Plant growth promoting potential of a bacterial isolate from Tea garden in Assam

Tea is an economically important crop cultivated under warm and humid conditions. Assam is one of the largest tea-producing states in India. The tropical climatic condition gives the tea its unique malty taste but it also makes tea more prone to fungal diseases, which ultimately results in economic loss. Factors like insect/pathogen attack, drought, and heavy metals contribute to significant loss in tea production. Fungal diseases are significant contributors in reduced productivity of tea crops. Specifically, in the tea sector, estimated crop loss due to disease, pest, and weeds is reported to be around 85 million kg. Traditionally, chemical fertilizers, pesticides and insecticides are routinely used in tea gardens to tackle biotic stress factors. These chemicals are harmful for the ecosystem. The presence of pesticide residues in Assam Tea is a cause of great concern.

Plant Growth Promoting Rhizobacteria (PGPR) contributes in plant growth promotion activities, which eventually contributes to better farming. PGPRs colonize plant roots and benefit the plant system by solubilizing minerals such as phosphate, fixing Nitrogen in roots, producing phytohormones such as auxin; producing siderophore, iron scavenging molecules. They are also known to induce systemic resistance thereby developing robust mechanisms to resist biotic and abiotic stress.

Although PGPR associated with crops such as wheat, maize, rice, etc. have been widely studied, it is important to note that, despite Assam representing the largest tea producing states, the rhizosphere of tea has been poorly explored. Even in comparison with other crops, this commercial crop is highly ignored. Thus, it is important to characterize bacteria isolated from the tea rhizosphere and understand their functional potential for PGP traits, including biocontrol activity against pathogenic fungi.

Researchers from Assam University, NCMR-NCCS Pune and SPPU Pune conducted a study in which 23 distinct bacterial morphotypes were isolated from the tea garden of Assam, India. The isolates were screened for their plant growth promotion (PGP) and antifungal traits against three pathogenic fungi, namely Rhizoctonia solani, Corticium rolfsii, and Fomes lamaensis. Out of 23 isolates, 7 isolates showed potential in antifungal activities, amongt which, isolate A6 was found to have promising PGP and antifungal traits. Isolate A6 also exhibited biosurfactant production abilities. Biochemical and molecular characterization revealed its identity as Brevibacterium sediminis.

Biofilm – forming ability of fresh A6 culture was also assessed. Biofilm formation is considered as a prerequisite to colonize plant roots. Only after root colonization, the bacterium can perform the PGP activities. The finding of the study revealed that the isolate A6 forms moderately adherent biofilm. Biosurfactants now addressed as ‘green surfactants’ are well documented in the literature for plant growth promotion by their detrimental effect on pathogens. Hence, these biosurfactants and/or biosurfactant producing microbes are potential substitutes for the harsh chemical pesticides and insecticides being currently used in agriculture.

The study indicated isolate A6’s ability to exhibit PGP properties including the biocontrol activity and biosurfactant production and also to withstand the environmental stress such as its ability to grow and remain metabolically active in acidic pH. Also, the current findings need validation of reproducibility in tea plants. However, this study suggest and indicate that the bacterial isolate Brevibacterium sediminis A6 can be a potential PGPR candidate to be used in combination with other PGPR isolates for improving crop health and eventually the overall crop productivity.


Root-associated microbiome of oxalogenic plant reveals distinct bacterial diversity

Colocasia esculenta (wikimedia)

Colocasia esculenta (Linn) also known as Taro is a tropical plant primarily grown as a vegetable food for its edible corm, and secondarily as a leaf vegetable. Colocasia esculenta grows relatively low to the ground and is a tuberous plant in the family Araceae. Colocasia esculenta has been documented to have oxalogenic properties. Oxalate is found in different environments such as soil and gastrointestinal tracts. Oxalate metabolizing bacteria also known as oxalotrophic bacteria can metabolize oxalate for carbon and energy source. Some plants produce the oxalate crystals as a defense against the herbivory. Oxalotrophy is involved in root colonization by plant-associated bacterial species that may have a positive role in plant growth.

A collaborative study was conducted by researchers at NCMR-NCCS Pune, Yenepoya Research Centre Mangalore, SPPU Pune, University of Nevada, Las Vegas, USA and Zeal College of Engineering and Research Narhe, Pune with the aim of understanding the rhizospheric microbial communities in an oxalogenic plant with the prospects of recognizing possible bacterial species for their capability to metabolize oxalates.

Researchers collected naturally growing Colocasia esculenta (Local name: Arum) plants from a botanical garden near National Centre for Cell Science, Pune. The plant roots and surrounded area were selected and sampled as non-rhizospheric (NS), rhizospheric (S) and rhizoplane (P) soil fractions.  DNA isolation and further 16S rRNA gene amplification and sequencing were done for the samples. Taxonomic assignments and statistical analysis was performed.

Total 852 sequences were obtained from the three root compartments. Out of these, 311 corresponded to rhizosphere, 250 to rhizoplane and 291 were from non-rhizospheric soil. Bacteria belonging to phylum Proteobacteria were recorded relatively higher across all samples. Firmicutes in rhizosphere (S) soil, Actinobacteria in the non-rhizospheric (NS) soil whereas, Bacteroidetes (12%) in the rhizoplane (P) soil were found to the second most abundant groups. Flavobacteriaceae, Enterobacteriaceae, Moraxellaceae and Pseudomonadaceae were the major contributors in the rhizoplane microbial community assemblage. Paenibacillaceae was the major contributor to the rhizospheric microbial community. There were no species belonging to Firmicutes that were shared by nonrhizospheric (NS) and rhizoplane (P) soil samples. However, 6 bacterial species were shared by non-rhizospheric and rhizospheric soil samples. 6 bacterial species were exclusively present in the rhizoplane compartment which constituted of species belonging to genus Exiguobacterium, Paenibacillus, and Solibacillus.

In this study, the results indicate a clear distinction in the microbial community diversity at the phylum level. The complete absence of members of the phyla Cyanobacteria, Gemmatemonadetes and Planctomycetes from the rhizosphere and rhizoplane microbial population supports the role of root exudates in significantly influencing and designing the microbiome. Since Colocasia esculenta is an oxalogenic plant and has been known to release oxalates in the root exudates, the predominance of Proteobacteria in the rhizosphere and rhizoplane microbial communities indicates the oxalotrophic activity which might be a major functional trait of the communities associated. The study concluded that, the rhizoplane has a distinctive composition of microbial partners as compared to the rhizosphere and bulk soil communities in Colocasia esculenta.


Pea plant shapes its rhizosphere microbiome for nutrient uptake and combating stress

-By Kranti Karande

Legume crops like Pea are used as rotation crops along with rice cultivation in long term conservation agriculture experiments in the acidic soils of the North East region of India. Rhizosphere microbiomes present in the soil have significant influence on plant growth and productivity. The study aims at understanding the bacterial composition of microbiomes present in bulk soil as compared to the rhizosphere. It also aims to understand how the pea plant influences the bacterial communities present in soil and the rhizosphere microbiome in order to improve nutrient uptake and stress improvement. Pea cultivation is a practice used in conservation agriculture which strives to preserve and enrich the environmental resources to sustain and improve crop productivity. The study conducted will help devise future strategies to expand pea cultivation and improve soil health in the region. 

Crop rotation is an important and effective strategy as part of conservation agriculture practices. The North East region of India is a fragile, marginal, inaccessible and diverse ecosystem. Generally a mono-cropping system of rice is followed in this region.  Zero tillage (without disturbing the soil) cultivation of pea (Pisum sativum L.) has been considered beneficial to enhance the cropping intensity in the region. The majority of soils in North-East India are acidic in nature. The pH of soil among many other environmental factors has a significant influence on the type of nutrients and microorganisms present in the soil which in turn have an influence on the productivity of crops. Similarly, nutrient and residue management practices like the application of chemical fertilizers often influence the endogenous microbial communities. 

Sample collection for the study was done from experimental fields of the ICAR Research Complex for NEH Region, Umiam, Meghalaya, located in Eastern Himalayan region. Different tillage and residue management treatments were maintained in these fields for the last eight years by alternatively cultivating rice followed by pea cultivation. For microbial community analysis, bulk soil and pea rhizosphere samples were collected from each treatment plot. All the samples were processed for community DNA extraction. Analysis of the chemical properties of the soil samples was done using available methods. Rhizosphere soils were harvested from roots of pea plants. 

Soil pH (1:2.5) was found to be influenced by tillage and nutrient management practices at depth  0-15 cm. The combined effect of tillage and nutrient management practices on available N, P and K content and SOC,TOC of soil were significant. The rhizosphere showed higher diversity indices in comparison to the bulk soil samples. A total of 71 bacterial phyla were detected in the bulk soil and rhizosphere samples. A higher abundance of Firmicutes was recorded in bulk soil (~41.7%) in comparison to the rhizosphere (~17.8%). On the contrary, Proteobacteria were highly abundant in the rhizosphere (~43.9%) in comparison to bulk soil (~18.6%) samples. Significantly higher abundance of Proteobacteria and Bacteroidetes was observed in pea rhizosphere samples in comparison to bulk soil. 

Impact of residue management practices on abundance of specific microbial communities was observed across both rhizosphere and bulk soil samples. The impact of tillage history was also observed on the enrichment of specific OTUs in the bulk soil and rhizospheric soil. Differences in the abundance of 11 genera were recorded in the rhizosphere sample across the history of different tillage treatment. All these genera showed higher abundance in the conventional tillage fields. The correlation between soil properties and microbial community structure was also studied as part of the study. Significant correlations were observed between relative abundance of few bacterial phyla & genera and soil properties in both bulk soil and rhizospheric soil samples. However, the number of significant correlations was low in rhizosphere samples, in comparison to bulk soil samples. 

The study was designed to investigate the effect of long-term exposure to various tillage and residue management practices on the bacterial community structures of the bulk soils and how pea plant (a rotation crop) shapes the rhizosphere communities. A higher species diversity and evenness was observed in rhizospheric samples. There was no significant difference in bacterial richness and evenness among different tillage and residue management treatments in both rhizospheric and bulk soil samples. This is an indication that the plant rhizosphere effect (a plant’s ability to alter microbial communities in rhizospheric soil) is the key driver of alpha diversity. Plants can alter the microbial communities by secreting a variety of nutrients and bioactive molecules into the rhizosphere. Enrichment of specific OYUs in the Pea rhizosphere were also confirmed which can be attributed to the selection pressure of the Pea root. The results of the Pea rhizosphere and bulk soils were consistent with the fact that the majority of members of microbial communities in the host plant are horizontally acquired from the surrounding environment, and the soil is the main reservoir of a plant rhizosphere microbiome. The genus Nitrobacter was at higher abundance in pea rhizosphere samples than bulk soils, suggesting its enrichment by the host plant as Nitrobacter converts nitrite to nitrate making nitrogen more readily available to the host plant. Higher abundance of genes related to nitrogen fixation, phytohormone and siderophore production, phosphate solubilization in the rhizosphere soil substantiate the conclusion that the selection of bacterial communities is always based on plant growth promoting potential in the rhizosphere. 

The study concluded that pea plant is the most dominating selection factor shaping the microbial communities under diverse residue management and tillage treatments. The rhizospheric soil was found to be enriched with bacterial taxa known for plant growth promotion which indicates that the plant plays a role in selecting the rhizospheric communities to meet its requirement of nutrient uptake and combating stress.


The Importance of Studying Soil Microbes and their Interactions

-By Kranti Karande

A large number of micro-organisms are present in the soil ecosystem. There is a popular phrase that, microbes in a handful of soil are more in number compared to the total number of human beings that have ever existed on this planet. Soil life consists of microbes, nematodes, earthworms, ants, other insects, etc. With an estimated 100 billion bacteria that can be found in a handful of soil, it is the largest group of organism in this life-sustaining ecosystem. It is an astonishing reality that this handful of soil contains about 500 individual species of fungi and its mycelium can run up to 50 km in length. Staggering, isn’t it!

Among microbes, bacteria are present in large number in soil. Soil bacteria are mainly responsible for nitrogen fixation. Actinomyecetes, a group of bacteria break large lignin molecules into small molecules. Although not as commonly abundant as bacteria, fungi also significantly contribute in soil health by decomposing organic matter and nutrient recycling. Microbes contribute to soil in various ways by increasing its fertility, aggregation ability and by fixing nitrogen.

Soil ecosystem plays an important role in cultivating high yielding crops. Microbes being the major community of the soil, it is important to study them in order to conserve and nurture soil ecosystem. Studying soil microbes will help in increasing soil fertility and indirectly will contribute for betterment of farmers’ lives and for betterment of society.

Isn’t it interesting to study how these tiny microbes contribute in overall plant health? The very first interaction between plants and microorganisms occurs in soil. Every plant is associated with a unique rhizosphere (root microbial community). The rhizosphere microbial community is selected from large number of microorganisms present in the soil. The symbiotic association (beneficial for both) between rhizosphere and plant leads to complex interactions contributing to plant growth.

The interactions between these three components: plants, microbes and soil system play a critical role in maintaining health of the plant. However, the complexity of these interactions is not yet clear. Research group led by Dr. Kamlesh Jangid at NCMR, NCCS Pune is trying to understand this complex interaction.

Animals call for help when in need, but can you imagine how bacteria might be communicating with each other, especially in the complex soil ecosystem? You may wonder whether they use mobile phones. Not really, but they do have a very advanced communication system. Bacteria produce and release signalling molecules called as Auto inducers (AIs), which are then sensed by neighbouring organisms enabling them to differentiate between self and non-self. Isn’t it fascinating? This mechanism of cell-to-cell communication is known as quorum sensing.

While the mechanism was first discovered in 1970s by the team of Kenneth Nealson, Terry Platt and J. Woodland Hastings, it was not until 1994 that the term “quorum” was associated with this density-dependant mechanism by Fuqua , Winans and Greenberg. Quorum is a mechanism by which bacteria plan and fine-tune their actions as a group rather than as individual cells, thus co-ordinating gene expression and overall microbial population behaviour. Dr. Jangid’s group is discovering the presence of this mechanism across the bacterial community in soils. Studying this mechanism will help the scientific community to better understand the gene regulation in the soil microbes and will answer the questions related to their functional roles.

While studying the most abundant bacteria in soil, affiliated with the phylum Actinobacteria, Dr. Jangid’s group discovered that quorum sensing is extremely under explored partly due to the lack of sensor systems that can detect the huge diversity of AI molecules secreted by this group of bacteria. Specifically, only nine out of the 342 genera in the phylum Actinobacteria are experimentally proven to have this communication mechanism. Dr. Jangid’s group is now developing sensor systems for detecting signalling molecules produced by these bacteria to better understand quorum sensing in this phylum. This research can likely contribute to agricultural, biotechnological, medical and ecological fields.

If we understand the distribution of quorum sensing in soil bacteria, we will be able to modulate soil communities to enhance soil health and increase overall crop productivity. In addition, this will facilitate our understanding of the communication between microbes present in the rhizosphere and why plants are associated with a unique rhizosphere (root microbial community).

It was a great pleasure to interact with Dr. Jangid. In the discussion, Dr. Jangid commented that, “Soil microbiology and bacterial quorum sensing are two separately followed niche fields and their interjection enables us to explore new paths for improving soil health and creating more sustainable agricultural practices. Quorum sensing is also being researched extensively for developing new synthetic analogues that block (or quench) this communication mechanism among pathogenic microbes rather than the conventional anti-microbial drugs in use. The advantage of quorum quenching is that unlike antimicrobial targets, we expect very little to none resurgence towards this approach”.

Link to Dr. Jangid’s lab webpage:

Dr. Kamlesh Jangid with his research team