Erinaceus europaeus) from Catalonia, Spain

PubMed Central

Molina-López, R. A.; Adelantado, C.; Arosemena, E. L.; Obón, E.; Darwich, L.; Calvo, M. A.

2012-01-01

There are some reports about the risk of manipulating wild hedgehogs since they can be reservoirs of potential zoonotic agents like dermatophytes. The aim of this study was to describe the integument mycobiota, with special attention to dermatophytes of wild European hedgehogs. Samples from spines and fur were cultured separately in Sabouraud dextrose agar (SDA) with antibiotic and dermatophyte test medium (DTM) plates. Nineteen different fungal genera were isolated from 91 cultures of 102 hedgehogs. The most prevalent genera were Cladosporium (79.1%), Penicillium (74.7%), Alternaria (64.8%), and Rhizopus (63.7%). A lower prevalence of Aspergillus (P = 0,035; χ 2 = 8,633) and Arthrinium (P = 0,043; χ 2 = 8,173) was isolated during the spring time and higher frequencies of Fusarium (P = 0,015; χ 2 = 10,533) during the autumn. The prevalence of Acremonium was significantly higher in young animals (70%, 26/37) than in adults (30%, 11/37) (P = 0,019; χ 2 = 5,915). Moreover, the majority of the saprophytic species that grew at the SDA culture were also detected at the DTM. Finally, no cases of ringworm were diagnosed and no dermatophytes spp. were isolated. Concluding, this study provides the first description of fungal mycobiota of the integument of wild European hedgehogs in Spain, showing a large number of saprophytic species and the absence of dermatophytes. PMID:23762757

Phylogeny and bioactivity of epiphytic Gram-positive bacteria isolated from three co-occurring antarctic macroalgae.

PubMed

Alvarado, Pamela; Huang, Ying; Wang, Jian; Garrido, Ignacio; Leiva, Sergio

2018-02-19

Marine macroalgae are emerging as an untapped source of novel microbial diversity and, therefore, of new bioactive secondary metabolites. This study was aimed at assessing the diversity and antimicrobial activity of the culturable Gram-positive bacteria associated with the surface of three co-occurring Antarctic macroalgae. Specimens of Adenocystis utricularis (brown alga), Iridaea cordata (red alga) and Monostroma hariotii (green alga) were collected from the intertidal zone of King George Island, Antarctica. Gram-positive bacteria were investigated by cultivation-based methods and 16S rRNA gene sequencing, and screened for antimicrobial activity against a panel of pathogenic microorganisms. Isolates were found to belong to 12 families, with a dominance of Microbacteriaceae and Micrococcaceae. Seventeen genera of Actinobacteria and 2 of Firmicutes were cultured from the three macroalgae, containing 29 phylotypes. Three phylotypes within Actinobacteria were regarded as potentially novel species. Sixteen isolates belonging to the genera Agrococcus, Arthrobacter, Micrococcus, Pseudarthrobacter, Pseudonocardia, Sanguibacter, Staphylococcus, Streptomyces and Tessaracoccus exhibited antibiotic activity against at least one of the indicator strains. The bacterial phylotype composition was distinct among the three macroalgae species, suggesting that these macroalgae host species-specific Gram-positive associates. The results highlight the importance of Antarctic macroalgae as a rich source of Gram-positive bacterial diversity and potentially novel species, and a reservoir of bacteria producing biologically active compounds with pharmacological potential.

First report of a sexual state in an ambrosia fungus: Ambrosiella cleistominuta sp. nov. associated with the ambrosia beetle Anisandrus maiche

USDA-ARS?s Scientific Manuscript database

Genera of ambrosia beetles in the tribe Xyleborini with large, mesonotal mycangia host unique fungal symbionts in the genus Ambrosiella. The symbiont of a recent invasive to the USA from Asia, Anisandrus maiche, had not been previously characterized. We consistently isolated a novel fungus, Ambrosie...

Diversity patterns, ecology and biological activities of fungal communities associated with the endemic macroalgae across the Antarctic peninsula

Treesearch

Laura E. Furbino; Valaria M. Godinho; Iara F. Santiago; Franciane M. Pellizari; Tania M.A. Alves; Carlos L. Zani; Policarpo A.S. Junior; Alvaro J. Romanha; Amanda G.O. Carvalho; Laura H.V.G. Gil; Carlos A. Rosa; Andrew M. Minnis; Luiz H. Rosa

2014-01-01

We surveyed diversity patterns and engaged in bioprospecting for bioactive compounds of fungi associated with the endemic macroalgae, Monostroma hariotii and Pyropia endiviifolia, in Antarctica. A total of 239 fungal isolates were obtained, which were identified to represent 48 taxa and 18 genera using molecular methods. The fungal...

First report of Botryosphearia dothidea causing white rot on apple fruit in Maryland

USDA-ARS?s Scientific Manuscript database

Botryosphaeria dothidea [Fr. : Moug.] Ces. & De Not. infects over 80 genera of woody plants causing stem cankers on grapevine, apple, pear, and almond trees and also causes white rot on apple fruit in the field and during storage. A B. dothidea isolate was obtained from decayed ‘Fuji’ apple fruit ex...

Bacteria and Archaea in acidic environments and a key to morphological identification

USGS Publications Warehouse

Robbins, E.I.

2000-01-01

Natural and anthropogenic acidic environments are dominated by bacteria and Archaea. As many as 86 genera or species have been identified or isolated from pH <4.5 environments. This paper reviews the worldwide literature and provide tables of morphological characteristics, habitat information and a key for light microscope identification for the non-microbiologist.

A phylogenetic overview of the antrodia clade (Basidiomycota, Polyporales)

Treesearch

Beatriz Ortiz-Santana; Daniel L. Lindner; Otto Miettinen; Alfredo Justo; David S. Hibbett

2013-01-01

Phylogenetic relationships among members of the antrodia clade were investigated with molecular data from two nuclear ribosomal DNA regions, LSU and ITS. A total of 123 species representing 26 genera producing a brown rot were included in the present study. Three DNA datasets (combined LSU-ITS dataset, LSU dataset, ITS dataset) comprising sequences of 449 isolates were...

Microbial Degradation of Asphalt1

PubMed Central

Phillips, U. A.; Traxler, R. W.

1963-01-01

Organisms of the genera Pseudomonas, Chromobacterium, and Bacillus capable of degrading asphalt were isolated by enrichment cultures. The asphalt degradation by these organisms varied from 3 to 25% after incubation for 1 week. The effects of temperature, pH, and atmosphere of incubation on asphalt degradation were investigated and were shown to vary with different organisms on the same substrate. PMID:16349633

Occurrence, structure, and nitrogen-fixation of root nodules of actinorhizal Arizona alder

Treesearch

J. O. Dawson; Gerald J. Gottfried; D. Hahn

2005-01-01

Actinorhizal plants are nodulated by the symbiotic, nitrogen-fixing actinomycete Frankia. The genus Alnus in the family Betulaceae is one of the 24 genera in 8 families of angiospermous plants that are actinorhizal. Arizona alder (Alnus oblongifolia Torr.) occurs in isolated populations associated with the watersheds of Madrean Sky Islands in the...

Distribution of Cenozoic plant relicts in China explained by drought in dry season.

PubMed

Huang, Yongjiang; Jacques, Frédéric M B; Su, Tao; Ferguson, David K; Tang, Hui; Chen, Wenyun; Zhou, Zhekun

2015-09-15

Cenozoic plant relicts are those groups that were once widespread in the Northern Hemisphere but are now restricted to some small isolated areas as a result of drastic climatic changes. They are good proxies to study how plants respond to climatic changes since their modern climatic requirements are known. Herein we look at the modern distribution of 65 palaeoendemic genera in China and compare it with the Chinese climatic pattern, in order to find a link between the plant distribution and climate. Central China and Taiwan Island are shown to be diversity centres of Cenozoic relict genera, consistent with the fact that these two regions have a shorter dry season with comparatively humid autumn and spring in China. Species distribution models indicate that the precipitation parameters are the most important variables to explain the distribution of relict genera. The Cenozoic wide-scale distribution of relict plants in the Northern Hemisphere is therefore considered to be linked to the widespread humid climate at that time, and the subsequent contraction of their distributional ranges was probably caused by the drying trend along with global cooling.

Distribution of Cenozoic plant relicts in China explained by drought in dry season

PubMed Central

Huang, Yongjiang; Jacques, Frédéric M. B.; Su, Tao; Ferguson, David K.; Tang, Hui; Chen, Wenyun; Zhou, Zhekun

2015-01-01

Cenozoic plant relicts are those groups that were once widespread in the Northern Hemisphere but are now restricted to some small isolated areas as a result of drastic climatic changes. They are good proxies to study how plants respond to climatic changes since their modern climatic requirements are known. Herein we look at the modern distribution of 65 palaeoendemic genera in China and compare it with the Chinese climatic pattern, in order to find a link between the plant distribution and climate. Central China and Taiwan Island are shown to be diversity centres of Cenozoic relict genera, consistent with the fact that these two regions have a shorter dry season with comparatively humid autumn and spring in China. Species distribution models indicate that the precipitation parameters are the most important variables to explain the distribution of relict genera. The Cenozoic wide-scale distribution of relict plants in the Northern Hemisphere is therefore considered to be linked to the widespread humid climate at that time, and the subsequent contraction of their distributional ranges was probably caused by the drying trend along with global cooling. PMID:26369980

Bacterial communities in ancient permafrost profiles of Svalbard, Arctic.

PubMed

Singh, Purnima; Singh, Shiv M; Singh, Ram N; Naik, Simantini; Roy, Utpal; Srivastava, Alok; Bölter, Manfred

2017-12-01

Permafrost soils are unique habitats in polar environment and are of great ecological relevance. The present study focuses on the characterization of bacterial communities from permafrost profiles of Svalbard, Arctic. Counts of culturable bacteria range from 1.50 × 10 3 to 2.22 × 10 5 CFU g -1 , total bacterial numbers range from 1.14 × 10 5 to 5.52 × 10 5 cells g -1 soil. Bacterial isolates are identified through 16S rRNA gene sequencing. Arthrobacter and Pseudomonas are the most dominant genera, and A. sulfonivorans, A. bergeri, P. mandelii, and P. jessenii as the dominant species. Other species belong to genera Acinetobacter, Bacillus, Enterobacter, Nesterenkonia, Psychrobacter, Rhizobium, Rhodococcus, Sphingobacterium, Sphingopyxis, Stenotrophomonas, and Virgibacillus. To the best of our knowledge, genera Acinetobacter, Enterobacter, Nesterenkonia, Psychrobacter, Rhizobium, Sphingobacterium, Sphingopyxis, Stenotrophomonas, and Virgibacillus are the first northernmost records from Arctic permafrost. The present study fills the knowledge gap of culturable bacterial communities and their chronological characterization from permafrost soils of Ny-Ålesund (79°N), Arctic. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Identification and Removal of Contaminant Sequences From Ribosomal Gene Databases: Lessons From the Census of Deep Life

PubMed Central

Sheik, Cody S.; Reese, Brandi Kiel; Twing, Katrina I.; Sylvan, Jason B.; Grim, Sharon L.; Schrenk, Matthew O.; Sogin, Mitchell L.; Colwell, Frederick S.

2018-01-01

Earth’s subsurface environment is one of the largest, yet least studied, biomes on Earth, and many questions remain regarding what microorganisms are indigenous to the subsurface. Through the activity of the Census of Deep Life (CoDL) and the Deep Carbon Observatory, an open access 16S ribosomal RNA gene sequence database from diverse subsurface environments has been compiled. However, due to low quantities of biomass in the deep subsurface, the potential for incorporation of contaminants from reagents used during sample collection, processing, and/or sequencing is high. Thus, to understand the ecology of subsurface microorganisms (i.e., the distribution, richness, or survival), it is necessary to minimize, identify, and remove contaminant sequences that will skew the relative abundances of all taxa in the sample. In this meta-analysis, we identify putative contaminants associated with the CoDL dataset, recommend best practices for removing contaminants from samples, and propose a series of best practices for subsurface microbiology sampling. The most abundant putative contaminant genera observed, independent of evenness across samples, were Propionibacterium, Aquabacterium, Ralstonia, and Acinetobacter. While the top five most frequently observed genera were Pseudomonas, Propionibacterium, Acinetobacter, Ralstonia, and Sphingomonas. The majority of the most frequently observed genera (high evenness) were associated with reagent or potential human contamination. Additionally, in DNA extraction blanks, we observed potential archaeal contaminants, including methanogens, which have not been discussed in previous contamination studies. Such contaminants would directly affect the interpretation of subsurface molecular studies, as methanogenesis is an important subsurface biogeochemical process. Utilizing previously identified contaminant genera, we found that ∼27% of the total dataset were identified as contaminant sequences that likely originate from DNA extraction and DNA cleanup methods. Thus, controls must be taken at every step of the collection and processing procedure when working with low biomass environments such as, but not limited to, portions of Earth’s deep subsurface. Taken together, we stress that the CoDL dataset is an incredible resource for the broader research community interested in subsurface life, and steps to remove contamination derived sequences must be taken prior to using this dataset. PMID:29780369

Identification and Removal of Contaminant Sequences From Ribosomal Gene Databases: Lessons From the Census of Deep Life.

PubMed

Sheik, Cody S; Reese, Brandi Kiel; Twing, Katrina I; Sylvan, Jason B; Grim, Sharon L; Schrenk, Matthew O; Sogin, Mitchell L; Colwell, Frederick S

2018-01-01

Earth's subsurface environment is one of the largest, yet least studied, biomes on Earth, and many questions remain regarding what microorganisms are indigenous to the subsurface. Through the activity of the Census of Deep Life (CoDL) and the Deep Carbon Observatory, an open access 16S ribosomal RNA gene sequence database from diverse subsurface environments has been compiled. However, due to low quantities of biomass in the deep subsurface, the potential for incorporation of contaminants from reagents used during sample collection, processing, and/or sequencing is high. Thus, to understand the ecology of subsurface microorganisms (i.e., the distribution, richness, or survival), it is necessary to minimize, identify, and remove contaminant sequences that will skew the relative abundances of all taxa in the sample. In this meta-analysis, we identify putative contaminants associated with the CoDL dataset, recommend best practices for removing contaminants from samples, and propose a series of best practices for subsurface microbiology sampling. The most abundant putative contaminant genera observed, independent of evenness across samples, were Propionibacterium , Aquabacterium , Ralstonia , and Acinetobacter . While the top five most frequently observed genera were Pseudomonas , Propionibacterium , Acinetobacter , Ralstonia , and Sphingomonas . The majority of the most frequently observed genera (high evenness) were associated with reagent or potential human contamination. Additionally, in DNA extraction blanks, we observed potential archaeal contaminants, including methanogens, which have not been discussed in previous contamination studies. Such contaminants would directly affect the interpretation of subsurface molecular studies, as methanogenesis is an important subsurface biogeochemical process. Utilizing previously identified contaminant genera, we found that ∼27% of the total dataset were identified as contaminant sequences that likely originate from DNA extraction and DNA cleanup methods. Thus, controls must be taken at every step of the collection and processing procedure when working with low biomass environments such as, but not limited to, portions of Earth's deep subsurface. Taken together, we stress that the CoDL dataset is an incredible resource for the broader research community interested in subsurface life, and steps to remove contamination derived sequences must be taken prior to using this dataset.

Exploring the Diversity and Antimicrobial Potential of Marine Actinobacteria from the Comau Fjord in Northern Patagonia, Chile

PubMed Central

Undabarrena, Agustina; Beltrametti, Fabrizio; Claverías, Fernanda P.; González, Myriam; Moore, Edward R. B.; Seeger, Michael; Cámara, Beatriz

2016-01-01

Bioprospecting natural products in marine bacteria from fjord environments are attractive due to their unique geographical features. Although, Actinobacteria are well known for producing a myriad of bioactive compounds, investigations regarding fjord-derived marine Actinobacteria are scarce. In this study, the diversity and biotechnological potential of Actinobacteria isolated from marine sediments within the Comau fjord, in Northern Chilean Patagonia, were assessed by culture-based approaches. The 16S rRNA gene sequences revealed that members phylogenetically related to the Micrococcaceae, Dermabacteraceae, Brevibacteriaceae, Corynebacteriaceae, Microbacteriaceae, Dietziaceae, Nocardiaceae, and Streptomycetaceae families were present at the Comau fjord. A high diversity of cultivable Actinobacteria (10 genera) was retrieved by using only five different isolation media. Four isolates belonging to Arthrobacter, Brevibacterium, Corynebacterium and Kocuria genera showed 16S rRNA gene identity <98.7% suggesting that they are novel species. Physiological features such as salt tolerance, artificial sea water requirement, growth temperature, pigmentation and antimicrobial activity were evaluated. Arthrobacter, Brachybacterium, Curtobacterium, Rhodococcus, and Streptomyces isolates showed strong inhibition against both Gram-negative Pseudomonas aeruginosa, Escherichia coli and Salmonella enterica and Gram-positive Staphylococcus aureus, Listeria monocytogenes. Antimicrobial activities in Brachybacterium, Curtobacterium, and Rhodococcus have been scarcely reported, suggesting that non-mycelial strains are a suitable source of bioactive compounds. In addition, all strains bear at least one of the biosynthetic genes coding for NRPS (91%), PKS I (18%), and PKS II (73%). Our results indicate that the Comau fjord is a promising source of novel Actinobacteria with biotechnological potential for producing biologically active compounds. PMID:27486455

Serovars, bacteriophage types and antimicrobial sensitivities associated with salmonellosis in dogs in the UK (1954-2012).

PubMed

Philbey, A W; Mather, H A; Gibbons, J F; Thompson, H; Taylor, D J; Coia, J E

2014-01-25

Serovars and bacteriophage (phage) types were determined for 442 isolates of Salmonella enterica from dogs in the UK submitted to the Scottish Salmonella Reference Laboratory from 1954 to 2012. The most frequent serovars were Salmonella Typhimurium (196 isolates; 44.3 per cent), Dublin (40 isolates; 9.0 per cent), Enteritidis (28 isolates; 6.3 per cent), Montevideo (19 isolates; 4.3 per cent), Virchow (10 isolates; 2.3 per cent), Heidelberg (8 isolates; 1.8 per cent) and Derby (8 isolates; 1.8 per cent), along with 55 other recognised serovars among 127 other isolates, and six incompletely classified isolates. Serovars were frequently represented by strains commonly associated with poultry, cattle or pigs and their products. Among 196 Salmonella Typhimurium isolates from dogs, the most frequent phage types (definitive types) were the multiple antimicrobial-resistant strains DT104 (62 isolates), DT204c (18 isolates) and DT193 (8 isolates), along with antimicrobial sensitive wild finch strains DT40 (13 isolates) and DT56 variant (8 isolates). Eleven of 28 isolates of Salmonella Enteritidis were phage type 4. S enterica was frequently recovered from faecal or intestinal samples of dogs with diarrhoea, although many dogs had concurrent infection with other enteric pathogens. Salmonella Dublin was recovered from the brain and/or cerebrospinal fluid of two dogs with meningoencephalitis. Salmonella Kedougou was isolated from the joint fluid of a dog with septic arthritis. Salmonella Typhimurium and Salmonella Dublin were each recovered from the vaginas of bitches that had aborted. Isolates of Salmonella Enteritidis phage types 1, 4 and 8, Salmonella Typhimurium DT104, Salmonella Dublin and Salmonella Indiana were isolated from clinically healthy dogs in households where the same strains were recovered from human beings with diarrhoea. The pattern ampicillin-chloramphenicol-spectinomycin-streptomycin-sulfamethoxazole-tetracycline (ACSpSSuT) was the most frequent resistance phenotype and was observed in 44 (13.3 per cent) of 330 isolates. Dogs in the UK are exposed to a wide variety of serovars of S enterica, sometimes associated with clinical disease, and represent a zoonotic risk.

Diversity of Bacillus-like bacterial community in the rhizospheric and non-rhizospheric soil of halophytes (Salsola stocksii and Atriplex amnicola) and characterization of osmoregulatory genes in halophilic Bacilli.

PubMed

Mukhtar, Salma; Mehnaz, Samina; Mirza, Muhammad Sajjad; Mirza, Babur Saeed; Malik, Kauser Abdulla

2018-04-27

Salinity is one of the major abiotic stresses, with a total of 3% of the world's land mass being affected by salinity. Approximately 6.3 million hectares of land in Pakistan is affected by salinity to varying degree and most of the areas are arid to semiarid with low annual precipitation. The aim of present study is to identify and characterize Bacillus and Bacillus-derived bacterial genera from the rhizospheric and non-rhizospheric soil samples from Khewra Salt Mine, Pakistan by using culture-independent as well as culture-dependent methods. Seven Bacillus-like bacterial genera Bacillus, Halobacillus, Virgibacillus, Brevibacillus, Paenibacillus, Tumebacillus and Lysinibacillus were detected by using pyrosequencing analysis whereas only four genera Bacillus, Halobacillus, Oceanobacillus and Virgibacillus were identified by culture-dependent methods. Most of Bacillus-like isolates identified in this study were moderately halophilic, alkaliphilic and mesophilic bacteria and were considered as a good source of hydrolytic enzymes because of their ability to degrade proteins, carbohydrates and lipids. Eight Bacillus-like strains from the genera Bacillus, Halobacillus, Oceanobacillus and Virgibacillus showed positive results for the presence of ectABC gene cluster (ectoine), six strains could synthesize betaine from choline and six strains tested positive for the synthesis of proline from either glutamate or ornithine by using proline dehydrogenase enzyme.

Trichocomaceae: biodiversity of Aspergillus spp and Penicillium spp residing in libraries.

PubMed

Leite, Diniz Pereira; Yamamoto, Ana Caroline Akeme; Amadio, Janaína Vasconcellos Ribeiro de Souza; Martins, Evelin Rodrigues; do Santos, Fábio Alexandre Leal; Simões, Sara de Almeida Alves; Hahn, Rosane Christine

2012-10-19

Atmospheric air is the most common vehicle for the dispersion of fungi. Fungi belonging to the genera Aspergillus and Penicillium are cosmopolitan and are classified in the family Trichocomaceae. Species of the genera are commonly found in soil, decaying organic materials, animal feed, stored grains, and other materials. This study aimed to determine the taxonomic diversity of airborne fungi of the genera Aspergillus and Penicillium residing in the dust of library environments to contribute to current knowledge of these characteristic genera. Three libraries in the city of Cuiaba, State of Mato Grosso, Brazil, were selected as the study areas. A total of 168 samples were collected at randomized sites within each library in areas containing journals, archives, in study rooms, and in collection storage areas in two different periods, the dry season (n = 42)  and the rainy season (n = 42). Samples were collected by exposing Petri dishes containing Sabouraud agar with chloramphenicol to the environmental air. Additional samples were collected with sterile swabs which were rubbed over the surface of randomly chosen books on the shelves; the swabs were subsequently incubated in the laboratory. The genus Aspergillus was highlighted as one of the principal airborne fungi present in indoor environments. Aspergillus spp was identified in 1,277 (89.6%) samples and Penicillium spp in 148 (10.4%). The dry period exhibited a greater number of isolates of the two taxons.

Characterization of Epiphytic Bacterial Communities from Grapes, Leaves, Bark and Soil of Grapevine Plants Grown, and Their Relations

PubMed Central

Martins, Guilherme; Lauga, Béatrice; Miot-Sertier, Cécile; Mercier, Anne; Lonvaud, Aline; Soulas, Marie-Louise; Soulas, Guy; Masneuf-Pomarède, Isabelle

2013-01-01

Despite its importance in plant health and crop quality, the diversity of epiphytic bacteria on grape berries and other plant parts, like leaves and bark, remains poorly described, as does the role of telluric bacteria in plant colonization. In this study, we compare the bacterial community size and structure in vineyard soils, as well as on grapevine bark, leaves and berries. Analyses of culturable bacteria revealed differences in the size and structure of the populations in each ecosystem. The highest bacteria population counts and the greatest diversity of genera were found in soil samples, followed by bark, grapes and leaves. The identification of isolates revealed that some genera – Pseudomonas, Curtobacterium, and Bacillus – were present in all ecosystems, but in different amounts, while others were ecosystem-specific. About 50% of the genera were common to soil and bark, but absent from leaves and grapes. The opposite was also observed: grape and leaf samples presented 50% of genera in common that were absent from trunk and soil. The bacterial community structure analyzed by T-RFLP indicated similarities between the profiles of leaves and grapes, on the one hand, and bark and soil, on the other, reflecting the number of shared T-RFs. The results suggest an interaction between telluric bacterial communities and the epiphytic bacteria present on the different grapevine parts. PMID:24023666

Inheritance and Establishment of Gut Microbiota in Chickens

PubMed Central

Ding, Jinmei; Dai, Ronghua; Yang, Lingyu; He, Chuan; Xu, Ke; Liu, Shuyun; Zhao, Wenjing; Xiao, Lu; Luo, Lingxiao; Zhang, Yan; Meng, He

2017-01-01

In mammals, the microbiota can be transmitted from the placenta, uterus, and vagina of the mother to the infant. Unlike mammals, development of the avian embryo is a process isolated from the mother and thus in the avian embryo the gut microbial developmental process remains elusive. To explore the establishment and inheritance of the gut microbiome in the avian embryo, we used the chicken as the model organism to investigate the gut microbial composition in embryos, chicks, and maternal hens. We observed: (1) 28 phyla and 162 genera of microbes in embryos where the dominated genus was Halomonas (79%). (2) 65 genera were core microbiota in all stages with 42% and 62% gut microbial genera of embryo were found in maternal hen and chick, respectively. There was a moderate correlation (0.40) between the embryo and maternal, and 0.52 between the embryo and chick at the family level. (3) Gut microbes that are involved in substance metabolism, infectious disease, and environmental adaptation are enriched in embryos, chicks, and maternal hens, respectively. (4) 94% genera of gut microbial composition were similar among three different chicken breeds which were maintained under similar conditions. Our findings provide evidence to support the hypothesis that part of the microbial colonizers harbored in early embryos were inherited from maternal hens, and the gut microbial abundance and diversity were influenced by environmental factors and host genetic variation during development. PMID:29067020

Esculin-based medium for isolation and identification of Cryptococcus neoformans.

PubMed Central

Edberg, S C; Chaskes, S J; Alture-Werber, E; Singer, J M

1980-01-01

A simple medium was developed, using esculin as the substrate, for the isolation and identification of Cryptococcus neoformans. C. neoformans produced a brown-black pigment on the medium; all other yeasts produced no pigment or were light yellow. Esculin is beta-glucose-6,7-dihydroxycoumarin. C. neoformans produced pigment because the 6,7-dihydroxycoumarin component of the esculin molecule was converted to a melanin-like pigment. We think the reaction was similar to the conversion of diphenols, aminophenols, and diaminobenzenes to melanin. Laboratory studies with isolates of C. neoformans, C. albidus, C. luteolus, and C. terreus and representatives of the genera Candida, Torulopsis, Geotrichum, and Rhodotorula, plus environmental field studies, demonstrated that over 95% of C. neoformans isolates were correctly identified, whereas all other fungi were excluded. Esculin agar was a sensitive, specific medium for the isolation and identification of C. neoformans. It was inexpensive and had a long storage life. Images PMID:7012169

Viability and molecular authentication of Coccidioides spp. isolates from the Instituto de Medicina Tropical de São Paulo culture collection, Brazil.

PubMed

Cavalcanti, Sarah Desirée Barbosa; Vidal, Mônica Scarpelli Martinelli; Sousa, Maria da Glória Teixeira de; Del Negro, Gilda Maria Barbaro

2013-01-01

Coccidioidomycosis is an emerging fungal disease in Brazil; adequate maintenance and authentication of Coccidioides isolates are essential for research into genetic diversity of the environmental organisms, as well as for understanding the human disease. Seventeen Coccidioides isolates maintained under mineral oil since 1975 in the Instituto de Medicina Tropical de São Paulo (IMTSP) culture collection, Brazil, were evaluated with respect to their viability, morphological characteristics and genetic features in order to authenticate these fungal cultures. Only five isolates were viable after almost 30 years, showing typical morphological characteristics, and sequencing analysis using Coi-F and Coi-R primers revealed 99% identity with Coccidioides genera. These five isolates were then preserved in liquid nitrogen and sterile water, and remained viable after two years of storage under these conditions, maintaining the same features.

Novel nuclei isolation buffer for flow cytometric genome size estimation of Zingiberaceae: a comparison with common isolation buffers

PubMed Central

Sadhu, Abhishek; Bhadra, Sreetama; Bandyopadhyay, Maumita

2016-01-01

Background and Aims Cytological parameters such as chromosome numbers and genome sizes of plants are used routinely for studying evolutionary aspects of polyploid plants. Members of Zingiberaceae show a wide range of inter- and intrageneric variation in their reproductive habits and ploidy levels. Conventional cytological study in this group of plants is severely hampered by the presence of diverse secondary metabolites, which also affect their genome size estimation using flow cytometry. None of the several nuclei isolation buffers used in flow cytometry could be used very successfully for members of Zingiberaceae to isolate good quality nuclei from both shoot and root tissues. Methods The competency of eight nuclei isolation buffers was compared with a newly formulated buffer, MB01, in six different genera of Zingiberaceae based on the fluorescence intensity of propidium iodide-stained nuclei using flow cytometric parameters, namely coefficient of variation of the G0/G1 peak, debris factor and nuclei yield factor. Isolated nuclei were studied using fluorescence microscopy and bio-scanning electron microscopy to analyse stain–nuclei interaction and nuclei topology, respectively. Genome contents of 21 species belonging to these six genera were determined using MB01. Key Results Flow cytometric parameters showed significant differences among the analysed buffers. MB01 exhibited the best combination of analysed parameters; photomicrographs obtained from fluorescence and electron microscopy supported the superiority of MB01 buffer over other buffers. Among the 21 species studied, nuclear DNA contents of 14 species are reported for the first time. Conclusions Results of the present study substantiate the enhanced efficacy of MB01, compared to other buffers tested, in the generation of acceptable cytograms from all species of Zingiberaceae studied. Our study facilitates new ways of sample preparation for further flow cytometric analysis of genome size of other members belonging to this highly complex polyploid family. PMID:27594649

Novel nuclei isolation buffer for flow cytometric genome size estimation of Zingiberaceae: a comparison with common isolation buffers.

PubMed

Sadhu, Abhishek; Bhadra, Sreetama; Bandyopadhyay, Maumita

2016-11-01

Cytological parameters such as chromosome numbers and genome sizes of plants are used routinely for studying evolutionary aspects of polyploid plants. Members of Zingiberaceae show a wide range of inter- and intrageneric variation in their reproductive habits and ploidy levels. Conventional cytological study in this group of plants is severely hampered by the presence of diverse secondary metabolites, which also affect their genome size estimation using flow cytometry. None of the several nuclei isolation buffers used in flow cytometry could be used very successfully for members of Zingiberaceae to isolate good quality nuclei from both shoot and root tissues. The competency of eight nuclei isolation buffers was compared with a newly formulated buffer, MB01, in six different genera of Zingiberaceae based on the fluorescence intensity of propidium iodide-stained nuclei using flow cytometric parameters, namely coefficient of variation of the G 0 /G 1 peak, debris factor and nuclei yield factor. Isolated nuclei were studied using fluorescence microscopy and bio-scanning electron microscopy to analyse stain-nuclei interaction and nuclei topology, respectively. Genome contents of 21 species belonging to these six genera were determined using MB01. Flow cytometric parameters showed significant differences among the analysed buffers. MB01 exhibited the best combination of analysed parameters; photomicrographs obtained from fluorescence and electron microscopy supported the superiority of MB01 buffer over other buffers. Among the 21 species studied, nuclear DNA contents of 14 species are reported for the first time. Results of the present study substantiate the enhanced efficacy of MB01, compared to other buffers tested, in the generation of acceptable cytograms from all species of Zingiberaceae studied. Our study facilitates new ways of sample preparation for further flow cytometric analysis of genome size of other members belonging to this highly complex polyploid family. © The Author 2016. Published by Oxford University Press on behalf of the Annals of Botany Company. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

Seasonal and regional diversity of maple sap microbiota revealed using community PCR fingerprinting and 16S rRNA gene clone libraries.

PubMed

Filteau, Marie; Lagacé, Luc; LaPointe, Gisèle; Roy, Denis

2010-04-01

An arbitrary primed community PCR fingerprinting technique based on capillary electrophoresis was developed to study maple sap microbial community characteristics among 19 production sites in Québec over the tapping season. Presumptive fragment identification was made with corresponding fingerprint profiles of bacterial isolate cultures. Maple sap microbial communities were subsequently compared using a representative subset of 13 16S rRNA gene clone libraries followed by gene sequence analysis. Results from both methods indicated that all maple sap production sites and flow periods shared common microbiota members, but distinctive features also existed. Changes over the season in relative abundance of predominant populations showed evidence of a common pattern. Pseudomonas (64%) and Rahnella (8%) were the most abundantly and frequently represented genera of the 2239 sequences analyzed. Janthinobacterium, Leuconostoc, Lactococcus, Weissella, Epilithonimonas and Sphingomonas were revealed as occasional contaminants in maple sap. Maple sap microbiota showed a low level of deep diversity along with a high variation of similar 16S rRNA gene sequences within the Pseudomonas genus. Predominance of Pseudomonas is suggested as a typical feature of maple sap microbiota across geographical regions, production sites, and sap flow periods.

A new genus and species of micro bee fly from the Earliest Eocene French amber (Diptera: Mythicomyiidae: Psiloderoidinae).

PubMed

Myskowiak, Justine; Garrouste, Romain; Nel, Andre

2016-05-26

Mythicomyiidae, or micro bee flies, are tiny flies (0.5-5.0 mm) that are found throughout most parts of the world except the highest altitudes and latitudes (Greathead & Evenhuis 2001). Including all extinct and extant taxa, the Mythicomyiidae currently comprise more than 380 valid taxonomic species distributed among 30 genera. The subfamily Psiloderoidinae is especially well represented among the fossil Mythicomyiidae by seven Cretaceous or Cenozoic genera. We here describe a new genus and a new species of this subfamily based on fossils from the Earliest Eocene of Oise (France). A Psiloderoidinae, Proplatypygus matilei Nel & DePloëg, 2004, is already described in this amber. Another mythicomyiid, Eurodoliopteryx inexpectatus Nel, 2006, is the most frequent bombylioid in this amber (Nel & DePloëg, 2004; Nel, 2006).

Comparative genetics of disease resistance within the solanaceae.

PubMed Central

Grube, R C; Radwanski, E R; Jahn, M

2000-01-01

Genomic positions of phenotypically defined disease resistance genes (R genes) and R gene homologues were analyzed in three solanaceous crop genera, Lycopersicon (tomato), Solanum (potato), and Capsicum (pepper). R genes occurred at corresponding positions in two or more genomes more frequently than expected by chance; however, in only two cases, both involving Phytophthora spp., did genes at corresponding positions have specificity for closely related pathogen taxa. In contrast, resistances to Globodera spp., potato virus Y, tobacco mosaic virus, and tomato spotted wilt virus were mapped in two or more genera and did not occur in corresponding positions. Without exception, pepper homologues of the cloned R genes Sw-5, N, Pto, Prf, and I2 were found in syntenous positions in other solanaceous genomes and in some cases also mapped to additional positions near phenotypically defined solanaceous R genes. This detailed analysis and synthesis of all available data for solanaceous R genes suggests a working hypothesis regarding the evolution of R genes. Specifically, while the taxonomic specificity of host R genes may be evolving rapidly, general functions of R alleles (e.g., initiation of resistance response) may be conserved at homologous loci in related plant genera. PMID:10835406

Differential Response of Coral Assemblages to Thermal Stress Underscores the Complexity in Predicting Bleaching Susceptibility

PubMed Central

Toh, Kok Ben; Ng, Chin Soon Lionel; Cabaitan, Patrick; Tun, Karenne; Goh, Eugene; Afiq-Rosli, Lutfi; Taira, Daisuke; Du, Rosa Celia Poquita; Loke, Hai Xin; Khalis, Aizat; Li, Jinghan; Song, Tiancheng

2016-01-01

Coral bleaching events have been predicted to occur more frequently in the coming decades with global warming. The susceptibility of corals to bleaching during thermal stress episodes is dependent on many factors and an understanding of these underlying drivers is crucial for conservation management. In 2013, a mild bleaching episode ensued in response to elevated sea temperature on the sediment-burdened reefs in Singapore. Surveys of seven sites highlighted variable bleaching susceptibility among coral genera–Pachyseris and Podabacia were the most impacted (31% of colonies of both genera bleached). The most susceptible genera such as Acropora and Pocillopora, which were expected to bleach, did not. Susceptibility varied between less than 6% and more than 11% of the corals bleached, at four and three sites respectively. Analysis of four of the most bleached genera revealed that a statistical model that included a combination of the factors (genus, colony size and site) provided a better explanation of the observed bleaching patterns than any single factor alone. This underscored the complexity in predicting the coral susceptibility to future thermal stress events and the importance of monitoring coral bleaching episodes to facilitate more effective management of coral reefs under climate change. PMID:27438593

Fungal flora associated with combine harvester wheat and sorghum dusts from Egypt.

PubMed

Abdel-Hafez, S I; Moubasher, A H; Shoreit, A A; Ismail, M A

1990-01-01

107 species and 8 species varieties belonging to 44 genera were collected from combine harvester wheat and sorghum dusts (35 genera and 91 species + 4 varieties) and from the atmosphere of their hay sites (26 genera and 69 species + 4 varieties) on glucose- and cellulose-Czapek's Dox agar at 28 degrees C and 45 degrees C. The mycoflora of wheat and sorghum dusts were basically similar on the two types of media and the most common fungi were: Alternaria alternata, Aspergillus flavus, A. fumigatus, A. niger, A. ochraceus, A. sydowii, A. terreus, Cochliobolus spicifer, Emericella nidulans, Fusarium moniliforme, Penicillium chrysogenum, P. duclauxii, P. funiculosum and P. oxalicum. Truly thermophilic species were frequently encountered from the two substrates: Chaetomium thermophilum, Humicola grisea var. thermoidae, H. insolens, Malbranchea pulchella var., sulphurea, Rhizomucor pusillus, Sporotrichum thermophilum, Talaromyces thermophilus, Thermoascus thermophilus and Thermomyces lanuginosus. The airborne fungi in the two atmospheres were basically similar and the most prevalent species were members of Alternaria (1 species), Aspergillus (18 species + 2 varieties), Chaetomium (2 species), Cochliobolus(3 species), Emericella (3 species + 2 varieties), Fusarium (3 species), Mucor (1 species), Penicillium (14 species) and Stachybotrys (1 species).

Persistence of microbial communities including Pseudomonas aeruginosa in a hospital environment: a potential health hazard

PubMed Central

2014-01-01

Background The persistence of microbial communities and how they change in indoor environments is of immense interest to public health. Moreover, hospital acquired infections are significant contributors to morbidity and mortality. Evidence suggests that, in hospital environments agent transfer between surfaces causes healthcare associated infections in humans, and that surfaces are an important transmission route and may act as a reservoir for some of the pathogens. This study aimed to evaluate the diversity of microorganisms that persist on noncritical equipment and surfaces in a main hospital in Portugal, and are able to grow in selective media for Pseudomonas, and relate them with the presence of Pseudomonas aeruginosa. Results During 2 years, a total of 290 environmental samples were analyzed, in 3 different wards. The percentage of equipment in each ward that showed low contamination level varied between 22% and 38%, and more than 50% of the equipment sampled was highly contaminated. P. aeruginosa was repeatedly isolated from sinks (10 times), from the taps’ biofilm (16 times), and from the showers and bedside tables (two times). Two ERIC clones were isolated more than once. The contamination level of the different taps analyzed showed correlation with the contamination level of the hand gels support, soaps and sinks. Ten different bacteria genera were frequently isolated in the selective media for Pseudomonas. Organisms usually associated with nosocomial infections as Stenotrophomonas maltophilia, Enterococcus feacalis, Serratia nematodiphila were also repeatedly isolated on the same equipment. Conclusions The environment may act as a reservoir for at least some of the pathogens implicated in nosocomial infections. The bacterial contamination level was related to the presence of humidity on the surfaces, and tap water (biofilm) was a point of dispersion of bacterial species, including potentially pathogenic organisms. The materials of the equipment sampled could not be related to the microbial contamination level. The presence of a disinfectant in the isolation medium suggests that the number of microorganism in the environment could be higher and shows the diversity of disinfectant resistant species. The statistical analysis suggests that the presence of bacteria could increase the risk of transmission by hand manipulation. PMID:24885173

Diversity of proteolytic microbes isolated from Antarctic freshwater lakes and characteristics of their cold-active proteases

NASA Astrophysics Data System (ADS)

Matsui, Mihoko; Kawamata, Akinori; Kosugi, Makiko; Imura, Satoshi; Kurosawa, Norio

2017-09-01

Despite being an extreme environment, the water temperature of freshwater lakes in Antarctica reaches 10 °C in summer, accelerating biological activity. In these environments, proteolytic microbial decomposers may play a large role in protein hydrolysis. We isolated 71 microbial strains showing proteolytic activity at 4 °C from three Antarctic freshwater lakes. They were classified as bacteria (63 isolates) and eukaryotes (8 isolates). The bacterial isolates were classified into the genera Flavobacterium (28 isolates), Pseudomonas (14 isolates), Arthrobacter (10 isolates), Psychrobacter (7 isolates), Cryobacterium (2 isolates), Hymenobacter (1 isolate), and Polaromonas (1 isolate). Five isolates of Flavobacterium and one of Hymenobacter seemed to belong to novel species. All eukaryotic isolates belonged to Glaciozyma antarctica, a psychrophilic yeast species originally isolated from the Weddell Sea near the Joinville Island, Antarctica. A half of representative strains were psychrophilic and did not grow at temperatures above 25 °C. The protease secreted by Pseudomonas prosekii strain ANS4-1 showed the highest activity among all proteases from representative isolates. The results of inhibitor tests indicated that nearly all the isolates secreted metalloproteases. Proteases from four representative isolates retained more than 30% maximal activity at 0 °C. These results expand our knowledge about microbial protein degradation in Antarctic freshwater lakes.

Cultured bacterial diversity and human impact on alpine glacier cryoconite.

PubMed

Lee, Yung Mi; Kim, So-Yeon; Jung, Jia; Kim, Eun Hye; Cho, Kyeung Hee; Schinner, Franz; Margesin, Rosa; Hong, Soon Gyu; Lee, Hong Kum

2011-06-01

The anthropogenic effect on the microbial communities in alpine glacier cryoconites was investigated by cultivation and physiological characterization of bacteria from six cryoconite samples taken at sites with different amounts of human impact. Two hundred and forty seven bacterial isolates were included in Actinobacteria (9%, particularly Arthrobacter), Bacteroidetes (14%, particularly Olleya), Firmicutes (0.8%), Alphaproteobacteria (2%), Betaproteobacteria (16%, particularly Janthinobacterium), and Gammaproteobacteria (59%, particularly Pseudomonas). Among them, isolates of Arthrobacter were detected only in samples from sites with no human impact, while isolates affiliated with Enterobacteriaceae were detected only in samples from sites with strong human impact. Bacterial isolates included in Actinobacteria and Bacteroidetes were frequently isolated from pristine sites and showed low maximum growth temperature and enzyme secretion. Bacterial isolates included in Gammaproteobacteria were more frequently isolated from sites with stronger human impact and showed high maximum growth temperature and enzyme secretion. Ecotypic differences were not evident among isolates of Janthinobacterium lividum, Pseudomonas fluorescens, and Pseudomonas veronii, which were frequently isolated from sites with different degrees of anthropogenic effect.

Bacteriology of the teeth from a great white shark: potential medical implications for shark bite victims.

PubMed Central

Buck, J D; Spotte, S; Gadbaw, J J

1984-01-01

Bacteria were cultured for the first time from the teeth of a great white shark (Carcharodon carcharias). Isolates included Vibrio alginolyticus, Vibrio fluvialis, Vibrio parahaemolyticus, and other genera. All are common in the marine environment and some may be associated with wound infections in humans. Shark bite lacerations may serve as a source of these potentially infectious bacteria, particularly Vibrio spp., and should be treated immediately. Antibiotic susceptibility patterns are shown for representatives of Vibrio isolates and indicate that a variety of new agents may be appropriate chemotherapy for shark bite victims. PMID:6511869

Description of Paralactobacillus selangorensis gen. nov., sp. nov., a new lactic acid bacterium isolated from chili bo, a Malaysian food ingredient.

PubMed

Leisner, J J; Vancanneyt, M; Goris, J; Christensen, H; Rusul, G

2000-01-01

Paralactobacillus selangorensis gen. nov., sp. nov. is described. This organism, isolated from a Malaysian food ingredient called chili bo, is an obligatory homofermentative, rod-shaped lactic acid bacterium. The G+C content is 46.1-46.2+/-0.3 mol%. Earlier 16S rRNA studies showed that this organism constitutes a new taxon distantly related to the Lactobacillus casei-Pediococcus group. A phenotypic description that distinguishes Paralactobacillus selangorensis from other genera of lactic acid bacteria is presented. The type strain of Paralactobacillus selangorensis is LMG 17710T.

Bacteriology of the teeth from a great white shark: potential medical implications for shark bite victims.

PubMed

Buck, J D; Spotte, S; Gadbaw, J J

1984-11-01

Bacteria were cultured for the first time from the teeth of a great white shark (Carcharodon carcharias). Isolates included Vibrio alginolyticus, Vibrio fluvialis, Vibrio parahaemolyticus, and other genera. All are common in the marine environment and some may be associated with wound infections in humans. Shark bite lacerations may serve as a source of these potentially infectious bacteria, particularly Vibrio spp., and should be treated immediately. Antibiotic susceptibility patterns are shown for representatives of Vibrio isolates and indicate that a variety of new agents may be appropriate chemotherapy for shark bite victims.

Bacteria Responsible for Mucilage-Layer Decomposition in Kona Coffee Cherries1

PubMed Central

Frank, Hilmer A.; Lum, Norma A.; Cruz, Amy S. Dela

1965-01-01

The predominant microbial flora present during decomposition of the mucilage layer of Kona coffee cherries were gram-negative bacteria which fermented lactose rapidly. Cultures isolated from coffee cherries under-going fermentation included species of Erwinia, Paracolobactrum, and Escherichia. Unblemished cherry surfaces and coffee plantation soil also had a microflora containing a high proportion of bacteria belonging to these three genera. Of 168 isolates tested, the 44 strains capable of demucilaging depulped coffee cherries were all members of Erwinia dissolvens. Supernatant growth medium liquids, after removal of E. dissolvens cells, actively decomposed the mucilage layer of depulped cherries. PMID:14325879

Description of Martiniozyma gen. nov. and transfer of seven Candida species to Saturnispora as new combinations

USDA-ARS?s Scientific Manuscript database

DNA sequence analysis has shown Candida abiesophila (NRRL Y-11514T, CBS 5366T) and Candida asiatica (NRRL Y-63747T, CBS 10863T) to be members of a small clade that is phylogenetically separate from other yeasts. In view of their isolation from neighboring genera, such as Pichia and Saturnispora, the...

Diversity and physiology of polyhydroxyalkanoate-producing and -degrading strains in microbial mats.

PubMed

Villanueva, Laura; Del Campo, Javier; Guerrero, Ricardo

2010-10-01

Photosynthetic microbial mats are sources of microbial diversity and physiological strategies that reflect the physical and metabolic interactions between their resident species. This study focused on the diversity and activity of polyhydroxyalkanoate-producing and -degrading bacteria and their close partnership with cyanobacteria in an estuarine and a hypersaline microbial mat. The aerobic heterotrophic population was characterized on the basis of lipid biomarkers (respiratory quinones, sphingoid bases), polyhydroxyalkanoate determination, biochemical analysis of the isolates, and interaction assays. Most of the polyhydroxyalkanoate-producing isolates obtained from an estuarine mat belonged to the Halomonas and Labrenzia genera, while species of Sphingomonas and Bacillus were more prevalent in the hypersaline mat. Besides, the characterization of heterotrophic bacteria coisolated with filamentous cyanobacteria after selection suggested a specific association between them and diversification of the heterotrophic partner belonging to the Halomonas genus. Preliminary experiments suggested that syntrophic associations between strains of the Pseudoalteromonas and Halomonas genera explain the dynamics of polyhydroxyalkanoate accumulation in some microbial mats. These metabolic interactions and the diversity of the bacteria that participate in them are most likely supported by the strong mutual dependence of the partners. © 2010 Federation of European Microbiological Societies. Published by Blackwell Publishing Ltd. All rights reserved.

Enzymatic bioremediation of polyaromatic hydrocarbons by fungal consortia enriched from petroleum contaminated soil and oil seeds.

PubMed

Balaji, V; Arulazhagan, P; Ebenezer, P

2014-05-01

The present study focuses on fungal strains capable of secreting extracellular enzymes by utilizing hydrocarbons present in the contaminated soil. Fungal strains were enriched from petroleum hydrocarbons contaminated soil samples collected from Chennai city, India. The potential fungi were isolated and screened for their enzyme secretion such as lipase, laccase, peroxidase and protease and also evaluated fungal enzyme mediated PAHs degradation. Total, 21 potential PAHs degrading fungi were isolated from PAHs contaminated soil, which belongs to 9 genera such as Aspergillus, Curvularia, Drechslera, Fusarium, Lasiodiplodia, Mucor Penicillium, Rhizopus, Trichoderma, and two oilseed-associated fungal genera such as Colletotrichum and Lasiodiplodia were used to test their efficacy in degradation of PAHs in polluted soil. Maximum lipase production was obtained with P. chrysogenum, M. racemosus and L. theobromae VBE1 under optimized cultural condition, which utilized PAHs in contaminated soil as sole carbon source. Fungal strains, P. chrysogenum, M. racemosus and L. theobromae VBE1, as consortia, used in the present study were capable of degrading branched alkane isoprenoids such as pristine (C17) and pyrene (C18) present in PAHs contaminated soil with high lipase production. The fungal consortia acts as potential candidate for bioremediation of PAHs contaminated environments.

Moraxella lincolnii sp. nov., isolated from the human respiratory tract, and reevaluation of the taxonomic position of Moraxella osloensis.

PubMed

Vandamme, P; Gillis, M; Vancanneyt, M; Hoste, B; Kersters, K; Falsen, E

1993-07-01

A polyphasic taxonomic study was performed to determine the relationships of 10 Moraxella-like strains isolated mainly from the human respiratory tract in Sweden. Two of the strains formed a separate subgroup on the basis of both their protein contents and their fatty acid contents. However, the overall protein and fatty acid profiles revealed that all 10 strains were highly related. Representative strains of the two subgroups exhibited high DNA binding values (98%) with each other and had an identical DNA base ratio (44 mol% G+C). DNA-rRNA hybridizations revealed that this taxon can be included in the genus Moraxella, which is only distantly related to phenotypically similar genera, such as the genera Neisseria and Kingella. The results of an extensive phenotypic analysis indicated that the general biochemical profile of the 10 strains conforms with the description of the genus Moraxella given in Bergey's Manual of Systematic Bacteriology. We therefore consider these organisms members of a new Moraxella species, for which the name Moraxella lincolnii is proposed. Furthermore, we also conclude that Moraxella osloensis belongs, genotypically as well as phenotypically, to the genus Moraxella.

Indole-3-Acetic Acid-Producing Yeasts in the Phyllosphere of the Carnivorous Plant Drosera indica L

PubMed Central

Shin, Li-Ying; Wei, Jyuan-Yu; Fu, Shih-Feng; Chou, Jui-Yu

2014-01-01

Yeasts are widely distributed in nature and exist in association with other microorganisms as normal inhabitants of soil, vegetation, and aqueous environments. In this study, 12 yeast strains were enriched and isolated from leaf samples of the carnivorous plant Drosera indica L., which is currently threatened because of restricted habitats and use in herbal industries. According to similarities in large subunit and small subunit ribosomal RNA gene sequences, we identified 2 yeast species in 2 genera of the phylum Ascomycota, and 5 yeast species in 5 genera of the phylum Basidiomycota. All of the isolated yeasts produced indole-3-acetic acid (IAA) when cultivated in YPD broth supplemented with 0.1% L-tryptophan. Growth conditions, such as the pH and temperature of the medium, influenced yeast IAA production. Our results also suggested the existence of a tryptophan-independent IAA biosynthetic pathway. We evaluated the effects of various concentrations of exogenous IAA on yeast growth and observed that IAA produced by wild yeasts modifies auxin-inducible gene expression in Arabidopsis. Our data suggest that yeasts can promote plant growth and support ongoing prospecting of yeast strains for inclusion into biofertilizer for sustainable agriculture. PMID:25464336

Carbohydrate catabolic diversity of bifidobacteria and lactobacilli of human origin.

PubMed

McLaughlin, Heather P; Motherway, Mary O'Connell; Lakshminarayanan, Bhuvaneswari; Stanton, Catherine; Paul Ross, R; Brulc, Jennifer; Menon, Ravi; O'Toole, Paul W; van Sinderen, Douwe

2015-06-16

Because increased proportions of particular commensal bacteria such as bifidobacteria and lactobacilli have been linked to human health through a variety of mechanisms, there is corresponding interest in identifying carbohydrates that promote growth and metabolic activity of these bacteria. We evaluated the ability of 20 carbohydrates, including several commercially available carbohydrates that are sold as prebiotic ingredients, to support growth of 32 human-derived isolates belonging to the genera Bifidobacterium and Lactobacillus, including those isolated from healthy elderly subjects. In general, bifidobacterial strains were shown to display more diverse carbohydrate utilization profiles compared to the tested Lactobacillus species, with several bifidobacterial strains capable of metabolizing xylo-oligosaccharide (XOS), arabinoxylan, maltodextrin, galactan and carbohydrates containing fructo-oligosaccharide (FOS) components. In contrast, maltodextrin, galactan, arabinogalactan and galactomannan did not support robust growth (≥0.8 OD600 nm) of any of the Lactobacillus strains assessed. Carbohydrate fermentation was variable among strains tested of the same species for both genera. This study advances our knowledge of polysaccharide utilization by human gut commensals, and provides information for the rational design of selective prebiotic food ingredients. Copyright © 2015 Elsevier B.V. All rights reserved.

Colony-PCR Is a Rapid Method for DNA Amplification of Hyphomycetes

PubMed Central

Walch, Georg; Knapp, Maria; Rainer, Georg; Peintner, Ursula

2016-01-01

Fungal pure cultures identified with both classical morphological methods and through barcoding sequences are a basic requirement for reliable reference sequences in public databases. Improved techniques for an accelerated DNA barcode reference library construction will result in considerably improved sequence databases covering a wider taxonomic range. Fast, cheap, and reliable methods for obtaining DNA sequences from fungal isolates are, therefore, a valuable tool for the scientific community. Direct colony PCR was already successfully established for yeasts, but has not been evaluated for a wide range of anamorphic soil fungi up to now, and a direct amplification protocol for hyphomycetes without tissue pre-treatment has not been published so far. Here, we present a colony PCR technique directly from fungal hyphae without previous DNA extraction or other prior manipulation. Seven hundred eighty-eight fungal strains from 48 genera were tested with a success rate of 86%. PCR success varied considerably: DNA of fungi belonging to the genera Cladosporium, Geomyces, Fusarium, and Mortierella could be amplified with high success. DNA of soil-borne yeasts was always successfully amplified. Absidia, Mucor, Trichoderma, and Penicillium isolates had noticeably lower PCR success. PMID:29376929

Resolving the polyphyletic nature of Pyricularia (Pyriculariaceae)

PubMed Central

Klaubauf, S.; Tharreau, D.; Fournier, E.; Groenewald, J.Z.; Crous, P.W.; de Vries, R.P.; Lebrun, M.-H.

2014-01-01

Species of Pyricularia (magnaporthe-like sexual morphs) are responsible for major diseases on grasses. Pyricularia oryzae (sexual morph Magnaporthe oryzae) is responsible for the major disease of rice called rice blast disease, and foliar diseases of wheat and millet, while Pyricularia grisea (sexual morph Magnaporthe grisea) is responsible for foliar diseases of Digitaria. Magnaporthe salvinii, M. poae and M. rhizophila produce asexual spores that differ from those of Pyricularia sensu stricto that has pyriform, 2-septate conidia produced on conidiophores with sympodial proliferation. Magnaporthe salvinii was recently allocated to Nakataea, while M. poae and M. rhizophila were placed in Magnaporthiopsis. To clarify the taxonomic relationships among species that are magnaporthe- or pyricularia-like in morphology, we analysed phylogenetic relationships among isolates representing a wide range of host plants by using partial DNA sequences of multiple genes such as LSU, ITS, RPB1, actin and calmodulin. Species of Pyricularia s. str. belong to a monophyletic clade that includes all P. oryzae/P. grisea isolates tested, defining the Pyriculariaceae, which is sister to the Ophioceraceae, representing two novel families. These clades are clearly distinct from species belonging to the Gaeumannomyces pro parte/Magnaporthiopsis/Nakataea generic complex that are monophyletic and define the Magnaporthaceae. A few magnaporthe- and pyricularia-like species are unrelated to Magnaporthaceae and Pyriculariaceae. Pyricularia oryzae/P. grisea isolates cluster into two related clades. Host plants such as Eleusine, Oryza, Setaria or Triticum were exclusively infected by isolates from P. oryzae, while some host plant such as Cenchrus, Echinochloa, Lolium, Pennisetum or Zingiber were infected by different Pyricularia species. This demonstrates that host range cannot be used as taxonomic criterion without extensive pathotyping. Our results also show that the typical pyriform, 2-septate conidium morphology of P. grisea/P. oryzae is restricted to Pyricularia and Neopyricularia, while most other genera have obclavate to more ellipsoid 2-septate conidia. Some related genera (Deightoniella, Macgarvieomyces) have evolved 1-septate conidia. Therefore, conidium morphology cannot be used as taxonomic criterion at generic level without phylogenetic data. We also identified 10 novel genera, and seven novel species. A re-evaluation of generic and species concepts within Pyriculariaceae is presented, and novelties are proposed based on morphological and phylogenetic data. PMID:25492987

Carbaryl degradation by bacterial isolates from a soil ecosystem of the Gaza Strip

PubMed Central

Hamada, Mazen; Matar, Ammar; Bashir, Abdallah

2015-01-01

Abstract Carbaryl is an important and widely used insecticide that pollutes soil and water systems. Bacteria from the local soil ecosystem of the Gaza Strip capable of utilizing carbaryl as the sole source of carbon and nitrogen were isolated and identified as belonging to Bacillus, Morganella, Pseudomonas, Aeromonas and Corynebacterium genera. Carbaryl biodegradation by Bacillus, Morganella and Corynebacterium isolates was analyzed in minimal liquid media supplemented with carbaryl as the only source of carbon and nitrogen. Bacillus and Morganella exhibited 94.6% and 87.3% carbaryl degradation, respectively, while Corynebacterium showed only moderate carbaryl degradation at 48.8%. These results indicate that bacterial isolates from a local soil ecosystem in the Gaza Strip are able to degrade carbaryl and can be used to decrease the risk of environmental contamination by this insecticide. PMID:26691466

Airborne fungi in child day care centers in Edirne City, Turkey.

PubMed

Aydogdu, Halide; Asan, Ahmet

2008-12-01

The purpose of this study was to determine the concentration, in terms of monthly and seasonal distribution and in relation to meteorological factors, of indoor and outdoor microfungi at selected sites in several child day care centers in the city of Edirne, Turkey. Samples were collected at one month intervals over a period of 12 months between January-December 2004, by exposing petri plates containing Peptone Dextrose Agar with Rose-Bengal and Streptomycin medium to the air for 10-15 min. A total of 2,071 microfungal colonies were counted on 192 petri plates. Thirty microfungal genera (Acremonium, Alternaria, Arthrinium, Aspergillus, Bahusakala, Beauveria, Ceuthospora, Chaetomium, Cladosporium, Curvularia, Drechslera, Epicoccum, Eurotium, Fusarium, Mycotypha, Myrotechium, Paecilomyces, Penicillium, Pestalotiopsis, Phoma, Ramichloridium, Rhizopus, Scopulariopsis, Stachybotrys, Stemphylium, Torula, Trichoderma, Trichothecium, Ulocladium, Verticillium) and 75 microfungal species were isolated from the air indoor and outdoor of the day care centers. The dominant microfungal genera were Cladosporium, Penicillium and Alternaria (44.11%, 18.94%, 14.67% of the total respectively), while the genus with the most species richness was Penicillium (26 species). Alternaria, Cladosporium, Penicillium and non-sporulating microfungi were found every month. Cladosporium was the dominant genus in both indoor and outdoor air. Although the predominant genus was the same in both indoor and outdoor air, Cladosporium was followed by Penicillium, Alternaria and Aspergillus genera in indoor air and by Alternaria, Penicillium and Aspergillus genera in outdoor air. While a positive correlation was found between the concentration of monthly outdoor microfungi and monthly average temperature, a negative correlation was found between the concentration of monthly outdoor microfungi and monthly average wind velocity. Also, some relationships were found between the monthly concentrations of the most predominant microfungal genera (Cladosporium, Penicillium and Alternaria) and various meteorological factors.

Microbial characterization of the Mars Odyssey spacecraft and its encapsulation facility.

PubMed

La Duc, Myron T; Nicholson, Wayne; Kern, Roger; Venkateswaran, Kasthuri

2003-10-01

Microbial characterization of the Mars Odyssey spacecraft and the Kennedy Space Center Spacecraft Assembly and Encapsulation Facility II (SAEF-II) was carried out by both culture-based and molecular methods. The most dominant cultivable microbes were species of Bacillus, with comamonads, microbacteria and actinomycetales also represented. Several spore-forming isolates were resistant to gamma-radiation, UV, H2O2 and desiccation, and one Acinetobacter radioresistens isolate and several Aureobasidium, isolated directly from the spacecraft, survived various conditions. Sequences arising in clone libraries were fairly consistent between the spacecraft and facility; predominant genera included Variovorax, Ralstonia and Aquaspirillum. This study improves our understanding of the microbial community structure, diversity and survival capabilities of microbes in an encapsulation facility and physically associated with colocated spacecraft.

First record of entomopathogenic fungi on autumn leaf Caterpillar (Doleschallia bisaltide)

NASA Astrophysics Data System (ADS)

Dayanti, A. K.; Sholahuddin; Yunus, A.; Subositi, D.

2018-03-01

Caricature plant is one of the medicinal plants in Indonesia to cure hemorrhoids, menstruation, and others. The cultivation constraints of caricature plant is autumn leaf caterpillars (Doleschallia bisaltide). Utilization of synthetic insecticides is not allowed to avoid bioaccumulation of chemical residues. Entomopathogenic fungi is an alternative way to control D. bisaltide. The objective of the research was to obtain isolates of entomopathogenic fungi of D. bisaltide. The research conducted by two steps, which were exsploration of infecfted D. bisaltide. The second step was identification of the fungi. Exploration results of 16 pupae of D. Bisaltide were infected by fungi. Identification done by classify the mcroscopic and microscopic fungi isolate characteristic. One from five fungal isolates were entomopathogenic fungi from Verticillium genera.

Microbial characterization of the Mars Odyssey spacecraft and its encapsulation facility

NASA Technical Reports Server (NTRS)

La Duc, Myron T.; Nicholson, Wayne; Kern, Roger; Venkateswaran, Kasthuri

2003-01-01

Microbial characterization of the Mars Odyssey spacecraft and the Kennedy Space Center Spacecraft Assembly and Encapsulation Facility II (SAEF-II) was carried out by both culture-based and molecular methods. The most dominant cultivable microbes were species of Bacillus, with comamonads, microbacteria and actinomycetales also represented. Several spore-forming isolates were resistant to gamma-radiation, UV, H2O2 and desiccation, and one Acinetobacter radioresistens isolate and several Aureobasidium, isolated directly from the spacecraft, survived various conditions. Sequences arising in clone libraries were fairly consistent between the spacecraft and facility; predominant genera included Variovorax, Ralstonia and Aquaspirillum. This study improves our understanding of the microbial community structure, diversity and survival capabilities of microbes in an encapsulation facility and physically associated with colocated spacecraft.

Phylogenetic and metabolic diversity of Tunisian forest wood-degrading fungi: a wealth of novelties and opportunities for biotechnology.

PubMed

Daâssi, Dalel; Zouari-Mechichi, Héla; Belbahri, Lassaad; Barriuso, Jorge; Martínez, María Jesús; Nasri, Moncef; Mechichi, Tahar

2016-06-01

In this study, 51 fungal strains were isolated from decaying wood samples collected from forests located in the Northwest of Tunisia in the vicinity of Bousalem, Ain Draham and Kef. Phylogenetic analysis based on the sequences of the internal transcribed spacers of the ribosomal DNA showed a high diversity among the 51 fungal isolates collection. Representatives of 25 genera and 29 species were identified, most of which were members of one of the following phyla (Ascomycota, Basidiomycota and Zygomycota). In addition to the phylogenetic diversity, a high diversity of secreted enzyme profiles was also detected among the fungal isolates. All fungal strains produced at least one of the following enzymes: laccase, cellulase, protease and/or lipase.

Identification of thermophilic bacterial strains producing thermotolerant hydrolytic enzymes from manure compost.

PubMed

Charbonneau, David M; Meddeb-Mouelhi, Fatma; Boissinot, Maurice; Sirois, Marc; Beauregard, Marc

2012-03-01

Ten thermophilic bacterial strains were isolated from manure compost. Phylogenetic analysis based on 16S rRNA genes and biochemical characterization allowed identification of four different species belonging to four genera: Geobacillus thermodenitrificans, Bacillus smithii, Ureibacillus suwonensis and Aneurinibacillus thermoaerophilus. PCR-RFLP profiles of the 16S-ITS-23S rRNA region allowed us to distinguish two subgroups among the G. thermodenitrificans isolates. Isolates were screened for thermotolerant hydrolytic activities (60-65°C). Thermotolerant lipolytic activities were detected for G. thermodenitrificans, A. thermoaerophilus and B. smithii. Thermotolerant protease, α-amylase and xylanase activities were also observed in the G. thermodenitrificans group. These species represent a source of potential novel thermostable enzymes for industrial applications.

Antagonistic activity of fungi of Olea europaea L. against Colletotrichum acutatum.

PubMed

Landum, Miguel C; Félix, Maria do Rosário; Alho, Joana; Garcia, Raquel; Cabrita, Maria João; Rei, Fernando; Varanda, Carla M R

2016-02-01

Fungi naturally present in olive trees were identified and tested for their antagonistic potential against Colletotrichum acutatum. A total of 14 isolates were identified, 12 belonged to genera Alternaria, Epicoccum, Fusarium, Aspergillus, Anthrinium, Chaetomium, Diaporthe, Nigrospora, one to family Xylariaceae and one was unclassified. All fungal isolates showed some inhibitory action over the growth of C. acutatum during dual culture growth, however, when agar-diffusible tests were performed only five fungal isolates caused C. acutatum growth inhibition: Alternaria sp. isolate 2 (26.8%), the fungus from Xylariaceae family (14.3%), Alternaria sp. isolate 1 (10.7%); Diaporthe sp. (10.7%), Nigrospora oryzae (3.5%). Volatile substances produced by these isolates were identified through gas-chromatography techniques, as phenylethyl alcohol, 4-methylquinazoline, benzothiazole, benzyl alcohol, lilial, galaxolide, among others. These inhibitory volatiles could play a significant role in reduction of C. acutatum expansion in olive and their study as potential biocontrol agents should be further explored. Copyright © 2015 Elsevier GmbH. All rights reserved.

Bacterial genus is a risk factor for major amputation in patients with diabetic foot.

PubMed

Cardoso, Natália Anício; Cisneiros, Lígia DE Loiola; Machado, Carla Jorge; Cenedezi, Juliana Merlin; Procópio, Ricardo Jayme; Navarro, Túlio Pinho

2017-01-01

to evaluate whether bacterial genus is a risk factor for major amputation in patients with diabetic foot and infected ulcer. we conducted a case-control, observational study of 189 patients with infected ulcers in diabetic feet admitted to the Vascular Surgery Service of the Risoleta Tolentino Neves Hospital, from January 2007 to December 2012. The bacteriological evaluation was performed in deep tissue cultures from the lesions and amputation was considered major when performed above the foot'smiddle tarsus. the patients'mean age was 61.9±12.7 years; 122 (64.6%) were men. The cultures were positive in 86.8%, being monomicrobial in 72% of the cases. In patients with major amputation, Acinetobacter spp. (24.4%), Morganella spp. (24.4%), Proteus spp. (23.1%) and Enterococcus spp. (19.2%) were the most frequent types of bacteria. The most commonly isolated species were Acinetobacter baumannii, Morganella morganii, Pseudomonas aeruginosa and Proteus mirabilis. As predictors of major amputation, we identified the isolation of the generaAcinetobacter spp. and Klebsiella spp., serum creatinine ≥1.3mg/dl and hemoglobin <11g/dl. the bacterial genera Acinetobacter spp. and Klebsiella spp. identified in infected ulcers of patients with diabetic foot were associated with a higher incidence of major amputation. avaliar se gênero bacteriano é fator de risco para amputação maior em pacientes com pé diabético e úlcera infectada. estudo observacional do tipo caso-controle de 189 pacientes com úlcera infectada em pé diabético admitidos pelo Serviço de Cirurgia Vascular do Hospital Risoleta Tolentino Neves, no período de janeiro de 2007 a dezembro de 2012. A avaliação bacteriológica foi realizada em cultura de tecido profundo das lesões e a amputação foi considerada como maior quando realizada acima do médio tarso do pé. a média de idade dos pacientes foi 61,9±12,7 anos e 122 (64,6%) eram homens. As culturas foram positivas em 86,8%, sendo monomicrobianas em 72% dos casos. Nos pacientes com amputação maior, os gêneros de bactérias mais frequentes foram Acinetobacter spp. (24,4%), Morganella spp. (24,4%), Proteus spp. (23,1%) e Enterococcus spp. (19,2%) e as espécies mais isoladas foram Acinetobacter baumannii, Morganella morganii, Pseudomonas aeruginosa e Proteus mirabilis. Identificou-se como fatores preditivos para amputação maior o isolamento dos gêneros Acinetobacter spp. e Klebsiella spp.,e níveis séricos de creatinina ≥1,3mg/dl e de hemoglobina <11g/dl. os gêneros bacterianos Acinetobacter spp. e Klebsiella spp. identificados nas úlceras infectadas dos pacientes com pé diabético associaram-se a maior incidência de amputação maior.

Biogeography of the Pistia clade (Araceae): based on chloroplast and mitochondrial DNA sequences and Bayesian divergence time inference.

PubMed

Renner, Susanne S; Zhang, Li-Bing

2004-06-01

Pistia stratiotes (water lettuce) and Lemna (duckweeds) are the only free-floating aquatic Araceae. The geographic origin and phylogenetic placement of these unrelated aroids present long-standing problems because of their highly modified reproductive structures and wide geographical distributions. We sampled chloroplast (trnL-trnF and rpl20-rps12 spacers, trnL intron) and mitochondrial sequences (nad1 b/c intron) for all genera implicated as close relatives of Pistia by morphological, restriction site, and sequencing data, and present a hypothesis about its geographic origin based on the consensus of trees obtained from the combined data, using Bayesian, maximum likelihood, parsimony, and distance analyses. Of the 14 genera closest to Pistia, only Alocasia, Arisaema, and Typhonium are species-rich, and the latter two were studied previously, facilitating the choice of representatives that span the roots of these genera. Results indicate that Pistia and the Seychelles endemic Protarum sechellarum are the basalmost branches in a grade comprising the tribes Colocasieae (Ariopsis, Steudnera, Remusatia, Alocasia, Colocasia), Arisaemateae (Arisaema, Pinellia), and Areae (Arum, Biarum, Dracunculus, Eminium, Helicodiceros, Theriophonum, Typhonium). Unexpectedly, all Areae genera are embedded in Typhonium, which throws new light on the geographic history of Areae. A Bayesian analysis of divergence times that explores the effects of multiple fossil and geological calibration points indicates that the Pistia lineage is 90 to 76 million years (my) old. The oldest fossils of the Pistia clade, though not Pistia itself, are 45-my-old leaves from Germany; the closest outgroup, Peltandreae (comprising a few species in Florida, the Mediterranean, and Madagascar), is known from 60-my-old leaves from Europe, Kazakhstan, North Dakota, and Tennessee. Based on the geographic ranges of close relatives, Pistia likely originated in the Tethys region, with Protarum then surviving on the Seychelles, which became isolated from Madagascar and India in the Late Cretaceous (85 my ago). Pistia and Protarum provide striking examples of ancient lineages that appear to have survived in unique or isolated habitats.

The evolution of trypanosomatid taxonomy.

PubMed

Kaufer, Alexa; Ellis, John; Stark, Damien; Barratt, Joel

2017-06-08

Trypanosomatids are protozoan parasites of the class Kinetoplastida predominately restricted to invertebrate hosts (i.e. possess a monoxenous life-cycle). However, several genera are pathogenic to humans, animals and plants, and have an invertebrate vector that facilitates their transmission (i.e. possess a dixenous life-cycle). Phytomonas is one dixenous genus that includes several plant pathogens transmitted by phytophagous insects. Trypanosoma and Leishmania are dixenous genera that infect vertebrates, including humans, and are transmitted by hematophagous invertebrates. Traditionally, monoxenous trypanosomatids such as Leptomonas were distinguished from morphologically similar dixenous species based on their restriction to an invertebrate host. Nonetheless, this criterion is somewhat flawed as exemplified by Leptomonas seymouri which reportedly infects vertebrates opportunistically. Similarly, Novymonas and Zelonia are presumably monoxenous genera yet sit comfortably in the dixenous clade occupied by Leishmania. The isolation of Leishmania macropodum from a biting midge (Forcipomyia spp.) rather than a phlebotomine sand fly calls into question the exclusivity of the Leishmania-sand fly relationship, and its suitability for defining the Leishmania genus. It is now accepted that classic genus-defining characteristics based on parasite morphology and host range are insufficient to form the sole basis of trypanosomatid taxonomy as this has led to several instances of paraphyly. While improvements have been made, resolution of evolutionary relationships within the Trypanosomatidae is confounded by our incomplete knowledge of its true diversity. The known trypanosomatids probably represent a fraction of those that exist and isolation of new species will help resolve relationships in this group with greater accuracy. This review incites a dialogue on how our understanding of the relationships between certain trypanosomatids has shifted, and discusses new knowledge that informs the present taxonomy of these important parasites.

Arsenite-oxidizing and arsenate-reducing bacteria associated with arsenic-rich groundwater in Taiwan

NASA Astrophysics Data System (ADS)

Liao, Vivian Hsiu-Chuan; Chu, Yu-Ju; Su, Yu-Chen; Hsiao, Sung-Yun; Wei, Chia-Cheng; Liu, Chen-Wuing; Liao, Chung-Min; Shen, Wei-Chiang; Chang, Fi-John

2011-04-01

Drinking highly arsenic-contaminated groundwater is a likely cause of blackfoot disease in Taiwan, but microorganisms that potentially control arsenic mobility in the subsurface remain unstudied. The objective of this study was to investigate the relevant arsenite-oxidizing and arsenate-reducing microbial community that exists in highly arsenic-contaminated groundwater in Taiwan. We cultured and identified arsenic-transforming bacteria, analyzed arsenic resistance and transformation, and determined the presence of genetic markers for arsenic transformation. In total, 11 arsenic-transforming bacterial strains with different colony morphologies and varying arsenic transformation abilities were isolated, including 10 facultative anaerobic arsenate-reducing bacteria and one strictly aerobic arsenite-oxidizing bacterium. All of the isolates exhibited high levels of arsenic resistance with minimum inhibitory concentrations of arsenic ranging from 2 to 200 mM. Strain AR-11 was able to rapidly oxidize arsenite to arsenate at concentrations relevant to environmental groundwater samples without the addition of any electron donors or acceptors. We provide evidence that arsenic-reduction activity may be conferred by the ars operon(s) that were not amplified by the designed primers currently in use. The 16S rRNA sequence analysis grouped the isolates into the following genera: Pseudomonas, Bacillus, Psychrobacter, Vibrio, Citrobacter, Enterobacter, and Bosea. Among these genera, we present the first report of the genus Psychrobacter being involved in arsenic reduction. Our results further support the hypothesis that bacteria capable of either oxidizing arsenite or reducing arsenate coexist and are ubiquitous in arsenic-contaminated groundwater.

Coral-Associated Actinobacteria: Diversity, Abundance, and Biotechnological Potentials

PubMed Central

Mahmoud, Huda M.; Kalendar, Aisha A.

2016-01-01

Marine Actinobacteria, particularly coral-associated Actinobacteria, have attracted attention recently. In this study, the abundance and diversity of Actinobacteria associated with three types of coral thriving in a thermally stressed coral reef system north of the Arabian Gulf were investigated. Coscinaraea columna, Platygyra daedalea and Porites harrisoni have been found to harbor equivalent numbers of culturable Actinobacteria in their tissues but not in their mucus. However, different culturable actinobacterial communities have been found to be associated with different coral hosts. Differences in the abundance and diversity of Actinobacteria were detected between the mucus and tissue of the same coral host. In addition, temporal and spatial variations in the abundance and diversity of the cultivable actinobacterial communities were detected. In total, 19 different actinobacterial genera, namely Micrococcus, Brachybacterium, Brevibacterium, Streptomyces, Micromonospora, Renibacterium, Nocardia, Microbacterium, Dietzia, Cellulomonas, Ornithinimicrobium, Rhodococcus, Agrococcus, Kineococcus, Dermacoccus, Devriesea, Kocuria, Marmoricola, and Arthrobacter, were isolated from the coral tissue and mucus samples. Furthermore, 82 isolates related to Micromonospora, Brachybacterium, Nocardia, Micrococcus, Arthrobacter, Rhodococcus, and Streptomyces showed antimicrobial activities against representative Gram-positive and/or Gram-negative bacteria. Even though Brevibacterium and Kocuria were the most dominant actinobacterial isolates, they failed to show any antimicrobial activity, whereas less dominant genera, such as Streptomyces, did show antimicrobial activity. Focusing on the diversity of coral-associated Actinobacteria may help to understand how corals thrive under harsh environmental conditions and may lead to the discovery of novel antimicrobial metabolites with potential biotechnological applications. PMID:26973601

Assessment of bacterial diversity during composting of agricultural byproducts

PubMed Central

2013-01-01

Background Composting is microbial decomposition of biodegradable materials and it is governed by physicochemical, physiological and microbiological factors. The importance of microbial communities (bacteria, actinomycetes and fungi) during composting is well established. However, the microbial diversity during composting may vary with the variety of composting materials and nutrient supplements. Therefore, it is necessary to study the diversity of microorganisms during composting of different agricultural byproducts like wheat bran, rice bran, rice husk, along with grass clippings and bulking agents. Here it has been attempted to assess the diversity of culturable bacteria during composting of agricultural byproducts. Results The culturable bacterial diversity was assessed during the process by isolating the most prominent bacteria. Bacterial population was found to be maximum during the mesophilic phase, but decreased during the thermophilic phase and declined further in the cooling and maturation phase of composting. The bacterial population ranged from 105 to 109 cfu g-1 compost. The predominant bacteria were characterized biochemically, followed by 16S rRNA gene sequencing. The isolated strains, both Gram-positive and Gram-negative groups belonged to the order Burkholderiales, Enterobacteriales, Actinobacteriales and Bacillales, which includes genera e.g. Staphylococcus, Serratia, Klebsiella, Enterobacter, Terribacillus, Lysinibacillus Kocuria, Microbacterium, Acidovorax and Comamonas. Genera like Kocuria, Microbacterium, Acidovorax, Comamonas and some new species of Bacillus were also identified for the first time from the compost made from agricultural byproducts. Conclusion The use of appropriate nitrogen amendments and bulking agents in composting resulted in good quality compost. The culture based strategy enabled us to isolate some novel bacterial isolates like Kocuria, Microbacterium, Acidovorax and Comamonas first time from agro-byproducts compost. These bacteria can be used as potential compost inoculants for accelerating composting process. PMID:23651653

Diversity and antimicrobial activity of culturable fungi from fishscale bamboo (Phyllostachys heteroclada) in China.

PubMed

Zhou, Ying-Ke; Shen, Xiao-Ye; Hou, Cheng-Lin

2017-06-01

An important and useful bamboo species, fishscale bamboo (Phyllostachys heteroclada Oliver), is broadly distributed in Southeast China and has multiple purposes, including uses in cuisine, weaving, Chinese medicine and ecological protection. However, no previous studies have focused on the endophytes of this plant. In our article, a total of 127 fungal strains were first isolated from the healthy branches and leaves of common P. heteroclada. These endophytic fungi could be directly categorized into 50 morphotypes according to their culture characteristics, and their internal transcribed spacer (ITS) regions were analyzed for molecular identification. Using the BLAST search tool of the NCBI database and phylogenetic tree analysis, these isolates were divided into two phyla, Ascomycota (95.28%) and Basidiomycota (4.72%), including at least six orders (Xylariales, Capnodiales, Pleosporales, Hypocreales, Chaetothyriales and Polyporales) and fourteen genera (Arthrinium, Pestalotiopsis, Epicoccum, Cladosporium, Nigrospora, Setophoma, Didymella, Calcarisporium, Preussia, Nemania, Creosphaeria, Ophiobolus, Phialophora and Perenniporia). It is fascinating that four genera, Calcarisporium, Preussia, Creosphaeria and Phialophora were isolated from bamboos for the first time. The inhibitory effects against clinical pathogens were also preliminarily screened, and four isolates FB43 (Calcarisporium arbuscula), FB06 (Preussia minima), FB16 (Setophoma sp.) and FB21 (Perenniporia medulla-pains) among the candidate strains displayed broad-spectrum activities according to the agar diffusion method and the disk diffusion assay. Strain FB16 (Setophoma sp.) especially indicated high bioactivity against both clinical bacteria and yeast. This study is the first report on the diversity and antimicrobial activity of the endophytic fungi associated with P. heteroclada, which could be regarded as a potential source of drug precursors and could be used in biocontrol development.

Multi-centre evaluation of mass spectrometric identification of anaerobic bacteria using the VITEK® MS system.

PubMed

Garner, O; Mochon, A; Branda, J; Burnham, C-A; Bythrow, M; Ferraro, M; Ginocchio, C; Jennemann, R; Manji, R; Procop, G W; Richter, S; Rychert, J; Sercia, L; Westblade, L; Lewinski, M

2014-04-01

Accurate and timely identification of anaerobic bacteria is critical to successful treatment. Classic phenotypic methods for identification require long turnaround times and can exhibit poor species level identification. Matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS) is an identification method that can provide rapid identification of anaerobes. We present a multi-centre study assessing the clinical performance of the VITEK(®) MS in the identification of anaerobic bacteria. Five different test sites analysed a collection of 651 unique anaerobic isolates comprising 11 different genera. Multiple species were included for several of the genera. Briefly, anaerobic isolates were applied directly to a well of a target plate. Matrix solution (α-cyano-4-hydroxycinnamic acid) was added and allowed to dry. Mass spectra results were generated with the VITEK(®) MS, and the comparative spectral analysis and organism identification were determined using the VITEK(®) MS database 2.0. Results were confirmed by 16S rRNA gene sequencing. Of the 651 isolates analysed, 91.2% (594/651) exhibited the correct species identification. An additional eight isolates were correctly identified to genus level, raising the rate of identification to 92.5%. Genus-level identification consisted of Actinomyces, Bacteroides and Prevotella species. Fusobacterium nucleatum, Actinomyces neuii and Bacteroides uniformis were notable for an increased percentage of no-identification results compared with the other anaerobes tested. VITEK(®) MS identification of clinically relevant anaerobes is highly accurate and represents a dramatic improvement over other phenotypic methods in accuracy and turnaround time. © 2013 The Authors Clinical Microbiology and Infection © 2013 European Society of Clinical Microbiology and Infectious Diseases.

The molecular variability analysis of the RNA 3 of fifteen isolates of Prunus necrotic ringspot virus sheds light on the minimal requirements for the synthesis of its subgenomic RNA.

PubMed

Aparicio, Frederic; Pallás, Vicente

2002-01-01

The nucleotide sequences of the RNA 3 of fifteen isolates of Prunus necrotic ringspot virus (PNRSV) varying in the symptomatology they cause in six different Prunus spp. were determined. Analysis of the molecular variability has allowed, in addition to study the phylogenetic relationships among them, to evaluate the minimal requirements for the synthesis of the subgenomic RNA in Ilarvirus genus and their comparison to other members of the Bromoviridae family. Computer assisted comparisons led recently to Jaspars (Virus Genes 17, 233-242, 1998) to propose that a hairpin structure in viral minus strand RNA is required for subgenomic promoter activity of viruses from at least two, and possibly all five, genera in the family of Bromoviridae. For PNRSV and Apple mosaic virus two stable hairpins were proposed whereas for the rest of Ilarviruses and the other four genera of the Bromoviridae family only one stable hairpin was predicted. Comparative analysis of this region among the fifteen PNRSV isolates characterized in this study revealed that two of them showed a 12-nt deletion that led to the disappearance of the most proximal hairpin to the initiation site. Interestingly, the only hairpin found in these two isolates is very similar in primary and secondary structure to the one previously shown in Brome mosaic virus to be required for the synthesis of the subgenomic RNA. In this hairpin, the molecular diversity was concentrated mostly at the loop whereas compensatory mutations were observed at the base of the stem strongly suggesting its functional relevance. The evolutionary implications of these observations are discussed.

The environmental and intrinsic yeast diversity of Cuban cocoa bean heap fermentations.

PubMed

Fernández Maura, Yurelkys; Balzarini, Tom; Clapé Borges, Pablo; Evrard, Pierre; De Vuyst, Luc; Daniel, H-M

2016-09-16

The environmental yeast diversity of spontaneous cocoa bean fermentations in east Cuba was investigated. Seven fermentations, 25 equipment- and handling-related samples, and 115 environmental samples, such as flowers, leaf and cocoa pod surfaces, as well as drosophilid insects, were analysed. The basic fermentation parameters temperature and pH were recorded during five fermentations for at least six days. A total of 435 yeast isolates were identified by a combination of PCR-fingerprinting of genomic DNA with the M13 primer and sequence analysis of DNA from representative isolates, using the internal transcribed spacer region, the D1/D2 region of the large subunit rRNA gene, and an actin gene-encoding fragment, as required. Among 65 yeast species detected, Pichia manshurica and Hanseniaspora opuntiae were the most frequently isolated species, obtained from five and four fermentations, followed in frequency by Pichia kudriavzevii from two fermentations. Saccharomyces cerevisiae was isolated only occasionally. Cocoa fermentation yeast species were also present on processing equipment. The repeated isolation of a preliminarily as Yamadazyma sp. classified species, a group of strains similar to Saccharomycopsis crataegensis from fermentations and equipment, and the isolation of fifteen other potentially novel yeast species in low numbers provides material for further studies. Environmental samples showed higher yeast diversity compared to the fermentations, included the most frequent fermentation species, whereas the most frequently isolated environmental species were Candida carpophila, Candida conglobata, and Candida quercitrusa. Potential selective advantages of the most frequently isolated species were only partly explained by the physiological traits tested. For instance, tolerance to higher ethanol concentrations was more frequent in strains of Pichia spp. and S. cerevisiae compared to Hanseniaspora spp.; the ability to also assimilate ethanol might have conferred a selective advantage to Pichia spp. In contrast, high glucose tolerance was common among strains of Hanseniaspora spp., Torulaspora delbrueckii, and Candida tropicalis, among which only Hanseniaspora spp. were frequently isolated. Copyright © 2016 Elsevier B.V. All rights reserved.

Screening of cloud microorganisms isolated at the Puy de Dôme (France) station for the production of biosurfactants

NASA Astrophysics Data System (ADS)

Renard, Pascal; Canet, Isabelle; Sancelme, Martine; Wirgot, Nolwenn; Deguillaume, Laurent; Delort, Anne-Marie

2016-09-01

A total of 480 microorganisms collected from 39 clouds sampled at the Puy de Dôme station (alt. 1465 m; 45°46'19'' N, 2°57'52'' E; Massif Central, France) were isolated and identified. This unique collection was screened for biosurfactant (surfactants of microbial origin) production by measuring the surface tension (σ) of the crude extracts, comprising the supernatants of the pure cultures, using the pendant drop technique. The results showed that 41 % of the tested strains were active producers (σ < 55 mN m-1), with 7 % being extremely active (σ < 30 mN m-1). The most efficient biosurfactant producers (σ < 45 mN m-1) belong to a few bacterial genera (Pseudomonas and Xanthomonas) from the Υ-Proteobacteria class (78 %) and a yeast genus (Udeniomyces) from the Basidiomycota phylum (11 %). Some Bacillus strains from the Firmicutes phylum were also active but represented a small fraction of the collected population. Strains from the Actinobacteria phylum in the collection examined in the present study showed moderate biosurfactant production (45<σ < 55 mN m-1). Pseudomonas (Υ-Proteobacteria), the most frequently detected genus in clouds, with some species issued from the phyllosphere, was the dominant group for the production of biosurfactants. We observed some correlations between the chemical composition of cloud water and the presence of biosurfactant-producing microorganisms, suggesting the "biogeography" of this production. Moreover, the potential impact of the production of biosurfactants by cloud microorganisms on atmospheric processes is discussed.

Extracellular enzymatic activities and physiological profiles of yeasts colonizing fruit trees.

PubMed

Molnárová, Jana; Vadkertiová, Renáta; Stratilová, Eva

2014-07-01

Yeasts form a significant and diverse part of the phyllosphere microbiota. Some yeasts that inhabit plants have been found to exhibit extracellular enzymatic activities. The aim of the present study was to investigate the ability of yeasts isolated from leaves, fruits, and blossoms of fruit trees cultivated in Southwest Slovakia to produce extracellular enzymes, and to discover whether the yeasts originating from these plant organs differ from each other in their physiological properties. In total, 92 strains belonging to 29 different species were tested for: extracellular protease, β-glucosidase, lipase, and polygalacturonase activities; fermentation abilities; the assimilation of xylose, saccharose and alcohols (methanol, ethanol, glycerol); and for growth in a medium with 33% glucose. The black yeast Aureobasidium pullulans showed the largest spectrum of activities of all the species tested. Almost 70% of the strains tested demonstrated some enzymatic activity, and more than 90% utilized one of the carbon compounds tested. Intraspecies variations were found for the species of the genera Cryptococcus and Pseudozyma. Interspecies differences of strains exhibiting some enzymatic activities and utilizing alcohols were also noted. The largest proportion of the yeasts exhibited β-glucosidase activity and assimilated alcohols independently of their origin. The highest number of strains positive for all activities tested was found among the yeasts associated with leaves. Yeasts isolated from blossoms assimilated saccharose and D-xylose the most frequently of all the yeasts tested. The majority of the fruit-inhabiting yeasts grew in the medium with higher osmotic pressure. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Biodegradation of naphthenic acid surrogates by axenic cultures.

PubMed

Yue, Siqing; Ramsay, Bruce A; Ramsay, Juliana A

2015-07-01

This is the first study to report that bacteria from the genera Ochrobactrum, Brevundimonas and Bacillus can be isolated by growth on naphthenic acids (NAs) extracted from oil sands process water (OSPW). These pure cultures were screened for their ability to use a range of aliphatic, cyclic and aromatic NA surrogates in 96-well microtiter plates using water-soluble tetrazolium redox dyes (Biolog Redox Dye H) as the indicator of metabolic activity. Of the three cultures, Ochrobactrum showed most metabolic activity on the widest range of NA surrogates. Brevundomonas and especially Ochrobactrum had higher metabolic activity on polycyclic aromatic compounds than other classes of NA surrogates. Bacillus also oxidized a wide range of NA surrogates but not as well as Ochrobactrum. Using this method to characterize NA utilisation, one can identify which NAs or NA classes in OSPW are more readily degraded. Since aromatic NAs have been shown to have an estrogenic effect and polycyclic monoaromatic compounds have been suggested to pose the greatest environmental threat among the NAs, these bacterial genera may play an important role in detoxification of OSPW. Furthermore, this study demonstrates that bacteria belonging to the genera Ochrobactrum and Bacillus can also degrade surrogates of tricyclic NAs.

Characterization of a novel extremely alkalophilic bacterium

NASA Technical Reports Server (NTRS)

Souza, K. A.; Deal, P. H.

1977-01-01

A new alkalophilic bacterium, isolated from a natural spring of high pH is characterized. It is a Gram-positive, non-sporulating, motile rod requiring aerobic and alkaline conditions for growth. The characteristics of this organism resemble those of the coryneform group of bacteria; however, there are no accepted genera within this group with which this organism can be closely matched. Therefore, a new genus may be warranted.

Diversity of Cultivated Fungi Associated with Conventional and Transgenic Sugarcane and the Interaction between Endophytic Trichoderma virens and the Host Plant

PubMed Central

Romão-Dumaresq, Aline Silva; Dourado, Manuella Nóbrega; Fávaro, Léia Cecilia de Lima; Mendes, Rodrigo; Ferreira, Anderson; Araújo, Welington Luiz

2016-01-01

Plant-associated fungi are considered a vast source for biotechnological processes whose potential has been poorly explored. The interactions and diversity of sugarcane, one of the most important crops in Brazil, have been rarely studied, mainly concerning fungal communities and their interactions with transgenic plants. Taking this into consideration, the purpose of this study was, based on culture dependent strategy, to determine the structure and diversity of the fungal community (root endophytes and rhizosphere) associated with two varieties of sugarcane, a non-genetically modified (SP80-1842) variety and its genetically modified counterpart (IMI-1, expressing imazapyr herbicide resistance). For this, the sugarcane varieties were evaluated in three sampling times (3, 10 and 17 months after planting) under two crop management (weeding and herbicide treatments). In addition, a strain of Trichoderma virens, an endophyte isolated from sugarcane with great potential as a biological control, growth promotion and enzyme production agent, was selected for the fungal-plant interaction assays. The results of the isolation, characterization and evaluation of fungal community changes showed that the sugarcane fungal community is composed of at least 35 different genera, mostly in the phylum Ascomycota. Many genera are observed at very low frequencies among a few most abundant genera, some of which were isolated from specific plant sites (e.g., the roots or the rhizosphere). An assessment of the possible effects upon the fungal community showed that the plant growth stage was the only factor that significantly affected the community’s structure. Moreover, if transgenic effects are present, they may be minor compared to other natural sources of variation. The results of interaction studies using the Green fluorescent protein (GFP)-expressing T. virens strain T.v.223 revealed that this fungus did not promote any phenotypic changes in the host plant and was found mostly in the roots where it formed a dense mycelial cover and was able to penetrate the intercellular spaces of the root epidermis upper layers. The ability of T. virens to colonize plant roots suggests a potential for protecting plant health, inhibiting pathogens or inducing systemic resistance. PMID:27415014

Allocatelliglobosispora scoriae gen. nov., sp. nov., isolated from volcanic ash.

PubMed

Lee, Dong Wan; Lee, Soon Dong

2011-02-01

A novel actinomycete, designated strain Sco-B14(T), was isolated from volcanic ash collected near Darangshi Oreum (a parasitic or satellite volcano) in Jeju, Republic of Korea. The organism formed well-developed, branched substrate mycelium, on which short chains of non-motile spores were arranged singly or in clusters. Aerial mycelium was not produced. Globose bodies were observed. The reverse colour of colonies was light brown to brown. Diffusible pigments were produced on ISP medium 3 and oatmeal-nitrate agar. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain Sco-B14(T) formed a lineage within the family Micromonosporaceae and was distinct from established genera. The 16S rRNA gene sequence similarity of strain Sco-B14(T) to members of related genera of the family was 95.0-95.7 % to type strains of Catellatospora species, 94.7 % to Hamadaea tsunoensis IMSNU 22005(T), 94.7 % to Longispora albida K97-0003(T) and 94.0 % to Catelliglobosispora koreensis LM 042(T). 3-Hydroxydiaminopimelic acid was the diagnostic diamino acid in the cell-wall peptidoglycan. Whole-cell sugars were glucose, rhamnose, ribose, xylose, arabinose, galactose and mannose. The polar lipids included diphosphatidylglycerol, phosphatidylethanolamine and phosphatidylinositol. The menaquinone profile contained MK-10(H(4)) (49 %), MK-9(H(4)) (24 %), MK-10(H(6)) (18 %) and MK-9(H(6)) (9 %). The predominant fatty acids were iso-C(15 : 0) and C(17 : 0). The DNA G+C content was 70.1 mol%. The combination of chemotaxonomic and phylogenetic data clearly separated the isolate from the type strains of all genera in the family Micromonosporaceae. On the basis of the phylogenetic and chemotaxonomic data presented in this paper, strain Sco-B14(T) is considered to represent a novel species of a new genus in the family Micromonosporaceae, for which the name Allocatelliglobosispora scoriae gen. nov., sp. nov. is proposed. The type strain of Allocatelliglobosispora scoriae is Sco-B14(T) (=KCTC 19661(T) =DSM 45362(T)).

Diversity and evolutionary origins of fungi associated with seeds of a neotropical pioneer tree: a case study for analysing fungal environmental samples.

PubMed

U'ren, Jana M; Dalling, James W; Gallery, Rachel E; Maddison, David R; Davis, E Christine; Gibson, Cara M; Arnold, A Elizabeth

2009-04-01

Fungi associated with seeds of tropical trees pervasively affect seed survival and germination, and thus are an important, but understudied, component of forest ecology. Here, we examine the diversity and evolutionary origins of fungi isolated from seeds of an important pioneer tree (Cecropia insignis, Cecropiaceae) following burial in soil for five months in a tropical moist forest in Panama. Our approach, which relied on molecular sequence data because most isolates did not sporulate in culture, provides an opportunity to evaluate several methods currently used to analyse environmental samples of fungi. First, intra- and interspecific divergence were estimated for the nu-rITS and 5.8S gene for four genera of Ascomycota that are commonly recovered from seeds. Using these values we estimated species boundaries for 527 isolates, showing that seed-associated fungi are highly diverse, horizontally transmitted, and genotypically congruent with some foliar endophytes from the same site. We then examined methods for inferring the taxonomic placement and phylogenetic relationships of these fungi, evaluating the effects of manual versus automated alignment, model selection, and inference methods, as well as the quality of BLAST-based identification using GenBank. We found that common methods such as neighbor-joining and Bayesian inference differ in their sensitivity to alignment methods; analyses of particular fungal genera differ in their sensitivity to alignments; and numerous and sometimes intricate disparities exist between BLAST-based versus phylogeny-based identification methods. Lastly, we used our most robust methods to infer phylogenetic relationships of seed-associated fungi in four focal genera, and reconstructed ancestral states to generate preliminary hypotheses regarding the evolutionary origins of this guild. Our results illustrate the dynamic evolutionary relationships among endophytic fungi, pathogens, and seed-associated fungi, and the apparent evolutionary distinctiveness of saprotrophs. Our study also elucidates the diversity, taxonomy, and ecology of an important group of plant-associated fungi and highlights some of the advantages and challenges inherent in the use of ITS data for environmental sampling of fungi.

Genotypic diversity of oscillatoriacean strains belonging to the genera Geitlerinema and Spirulina determined by 16S rDNA restriction analysis.

PubMed

Margheri, Maria C; Piccardi, Raffaella; Ventura, Stefano; Viti, Carlo; Giovannetti, Luciana

2003-05-01

Genotypic diversity of several cyanobacterial strains mostly isolated from marine or brackish waters, belonging to the genera Geitlerinema and Spirulina, was investigated by amplified 16S ribosomal DNA restriction analysis and compared with morphological features and response to salinity. Cluster analysis was performed on amplified 16S rDNA restriction profiles of these strains along with profiles obtained from sequence data of five Spirulina-like strains, including three representatives of the new genus Halospirulina. Our strains with tightly coiled trichomes from hypersaline waters could be assigned to the Halospirulina genus. Among the uncoiled strains, the two strains of hypersaline origin clustered together and were found to be distant from their counterparts of marine and freshwater habitat. Moreover, another cluster, formed by alkali-tolerant strains with tightly coiled trichomes, was well delineated.

The Strange, Expanding World of Animal Hepaciviruses

PubMed Central

Hartlage, Alex S.; Cullen, John M.; Kapoor, Amit

2017-01-01

Hepaciviruses and pegiviruses constitute two closely related sister genera of the family Flaviviridae. In the past five years, the known phylogenetic diversity of the hepacivirus genera has absolutely exploded. What was once an isolated infection in humans (and possibly other primates) has now expanded to include horses, rodents, bats, colobus monkeys, cows, and, most recently, catsharks, shedding new light on the genetic diversity and host range of hepaciviruses. Interestingly, despite the identification of these many animal and primate hepaciviruses, the equine hepaciviruses remain the closest genetic relatives of the human hepaciviruses, providing an intriguing clue to the zoonotic source of hepatitis C virus. This review summarizes the significance of these studies and discusses current thinking about the origin and evolution of the animal hepaciviruses as well as their potential usage as surrogate models for the study of hepatitis C virus. PMID:27741408

Heterotrophic bacterial flora in aquaculture area around Xuejiadao

NASA Astrophysics Data System (ADS)

Du, Zongjun; Li, Yun; Yu, Dehua; Wang, Xianghong; Chen, Jixiang; Robertson, P. A. W.; Austin, B.; Xu, Huaishu

2002-10-01

From Oct., 1999 to Oct., 2000, the heterotrophic bacterial flora in the aquaculture area around Xuejiadao was investigated. The result shows that the populations of the heterotrophic bacteria are heavier in summer and autumn than those in winter and spring. The average populations in seawater, sediment, the surface of seaweed and the surface of fish are 1.4×104cfu mL-1, 5.4×106cfu g-1, 1.5×106cfu g-1 and 1.8×103cfu cm-2, respectively. A total of 301 strains were isolated, among them 259 were Gram-negative. All the Gram-negative bacteria belong to 13 genera and some genera of Enterobacteriaceae. The communities of bacteria are slightly different among the samples. In the body surface of fish, Genus vibrio is dominant. In the remaining samples, dominant genus is Aeromonas.

Diverse bacteria isolated from microtherm oil-production water.

PubMed

Sun, Ji-Quan; Xu, Lian; Zhang, Zhao; Li, Yan; Tang, Yue-Qin; Wu, Xiao-Lei

2014-02-01

In total, 435 pure bacterial strains were isolated from microtherm oil-production water from the Karamay Oilfield, Xinjiang, China, by using four media: oil-production water medium (Cai medium), oil-production water supplemented with mineral salt medium (CW medium), oil-production water supplemented with yeast extract medium (CY medium), and blood agar medium (X medium). The bacterial isolates were affiliated with 61 phylogenetic groups that belong to 32 genera in the phyla Actinobacteria, Firmicutes, and Proteobacteria. Except for the Rhizobium, Dietzia, and Pseudomonas strains that were isolated using all the four media, using different media led to the isolation of bacteria with different functions. Similarly, nonheme diiron alkane monooxygenase genes (alkB/alkM) also clustered according to the isolation medium. Among the bacterial strains, more than 24 % of the isolates could use n-hexadecane as the sole carbon source for growth. For the first time, the alkane-degrading ability and alkB/alkM were detected in Rhizobium, Rhodobacter, Trichococcus, Micrococcus, Enterococcus, and Bavariicoccus strains, and the alkM gene was detected in Firmicutes strains.

Distribution and identification of culturable airborne microorganisms in a Swiss milk processing facility.

PubMed

Brandl, Helmut; Fricker-Feer, Claudia; Ziegler, Dominik; Mandal, Jyotshna; Stephan, Roger; Lehner, Angelika

2014-01-01

Airborne communities (mainly bacteria) were sampled and characterized (concentration levels and diversity) at 1 outdoor and 6 indoor sites within a Swiss dairy production facility. Air samples were collected on 2 sampling dates in different seasons, one in February and one in July 2012 using impaction bioaerosol samplers. After cultivation, isolates were identified by mass spectrometry (matrix-assisted laser desorption/ionization-time-of-flight) and molecular (sequencing of 16S rRNA and rpoB genes) methods. In general, total airborne particle loads and total bacterial counts were higher in winter than in summer, but remained constant within each indoor sampling site at both sampling times (February and July). Bacterial numbers were generally very low (<100 cfu/m(3) of air) during the different steps of milk powder production. Elevated bacterial concentrations (with mean values of 391 ± 142 and 179 ± 33 cfu/m(3) of air during winter and summer sampling, respectively; n=15) occurred mainly in the "logistics area," where products in closed tins are packed in secondary packaging material and prepared for shipping. However, total bacterial counts at the outdoor site varied, with a 5- to 6-fold higher concentration observed in winter compared with summer. Twenty-five gram-positive and gram-negative genera were identified as part of the airborne microflora, with Bacillus and Staphylococcus being the most frequent genera identified. Overall, the culturable microflora community showed a composition typical and representative for the specific location. Bacterial counts were highly correlated with total airborne particles in the size range 1 to 5 µm, indicating that a simple surveillance system based upon counting of airborne particles could be implemented. The data generated in this study could be used to evaluate the effectiveness of the dairy plant's sanitation program and to identify potential sources of airborne contamination, resulting in increased food safety. Copyright © 2014 American Dairy Science Association. Published by Elsevier Inc. All rights reserved.

Biodegradation of diesel fuel hydrocarbons by mangrove fungi from Red Sea Coast of Saudi Arabia.

PubMed

Ameen, Fuad; Moslem, Mohamed; Hadi, Sarfaraz; Al-Sabri, Ahmed E

2016-03-01

Mangrove sediments were collected from major mangrove stands on the Red Sea Coast of Saudi Arabia. Forty five isolates belonging to 12 genera were purified and five isolates as well as their consortium were found to be able to grow in association with petroleum oil as sole carbon source under in vitro conditions. The isolated strains were identified based on internal transcribed spacer (ITS) rDNA sequence analysis. The fungal strains with the greatest potentiality to degrade diesel oil, without developing antagonistic activity, were identified as Alternaria alternata, Aspergillus terreus, Cladosporium sphaerospermum, Eupenicillium hirayamae and Paecilomyces variotii. As compared to the controls, these fungi accumulated significantly higher biomass, produced extracellular enzymes and liberated larger volumes of CO2. These observations with GC-MS data confirm that these isolates displayed rapid diesel oil bioremoval and when used together as a consortium, there was no antagonistic activity.

Biodegradation of diesel fuel hydrocarbons by mangrove fungi from Red Sea Coast of Saudi Arabia

PubMed Central

Ameen, Fuad; Moslem, Mohamed; Hadi, Sarfaraz; Al-Sabri, Ahmed E.

2015-01-01

Mangrove sediments were collected from major mangrove stands on the Red Sea Coast of Saudi Arabia. Forty five isolates belonging to 12 genera were purified and five isolates as well as their consortium were found to be able to grow in association with petroleum oil as sole carbon source under in vitro conditions. The isolated strains were identified based on internal transcribed spacer (ITS) rDNA sequence analysis. The fungal strains with the greatest potentiality to degrade diesel oil, without developing antagonistic activity, were identified as Alternaria alternata, Aspergillus terreus, Cladosporium sphaerospermum, Eupenicillium hirayamae and Paecilomyces variotii. As compared to the controls, these fungi accumulated significantly higher biomass, produced extracellular enzymes and liberated larger volumes of CO2. These observations with GC–MS data confirm that these isolates displayed rapid diesel oil bioremoval and when used together as a consortium, there was no antagonistic activity. PMID:26981002

Candidiasis in pediatric patients with cancer interned in a university hospital

PubMed Central

De Carvalho Parahym, Ana Maria Rabelo; De Melo, Luciana Resende Bandeira; De Morais, Vera Lúcia Lins; Neves, Rejane Pereira

2009-01-01

Fungi are common causes of infection in immunocompromised patients. Candida species are frequently involved in these cases. In order to investigate candidiasis in pediatric patients with cancer, clinical samples were collected from one hundred and twenty two patients interned in the Oswaldo Cruz University Hospital in Recife, Brazil. Yeasts were isolated from thirty-four clinical samples. The species isolated were: Candida albicans (fourteen isolates), C. parapsilosis (nine isolates), C. guilliermondii (two isolates) and C. tropicalis (two isolates). We found that candidemia was most frequent in patients with malignant hematology and that C. parapsilosis infections caused the highest mortality. PMID:24031365

The blow fly, Chrysomya megacephala, and the house fly, Musca domestica, as mechanical vectors of pathogenic bacteria in Northeast Thailand.

PubMed

Chaiwong, T; Srivoramas, T; Sueabsamran, P; Sukontason, K; Sanford, M R; Sukontason, K L

2014-06-01

The Oriental latrine fly, Chrysomya megacephala (Fabricius) (Diptera: Calliphoridae) and the house fly, Musca domestica L., (Diptera: Muscidae) are synanthropic flies which are adapted to live in close association with human habitations, thereby making them likely mechanical vectors of several pathogens to humans. There were two main aims of this study. The first aim was to determine the prevalence of these two fly species from five types of human habitations including: fresh-food markets, garbage piles, restaurants, school cafeterias and paddy fields, in the Muang Ubon Ratchathani and Warinchamrap districts of Ubon Ratchathani province of Northeast Thailand. Flies collection were conducted monthly from September 2010-October 2011 using a reconstructable funnel trap, containing 1 day-tainted beef offal as bait. A total of 7 750 flies (6 401 C. megacephala and 1 349 M.domestica) were collected. The second aim was to examine the potential of these flies to carry pathogenic bacteria. Bacteria were isolated from 994 individual flies collected using a sweep net (555 C. megacephala and 439 M. domestica). A total of 15 bacterial genera were isolated from the external surfaces, comprising ten genera of gram-negative bacteria and five gram-positive bacteria. The most common bacteria isolated from both species were coagulase-negative staphylococci, followed by Streptococcus group D non-enterococci. Human pathogenic enteric bacteria isolated were Salmonella sp., Shigella sp., Escherichia coli O157:H7, Salmonella typhi, Bacillus sp., and Enterococcus sp., of which S. typhi is the first report of isolation from these fly species. Other human pathogens included Staphylococcus aureus and Pseudomonas aeruginosa. Not only were the number of C. megacephala positive for bacteria significantly higher than for M. domestica, but they were also carrying ~11-12 times greater bacterial load than M. domestica. These data suggest that both fly species should be considered potential mechanical vectors of bacterial pathogens associated with human habitations year-round in this region of Northeast Thailand.

Diversity and Antimicrobial Activity of Culturable Endophytic Fungi Isolated from Moso Bamboo Seeds

PubMed Central

Cai, Chun-Ju; Fan, Li; Gao, Jian; Hou, Cheng-Lin

2014-01-01

Bamboos, regarded as therapeutic agents in ethnomedicine, have been used to inhibit inflammation and enhance natural immunity for a long time in Asia, and there are many bamboo associated fungi with medical and edible value. In the present study, a total of 350 fungal strains were isolated from the uncommon moso bamboo (Phyllostachys edulis) seeds for the first time. The molecular diversity of these endophytic fungi was investigated and bioactive compound producers were screened for the first time. All the fungal endophytes were categorized into 69 morphotypes according to culturable characteristics and their internal transcriber spacer (ITS) regions were analyzed by BLAST search with the NCBI database. The fungal isolates showed high diversity and were divided in Ascomycota (98.0%) and Basidiomycota (2.0%), including at least 19 genera in nine orders. Four particular genera were considered to be newly recorded bambusicolous fungi, including Leptosphaerulina, Simplicillium, Sebacina and an unknown genus in Basidiomycetes. Furthermore, inhibitory effects against clinical pathogens and phytopathogens were screened preliminarily and strains B09 (Cladosporium sp.), B34 (Curvularia sp.), B35 (undefined genus 1), B38 (Penicillium sp.) and zzz816 (Shiraia sp.) displayed broad-spectrum activity against clinical bacteria and yeasts by the agar diffusion method. The crude extracts of isolates B09, B34, B35, B38 and zzz816 under submerged fermentation, also demonstrated various levels of bioactivities against bambusicolous pathogenic fungi. This study is the first report on the antimicrobial activity of endophytic fungi associated with moso bamboo seeds, and the results show that they could be exploited as a potential source of bioactive compounds and plant defense activators. In addition, it is the first time that strains of Shiraia sp. have been isolated and cultured from moso bamboo seeds, and one of them (zzz816) could produce hypocrellin A at high yield, which is significantly different from the other strains published. PMID:24759896

Bacteriological aspects implicated in abdominal surgical emergencies.

PubMed

Israil, A M; Delcaru, C; Palade, R S; Chifiriuc, C; Iordache, C; Vasile, D; Grigoriu, M; Voiculescu, D

2010-01-01

The purpose of the present study was to establish the microbial etiology of abdominal surgical emergencies as well as the relationship between the bacterial etiology and the virulence factors produced by the respective isolated strains. 110 bacterial strains were isolated from 100 randomized clinical cases, operated during 2009-2010 in the First Surgical Clinic of the University Hospital of Bucharest. The clinical cases (sex ratio 52 M/48F aged between 22-85 years old) were classified into three risk groups, as related to their severity. The isolated strains were characterized by cultural, microscopic and biochemical methods. After identification, the bacterial strains were investigated for their virulence potential (adherence to abiotic surface and production of soluble virulence factors). The specimens were collected from different clinical pathologies: diffuse acute peritonitis, biliary duct infections, severe acute pancreatitis followed by septic processes etc. The 110 bacterial (72 aerobic and 38 anaerobic) strains were isolated only in 70 out of 100 cases. Out of these 70 cases, in 45 already submitted to pre-operatory empiric broad spectrum antibiotic therapy, there were isolated 74 strains, whereas in 25 cases without any treatment, there were isolated 36 strains. The etiology was either mono-specific or multi-specific (aerobic-anaerobic associations, especially in old persons). Out of the 30 negative culture cases, 16 were already submitted to pre-operatory parenteral empiric antibiotic therapy at the moment of specimen collection. The aerobic etiology was dominated by Enterobacteriaceae. The most frequent anaerobic species belonged to Clostridium, Peptococcus and Bacteroides genera. It is to be mentioned that the isolation of Bifidobacterium and Veillonella spp. in 11 (10%) severe cases of the studied abdominal surgical emergencies is pleading for the fact that in certain conditions, bacteria belonging usually to commensal gut flora can turn to pathogenic becoming responsive for life-threatening cases. All aerobic and anaerobic strains exhibited some of the following virulence factors: mucinase, esculinase, pore-forming toxins (lecithinase), proteolytic enzymes, adherence ability (slime factor). The presence of these virulence factors (VF) could explain the severity of the clinical aspects. The bacterial etiology of the abdominal surgical emergencies exhibited a very large spectrum, the highest number of strains being of endogenous origin (Enterobacteriaceae and anaerobic strains). It was demonstrated that the isolated strains produced (cell associated and soluble) VF proving in this way their role as important virulence sources in the hospital environment and explaining the large diversity and severity of the clinical abdominal pathology. The results of the present study are also pleading for periodical readjustments of the pre-operatory empiric antibiotic therapy.

Actinomyces hominis sp. nov., isolated from a wound swab.

PubMed

Funke, Guido; Englert, Ralf; Frodl, Reinhard; Bernard, Kathryn A; Stenger, Steffen

2010-07-01

A coryneform bacterium (strain 1094(T)) was isolated from a wound swab taken from an 89-year-old female patient. Chemotaxonomic investigations suggested that this bacterium was related to the genera Actinomyces, Arcanobacterium and Actinobaculum. Phylogenetic analysis of 16S rRNA gene sequences showed that strain 1094(T) was most closely related to Actinomyces europaeus CCUG 32789 A(T) (94.3 % similarity). Phenotypically, the isolate could be separated from its closest phylogenetic neighbours on the basis of being positive for catalase, CAMP reaction, acid phosphatase, N-acetyl-beta-glucosaminidase and raffinose fermentation. Based on the data presented, it is proposed that strain 1094(T) should be classified in a novel species, Actinomyces hominis sp. nov. The type strain is 1094(T) (=CCUG 57540(T) =DSM 22168(T)).

[Diversity of actinomycetes associated with root-knot nematode and their potential for nematode control].

PubMed

Luo, Hong-li; Sun, Man-hong; Xie, Jian-ping; Liu, Zhi-heng; Huang, Ying

2006-08-01

Twenty actinomycetes were isolated from root-knot nematode eggs and females collected from 11 plant root samples infested by Meloidogyne spp.. The isolates were assigned to the genera Streptomyces, Nocardia and Pseudonocardia respectively, based on analysis of morphological characteristics, cell-wall DAPs and 16S rRNA gene sequences. 80% of them were streptomycetes. Biocontrol potential of the isolates against Meloidogyne hapla was evaluated in liquid culture in vitro. The average percentages of egg parasitism, egg hatching, and juvenile mortality were 54.1, 40.4 and 26.2, respectively. Three Streptomyces strains and one Nocardia strain with high pathogenicity in vitro were selected to determine their ability to reduce tomato root galls in greenhouse. The results demonstrated good biocontrol efficacy (31.4%-56.4%) of the strains.

Keratinophilic fungi isolated from soils of long-term fold-grazed, degraded pastures in national parks of Slovakia.

PubMed

Javoreková, Soňa; Labuda, Roman; Maková, Jana; Novák, Ján; Medo, Juraj; Majerčíková, Kamila

2012-09-01

A total of 939 isolates of 11 genera representing 15 species of keratinophilic fungi were isolated and identified from the soils of three long-term fold-grazed pastures in national parks of Slovakia (Pod Ploskou, Strungový príslop, and Pod Kečkou) and one non-fold-grazed pasture in sierra Stolicke vrchy (Diel) using the hair-baiting technique. Keratinophilic fungi were present in all soil samples with a prevalence of Trichophyton ajelloi and Paecilomyces lilacinus. These fungi were more abundant in soil from fold-grazed pasture (Strungový príslop) compared to non-fold-grazed pasture (Diel). The occurrence of the other keratinophilic fungi was substantially lower, likely because of low pH in some soils.

[Screening and characterization of marine bacteria with antibacterial and cytotoxic activities, and existence of PKS I and NRPS genes in bioactive strains].

PubMed

Zhu, Peng; Zheng, Li; Li, Jing; Shao, Jian-zhong; Yan, Xiao-jun

2007-04-01

Antibacterial and cytotoxic activities were screened for marine bacteria which have been isolated from organism, sediments and seawater in China coastal area. The results showed that 42 isolates had antimicrobial activity and 12 isolates had cytotoxicity. Molecular phylogenetic analysis of marine bacteria with cytotoxicity based on 16S rRNA sequences indicated that they were belong to the genera Aerococcus, Agrobacterium, Alteromona, Bacillus, Exiguobacterium, Paracoccus, Pseudoalteromons, Rheinheimera. Furthermore, marine bacteria with cytotoxicity were also screened for PKS I and NRPS genes which could be responsible for bioactive secondary metabolites biosynthesis, 4 strains having KS domain or A domain were obtained, which provide strong evidence that marine bioactive bacteria can produce natural products through PKS and NRPS pathways.

High-quality draft genome sequence of Effusibacillus lacus strain skLN1T, facultative anaerobic spore-former isolated from freshwater lake sediment.

PubMed

Watanabe, Miho; Tokizawa, Riho; Kojima, Hisaya; Fukui, Manabu

2017-01-01

10.1601/nm.25721 strain skLN1 T is the type strain of the type species in the genus 10.1601/nm.25720 which is the one of the genera in the family 10.1601/nm.5070 within the phylum 10.1601/nm.3874. 10.1601/nm.25721 strain skLN1 T is a Gram-positive, spore-forming thermophilic neutrophile isolated from freshwater lake sediment. Here, we present the draft genome sequence of strain skLN1 T , which consists of 3,902,380 bp with a G + C content of 50.38%.

Biodegradation of Metal-EDTA Complexes by an Enriched Microbial Population

PubMed Central

Thomas, Russell A. P.; Lawlor, Kirsten; Bailey, Mark; Macaskie, Lynne E.

1998-01-01

A mixed culture utilizing EDTA as the sole carbon source was isolated from a mixed inoculum of water from the River Mersey (United Kingdom) and sludge from an industrial effluent treatment plant. Fourteen component organisms were isolated from the culture, including representatives of the genera Methylobacterium, Variovorax, Enterobacter, Aureobacterium, and Bacillus. The mixed culture biodegraded metal-EDTA complexes slowly; the biodegradability was in the order Fe>Cu>Co>Ni>Cd. By incorporation of inorganic phosphate into the medium as a precipitant ligand, heavy metals were removed in parallel to EDTA degradation. The mixed culture also utilized a number of possible EDTA degradation intermediates as carbon sources. PMID:9546167

Molecular phylogeny of Panaspis and Afroablepharus skinks (Squamata: Scincidae) in the savannas of sub-Saharan Africa.

PubMed

Medina, Maria F; Bauer, Aaron M; Branch, William R; Schmitz, Andreas; Conradie, Werner; Nagy, Zoltán T; Hibbitts, Toby J; Ernst, Raffael; Portik, Daniel M; Nielsen, Stuart V; Colston, Timothy J; Kusamba, Chifundera; Behangana, Mathias; Rödel, Mark-Oliver; Greenbaum, Eli

2016-07-01

African snake-eyed skinks are relatively small lizards of the genera Panaspis and Afroablepharus. Species allocation of these genera frequently changed during the 20th century based on morphology, ecology, and biogeography. Members of these genera occur primarily in savanna habitats throughout sub-Saharan Africa and include species whose highly conserved morphology poses challenges for taxonomic studies. We sequenced two mitochondrial (16S and cyt b) and two nuclear genes (PDC and RAG1) from 76 Panaspis and Afroablepharus samples from across eastern, central, and southern Africa. Concatenated gene-tree and divergence-dating analyses were conducted to infer phylogenies and biogeographic patterns. Molecular data sets revealed several cryptic lineages, with most radiations occurring during the mid-Miocene to Pliocene. We infer that rifting processes (including the formation of the East African Rift System) and climatic oscillations contributed to the expansion and contraction of savannas, and caused cladogenesis in snake-eyed skinks. Species in Panaspis and Afroablepharus used in this study, including type species for both genera, formed a monophyletic group. As a result, the latter genus should be synonymized with the former, which has priority. Conservatively, we continue to include the West African species P. breviceps and P. togoensis within an expanded Panaspis, but note that they occur in relatively divergent clades, and their taxonomic status may change with improved taxon sampling. Divergence estimates and cryptic speciation patterns of snake-eyed skinks were consistent with previous studies of other savanna vertebrate lineages from the same areas examined in this study. Copyright © 2016 Elsevier Inc. All rights reserved.

[Isolation of actinobacteria with antibiotic associated with soft coral Nephthea sp].

PubMed

Ma, Liang; Zhang, Wenjun; Zhu, Yiguang; Wu, Zhengchao; Saurav, Kumar; Hang, Hui; Zhang, Changsheng

2013-10-04

The present study aims to isolate and identify actinobacteria associated with the soft coral Nephthea sp., and to isolate natural products from these actinobacteria under the guidance of PCR screening for polyketides synthase (PKS) genes. Eleven selective media were used to isolate actinobacteria associated with the soft coral Nephthea sp. collected from Yongxin Island. The isolated actinobacteria were classified on the basis of phylogenetic tree analysis of their 16S rRNA genes. Degenerated primers targeted on conserved KS (ketoacyl-synthase) domain of type I PKS genes were used to screen for potential isolates. The positive isolates were cultured in three different media to check their producing profiles. One bioactive strain that is rich in metabolites was subjected to larger scale fermentation for isolating bioactive natural products. A total of 20 strains were isolated from Nephthea sp., and were categorized into 3 genera including Streptomyces, Dietzia and Salinospora, among which 18 strains were positive in screening with type I PKS genes. Two bioactive compounds rifamycin S and rifamycin W were isolated and identified from Salinospora arenicola SH04. This is the first report of isolating indigenous marine actinobacteria Salinospora from the soft coral Nephthea sp. It provides an example of isolating bioactive secondary metabolites from cultivable actinobacteria associated with Nephthea sp. by PCR screening.

Identification and differentiation of species and strains of Arthrobacter and Microbacterium barkeri isolated from smear cheeses with Amplified Ribosmal DNA Restriction Analysis (ARDRA) and pulsed field gel electrophoresis (PFGE).

PubMed

Hoppe-Seyler, T S; Jaeger, B; Bockelmann, W; Noordman, W H; Geis, A; Heller, K J

2003-09-01

ARDRA (Amplified Ribosomal-DNA Restriction Analysis) was used to differentiate among species and genera of Arthrobacter and Microbacteria. Species-specific restriction patterns of PCR-products were obtained with NciI for Arthrobacter citreus (DSM 20133T), A. sulfureus (DSM 20167T), A. globiformis (DSM 20124T) and A. nicotianae strains (DSM 20123T, MGE 10D, CA13, CA14, isolate 95293, 95294, and 95299), A. rhombi CCUG 38813T, and CCUG 38812, and Microbacterium barkeri strains (DSM 30123T, MGE 10D, CA12 and CA15, isolate 95292, and isolate 95207). All yellow pigmented coryneforme bacteria isolated from the smear of surface ripened cheeses were identified as either A. nicotianae or M. barkeri strains. Using pulsed field gel electrophoresis (PFGE) strain specific restriction pattern for all Arthrobacter species and Microbacteria tested were obtained with restriction enzymes AscI and SpeI.

Rapid isolation of a facultative anaerobic electrochemically active bacterium capable of oxidizing acetate for electrogenesis and azo dyes reduction.

PubMed

Shen, Nan; Yuan, Shi-Jie; Wu, Chao; Cheng, Yuan-Yuan; Song, Xiang-Ning; Li, Wen-Wei; Tong, Zhong-Hua; Yu, Han-Qing

2014-05-01

In this study, 27 strains of electrochemically active bacteria (EAB) were rapidly isolated and their capabilities of extracellular electron transfer were identified using a photometric method based on WO3 nanoclusters. These strains caused color change of WO3 from white to blue in a 24-well agar plate within 40 h. Most of the isolated EAB strains belonged to the genera of Aeromonas and Shewanella. One isolate, Pantoea agglomerans S5-44, was identified as an EAB that can utilize acetate as the carbon source to produce electricity and reduce azo dyes under anaerobic conditions. The results confirmed the capability of P. agglomerans S5-44 for extracellular electron transfer. The isolation of this acetate-utilizing, facultative EBA reveals the metabolic diversity of environmental bacteria. Such strains have great potential for environmental applications, especially at interfaces of aerobic and anaerobic environments, where acetate is the main available carbon source.

Evaluation of the Vitek 2 ANC card for identification of clinical isolates of anaerobic bacteria.

PubMed

Lee, E H L; Degener, J E; Welling, G W; Veloo, A C M

2011-05-01

An evaluation of the Vitek 2 ANC card (bioMérieux, Marcy l'Etoile, France) was performed with 301 anaerobic isolates. Each strain was identified by 16S rRNA gene sequencing, which is considered to be the reference method. The Vitek 2 ANC card correctly identified 239 (79.4%) of the 301 clinical isolates to the genus level, including 100 species that were not represented in the database. Correct species identification was obtained for 60.1% (181/301) of the clinical isolates. For the isolates not identified to the species level, a correct genus identification was obtained for 47.0% of them (47/100), and 16 were accurately designated not identified. Although the Vitek 2 ANC card allows the rapid and acceptable identification of the most common clinically important anaerobic bacteria within 6 h, improvement is required for the identification of members of the genera Fusobacterium, Prevotella, and Actinomyces and certain Gram-positive anaerobic cocci (GPAC).

Isolation and characterization of probiotics from dairies

PubMed Central

Haghshenas, Babak; Nami, Yousef; Almasi, Ali; Abdullah, Norhafizah; Radiah, Dayang; Rosli, Rozita; Barzegari, Abolfazl; Khosroushahi, Ahmad Yari

2017-01-01

Background and Objectives: Probiotics are live microorganisms, which show beneficial health effects on hosts once consumed in sufficient amounts. LAB group can be isolated and characterized from traditional dairy sources. This study aimed at isolating, identifying, and in vitro characterizing (low pH/high bile salt tolerance, antibacterial activity, and antibiotic susceptibility) LAB strains from traditional Iranian dairy products. Materials and Methods: Isolated strains were identified by Gram staining, catalase assay, and 3 molecular identification methods; namely, (GTG) 5-PCR fingerprinting, ARDRA, and 16S rDNA gene sequencing. Results: A total of 19 LAB strains belonging to 4 genera (Lactococcus, Leuconostoc, Lactobacillus and Enterococcus) were identified. Conclusion: The experiments revealed that L. plantarum 15HN, L. lactis subsp. cremoris 44L and E. mundtii 50H strains, which were isolated from shiraz, cheese and shiraz, respectively, displayed a desirable tolerance to low pH and high bile salts, favorable anti-pathogen activity, and acceptable antibiotic susceptibility; hence, they could be considered as novel probiotic candidates and applied in the food industry. PMID:29238459

Bacteria profile and antibiogram of the bacteria isolated from the exposed pulp of dog canine teeth.

PubMed

Almansa Ruiz, José Carlos; Jonker, Annelize; Bosman, Anna-Mari; Steenkamp, Gerhard

2018-04-27

Twenty-seven microbiological samples were taken from root canals (RC) of the canine teeth of 20 dogs where the pulps were non-vital and exposed due to complicated crown fractures. These pulps were cultured for aerobic/anaerobic bacteria. Antimicrobial susceptibility of isolates was determined using the Kirby-Bauer diffusion test. A total of 49 cultivable isolates, belonging to 27 different microbial species and 18 different genera, were recovered from the 27 RCs sampled. Twenty (40.81 per cent) of the cultivable isolates were Gram positive while 29 (59.19 per cent) were Gram negative. Facultative anaerobes were the most common bacteria (77.56 per cent). Aerobic isolates represented 18.36 per cent, and strict anaerobes 4.08 per cent. The antimicrobials with the highest in vitro efficacy were gentamicin (100 per cent) and enrofloxacin (93.32 per cent). © British Veterinary Association (unless otherwise stated in the text of the article) 2018. All rights reserved. No commercial use is permitted unless otherwise expressly granted.

Typing and Subtyping of 83 Clinical Isolates Purified from Surgically Implanted Silicone Feeding Tubes by Random Amplified Polymorphic DNA Amplification

PubMed Central

Dautle, Melanie P.; Ulrich, Ricky L.; Hughes, Thomas A.

2002-01-01

In this study, 83 clinical isolates purified from biofilms colonizing 18 silicone gastrostomy devices (12 “buttons” and six tubes converted to skin level devices) were selected for subtype characterization utilizing genetic analysis. The tubes, previously used for feeding, remained in place for 3 to 47 months (mean, 20.0 months) in children ranging in age from 6 months to 17 years. Classification of specific microbes using random amplified polymorphic DNA (RAPD) analysis revealed genetic similarities and differences among isolates belonging to the same genus. Both gram-positive and -negative bacteria were investigated, including 2 isolates of Bacillus brevis, 4 isolates of Bacillus licheniformis, 2 isolates of Bacillus pumilus, 3 isolates of Enterococcus durans, 19 isolates of Enterococcus faecalis, 8 isolates of Enterococcus faecium, 2 isolates of Enterococcus hirae, 7 isolates of Escherichia coli, 8 isolates of Lactobacillus plantarum, 19 isolates of Staphylococcus aureus, 2 isolates of Staphylococcus epidermidis, and 7 isolates of Staphylococcus saprophyticus. Amplified DNA fragments (amplicons) provided species-specific fingerprints for comparison by agarose gel electrophoresis. A total of 62 distinct RAPD types were categorized from the five genera studied. Typing analysis suggested cross acquisition of E. coli, E. faecalis, and S. aureus in three patient pairs. Genomic polymorphism detection proved efficient and reliable for classifying bacterial subtypes isolated from biofilms adhering to various portions of commonly employed enteral access tubes. PMID:11825951

Rare alluvial sands of El Monte Valley, California (San Diego County), support high herpetofaunal species richness and diversity, despite severe habitat disturbance

USGS Publications Warehouse

Richmond, Jonathan Q.; Rochester, Carlton J.; Smith, Nathan W.; Nordland, Jeffrey A.; Fisher, Robert N.

2016-01-01

We characterized the species richness, diversity, and distribution of amphibians and reptiles inhabiting El Monte Valley, a heavily disturbed, alluvium-filled basin within the lower San Diego River in Lakeside, California. This rare habitat type in coastal southern California is designated as a critical sand resource by the state of California and is currently under consideration for a large-scale sand mining operation with subsequent habitat restoration. We conducted field surveys from June 2015 to May 2016 using drift fence lines with funnel traps, coverboard arrays, walking transects, and road driving. We recorded 1,208 total captures, revealing high species richness and diversity, but with marked unevenness in species' abundances. Snakes were the most species-rich taxonomic group (13 species representing 11 genera), followed by lizards (11 species representing 9 genera). After the southern Pacific rattlesnake (Crotalus oreganus helleri), the California glossy snake (Arizona elegans occidentalis) was the second most frequently detected snake species (n = 23 captures). Amphibian species richness was limited to only three species in three genera. Despite the relatively limited 12-month sampling period, a longstanding drought, and severe habitat disturbance, our study demonstrates that El Monte Valley harbors a rich herpetofauna that includes many sensitive species.

Ubiquity and Diversity of Dissimilatory (Per)chlorate-Reducing Bacteria

PubMed Central

Coates, John D.; Michaelidou, Urania; Bruce, Royce A.; O’Connor, Susan M.; Crespi, Jill N.; Achenbach, Laurie A.

1999-01-01

Environmental contamination with compounds containing oxyanions of chlorine, such as perchlorate or chlorate [(per)chlorate] or chlorine dioxide, has been a constantly growing problem over the last 100 years. Although the fact that microbes reduce these compounds has been recognized for more than 50 years, only six organisms which can obtain energy for growth by this metabolic process have been described. As part of a study to investigate the diversity and ubiquity of microorganisms involved in the microbial reduction of (per)chlorate, we enumerated the (per)chlorate-reducing bacteria (ClRB) in very diverse environments, including pristine and hydrocarbon-contaminated soils, aquatic sediments, paper mill waste sludges, and farm animal waste lagoons. In all of the environments tested, the acetate-oxidizing ClRB represented a significant population, whose size ranged from 2.31 × 103 to 2.4 × 106 cells per g of sample. In addition, we isolated 13 ClRB from these environments. All of these organisms could grow anaerobically by coupling complete oxidation of acetate to reduction of (per)chlorate. Chloride was the sole end product of this reductive metabolism. All of the isolates could also use oxygen as a sole electron acceptor, and most, but not all, could use nitrate. The alternative electron donors included simple volatile fatty acids, such as propionate, butyrate, or valerate, as well as simple organic acids, such as lactate or pyruvate. Oxidized-minus-reduced difference spectra of washed whole-cell suspensions of the isolates had absorbance maxima close to 425, 525, and 550 nm, which are characteristic of type c cytochromes. In addition, washed cell suspensions of all of the ClRB isolates could dismutate chlorite, an intermediate in the reductive metabolism of (per)chlorate, into chloride and molecular oxygen. Chlorite dismutation was a result of the activity of a single enzyme which in pure form had a specific activity of approximately 1,928 μmol of chlorite per mg of protein per min. Analyses of the 16S ribosomal DNA sequences of the organisms indicated that they all belonged to the alpha, beta, or gamma subclass of the Proteobacteria. Several were closely related to members of previously described genera that are not recognized for the ability to reduce (per)chlorate, such as the genera Pseudomonas and Azospirllum. However, many were not closely related to any previously described organism and represented new genera within the Proteobacteria. The results of this study significantly increase the limited number of microbial isolates that are known to be capable of dissimilatory (per)chlorate reduction and demonstrate the hitherto unrecognized phylogenetic diversity and ubiquity of the microorganisms that exhibit this type of metabolism. PMID:10583970

Gram-positive Rod Surveillance for Early Anthrax Detection

PubMed Central

Begier, Elizabeth M.; Barrett, Nancy L.; Mshar, Patricia A.; Johnson, David G.

2005-01-01

Connecticut established telephone-based gram-positive rod (GPR) reporting primarily to detect inhalational anthrax cases more quickly. From March to December 2003, annualized incidence of blood isolates was 21.3/100,000 persons; reports included 293 Corynebacterium spp., 193 Bacillus spp., 73 Clostridium spp., 26 Lactobacillus spp., and 49 other genera. Around-the-clock GPR reporting has described GPR epidemiology and enhanced rapid communication with clinical laboratories. PMID:16229790

MALDI-TOF Mass Spectrometry Is a Fast and Reliable Platform for Identification and Ecological Studies of Species from Family Rhizobiaceae

PubMed Central

Ferreira, Laura; Sánchez-Juanes, Fernando; García-Fraile, Paula; Rivas, Raúl; Mateos, Pedro F.; Martínez-Molina, Eustoquio; González-Buitrago, José Manuel; Velázquez, Encarna

2011-01-01

Family Rhizobiaceae includes fast growing bacteria currently arranged into three genera, Rhizobium, Ensifer and Shinella, that contain pathogenic, symbiotic and saprophytic species. The identification of these species is not possible on the basis of physiological or biochemical traits and should be based on sequencing of several genes. Therefore alternative methods are necessary for rapid and reliable identification of members from family Rhizobiaceae. In this work we evaluated the suitability of Matrix-Assisted Laser Desorption Ionization-Time-of-Flight Mass Spectrometry (MALDI-TOF MS) for this purpose. Firstly, we evaluated the capability of this methodology to differentiate among species of family Rhizobiaceae including those closely related and then we extended the database of MALDI Biotyper 2.0 including the type strains of 56 species from genera Rhizobium, Ensifer and Shinella. Secondly, we evaluated the identification potential of this methodology by using several strains isolated from different sources previously identified on the basis of their rrs, recA and atpD gene sequences. The 100% of these strains were correctly identified showing that MALDI-TOF MS is an excellent tool for identification of fast growing rhizobia applicable to large populations of isolates in ecological and taxonomic studies. PMID:21655291

Bacterial community associated with the trunk latex of Hancornia speciosa Gomes (Apocynaceae) grown in the northeast of Brazil.

PubMed

Silva, Thais Freitas da; Coelho, Marcia Reed Rodrigues; Vollú, Renata Estebanez; de Vasconcelos Goulart, Fátima Regina; Alviano, Daniela Sales; Alviano, Celuta Sales; Seldin, Lucy

2011-03-01

Prevention or cure of different illnesses through the use of plant latex is a worldwide known concept. The antifungal activity of Hancornia speciosa latex has been observed against Candida albicans. However, H. speciosa latex is not a sterile plant exudate and secondary metabolites produced by bacteria could be involved in fungal inhibition. In the present study, the bacterial communities of the latex from three H. speciosa trees were characterized using traditional plating and molecular methods. Twelve strains isolated from the latex samples were clustered into four groups by amplified ribosomal DNA restriction analysis (ARDRA). One representative of each group was sequenced and they were identified as belonging to the genera Bacillus, Klebsiella, Enterobacter and Escherichia. None of the 12 isolates showed antifungal activity against C. albicans. A lack of a microbial origin for the antifungal properties of latex was noted. DGGE profiles generated from each of the three latex samples showed unique patterns. Sequencing of the DGGE bands demonstrated the affiliation with the genera Klebsiella, Pantoea, Enterobacter and Burkholderia. In addition, clone libraries were generated and the phylogenetic distribution of the 50 analyzed clones was similar to that obtained using DGGE. The presence of some potential pathogens should be considered before using H. speciosa latex in folk medicine.

Seasonal Microbial Conditions of Locally Made Yoghurt (Shalom) Marketed in Some Regions of Cameroon

PubMed Central

Moh, Lamye Glory; Keilah, Lunga Paul; Etienne, Pamo Tedonkeng

2017-01-01

The microbial conditions of locally made yoghurt (shalom) marketed in three areas of Cameroon were evaluated during the dry and rainy seasons alongside three commercial brands. A total of ninety-six samples were collected and the microbial conditions were based on total aerobic bacteria (TEB), coliforms, yeasts, and moulds counts as well as the identification of coliforms and yeasts using identification kits. Generally, there was a significant increase (p ≤ 0.05) in total aerobic and coliform counts (especially samples from Bamenda), but a decrease in yeast and mould counts of the same samples during the rainy season when compared to those obtained during the dry season. These counts were mostly greater than the recommended standards. Twenty-one Enterobacteriaceae species belonging to 15 genera were identified from 72 bacterial isolates previously considered as all coliforms. Pantoea sp. (27.77%) was highly represented, found in 41% (dry season) and 50% (rainy season) of samples. In addition, sixteen yeast species belonging to 8 genera were equally identified from 55 yeast isolates and Candida sp. (76.36%) was the most represented. This result suggests that unhygienic practices during production, ignorance, warmer weather, duration of selling, and inadequate refrigeration are the principal causes of higher levels of contamination and unsafe yoghurts. PMID:29423400