Description of a novel taxon associated with Sugarcane Grassy Shoot (SCGS) disease

Phytoplasma is a group of extremely small bacteria (mollicutes). They don’t have a cell wall and any particular shape (pleomorphic). Phytoplasma was first identified by a Japanese scientist Yoji Doi as ‘mycoplasma-like-organisms’ in 1967. They are bacterial parasites of plants and insects. Phytoplasmas reside in plant’s phloem tissue while insects serve as vectors for the transmission of infection from plant to plant. Once disease caused by phytoplasma is established, entire fields of crops might be wiped out. Sugarcane is the world’s fourth largest and commercially important crop. Sugarcane Grassy Shoot disease is related to Rice Yellow Dwarf (RYD) phytoplasma which occurs in sugarcane growing countries throughout the world.

The major characteristic of SCGS disease are stunting, profuse tillering, side shoots, chlorotic stripes and bleached white leaf blades. The common symptoms of SCGS in sugarcane plant are narrowing and partially or almost chlorotic leaf lamina, excessive tillering and witches’ broom symptoms. Severely infected younger plants appear yellowish. The phytoplasma infection often leads to stunted growth, reduction in leaf size, and excessive proliferation of shoots.

Complete leaf chlorosis in SCGS disease &
Grassy appearance of phytoplasma-infected sugarcane plant

It’s important to study the genome of phytoplasma to understand how this tiny microbe causes infection in plants and gets transmitted through insect vectors. Phytoplasma DNA is difficult to isolate and then sequence it further, as researchers have not yet been active in this organism’s laboratory cultivation. Recently, the researchers at NCMR Pune successfully isolated and sequenced sugarcane phytoplasma. In this study, researchers demonstrated the phylogenetic position of 16SrXI-B group phytoplasmas by characterizing the phytoplasma strain associated with Sugarcane Grassy Shoot (SCGS) disease based on comparative genome features and phylogenetic analyses with its closely related phytoplasma taxa and proposed a novel ‘Ca. Phytoplasma’ taxon. This study is the first description of phytoplasma from India and the first description of phytoplasma species based on genome sequences.

Reference: https://pubmed.ncbi.nlm.nih.gov/33289626/

Identification of a strain related to phytoplasma infection in marigold in India

Phytoplasma is a group of extremely small bacteria. They don’t have a cell wall and any particular shape. They are bacterial parasites of plants and insects. Marigold is an important floricultural crop which has been reported as phytoplasma host from many countries like Mexico, India and Hungary. The state of Karnataka is one among the leading producer of Marigold flowers in India. Marigold is the most widely cultivated commercial flower of Karnataka, it has a significant role in the national and international flower trade. Phyllody and associated symptoms of phytoplasma infection have a direct negative impact on the quality and market value of marigold flowers.

Typical disease symptoms on marigold plants, from the left: healthy marigold plant with normal inflorescence, and with virescence and phyllody symptoms.

Researchers conducted field surveys in the marigold growing areas of Karnataka from April 2016 to July 2018 to assess the presence of phytoplasma associated symptoms in the crop. A total of ten symptomatic and two asymptomatic samples were collected and the percentage of disease incidence was determined by taking into account the number of diseased plants for every 100 plants evaluated. DNA extraction was done from the leaves of symptomatic and asymptomatic plants. Characterization of phytoplasma was done using direct and semi-nested PCR assays. The virtual RFLP patterns were generated and compared with the reference phytoplasma strains of different 16Sr groups. The assembled 16Sr sequences and the sequences retrieved from the GenBank were aligned and
a phylogenetic tree was constructed.

The symptoms of phyllody, yellowing, discoloration of florets, stunted growth, purpling and crinkled leaves were observed on marigold plants. The virtual RFLP patterns resulted identical with the one of papaya yellow crinkle phytoplasma, ‘Candidatus Phytoplasma australasia’ classified in the 16SrII group, subgroup D with the similarity coefficient of 1.00. In this study, the symptomatic samples of marigold collected from different fields resulted infected with a ‘Ca. P. australasia’-related strain, which has not been reported in India in this plant species. This study is the first report of 16SrII phytoplasmas associated with marigold phyllody from the Karnataka state.

Reference: http://www.indianjournals.com/ijor.aspx?target=ijor:mollicutes&volume=10&issue=1&article=010

A threat to Sandalwood cultivation in Marayoor Sandalwood Reserve through phytoplasma infections

Santalum album, commonly known as Indian Sandalwood is a semi parasitic plant with fragrant wood and is one of the most valuable trees across the globe. The wood and roots contain ‘sandal oil’ which is valued for use in perfumes, incense, cosmetics, soaps, and medicines. The bark contains tannin, which is used for dye production. The states of Karnataka, Tamil Nadu and Kerala are recognized for natural populations of sandalwood contributing 90% of its distribution in India.

Sandalwood Spike Disease (SSD) is the most destructive disease of sandalwood and one of the major cause for decline in sandalwood production. SSD is known to be associated with the presence of aster yellow (‘Candidatus phytoplasma asteris’ 16SrI-B) phytoplasma. Phytoplasma is a group of extremely small bacteria. They don’t have a cell wall and any particular shape. They are bacterial parasites of plants and insects. SSD is identified based on presence of chlorosis, reduction in leaf size, and shortened internodes, causing leaves to become crowded on twigs with a bushy appearance and stems standout stiffly with spike-like appearance.

Researchers collected the symptomatic sandalwood samples from the Marayoor sandalwood reserve in Kerala state and and they confirmed the presence of 16SrI-B phytoplasma, however 16SrXI-B group phytoplasmas were also identified. These phytoplasmas were present in single or in mixed infection in the collected sandalwood, sugarcane and Indian gooseberry samples from this area. This study is the first report of 16SrXI-B phytoplasma presence in SSD plants.

(A) A diseased and symptomatic sandalwood branch showing typical little leaf and spike symptoms,
(B) A dead sandalwood plant, due to spike disease

The study reconfirmed the earlier observation of the presence of aster yellows phytoplasmas in plants with SSD disease, but those reports were from Chamundi Hill areas of Karnataka state. There is a great fear of complete loss of sandalwood cultivation from Marayoor Sandalwood Reserve region, which is the only naturalised and largest reservoir in the world. The spread of SSD to the neighbouring sandalwood reserves of Marayoor will cause drastic damage. This study reports the first 16SrXI phytoplasmas detection in plants with SSD disease.

Reference: https://www.indianjournals.com/ijor.aspx?target=ijor:mollicutes&volume=10&issue=1&article=011

Phytoplasma associated with witches’ broom disease of a weed plant

(A) Healthy C. bonplandianum plant twigs with inflorescences
(B and C) Symptomatic plants showing witches’ broom, yellowing and little leaf symptoms

Croton bonplandianum is an exotic weed which is wide spreaded in South America and in many countries of the Indian subcontinent. C.bonplandianum is commonly known as three-leaved caper, “Ban Tulsi”, or “Kala Bhangra”. In India, this weed primarily grows in barren lands with sandy clay soil, and is commonly found in the fields of paddy, sugarcane, vegetable and fields of pulse crops. This weed is used in traditional medicine. Other species of the genus Croton are used as ornamentals, indoor plants and are potential biofuel source.

Phytoplasma is a group of extremely small bacteria. They don’t have a cell wall and any particular shape. Phytoplasma was first identified by a Japanese scientist Yoji Doi as ‘mycoplasma-like-organisms’ in 1967. They are bacterial parasites of plants and insects.  The study was conducted by researchers at NCMR pune in order to understand whether there is any phytoplasma association with the witches’ broom disease in C.bonplandianum plant. In this study, four symptomatic plants showing typical witches’ broom, little leaf, yellowing, virescence and phyllody symptoms along with healthy samples were collected from Baramati, India. To confirm the phytoplasma presence, leaves and floral whorls were used for total DNA extraction and further experiments were performed.

The study reported 16SrII group phytoplasma association with witches’ broom disease of C. bonplandianum. This is the first identification of a ‘Candidatus Phytoplasma australasia’-related strains in C. bonplandianum showing witches’ broom symptoms. Studying phytoplasma infection in these weeds becomes highly significant in agriculture as they cause devastating yield losses in diverse crops worldwide. Early identification of phytoplasmas infecting weed is crucial to verify the possibility of the spread of phytoplasmas diseases to commercial crops.

Reference: http://www.indianjournals.com/Mobile/SearchResult.aspx?query=1&mode=gen#&ui-state=dialog

First Phytoplasma whole genome sequence from India

-By Kranti Karande

Phytoplasma is a group of extremely small bacteria. They don’t have a cell wall and any particular shape. Phytoplasma was first identified by a Japanese scientist Yoji Doi as ‘mycoplasma-like-organisms’ in 1967. They are bacterial parasites of plants and insects. 

Sugarcane Grassy Shoot (SCGS) is a disease caused by phytoplasma and the disease leads to 5% to 20% crop loss. SCGS phytoplasma causes severe proliferation of tillers leading to the typical grassy appearance of sugarcane, hence the name grassy shoot is given. Another disease called Bermuda Grass White leaf (BGWL) disease is a destructive phytoplasma disease of Bermuda grass.

Research group of Dr. Amit Yadav at NCMR, NCCS Pune performed whole genome sequencing of two phytoplasma associated with these two diseases. This is the first whole genome sequence of phytoplasma published from India. This sequence data might help in taxonomical characterization of other phytoplasma belonging to the same group.

A sugarcane plant sample (strain SCGS) exhibiting grassy shoot symptoms and a Bermuda grass sample (strain LW01) showing white leaf symptoms were collected from Pune, Maharashtra, India. The presence of phytoplasma was confirmed by 16S rRNA gene sequencing. Researcher confirmed that these phytoplasma strains belonged to the 16SrXI and 16SrXIV phytoplasma groups, respectively. Both genomes were annotated using the NCBI Prokaryotic Genome Annotation Pipeline

The final SCGS assembly contained 29 scaffolds corresponding to 505,173 base pairs of DNA. The genome was found to be 95.43% complete and the GC content was 19.86%.The SCGS genome was predicted to have 404 protein-coding genes, 12 tRNA and two rRNA genes.

Similarly, the LW01 assembly contained 21 scaffolds corresponding to 483,935 base pairs of DNA. This genome was found to be 91.32 % complete and the GC content was 20.46 %. The LW01 genome was predicted to have 425 protein-coding genes, 13 tRNA and three rRNA genes.

Reference: https://www.ncbi.nlm.nih.gov/pubmed/32040378

Phytoplasma: A tiny microbe affecting multiple plant species

By Kranti Karande

Phytoplasma is a group of extremely small bacteria (mollicutes). They don’t have a cell wall and any particular shape (pleomorphic). Phytoplasma was first identified by a Japanese scientist Yoji Doi as ‘mycoplasma-like-organisms’ in 1967. They are bacterial parasites of plants and insects. Phytoplasmas reside in plant’s phloem tissue while insects serve as vectors for the transmission of infection from plant to plant. Once disease caused by phytoplasma is established, entire fields of crops might be wiped out. Indian sandalwood production has been drastically reduced due to phytoplasma infection during the last few decades.

The major characteristic symptom of phytoplasma-caused disease is abnormal growth of the floral organ,green flowers development (phyllody) and numerous growth of tree branches which appears like ‘Witches’ boom’ and reduction in leaf size called ‘little leaf’. Phytoplasma infection also causes curling and yellowing of the leaves (virescence). Disease caused by phytoplasma is called Sandalwood Spike Disease (SSD) in sandalwood plants, as leaves show growth in ‘spike-like’ structure. In few species of plants, such as onion and bamboo, the symptoms of witches’ broom and shortening of plant height (stunting) are observed due to phytoplasma infection.

Some plant pathogens produce virulence factors (effectors) that modulate or interfere with normal host processes for the pathogen’s benefit. Phytoplasma is reported to express secretory proteins including SAP proteins. The major obstacle limiting research in phytoplasma disease is that the organism is difficult to cultivate in vitro (laboratory cultivation).

Dr. Amit Yadav’s research group at NCMR, NCCS Pune is interested in understanding these pathogenic microbes which cause disease in over a thousand species of plants and affect agricultural productivity around the world. They’re interested in understanding genetic factors related to pathogenicity and phytoplasma transmission. They study phytoplasma taxonomy and the role of insect gut micro biome in vectoring ability of the insects.

It’s important to study the genome of this organism to understand how this tiny microbe causes infection in plants and gets transmitted through insect vectors. Phytoplasma DNA is difficult to isolate and then sequence it further, as researchers have not yet been active in this organism’s laboratory cultivation. Dr. Yadav’s research group is currently working on 40-45 symptomatic plants associated with phytoplasma infection. Recently, the group was successful in isolating and sequencing sugarcane phytoplasma. Dr. Yadav’s group is interested in studying other phytoplasma species that are prevalent in India; mainly associated with diseases in economically important pulse crops, sandalwood and weed species; and will be the first to publish phytoplasma genome sequence from India.

There is no cure yet available for this infection. Phytoplasmas are transmitted from plants to plants via the insect vectors. Weeds are also known to be secondary phytoplasma carriers. The weeds around the field are not eradicated by farmers, insects introduce phytoplasma to these weeds and then again to the new crop transmitting phytoplasma infection. Dr. Yadav’s group is also interested in studying the insects’ vector families and mechanism involved in the transmission of infection with Phytoplasma.

Some researchers are trying to understand if phytoplasma are beneficial for the insect vectors transmitting phytoplasma, and why some insects act as transmitters and some not.

Phytoplasmas have one of the smallest genomes as compared to other common bacteria. They completely rely on their host for nutrient supply, growth, spread and reproduction. “How organism with such a small genome affects over 1000 plant species is a curious question that drives me in this study,” said Kiran Kirdat, researcher from Dr. Yadav’s group. She also commented that “Dr. Yadav has been a great motivator for me”.

Dr. Yadav’s group has reported novel species of phytoplasma from various economically important plants like from Mango, Sandalwood, Sugarcane, Tamarind etc. Along with taxonomy study their research focus is also on understanding role of insect gut microbiome in the vectoring ability of these insects. They are interested in understanding the diversity of microbiota in the gut of insect vectors. The Wikipedia page of ‘Sugarcane Grassy Shoot Disease’ has been created by Dr Yadav and he has contributed significantly in other phytoplasma related article on Wikipedia.

Dr. Yadav said that, “People are more aware of phytoplasma associated diseases than a decade ago, when I started working on this notorious bacterium. However, much needs to be done further. Many crops like Sugarcane, Sesame, Sandalwood, coconut in India are facing great challenge to sustain due to phytoplasma infection. We are working on two different aspect to study phytoplasma; one is to understand how this pathogen spread the disease from one plant to other through insect vector and other is to study the genome of this organism to find out disease biology. We are also working on development of reliable and robust detection of phytoplasmas to help on field workers.”

Phytoplasma affects many economically important plant species and thus is a major threat to agriculture economy. Understanding the epidemiology of the phytoplasma diseases, pathogen and genomics of this tiny microorganism will help to cure the infection in future.