Komal Kamra | University of Delhi (original) (raw)

Papers by Komal Kamra

European Journal of Protistology, 2020

It is very rare to meet protistologists who are not passionate about their study subject. The vas... more It is very rare to meet protistologists who are not passionate about their study subject. The vast majority of people, however, never get the chance to hear about the work of these researchers. Although every researcher working on protists is likely to be aware of this situation, efforts made and tools employed for dissemination of knowledge are rarely documented. Following a proposal by the Italian Society of Protistology, a workshop at the 2019 VIII European Congress of Protistology in Rome, Italy, was dedicated to protistological knowledge dissemination. Through the many interventions, we discovered the diversity of efforts to reveal the protistan world to the general public, including museum exhibitions and activities, public understanding of science events, citizen science projects, specific book publications, the use of protists in teaching at all levels from primary school children to university undergraduate students, and to a global audience via social media. The participation of the workshop delegates in the discussions indicated that presentations on the wonderful world of protists to the public not only increase the visibility and accessibility of protistology research, but are also very important for the scientific community. Here we report on some of the key aspects of the presentations given in the dissemination workshop.

Canadian Journal of Microbiology, 2014

Influenza virus remains one of the most important disease-causing viruses owing to its high adapt... more Influenza virus remains one of the most important disease-causing viruses owing to its high adaptability and even higher contagious nature. Thus, it poses a constant threat of pandemic, engulfing a large population within the smallest possible time interval. A similar threat was anticipated with the identification of the novel H7N9 virus in China on 30 March 2013. Detection of transmission of the virus between humans has caused a stir with the identification of family clusters along with sporadic infections all across China. In this review we analyze the potential of the novel H7N9 virus as a probable cause of a pandemic and the possible consequences thereof.

Acta Protozoologica, 2001

Summary. Stylonychia ammermanni sp. n. is widely distributed in the backwaters of the Yamuna rive... more Summary. Stylonychia ammermanni sp. n. is widely distributed in the backwaters of the Yamuna river of Delhi region. The cell measures about 135 x 50µm and the vegetative ciliature consists of an adoral zone of membranelles, two parallel undulating membranes, ...

International journal of systematic and evolutionary microbiology, 2020

The spirotrichean ciliate Stylonychia notophora has previously been recorded in India although th... more The spirotrichean ciliate Stylonychia notophora has previously been recorded in India although the descriptions are lacking in detail. It has been suggested several times that the Indian population, S. notophora sensu Sapra and Dass, 1970 collected along the Delhi stretch of the River Yamuna, is identical to Tetmemena pustulata, but this has never been confirmed due to insufficient data for the former. The present study includes detailed descriptions (classical and molecular) of populations of Tetmemena isolated from six locations along the River Yamuna, India. These include four from the Delhi stretch including that from which Sapra and Dass, 1970 isolated their population of S. notophora. Due to the lack of a sufficiently detailed description, the taxonomic status of S. notophora sensu Sapra and Dass, 1970 was not clear. Comparisons among the populations isolated in the present study with previous descriptions of T. pustulata and S. notophora sensu Sapra and Dass, 1970 show only m...

Acta Protozoologica, 2010

The Silent Valley National Park in the state of Kerala, India, ranks high among the biodiversity ... more The Silent Valley National Park in the state of Kerala, India, ranks high among the biodiversity hotspots of the world with 4.8 as the alpha diversity index. The Valley is surrounded by mountain ranges and has a diverse topography with a mosaic of varied habitats that have remained isolated from extraneous influences. The present report describes urostyloid ciliates from diverse ecozones within the core zone of the National Park. Six species of the urostyloids, including Anteholosticha angida n. sp. and Bakuella nilgiri n. sp., were found in soil samples. Anteholosticha angida n. sp. differs from its cogeners in having a unique combination of characters-presence of colourless cortical granules, ~53 macronuclear nodules, ~3 micronuclei, ciliature with 3-4 buccal cirri in a row and 4 dorsal kineties. Bakuella nilgiri n. sp. is characterized by the presence of colourless cortical granules, ~98 macronuclear nodules, 3-4 micronuclei, ciliature with 4-8 buccal cirri in a row and a mid-ven...

Acta Protozoologica, 1999

European Journal of Protistology

Journal of Eukaryotic Microbiology

Ciliated protists have attracted wide interest among researchers from the Indian subcontinent in ... more Ciliated protists have attracted wide interest among researchers from the Indian subcontinent in the last few years. An International Symposium on Ciliate Biology (ISCB) 2018 was held on 04–06 April 2018 at the India Habitat Centre, New Delhi, India. The symposium represented a synergy with International Research Coordination Network for Biodiversity of Ciliates (IRCN‐BC), an affiliate society of International Society of Protistologists (ISOP). The symposium provided a platform for Indian and International delegates to exchange knowledge, present their latest research findings, and establish collaborations as well as creating a networking opportunity for undergraduate and postgraduate students. Nine foreign delegates from 5 countries and 300 Indian delegates actively participated in the event which included 22 oral and 57 poster presentations.

PLOS ONE

Present study, investigates a poorly known species of the genus Sterkiella, i.e., S. tricirrata, ... more Present study, investigates a poorly known species of the genus Sterkiella, i.e., S. tricirrata, based on two populations isolated from soil samples collected from the Colfiorito Regional Park, Umbria Region, Italy and from the Silent Valley National Park, India. Both populations showed a highly similar morphology, however different ontogenetic pattern in between. The study confirms the validity of the species S. tricirrata which was considered to be a species within the Sterkiella histriomuscorum complex. The main ontogenetic difference between S. tricirrata and other species of the genus Sterkiella is the different mode of formation of anlagen V and VI of the proter in the former. In the phylogenetic analyses, Sterkiella tricirrata clusters with Sterkiella sinica within the stylonychine oxytrichids, in a clade away from the type species (Sterkiella cavicola) of the genus Sterkiella. The study highlights the importance of ontogenetic as well as molecular data in shedding light on the polyphyletic behavior of the genus Sterkiella. A detailed description of S. tricirrata based on morphology, ontogenesis and molecular phylogenetic methods is presented. Further, the improved diagnosis has been provided for the genus Sterkiella and the poorly known species S. tricirrata.

Frontiers in Microbiology

Thermophilic environments represent an interesting niche. Among thermophiles, the genus Thermus i... more Thermophilic environments represent an interesting niche. Among thermophiles, the genus Thermus is among the most studied genera. In this study, we have sequenced the genome of Thermus parvatiensis strain RL, a thermophile isolated from Himalayan hot water springs (temperature >96 • C) using PacBio RSII SMRT technique. The small genome (2.01 Mbp) comprises a chromosome (1.87 Mbp) and a plasmid (143 Kbp), designated in this study as pTP143. Annotation revealed a high number of repair genes, a squeezed genome but containing highly plastic plasmid with transposases, integrases, mobile elements and hypothetical proteins (44%). We performed a comparative genomic study of the group Thermus with an aim of analysing the phylogenetic relatedness as well as niche specific attributes prevalent among the group. We compared the reference genome RL with 16 Thermus genomes to assess their phylogenetic relationships based on 16S rRNA gene sequences, average nucleotide identity (ANI), conserved marker genes (31 and 400), pan genome and tetranucleotide frequency. The core genome of the analyzed genomes contained 1,177 core genes and many singleton genes were detected in individual genomes, reflecting a conserved core but adaptive pan repertoire. We demonstrated the presence of metagenomic islands (chromosome:5, plasmid:5) by recruiting raw metagenomic data (from the same niche) against the genomic replicons of T. parvatiensis. We also dissected the CRISPR loci wide all genomes and found widespread presence of this system across Thermus genomes. Additionally, we performed a comparative analysis of competence loci wide Thermus genomes and found evidence for recent horizontal acquisition of the locus and continued dispersal among members reflecting that natural competence is a beneficial survival trait among Thermus members and its acquisition depicts unending evolution in order to accomplish optimal fitness.

Indian Journal of Microbiology, 2017

Pseudomonas fluorescens Pt14 is a non-pathogenic and acidophilic bacterium isolated from acidic s... more Pseudomonas fluorescens Pt14 is a non-pathogenic and acidophilic bacterium isolated from acidic soil (pH 4.65). Genome sequencing of strain Pt14 was performed using Single Molecule Real Time (SMRT) sequencing to get insights into unique existence of this strain in acidic environment. Complete genome sequence of this strain revealed a chromosome of 5,841,722 bp having 5354 CDSs and 88 RNAs. Phylogenomic reconstruction based on 16S rRNA gene, Average Nucleotide Identity (ANI) values and marker proteins revealed that strain Pt14 shared a common clade with P. fluorescens strain A506 and strain SS101. ANI value of strain Pt14 in relation to strain A506 was found 99.23% demonstrating a very close sub-species association at genome level. Further, orthology determination among these three phylogenetic neighbors revealed 4726 core proteins. Functional analysis elucidated significantly higher abundance of sulphur metabolism ([19) which could be one of the reasons for the survival of strain Pt14 under acidic conditions (pH 4.65). Acidophilic bacteria have capability to oxidize sulphur into sulphuric acid which in turn can make the soil acidic and genome-wide analysis of P. fluorescens Pt14 demonstrated that this strain contributes towards making the soil acidic. Keywords Pseudomonas fluorescens Á Genomics Á Acidophilic Á SMRT sequencing Nucleotide sequence Accession Number: The complete genome sequence of Pseudomonas fluorescens strain Pt14 has been deposited at NCBI under Genbank Accession Number CP017296.1.

The Journal of eukaryotic microbiology, Jul 6, 2017

Recent advances in molecular technology have revolutionized research on all aspects of the biolog... more Recent advances in molecular technology have revolutionized research on all aspects of the biology of organisms, including ciliates, and created unprecedented opportunities for pursuing a more integrative approach to investigation of biodiversity. However, this goal is complicated by large gaps and inconsistencies that still exist in the foundation of basic information about biodiversity of ciliates. The present paper reviews issues relating to the taxonomy of ciliates and presents specific recommendations for best practice in the observation and documentation of their biodiversity. This effort stems from a workshop that explored ways to implement six Grand Challenges proposed by the International Research Coordination Network for Biodiversity of Ciliates (IRCN-BC). As part of its commitment to strengthening the knowledge base that supports research on biodiversity of ciliates, the IRCN-BC proposes to populate The Ciliate Guide, an online database, with biodiversity-related data and...

Standards in genomic sciences, 2016

Lampropedia cohaerens strain CT6(T), a non-motile, aerobic and coccoid strain was isolated from a... more Lampropedia cohaerens strain CT6(T), a non-motile, aerobic and coccoid strain was isolated from arsenic rich microbial mats (temperature ~45 °C) of a hot water spring located atop the Himalayan ranges at Manikaran, India. The present study reports the first genome sequence of type strain CT6(T) of genus Lampropedia cohaerens. Sequencing data was generated using the Illumina HiSeq 2000 platform and assembled with ABySS v 1.3.5. The 3,158,922 bp genome was assembled into 41 contigs with a mean GC content of 63.5 % and 2823 coding sequences. Strain CT6(T) was found to harbour genes involved in both the Entner-Duodoroff pathway and non-phosphorylated ED pathway. Strain CT6(T) also contained genes responsible for imparting resistance to arsenic, copper, cobalt, zinc, cadmium and magnesium, providing survival advantages at a thermal location. Additionally, the presence of genes associated with biofilm formation, pyrroloquinoline-quinone production, isoquinoline degradation and mineral pho...

International journal of systematic and evolutionary microbiology, Jan 10, 2016

A Gram-stain-negative, aerobic, rod shaped, non-spore forming yellow pigmented bacterial strain U... more A Gram-stain-negative, aerobic, rod shaped, non-spore forming yellow pigmented bacterial strain UM1T was isolated from the hexachlorocyclohexane (HCH) contaminated dumpsite located at Ummari village in Lucknow, India. The phylogenetic analysis based on 16S rRNA gene sequence similarity revealed that strain UM1T belongs to the genus Luteimonas with Luteimonas aestuarii B9T as the closest neighbour (97.2%). The DNA G+C content of strain UM1T was 64.3 mol%. The major polar lipids were diphosphatidylglycerol (DPG), phosphatidylethanolamine (PE) and phosphatidylglycerol (PG). Main fatty acids were iso-C15:0, iso-C11:0, iso-C11:0-3OH and summed feature 9 (C16:0 10-methyl and/or Iso-C17:1 ω9c). Ubiquinone (Q-8) was the only respiratory quinone. Spermidine was detected as the major polyamine. DNA-DNA relatedness value of strain UM1T with respect to its closest neighbour B9T was well below 70% (~49%). Thus, data obtained from phylogenetic analysis, DNA-DNA hybridization, chemotaxonomical and...

International Journal of Systematic and Evolutionary Microbiology, 2015

A biofilm-forming, Gram-stain-negative, aerobic, catalase-positive but oxidase-negative strain, d... more A biofilm-forming, Gram-stain-negative, aerobic, catalase-positive but oxidase-negative strain, designated CT6 T , was isolated from the microbial mats (,45 8C) of a hot water spring, located within the Himalayan ranges at Manikaran, Himachal Pradesh, India. Strain CT6 T formed white, smooth colonies with irregular margins. Transmission electron microscopy revealed coccoid, non-flagellated cells with wavy boundaries. Phylogenetic analyses based on 16S rRNA gene sequences showed that strain CT6 T belongs to the genus Lampropedia with a sequence similarity value of 95.4 % to the sole member of this genus, Lampropedia hyalina ATCC 11041 T. Strain CT6 T was found to have phosphatidylethanolamine and phosphatidylglycerol as the major polar lipids. The major cellular fatty acids were C 16 : 0 , summed feature 8 (C 18 : 1 v7c and/or C 18 : 1 v6c), C 14 : 0 , C 19 : 0 v8c cyclo and summed feature 3 (C 16 : 1 v7c and/or C 16 : 1 v6c). The major respiratory quinone was ubiquinone-8. The major polyamines were putrescine, spermidine and the betaproteobacterial-specific 2-hydroxyputrescine. The DNA G+C content was 63.5 mol%. Based on the genotypic, phenotypic, physiological and biochemical data, strain CT6 T is considered to represent a novel species of the genus Lampropedia, for which the name Lampropedia cohaerens sp. nov. is proposed (5DSM 100029 T 5KCTC 42939 T 5MCC 2711 T).

European Journal of Protistology, 2015

The oxytrichid ciliate Cyrtohymena citrina, isolated from a soil sample from India, is moderately... more The oxytrichid ciliate Cyrtohymena citrina, isolated from a soil sample from India, is moderately flexible, measures about 105×35μm in life and possesses citrine cortical granules, mainly arranged around cirri and dorsal cilia. Morphology and ontogenesis was investigated using live observation and protargol impregnation, and 18S rDNA was sequenced. Ontogenesis of an Indian population of Urosomoida agilis was also investigated. All three genera included in the Urosomoida-Notohymena-Cyrtohymena group have long been characterized by the ontogenetic feature that "anlagen V and VI of proter originate de novo". This ontogenetic feature has been considered as the sole synapomorphy and an important diagnostic feature of the group. Based on current observations on ontogenesis of C. citrina and U. agilis, and previous observations of C. shii, Notohymena saprai and N. australis, the aforesaid ontogenetic feature is no longer true for the group. Indian population of C. citrina clusters with C. muscorum, Paraurosomoida, Urosomoida, Notohymena and Paraurostyla, and is placed away from Oxytricha granulifera; all oxytrichids in the cluster show deviation(s) from any of the typical oxytrichid features like Oxytricha pattern undulating membrane, 18 frontoventral transverse cirri and fragmentation of dorsal kinety 3. Phylogenetic analyses supported non-monophyly of Cyrtohymena and other flexible-bodied oxytrichids.

Journal of Eukaryotic Microbiology, 2014

Kleinstyla dorsicirrata (Foissner, 1982) Foissner et al., 2002. comb. nov. (basionym: Gastrostyla... more Kleinstyla dorsicirrata (Foissner, 1982) Foissner et al., 2002. comb. nov. (basionym: Gastrostyla dorsicirrata) is a slightly flexible oxytrichid, measuring about 88-115 × 27-46 μm in life and possesses cortical granules. Kleinstyla dorsicirrata is the only oxytrichid known so far with incompletely fragmented dorsal kinety. Morphological and morphogenetic data recognise K. dorsicirrata as nonstylonychine oxytrichid. Molecular phylogeny of an Indian population was inferred using 18S rRNA gene sequences and was examined with respect to oxytrichids exhibiting variation in dorsal kinety fragmentation. Kleinstyla dorsicirrata clusters with Oxytricha lanceolata; this proximity is quite significant as both show deviation from typical oxytrichid fragmentation of dorsal kinety. Molecular phylogeny of Indian population confirms its nonstylonychine oxytrichid status.

European Journal of Protistology, 2015

For years, systematics of three species, Urosomoida agilis (Engelmann, 1862) Hemberger in Foissne... more For years, systematics of three species, Urosomoida agilis (Engelmann, 1862) Hemberger in Foissner, 1982, Urosomoida longa (Gelei and Szabados, 1950) Foissner et al., 1991 and Oxytricha lanceolata Shibuya, 1930, has remained unresolved due to lack of adequate molecular data. Though, it is known since several years that the three species are not very closely related. In the present paper, 18S rRNA gene sequences for two key species, U. agilis and U. longa, and their morphology and morphometry have been analyzed. Molecular phylogeny inferred from maximum likelihood, neighbour joining and maximum parsimony methods has adequately removed ambiguity over their systematics. In phylogenetic trees, U. agilis clustered consistently with non-stylonychine oxytrichids. Both Urosomoida longa and Oxytricha lanceolata clustered consistently away from U. agilis and O. granulifera, the type species of the genera Urosomoida and Oxytricha, respectively. As a result of the current molecular phylogenetic investigation and based on previously inferred morphological and morphogenetic data it is proposed to remove Urosomoida longa and Oxytricha lanceolata from Urosomoida and incertae sedis in Oxytricha, respectively, and establish two new generic combinations, Hemiurosomoida longa gen. nov., comb. nov. and Heterourosomoida lanceolata gen. nov., comb. nov. for them.

Journal of Eukaryotic Microbiology, 2013

Two marine urostylid ciliates, Anteholosticha multicirrata n. sp. and Anteholosticha pulchra (Kah... more Two marine urostylid ciliates, Anteholosticha multicirrata n. sp. and Anteholosticha pulchra (Kahl, 1932) Berger, 2003, were collected from South Korea. These species were identified based on morphology, morphogenesis, and SSU rRNA gene sequence comparison. Anteholosticha multicirrata n. sp. is characterized by the following features: body size 90-125 × 30-45 μm in vivo, shape slender to ellipsoidal in outline, with yellow-greenish cortical granules distributed along and between dorsal kineties and cirri; single contractile vacuole positioned on left at mid-body; three frontal, five to seven frontoterminal, one buccal, one to two pretransverse and four to six transverse cirri; three complete dorsal kineties; one left and one right marginal cirral row; about 117 macronuclear nodules; and three to four micronuclei observed during morphogenesis. In addition, based on the observations of morphogenesis, we found that A. pulchra has pretransverse cirri, which were not described in detail in previous studies. Nuclear small subunit ribosomal RNA (SSU rRNA) gene was used to analyse their phylogenetic relationship, and the gene tree supports that the genus Anteholosticha is a highly polyphyletic group.

European Journal of Protistology, 2020

It is very rare to meet protistologists who are not passionate about their study subject. The vas... more It is very rare to meet protistologists who are not passionate about their study subject. The vast majority of people, however, never get the chance to hear about the work of these researchers. Although every researcher working on protists is likely to be aware of this situation, efforts made and tools employed for dissemination of knowledge are rarely documented. Following a proposal by the Italian Society of Protistology, a workshop at the 2019 VIII European Congress of Protistology in Rome, Italy, was dedicated to protistological knowledge dissemination. Through the many interventions, we discovered the diversity of efforts to reveal the protistan world to the general public, including museum exhibitions and activities, public understanding of science events, citizen science projects, specific book publications, the use of protists in teaching at all levels from primary school children to university undergraduate students, and to a global audience via social media. The participation of the workshop delegates in the discussions indicated that presentations on the wonderful world of protists to the public not only increase the visibility and accessibility of protistology research, but are also very important for the scientific community. Here we report on some of the key aspects of the presentations given in the dissemination workshop.

Canadian Journal of Microbiology, 2014

Influenza virus remains one of the most important disease-causing viruses owing to its high adapt... more Influenza virus remains one of the most important disease-causing viruses owing to its high adaptability and even higher contagious nature. Thus, it poses a constant threat of pandemic, engulfing a large population within the smallest possible time interval. A similar threat was anticipated with the identification of the novel H7N9 virus in China on 30 March 2013. Detection of transmission of the virus between humans has caused a stir with the identification of family clusters along with sporadic infections all across China. In this review we analyze the potential of the novel H7N9 virus as a probable cause of a pandemic and the possible consequences thereof.

Acta Protozoologica, 2001

Summary. Stylonychia ammermanni sp. n. is widely distributed in the backwaters of the Yamuna rive... more Summary. Stylonychia ammermanni sp. n. is widely distributed in the backwaters of the Yamuna river of Delhi region. The cell measures about 135 x 50µm and the vegetative ciliature consists of an adoral zone of membranelles, two parallel undulating membranes, ...

International journal of systematic and evolutionary microbiology, 2020

The spirotrichean ciliate Stylonychia notophora has previously been recorded in India although th... more The spirotrichean ciliate Stylonychia notophora has previously been recorded in India although the descriptions are lacking in detail. It has been suggested several times that the Indian population, S. notophora sensu Sapra and Dass, 1970 collected along the Delhi stretch of the River Yamuna, is identical to Tetmemena pustulata, but this has never been confirmed due to insufficient data for the former. The present study includes detailed descriptions (classical and molecular) of populations of Tetmemena isolated from six locations along the River Yamuna, India. These include four from the Delhi stretch including that from which Sapra and Dass, 1970 isolated their population of S. notophora. Due to the lack of a sufficiently detailed description, the taxonomic status of S. notophora sensu Sapra and Dass, 1970 was not clear. Comparisons among the populations isolated in the present study with previous descriptions of T. pustulata and S. notophora sensu Sapra and Dass, 1970 show only m...

Acta Protozoologica, 2010

The Silent Valley National Park in the state of Kerala, India, ranks high among the biodiversity ... more The Silent Valley National Park in the state of Kerala, India, ranks high among the biodiversity hotspots of the world with 4.8 as the alpha diversity index. The Valley is surrounded by mountain ranges and has a diverse topography with a mosaic of varied habitats that have remained isolated from extraneous influences. The present report describes urostyloid ciliates from diverse ecozones within the core zone of the National Park. Six species of the urostyloids, including Anteholosticha angida n. sp. and Bakuella nilgiri n. sp., were found in soil samples. Anteholosticha angida n. sp. differs from its cogeners in having a unique combination of characters-presence of colourless cortical granules, ~53 macronuclear nodules, ~3 micronuclei, ciliature with 3-4 buccal cirri in a row and 4 dorsal kineties. Bakuella nilgiri n. sp. is characterized by the presence of colourless cortical granules, ~98 macronuclear nodules, 3-4 micronuclei, ciliature with 4-8 buccal cirri in a row and a mid-ven...

Acta Protozoologica, 1999

European Journal of Protistology

Journal of Eukaryotic Microbiology

Ciliated protists have attracted wide interest among researchers from the Indian subcontinent in ... more Ciliated protists have attracted wide interest among researchers from the Indian subcontinent in the last few years. An International Symposium on Ciliate Biology (ISCB) 2018 was held on 04–06 April 2018 at the India Habitat Centre, New Delhi, India. The symposium represented a synergy with International Research Coordination Network for Biodiversity of Ciliates (IRCN‐BC), an affiliate society of International Society of Protistologists (ISOP). The symposium provided a platform for Indian and International delegates to exchange knowledge, present their latest research findings, and establish collaborations as well as creating a networking opportunity for undergraduate and postgraduate students. Nine foreign delegates from 5 countries and 300 Indian delegates actively participated in the event which included 22 oral and 57 poster presentations.

PLOS ONE

Present study, investigates a poorly known species of the genus Sterkiella, i.e., S. tricirrata, ... more Present study, investigates a poorly known species of the genus Sterkiella, i.e., S. tricirrata, based on two populations isolated from soil samples collected from the Colfiorito Regional Park, Umbria Region, Italy and from the Silent Valley National Park, India. Both populations showed a highly similar morphology, however different ontogenetic pattern in between. The study confirms the validity of the species S. tricirrata which was considered to be a species within the Sterkiella histriomuscorum complex. The main ontogenetic difference between S. tricirrata and other species of the genus Sterkiella is the different mode of formation of anlagen V and VI of the proter in the former. In the phylogenetic analyses, Sterkiella tricirrata clusters with Sterkiella sinica within the stylonychine oxytrichids, in a clade away from the type species (Sterkiella cavicola) of the genus Sterkiella. The study highlights the importance of ontogenetic as well as molecular data in shedding light on the polyphyletic behavior of the genus Sterkiella. A detailed description of S. tricirrata based on morphology, ontogenesis and molecular phylogenetic methods is presented. Further, the improved diagnosis has been provided for the genus Sterkiella and the poorly known species S. tricirrata.

Frontiers in Microbiology

Thermophilic environments represent an interesting niche. Among thermophiles, the genus Thermus i... more Thermophilic environments represent an interesting niche. Among thermophiles, the genus Thermus is among the most studied genera. In this study, we have sequenced the genome of Thermus parvatiensis strain RL, a thermophile isolated from Himalayan hot water springs (temperature >96 • C) using PacBio RSII SMRT technique. The small genome (2.01 Mbp) comprises a chromosome (1.87 Mbp) and a plasmid (143 Kbp), designated in this study as pTP143. Annotation revealed a high number of repair genes, a squeezed genome but containing highly plastic plasmid with transposases, integrases, mobile elements and hypothetical proteins (44%). We performed a comparative genomic study of the group Thermus with an aim of analysing the phylogenetic relatedness as well as niche specific attributes prevalent among the group. We compared the reference genome RL with 16 Thermus genomes to assess their phylogenetic relationships based on 16S rRNA gene sequences, average nucleotide identity (ANI), conserved marker genes (31 and 400), pan genome and tetranucleotide frequency. The core genome of the analyzed genomes contained 1,177 core genes and many singleton genes were detected in individual genomes, reflecting a conserved core but adaptive pan repertoire. We demonstrated the presence of metagenomic islands (chromosome:5, plasmid:5) by recruiting raw metagenomic data (from the same niche) against the genomic replicons of T. parvatiensis. We also dissected the CRISPR loci wide all genomes and found widespread presence of this system across Thermus genomes. Additionally, we performed a comparative analysis of competence loci wide Thermus genomes and found evidence for recent horizontal acquisition of the locus and continued dispersal among members reflecting that natural competence is a beneficial survival trait among Thermus members and its acquisition depicts unending evolution in order to accomplish optimal fitness.

Indian Journal of Microbiology, 2017

Pseudomonas fluorescens Pt14 is a non-pathogenic and acidophilic bacterium isolated from acidic s... more Pseudomonas fluorescens Pt14 is a non-pathogenic and acidophilic bacterium isolated from acidic soil (pH 4.65). Genome sequencing of strain Pt14 was performed using Single Molecule Real Time (SMRT) sequencing to get insights into unique existence of this strain in acidic environment. Complete genome sequence of this strain revealed a chromosome of 5,841,722 bp having 5354 CDSs and 88 RNAs. Phylogenomic reconstruction based on 16S rRNA gene, Average Nucleotide Identity (ANI) values and marker proteins revealed that strain Pt14 shared a common clade with P. fluorescens strain A506 and strain SS101. ANI value of strain Pt14 in relation to strain A506 was found 99.23% demonstrating a very close sub-species association at genome level. Further, orthology determination among these three phylogenetic neighbors revealed 4726 core proteins. Functional analysis elucidated significantly higher abundance of sulphur metabolism ([19) which could be one of the reasons for the survival of strain Pt14 under acidic conditions (pH 4.65). Acidophilic bacteria have capability to oxidize sulphur into sulphuric acid which in turn can make the soil acidic and genome-wide analysis of P. fluorescens Pt14 demonstrated that this strain contributes towards making the soil acidic. Keywords Pseudomonas fluorescens Á Genomics Á Acidophilic Á SMRT sequencing Nucleotide sequence Accession Number: The complete genome sequence of Pseudomonas fluorescens strain Pt14 has been deposited at NCBI under Genbank Accession Number CP017296.1.

The Journal of eukaryotic microbiology, Jul 6, 2017

Recent advances in molecular technology have revolutionized research on all aspects of the biolog... more Recent advances in molecular technology have revolutionized research on all aspects of the biology of organisms, including ciliates, and created unprecedented opportunities for pursuing a more integrative approach to investigation of biodiversity. However, this goal is complicated by large gaps and inconsistencies that still exist in the foundation of basic information about biodiversity of ciliates. The present paper reviews issues relating to the taxonomy of ciliates and presents specific recommendations for best practice in the observation and documentation of their biodiversity. This effort stems from a workshop that explored ways to implement six Grand Challenges proposed by the International Research Coordination Network for Biodiversity of Ciliates (IRCN-BC). As part of its commitment to strengthening the knowledge base that supports research on biodiversity of ciliates, the IRCN-BC proposes to populate The Ciliate Guide, an online database, with biodiversity-related data and...

Standards in genomic sciences, 2016

Lampropedia cohaerens strain CT6(T), a non-motile, aerobic and coccoid strain was isolated from a... more Lampropedia cohaerens strain CT6(T), a non-motile, aerobic and coccoid strain was isolated from arsenic rich microbial mats (temperature ~45 °C) of a hot water spring located atop the Himalayan ranges at Manikaran, India. The present study reports the first genome sequence of type strain CT6(T) of genus Lampropedia cohaerens. Sequencing data was generated using the Illumina HiSeq 2000 platform and assembled with ABySS v 1.3.5. The 3,158,922 bp genome was assembled into 41 contigs with a mean GC content of 63.5 % and 2823 coding sequences. Strain CT6(T) was found to harbour genes involved in both the Entner-Duodoroff pathway and non-phosphorylated ED pathway. Strain CT6(T) also contained genes responsible for imparting resistance to arsenic, copper, cobalt, zinc, cadmium and magnesium, providing survival advantages at a thermal location. Additionally, the presence of genes associated with biofilm formation, pyrroloquinoline-quinone production, isoquinoline degradation and mineral pho...

International journal of systematic and evolutionary microbiology, Jan 10, 2016

A Gram-stain-negative, aerobic, rod shaped, non-spore forming yellow pigmented bacterial strain U... more A Gram-stain-negative, aerobic, rod shaped, non-spore forming yellow pigmented bacterial strain UM1T was isolated from the hexachlorocyclohexane (HCH) contaminated dumpsite located at Ummari village in Lucknow, India. The phylogenetic analysis based on 16S rRNA gene sequence similarity revealed that strain UM1T belongs to the genus Luteimonas with Luteimonas aestuarii B9T as the closest neighbour (97.2%). The DNA G+C content of strain UM1T was 64.3 mol%. The major polar lipids were diphosphatidylglycerol (DPG), phosphatidylethanolamine (PE) and phosphatidylglycerol (PG). Main fatty acids were iso-C15:0, iso-C11:0, iso-C11:0-3OH and summed feature 9 (C16:0 10-methyl and/or Iso-C17:1 ω9c). Ubiquinone (Q-8) was the only respiratory quinone. Spermidine was detected as the major polyamine. DNA-DNA relatedness value of strain UM1T with respect to its closest neighbour B9T was well below 70% (~49%). Thus, data obtained from phylogenetic analysis, DNA-DNA hybridization, chemotaxonomical and...

International Journal of Systematic and Evolutionary Microbiology, 2015

A biofilm-forming, Gram-stain-negative, aerobic, catalase-positive but oxidase-negative strain, d... more A biofilm-forming, Gram-stain-negative, aerobic, catalase-positive but oxidase-negative strain, designated CT6 T , was isolated from the microbial mats (,45 8C) of a hot water spring, located within the Himalayan ranges at Manikaran, Himachal Pradesh, India. Strain CT6 T formed white, smooth colonies with irregular margins. Transmission electron microscopy revealed coccoid, non-flagellated cells with wavy boundaries. Phylogenetic analyses based on 16S rRNA gene sequences showed that strain CT6 T belongs to the genus Lampropedia with a sequence similarity value of 95.4 % to the sole member of this genus, Lampropedia hyalina ATCC 11041 T. Strain CT6 T was found to have phosphatidylethanolamine and phosphatidylglycerol as the major polar lipids. The major cellular fatty acids were C 16 : 0 , summed feature 8 (C 18 : 1 v7c and/or C 18 : 1 v6c), C 14 : 0 , C 19 : 0 v8c cyclo and summed feature 3 (C 16 : 1 v7c and/or C 16 : 1 v6c). The major respiratory quinone was ubiquinone-8. The major polyamines were putrescine, spermidine and the betaproteobacterial-specific 2-hydroxyputrescine. The DNA G+C content was 63.5 mol%. Based on the genotypic, phenotypic, physiological and biochemical data, strain CT6 T is considered to represent a novel species of the genus Lampropedia, for which the name Lampropedia cohaerens sp. nov. is proposed (5DSM 100029 T 5KCTC 42939 T 5MCC 2711 T).

European Journal of Protistology, 2015

The oxytrichid ciliate Cyrtohymena citrina, isolated from a soil sample from India, is moderately... more The oxytrichid ciliate Cyrtohymena citrina, isolated from a soil sample from India, is moderately flexible, measures about 105×35μm in life and possesses citrine cortical granules, mainly arranged around cirri and dorsal cilia. Morphology and ontogenesis was investigated using live observation and protargol impregnation, and 18S rDNA was sequenced. Ontogenesis of an Indian population of Urosomoida agilis was also investigated. All three genera included in the Urosomoida-Notohymena-Cyrtohymena group have long been characterized by the ontogenetic feature that "anlagen V and VI of proter originate de novo". This ontogenetic feature has been considered as the sole synapomorphy and an important diagnostic feature of the group. Based on current observations on ontogenesis of C. citrina and U. agilis, and previous observations of C. shii, Notohymena saprai and N. australis, the aforesaid ontogenetic feature is no longer true for the group. Indian population of C. citrina clusters with C. muscorum, Paraurosomoida, Urosomoida, Notohymena and Paraurostyla, and is placed away from Oxytricha granulifera; all oxytrichids in the cluster show deviation(s) from any of the typical oxytrichid features like Oxytricha pattern undulating membrane, 18 frontoventral transverse cirri and fragmentation of dorsal kinety 3. Phylogenetic analyses supported non-monophyly of Cyrtohymena and other flexible-bodied oxytrichids.

Journal of Eukaryotic Microbiology, 2014

Kleinstyla dorsicirrata (Foissner, 1982) Foissner et al., 2002. comb. nov. (basionym: Gastrostyla... more Kleinstyla dorsicirrata (Foissner, 1982) Foissner et al., 2002. comb. nov. (basionym: Gastrostyla dorsicirrata) is a slightly flexible oxytrichid, measuring about 88-115 × 27-46 μm in life and possesses cortical granules. Kleinstyla dorsicirrata is the only oxytrichid known so far with incompletely fragmented dorsal kinety. Morphological and morphogenetic data recognise K. dorsicirrata as nonstylonychine oxytrichid. Molecular phylogeny of an Indian population was inferred using 18S rRNA gene sequences and was examined with respect to oxytrichids exhibiting variation in dorsal kinety fragmentation. Kleinstyla dorsicirrata clusters with Oxytricha lanceolata; this proximity is quite significant as both show deviation from typical oxytrichid fragmentation of dorsal kinety. Molecular phylogeny of Indian population confirms its nonstylonychine oxytrichid status.

European Journal of Protistology, 2015

For years, systematics of three species, Urosomoida agilis (Engelmann, 1862) Hemberger in Foissne... more For years, systematics of three species, Urosomoida agilis (Engelmann, 1862) Hemberger in Foissner, 1982, Urosomoida longa (Gelei and Szabados, 1950) Foissner et al., 1991 and Oxytricha lanceolata Shibuya, 1930, has remained unresolved due to lack of adequate molecular data. Though, it is known since several years that the three species are not very closely related. In the present paper, 18S rRNA gene sequences for two key species, U. agilis and U. longa, and their morphology and morphometry have been analyzed. Molecular phylogeny inferred from maximum likelihood, neighbour joining and maximum parsimony methods has adequately removed ambiguity over their systematics. In phylogenetic trees, U. agilis clustered consistently with non-stylonychine oxytrichids. Both Urosomoida longa and Oxytricha lanceolata clustered consistently away from U. agilis and O. granulifera, the type species of the genera Urosomoida and Oxytricha, respectively. As a result of the current molecular phylogenetic investigation and based on previously inferred morphological and morphogenetic data it is proposed to remove Urosomoida longa and Oxytricha lanceolata from Urosomoida and incertae sedis in Oxytricha, respectively, and establish two new generic combinations, Hemiurosomoida longa gen. nov., comb. nov. and Heterourosomoida lanceolata gen. nov., comb. nov. for them.

Journal of Eukaryotic Microbiology, 2013

Two marine urostylid ciliates, Anteholosticha multicirrata n. sp. and Anteholosticha pulchra (Kah... more Two marine urostylid ciliates, Anteholosticha multicirrata n. sp. and Anteholosticha pulchra (Kahl, 1932) Berger, 2003, were collected from South Korea. These species were identified based on morphology, morphogenesis, and SSU rRNA gene sequence comparison. Anteholosticha multicirrata n. sp. is characterized by the following features: body size 90-125 × 30-45 μm in vivo, shape slender to ellipsoidal in outline, with yellow-greenish cortical granules distributed along and between dorsal kineties and cirri; single contractile vacuole positioned on left at mid-body; three frontal, five to seven frontoterminal, one buccal, one to two pretransverse and four to six transverse cirri; three complete dorsal kineties; one left and one right marginal cirral row; about 117 macronuclear nodules; and three to four micronuclei observed during morphogenesis. In addition, based on the observations of morphogenesis, we found that A. pulchra has pretransverse cirri, which were not described in detail in previous studies. Nuclear small subunit ribosomal RNA (SSU rRNA) gene was used to analyse their phylogenetic relationship, and the gene tree supports that the genus Anteholosticha is a highly polyphyletic group.