Endophytic bacterial community of rice (Oryza sativa L.) from coastal saline zone of West Bengal: 16S rRNA gene based metagenomics approach

Community structure of endophytic bacteria of Sargassum thubergii in the intertidal zone of Qingdao in China

Endophytic bacteria are one of the symbiotic microbial groups closely related to host algae. However, less research on the endophytic bacteria of marine algae. In this study, the endophytic bacterial community of Sargassum thunbergii was investigated using the culture method and high-throughput sequencing. Thirty-nine endophytic bacterial strains, belonging to two phyla, five genera and sixteen species, were isolated, and Firmicutes, Bacillus and Metabacillus indicus were the dominant taxa at the phylum, genus and species level, respectively. High-throughput sequencing revealed 39 phyla and 574 genera of endophytic bacteria, and the dominant phylum was Proteobacteria, while the dominant genus was Ralstonia. The results also indicated that the endophytic bacteria of S. thunbergii included various groups with nitrogen fixation, salt tolerance, pollutant degradation, and antibacterial properties but also contained some pathogenic bacteria. Additionally, the endophytic bacterial community shared a large number of groups with the epiphytic bacteria and bacteria in the surrounding seawater, but the three groups of samples could be clustered separately. In conclusion, there are a variety of functional endophytic bacteria living in S. thunbergii, and the internal condition of algae is a selective factor for the formation of endophytic bacterial communities. This study enriched the database of endophytic bacteria in marine macroalgae, paving the way for further understanding of the interrelationships between endophytic bacteria, macroalgae, and the environment.

Microbiome Analysis Revealed Acholeplasma as a Possible Factor Influencing the Susceptibility to Bacterial Leaf Blight Disease of Two Domestic Rice Cultivars in Vietnam

The microbiomes of two important rice cultivars in Vietnam which differ by their susceptibility to the bacterial leaf blight (BLB) disease were analyzed through 16S rRNA amplicon technology. A higher number of operational taxonomic units and alpha-diversity indices were shown in the BLB-resistant LA cultivar than in the BLB-susceptible TB cultivar. The BLB pathogen Xanthomonas was scantly found (0.003%) in the LA cultivar, whereas was in a significantly higher ratio in the TB cultivar (1.82%), reflecting the susceptibility to BLB of these cultivars. Of special interest was the genus Acholeplasma presented in the BLB-resistant LA cultivar at a high relative abundance (22.32%), however, was minor in the BLB-sensitive TB cultivar (0.09%), raising a question about its roles in controlling the Xanthomonas low in the LA cultivar. It is proposed that Acholeplasma once entered the host plant would hamper other phytopathogens, i.e. Xanthomonas, by yet unknown mechanisms, of which the triggering of the host plants to produce secondary metabolites against pathogens could be a testable hypothesis.

Cutting edge tools in the field of soil microbiology

The study of the whole of the genetic material contained within the microbial populations found in a certain environment is made possible by metagenomics. This technique enables a thorough knowledge of the variety, function, and interactions of microbial communities that are notoriously difficult to research. Due to the limitations of conventional techniques such as culturing and PCR-based methodologies, soil microbiology is a particularly challenging field. Metagenomics has emerged as an effective technique for overcoming these obstacles and shedding light on the dynamic nature of the microbial communities in soil. This review focuses on the principle of metagenomics techniques, their potential applications and limitations in soil microbial diversity analysis. The effectiveness of target-based metagenomics in determining the function of individual genes and microorganisms in soil ecosystems is also highlighted. Targeted metagenomics, including high-throughput sequencing and stable-isotope probing, is essential for studying microbial taxa and genes in complex ecosystems. Shotgun metagenomics may reveal the diversity of soil bacteria, composition, and function impacted by land use and soil management. Sanger, Next Generation Sequencing, Illumina, and Ion Torrent sequencing revolutionise soil microbiome research. Oxford Nanopore Technology (ONT) and Pacific Biosciences (PacBio)'s third and fourth generation sequencing systems revolutionise long-read technology. GeoChip, clone libraries, metagenomics, and metabarcoding help comprehend soil microbial communities. The article indicates that metagenomics may improve environmental management and agriculture despite existing limitations.Metagenomics has revolutionised soil microbiology research by revealing the complete diversity, function, and interactions of microorganisms in soil. Metagenomics is anticipated to continue defining the future of soil microbiology research despite some limitations, such as the difficulty of locating the appropriate sequencing method for specific genes.

Deciphering endemic rhizosphere microbiome community's structure towards the host-derived heavy metals tolerance and plant growth promotion functions in serpentine geo-ecosystem

Environmental microbes in rhizosphere soil and surrounding plants have the potential to alter ecosystem functions. We investigated the microbial communities inhabiting the rhizosphere soils of both serpentine and non-serpentine rhizosphere zones to evaluate their heavy metal tolerance and ability to promote plant growth, utilizing 16S rRNA metabarcoding. The Biolog-EcoPlate technique was employed to determine how abiotic stress factors affect carbon utilization capacity by rhizospheric microbial communities in the serpentine geo-ecosystem. The phyla Proteobacteria, Acidobacteria, Bacteroidetes, and Nitrospirae colonized in the roots of Miscanthus sp., Biden sp., and Oryza sp. showed noticeable differences in different rhizosphere zones. The PICRUSt2-based analysis identified chromium/iron resistance genes (ceuE, chrA) and arsenic resistance genes (arsR, acr3, arsC) abundant in all the studied rhizosphere soils. Notably, nickel resistance genes (nikA, nikD, nikE, and nikR) from Arthrobacter, Microbacterium, and Streptomyces strongly correlate with functions related to solubilization of nickel and an increase in siderophore and IAA production. The abundance of Arthrobacter, Clostridium, Geobacter, Dechloromonas, Pseudomonas, and Flavobacterium was positively correlated with chromium and nickel but negatively correlated with the calcium/magnesium ratio. Our results contribute to a better understanding of the functions of plant-tolerant PGPR interaction in the heavy metal-contaminated rhizosphere and eco-physiological responses from long-term biological weathering.

Salinity Influences Endophytic Bacterial Communities in Rice Roots from the Indian Sundarban Area

In "Sundarbans", the coastal regions of the West Bengal, soil salinity has always been one of the major causes of reduction in yield in these regions. The use of endophytic is a well-demanded strategy to mitigate the problems of salt stress and rice productivity. The present study attempted to analyze rice root endogenous microbial diversity and their relationship with soil salinity and physicochemical factors in the salt stressed region of Sundarbans, India using amplicon metagenomics approaches. Our investigation indicates, that the unique microbiome slightly acidic nutrient enriched non-saline zone is characterized by microbial genera that reported either having plant growth promotion (Flavobacterium, Novosphingobium, and Kocuria) or biocontrol abilities (Leptotrichia), whereas high ionic alkaline saline stressed zone dominated with either salt-tolerant microbes or less characterized endophytes (Arcobacter and Vogesella). The number of genera represented by significantly abundant OTUs was higher in the non-saline zone compared to that of the saline stressed zone probably due to higher nutrient concentrations and the absence of abiotic stress factors including salinity. Physicochemical parameters like nitrogen, phosphorus, and potassium were found significantly positively correlated with Muribaculaceae highly enriched in the non-saline zone. However, relative dissolved oxygen was found significantly negatively correlated with Rikenellaceae and Desulfovibrionaceae, enriched in the non-saline soil. This study first provides the detailed characterizations of rice root endophytic bacterial communities as well as their diversity contributed by measured environmental parameters in salinity Sundarbans areas. Since this study deals with two gradients of salinity, connecting the microbial diversity with the salinity range could be targeted for the use as "bioindicator" taxa and bio-fertilizer formulation in salt-affected regions.

Potential Use of Microbial Community Genomes in Various Dimensions of Agriculture Productivity and Its Management: A Review

Agricultural productivity is highly influenced by its associated microbial community. With advancements in omics technology, metagenomics is known to play a vital role in microbial world studies by unlocking the uncultured microbial populations present in the environment. Metagenomics is a diagnostic tool to target unique signature loci of plant and animal pathogens as well as beneficial microorganisms from samples. Here, we reviewed various aspects of metagenomics from experimental methods to techniques used for sequencing, as well as diversified computational resources, including databases and software tools. Exhaustive focus and study are conducted on the application of metagenomics in agriculture, deciphering various areas, including pathogen and plant disease identification, disease resistance breeding, plant pest control, weed management, abiotic stress management, post-harvest management, discoveries in agriculture, source of novel molecules/compounds, biosurfactants and natural product, identification of biosynthetic molecules, use in genetically modified crops, and antibiotic-resistant genes. Metagenomics-wide association studies study in agriculture on crop productivity rates, intercropping analysis, and agronomic field is analyzed. This article is the first of its comprehensive study and prospects from an agriculture perspective, focusing on a wider range of applications of metagenomics and its association studies.

Insights into the relevance between bacterial endophytic communities and resistance of rice cultivars infected by Xanthomonas oryzae pv. oryzicola

Bacterial leaf streak (BLS) caused by Xanthomonas oryzae pv. oryzicola (Xoc), impacts the production of rice. However, several rice cultivars displayed resistance to Xoc in the field, but scarce information is available about the role of endophytic microbiota in disease resistance. In the present study, the endophytic bacterial communities of resistant and susceptible rice cultivars "CG2" and "IR24", respectively, were analyzed using high throughput 16S rRNA gene amplified sequencing and culture dependent method was further used for bacterial isolation. A total of 452,716 high-quality sequences representing 132 distinct OTUs (Proteobacteria, Actinobacteria, Bacteroidetes, and Firmicutes) and 46 isolates of 16 genera were explored from rice leaves infected with Xoc. Community diversity of endophytic bacteria were higher in the leaves of the resistant cultivars compared to susceptible cultivars upon Xoc infection. Strikingly, this diversity might contribute to natural defense of the resistant cultivar against pathogen. Pantoea, which is pathogen antagonist, was frequently detected in two cultivars and higher abundance were recorded in resistant cultivars. Different abundance genus includes endophytic isolates with marked antagonistic activity to Xoc. The increased proportions of antagonistic bacteria, may contribute to resistance of rice cultivar against Xoc and the Pantoea genus was recruited by Xoc infection play a key role in suppressing the development of BLS disease in rice. Taken together, this work reveals the association between endophytic bacteria and BLS resistance in rice and identification of antagonism-Xoc bacterial communities in rice.

SUPPLEMENTARY INFORMATION

The online version contains supplementary material available at 10.1007/s13205-021-02979-2.

Insights into endophytic bacterial diversity of rice grown across the different agro-ecological regions of West Bengal, India

Endophytes have recently garnered importance worldwide and multiple studies are being conducted to understand their important role and mechanism of interaction inside plants. But before we indulge in their functions it is necessary to dig into the microbiome. This will help to get a complete picture of the microbes intrinsic to their host and understand changes in community composition with respect to their habitats. To fulfil this requirement in our study we have attempted to dissect the endophytic diversity in roots of rice plant grown across the various agro-ecological zones of West Bengal by undergoing amplicon analysis of their 16S rRNA gene. Based on the measured environmental parameters agro-ecological zones can be divided into two groups: nutrient dense groups, representing zones like Gangetic, Northern hill and Terai-Teesta zone characterised by soil with higher levels of nitrogen (N) and total organic carbon and nutrient low groups representing Coastal saline, Red-laterite and Vindhyan zone mainly characterised by high electroconductivity and pH. Gammaproteobacteria, Alphaproteobacteria, Bacilli and Bacteroidetes were mostly abundant in nutrient dense sites whereas Clostridia and Planctomycetes were concentrated in nutrient low sites. Few genera (Aeromonas, Sulfurospirillum, Uliginosibacterium and Acidaminococcus) are present in samples cultivated in all the zones representing the core microbiome of rice in West Bengal, while some other genera like Lactococcus, Dickeya, Azonexus and Pectobacterium are unique to specific zone. Hence it can be concluded that this study has provided some insight in to the endophytic status of rice grown across the state of West Bengal.

Beneficial effects of endophytic Pantoea ananatis with ability to promote rice growth under saline stress

AIMS

Soil salinization severely inhibits plant growth, leading to a low crop yield. The aim of the current study was to isolate endophytic bacteria with the ability to promote rice growth under saline conditions.

METHODS AND RESULTS

We isolated eight salt-tolerant endophytic bacteria from rice roots. An isolated strain D1 was selected due to its ability to stimulate rice seed germination in the presence of NaCl, which was identified as Pantoea ananatis D1. It exhibited multiple plant growth-promoting traits including phosphate solubilization, production of indole-3-acetic acid, 1-aminocyclopropane-1-carboxylic acid (ACC) deaminase and siderophore. Inoculation of P. ananatis D1 obviously enhanced the rice root and shoot growth under normal and saline conditions. It also significantly increased the contents of chlorophyll, total soluble protein, and proline in salt-stressed rice seedlings. Moreover P. ananatis D1 could ameliorate the oxidative stress in rice induced by NaCl and Na₂ CO₃ treatment. The malondialdehyde content and various antioxidant enzyme activities were decreased by P. ananatis D1 inoculation in salt-affected rice. In addition, P. ananatis D1 showed a positive potential for limiting the Na⁺ accumulation and enhancing the K⁺ uptake, leading to an increase of 1·2-1·7 fold in K⁺ /Na⁺ ratio under saline environment.

CONCLUSIONS

Pantoea ananatis D1 has the ability to improve the salt tolerance of rice seedlings.

SIGNIFICANCE AND IMPACT OF THE STUDY

The application of plant growth-promoting bacteria (PGPB) is an eco-friendly strategy to improve plant tolerance towards abiotic stresses. We demonstrated that P. ananatis D1 could be used as an effective halotolerant PGPB to enhance rice growth in different salt-affected soils.

Exploring Rice Root Microbiome; The Variation, Specialization and Interaction of Bacteria and Fungi In Six Tropic Savanna Regions in Ghana

We investigated the root microbiomes of rice sampled from six major rice-producing regions in Ghana using Illumina MiSeq high-throughput amplicon sequencing analysis. The result showed that both bacterial and fungal community compositions were significantly varied across the regions. Bacterial communities were shaped predominantly by biotic factors, including root fungal diversity and abundance. In contrast, fungal communities were influenced by abiotic factors such as soil nitrate, total carbon and soil pH. A negative correlation between the diversity and abundance of root fungi with soil nitrate (NO3-) level was observed. It suggested that there were direct and indirect effects of NO3- on the root-associated bacterial and fungal community composition. The gradient of soil nitrate from North to South parts of Ghana may influence the composition of rice root microbiome. Bacterial community composition was shaped by fungal diversity and abundance; whereas fungal community composition was shaped by bacterial abundance. It suggested the mutualistic interaction of bacteria and fungi at the community level in the rice root microbiome. Specific bacterial and fungal taxa were detected abundantly in the ‘Northern’ regions of Ghana, which were very low or absent from the samples of other regions. The analysis of indicator species suggested that an ‘ecological specialization’ may have occurred which enabled specific microbial taxa to adapt to the local environment, such as the low-nitrate condition in the Northern regions.

Insights on aquatic microbiome of the Indian Sundarbans mangrove areas

BACKGROUND

Anthropogenic perturbations have strong impact on water quality and ecological health of mangrove areas of Indian Sundarbans. Diversity in microbial community composition is important causes for maintaining the health of the mangrove ecosystem. However, microbial communities of estuarine water in Indian Sundarbans mangrove areas and environmental determinants that contribute to those communities were seldom studied.

METHODS

Nevertheless, this study attempted first to report bacterial and archaeal communities simultaneously in the water from Matla River and Thakuran River of Maipith coastal areas more accurately using 16S rRNA gene-based amplicon approaches. Attempt also been made to assess the capability of the environmental parameters for explaining the variation in microbial community composition.

RESULTS

Our investigation indicates the dominancy of halophilic marine bacteria from families Flavobacteriaceae and OM1 clade in the water with lower nutrient load collected from costal regions of a small Island of Sundarban Mangroves (ISM). At higher eutrophic conditions, changes in bacterial communities in Open Marine Water (OMW) were detected, where some of the marine hydrocarbons degrading bacteria under families Oceanospirillaceae and Spongiibacteraceae were dominated. While most abundant bacterial family Rhodobacteracea almost equally (18% of the total community) dominated in both sites. Minor variation in the composition of archaeal community was also observed between OMW and ISM. Redundancy analysis indicates a combination of total nitrogen and dissolved inorganic nutrients for OMW and for ISM, salinity and total nitrogen was responsible for explaining the changes in their respective microbial community composition.

CONCLUSIONS

Our study contributes the first conclusive overview on how do multiple environmental/anthropogenic stressors (salinity, pollution, eutrophication, land-use) affect the Sundarban estuary water and consequently the microbial communities in concert. However, systematic approaches with more samples for evaluating the effect of environmental pollutions on mangrove microbial communities are recommended.

Agricultural and Other Biotechnological Applications Resulting from Trophic Plant-Endophyte Interactions

Endophytic microbiota plays a role not only in supplying plants with the basic nutrients indispensable for their growth, but also helps them in the mechanisms of adaptation to various environmental stresses (i.e., salinity, drought), which is important in the aspect of crop yields. From the agricultural and biotechnological points of view, the knowledge of endophytes and their roles in increasing crop yields, plant resistance to diseases, and helping to survive environmental stress is extremely desirable. This paper reviews some of the beneficial plant–microbe interactions that might be potentially used in both agriculture (plant growth stimulation effect, adaptation of host organisms in salinity and drought conditions, and support of defense mechanisms in plants), and in biotechnology (bioactive metabolites, application of endophytes for bioremediation and biotransformation processes, and production of biofertilizers and biopreparations). Importantly, relatively recent reports on endophytes from the last 10 years are summarized in this paper.