Bacterial Diversity and CAZyme Potential Revealed in Pandanus Rich Thermal Spring Cluster of India: A Non-cultivable 16S rRNA Sequencing Approach

Dixit, Sangita; Gaur, Mahendra; Subudhi, Enketeswara; Sahoo, Rajesh Kumar; Dey, Suchanda; Mahapatra, Lakshmi Datta; Mandal, Surajit De; Kumar, Nachimuthu Senthil; Anirudh, Hardik

doi:10.3389/fmicb.2021.760573

Cited by 8 publications

(4 citation statements)

References 68 publications

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“…More cellulase and hemicellulase sequences were identified in SKY hot spring than the counterpart numbers detected in an Indian hot spring metagenomic study using water–sediment samples lacking in-situ plant litters 3 . Besides, the metataxonomic described in this current study differed from Deulajhari hot springs and Obsidian Pool that contained Pandanus leaf litters and heat-tolerant plant Juncus tweedyi , respectively 16 , 28 . The microbial and enzyme diversity in SKY hot springs are far more complex than other heated in-situ or ex-situ studies supplemented with insoluble cellulosic biomass 31 – 33 , 42 .…”

Section: Discussionmentioning

confidence: 61%

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Thermophiles and carbohydrate-active enzymes (CAZymes) in biofilm microbial consortia that decompose lignocellulosic plant litters at high temperatures

Liew

Liang

Lau

et al. 2022

Sci Rep

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The SKY hot spring is a unique site filled with a thick layer of plant litter. With the advancement of next-generation sequencing, it is now possible to mine many new biocatalyst sequences. In this study, we aimed to (i) identify the metataxonomic of prokaryotes and eukaryotes in microbial mats using 16S and 18S rRNA markers, (ii) and explore carbohydrate degrading enzymes (CAZymes) that have a high potential for future applications. Green microbial mat, predominantly photosynthetic bacteria, was attached to submerged or floating leaves litter. At the spring head, the sediment mixture consisted of plant debris, predominantly brownish-reddish gelatinous microbial mat, pale tan biofilm, and grey-white filament biofilm. The population in the spring head had a higher percentage of archaea and hyperthermophiles than the green mat. Concurrently, we cataloged nearly 10,000 sequences of CAZymes in both green and brown biofilms using the shotgun metagenomic sequencing approach. These sequences include β-glucosidase, cellulase, xylanase, α-N-arabinofuranosidase, α-l-arabinofuranosidase, and other CAZymes. In conclusion, this work elucidated that SKY is a unique hot spring due to its rich lignocellulosic material, often absent in other hot springs. The data collected from this study serves as a repository of new thermostable macromolecules, in particular families of glycoside hydrolases.

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Section: Discussionmentioning

confidence: 61%

“…The scientific community also pays attention to biofilms at heated places 17 , 18 , 23 , 26 , 27 . Among the earlier publications, only a handful of hot springs contained plant residues, such as Obsidian Pool at Yellowstone Natural Park (USA) 16 , Deulajhari (India) 28 , and Malaysia SKY Hot Springs 29 .…”

Section: Introductionmentioning

confidence: 99%

Thermophiles and carbohydrate-active enzymes (CAZymes) in biofilm microbial consortia that decompose lignocellulosic plant litters at high temperatures

Liew

Liang

Lau

et al. 2022

Sci Rep

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“…All samples were sent to Guangzhou JiRui Gene Technology Co. Ltd. (China) for extraction of DNA and PCR amplification by the Illumina MiSeq Sequencing platform. PCR was performed from V3–V4 variable regions of 16S rRNA to taxonomically identify and analyze the bacteria (Liu et al, 2020 ; Dixit et al, 2021 ).…”

Section: Methodsmentioning

confidence: 99%

Lead induced structural and functional damage and microbiota dysbiosis in the intestine of crucian carp (Carassius auratus)

Liu,

Zhang,

et al. 2023

Front. Microbiol.

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Lead (Pb) is a hazardous pollutant in water environments that can cause significant damage to aquatic animals and humans. In this study, crucian carp (Carassius auratus) were exposed to waterborne Pb for 96 h; then, histopathological analysis, quantitative qPCR analysis, and 16S high-throughput sequencing were performed to explore the effects of Pb on intestinal bioaccumulation, structural damage, oxidative stress, immune response, and microbiota imbalance of C. auratus. After Pb exposure, the intestinal morphology was obviously damaged, including significantly increasing the thickness of the intestinal wall and the number of goblet cells and reducing the depth of intestinal crypts. Pb exposure reduced the mRNA expressions of Claudin-7 and villin-1 while significantly elevated the level of GST, GSH, CAT, IL-8, IL-10, IL-1, and TNF-α. Furthermore, 16S rRNA analysis showed that the Shannon and Simpson indices decreased at 48 h after Pb exposure, and the abundance of pathogenic bacteria (Erysipelotrichaceae, Weeksellaceae, and Vibrionaceae) increased after Pb exposure. In addition, the correlation network analysis found that Proteobacteria were negatively correlated with Firmicutes and positively correlated with Bacteroidetes. Functional prediction analysis of bacteria speculated that the change in intestinal microbiota led to the PPAR signaling pathway and peroxisome function of the intestine of crucian carp was increased, while the immune system and membrane transport function were decreased. Finally, canonical correlation analysis (CCA) found that there were correlations between the intestinal microbiota, morphology, antioxidant factors, and immune factors of crucian carp after Pb exposure. Taken together, our results demonstrated that intestinal flora dysbiosis, morphological disruption, oxidative stress, and immune injury are involved in the toxic damage of Pb exposure to the intestinal structure and function of crucian carp. Meanwhile, Pb exposure rapidly increased the abundance of pathogenic bacteria, leading to intestinal disorders, further aggravating the damage of Pb to intestinal structure and function. These findings provide us a basis for the link between gut microbiome changes and heavy metal toxicity, and gut microbiota can be used as biomarkers for the evaluation of heavy metal pollution in future.

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“…In various locations, including tropical hot springs and Yellowstone National Park, amplicon sequencing and shotgun metagenomics revealed the significance of carbohydrate-utilising microorganisms [ 14 , 15 ]. A study in an Indian hot spring employed functional gene prediction tools (Tax4Fun and Phylogenetic Investigation of Communities by Reconstruction of Unobserved States, PICRUSt) on amplicon data to estimate widespread carbohydrate utilisation across a thermal gradient (43–65 °C) [ 16 ]. MAGs and metatranscriptomic data from this site were subsequently analysed [ 7 , 17 ].…”

Section: Introductionmentioning

confidence: 99%

Integrating multi-platform assembly to recover MAGs from hot spring biofilms: insights into microbial diversity, biofilm formation, and carbohydrate degradation

Liew,

Shahar,

Shamsir

et al. 2024

Environmental Microbiome

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Background Hot spring biofilms provide a window into the survival strategies of microbial communities in extreme environments and offer potential for biotechnological applications. This study focused on green and brown biofilms thriving on submerged plant litter within the Sungai Klah hot spring in Malaysia, characterised by temperatures of 58–74 °C. Using Illumina shotgun metagenomics and Nanopore ligation sequencing, we investigated the microbial diversity and functional potential of metagenome-assembled genomes (MAGs) with specific focus on biofilm formation, heat stress response, and carbohydrate catabolism. Results Leveraging the power of both Illumina short-reads and Nanopore long-reads, we employed an Illumina-Nanopore hybrid assembly approach to construct MAGs with enhanced quality. The dereplication process, facilitated by the dRep tool, validated the efficiency of the hybrid assembly, yielding MAGs that reflected the intricate microbial diversity of these extreme ecosystems. The comprehensive analysis of these MAGs uncovered intriguing insights into the survival strategies of thermophilic taxa in the hot spring biofilms. Moreover, we examined the plant litter degradation potential within the biofilms, shedding light on the participation of diverse microbial taxa in the breakdown of starch, cellulose, and hemicellulose. We highlight that Chloroflexota and Armatimonadota MAGs exhibited a wide array of glycosyl hydrolases targeting various carbohydrate substrates, underscoring their metabolic versatility in utilisation of carbohydrates at elevated temperatures. Conclusions This study advances understanding of microbial ecology on plant litter under elevated temperature by revealing the functional adaptation of MAGs from hot spring biofilms. In addition, our findings highlight potential for biotechnology application through identification of thermophilic lignocellulose-degrading enzymes. By demonstrating the efficiency of hybrid assembly utilising Illumina-Nanopore reads, we highlight the value of combining multiple sequencing methods for a more thorough exploration of complex microbial communities.

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Bacterial Diversity and CAZyme Potential Revealed in Pandanus Rich Thermal Spring Cluster of India: A Non-cultivable 16S rRNA Sequencing Approach

Cited by 8 publications

References 68 publications

Thermophiles and carbohydrate-active enzymes (CAZymes) in biofilm microbial consortia that decompose lignocellulosic plant litters at high temperatures

Thermophiles and carbohydrate-active enzymes (CAZymes) in biofilm microbial consortia that decompose lignocellulosic plant litters at high temperatures

Lead induced structural and functional damage and microbiota dysbiosis in the intestine of crucian carp (Carassius auratus)

Integrating multi-platform assembly to recover MAGs from hot spring biofilms: insights into microbial diversity, biofilm formation, and carbohydrate degradation

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