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Malla MA, Ansari FA, Bux F, Kumari S. Re-vitalizing wastewater: Nutrient recovery and carbon capture through microbe-algae synergy using omics-biology. ENVIRONMENTAL RESEARCH 2024; 259:119439. [PMID: 38901811 DOI: 10.1016/j.envres.2024.119439] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/26/2024] [Revised: 05/23/2024] [Accepted: 06/17/2024] [Indexed: 06/22/2024]
Abstract
Increasing amounts of wastewater is the most pervasive and challenging environmental problem globally. Conventional treatment methods are costly and entail huge energy, carbon consumption and greenhouse gas emissions. Owing to their unique ability of carbon capturing and resource recovery, microalgae-microbiome based treatment is a potential approach and is widely used for carbon-neutral wastewater treatment. Microalgae-bacteria synergy (i.e., the functionally beneficial microbial synthetic communities) performs better and enhances carbon-sequestration and nutrient recovery from wastewater treatment plants. This review presents a comprehensive information regarding the potential of microalgae-microbiome as a sustainable agent for wastewater and discusses synergistic approaches for effective nutrient removal. Moreover, this review discusses, the role of omics-biology and Insilco approaches in unravelling and understanding the algae-microbe synergism and their response toward wastewater treatment. Finally, it discusses various microbiome engineering approaches for developing the effective microalgae-bacteria partners for carbon sequestration and nutrient recovery from wastewater, and summarizes future research perspectives on microalgae-microbiome based bioremediation.
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Affiliation(s)
- Muneer Ahmad Malla
- Institute for Water and Wastewater Technology, Durban University of Technology, Durban, South Africa
| | - Faiz Ahmad Ansari
- Institute for Water and Wastewater Technology, Durban University of Technology, Durban, South Africa
| | - Faizal Bux
- Institute for Water and Wastewater Technology, Durban University of Technology, Durban, South Africa
| | - Sheena Kumari
- Institute for Water and Wastewater Technology, Durban University of Technology, Durban, South Africa.
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Sivaprakasam N, Vaithiyanathan S, Gandhi K, Narayanan S, Kavitha PS, Rajasekaran R, Muthurajan R. Metagenomics approaches in unveiling the dynamics of Plant Growth-Promoting Microorganisms (PGPM) vis-à-vis Phytophthora sp. suppression in various crop ecological systems. Res Microbiol 2024; 175:104217. [PMID: 38857835 DOI: 10.1016/j.resmic.2024.104217] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2024] [Revised: 05/02/2024] [Accepted: 06/04/2024] [Indexed: 06/12/2024]
Abstract
Phytophthora species are destructive pathogens causing yield losses in different ecological systems, such as potato, black pepper, pepper, avocado, citrus, and tobacco. The diversity of plant growth-promoting microorganisms (PGPM) plays a crucial role in disease suppression. Knowledge of metagenomics approaches is essential for assessing the dynamics of PGPM and Phytophthora species across various ecosystems, facilitating effective management strategies for better crop protection. This review discusses the dynamic interplay between PGPM and Phytophthora sp. using metagenomics approaches that sheds light on the potential of PGPM strains tailored to specific crop ecosystems to bolster pathogen suppressiveness.
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Affiliation(s)
- Navarasu Sivaprakasam
- Department of Plant Pathology, Tamil Nadu Agricultural University, Coimbatore, Tamil Nadu, India
| | | | - Karthikeyan Gandhi
- Department of Plant Pathology, Tamil Nadu Agricultural University, Coimbatore, Tamil Nadu, India
| | - Swarnakumari Narayanan
- Department of Nematology, Tamil Nadu Agricultural University, Coimbatore, Tamil Nadu, India
| | - P S Kavitha
- School of Post Graduate Studies, Tamil Nadu Agricultural University, Coimbatore, Tamil Nadu, India
| | - Raghu Rajasekaran
- Centre for Plant Molecular Biology & Biotechnology, Tamil Nadu Agricultural University, Coimbatore, Tamil Nadu, India
| | - Raveendran Muthurajan
- Centre for Plant Molecular Biology & Biotechnology, Tamil Nadu Agricultural University, Coimbatore, Tamil Nadu, India
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Zhang X, Li Q, Zhong Z, Huang Z, Bian F. Characterization of the composition, structure, and functional potential of bamboo rhizosphere archaeal communities along a chromium gradient. Front Microbiol 2024; 15:1372403. [PMID: 38694797 PMCID: PMC11061513 DOI: 10.3389/fmicb.2024.1372403] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2024] [Accepted: 03/29/2024] [Indexed: 05/04/2024] Open
Abstract
Introduction Bamboo can be used in the phytoremediation of heavy metal pollution. However, the characteristics of the bamboo rhizosphere archaeal community in Cr-contaminated soil under field conditions remain unclear. Methods In this study, high-throughput sequencing was used to examine the rhizosphere soil archaeal communities of Lei bamboo (Phyllostachys precox) plantations along a Cr pollution gradient. Results The results revealed U-shaped relationships between Cr [total Cr (TCr) or HCl-extractable Cr (ACr)] and two alpha indices (Chao1 and Shannon) of archaea. We also established that high Cr concentrations were associated with a significant increase in the abundance of Thaumarchaeota and significant reductions in the abundances of Crenarchaeota and Euryarchaeota. The archaeal co-occurrence networks reduced in complexity with Cr pollution, decreasing the community's resistance to environmental disturbance. Candidatus nitrosotalea and Nitrososphaeraceae_unclassified (two genera of Thaumarchaeota) were identified as keystone taxa. The community structure of soil archaeal communities was also found to be affected by TCr, ACr, pH, total organic C, and available nutrient (N, P, and K) concentrations, with pH being identified as the most reliable predictor of the archaeal community in assessed soils. Discussion These findings enhance our understanding of microbial responses to Cr pollution and provide a basis for developing more refined approaches for the use of bamboo in the remediation of Cr-contaminated soils.
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Affiliation(s)
- Xiaoping Zhang
- Key Laboratory of State Forestry and Grassland Administration on Bamboo Forest Ecology and Resource Utilization, China National Bamboo Research Center, Hangzhou, China
- National Long-term Observation and Research Station for Forest Ecosystem in Hangzhou-Jiaxing-Huzhou Plain, Hangzhou, China
- Engineering Research Center of Biochar of Zhejiang Province, Hangzhou, China
| | - Qiaoling Li
- Key Laboratory of State Forestry and Grassland Administration on Bamboo Forest Ecology and Resource Utilization, China National Bamboo Research Center, Hangzhou, China
- National Long-term Observation and Research Station for Forest Ecosystem in Hangzhou-Jiaxing-Huzhou Plain, Hangzhou, China
| | - Zheke Zhong
- Key Laboratory of State Forestry and Grassland Administration on Bamboo Forest Ecology and Resource Utilization, China National Bamboo Research Center, Hangzhou, China
- National Long-term Observation and Research Station for Forest Ecosystem in Hangzhou-Jiaxing-Huzhou Plain, Hangzhou, China
- Key Laboratory of High Efficient Processing of Bamboo of Zhejiang Province, Hangzhou, China
| | - Zhiyuan Huang
- Key Laboratory of State Forestry and Grassland Administration on Bamboo Forest Ecology and Resource Utilization, China National Bamboo Research Center, Hangzhou, China
- National Long-term Observation and Research Station for Forest Ecosystem in Hangzhou-Jiaxing-Huzhou Plain, Hangzhou, China
| | - Fangyuan Bian
- Key Laboratory of State Forestry and Grassland Administration on Bamboo Forest Ecology and Resource Utilization, China National Bamboo Research Center, Hangzhou, China
- National Long-term Observation and Research Station for Forest Ecosystem in Hangzhou-Jiaxing-Huzhou Plain, Hangzhou, China
- Key Laboratory of High Efficient Processing of Bamboo of Zhejiang Province, Hangzhou, China
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Sharma S, Kumari M, Vakhlu J. Metatranscriptomic insight into the possible role of clay microbiome in skin disease management. INTERNATIONAL JOURNAL OF BIOMETEOROLOGY 2023; 67:1803-1811. [PMID: 37584759 DOI: 10.1007/s00484-023-02540-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Revised: 07/28/2023] [Accepted: 08/04/2023] [Indexed: 08/17/2023]
Abstract
Even though the scientific documentation is limited, microbiome of healing clay is gradually gaining attention of the scientific community, as a therapeutic force playing an indispensable role in skin disease management. The present study explores the metatranscriptome profile of the Chamliyal clay, widely known for its efficacy in managing various skin problems, using Illumina NextSeq sequencing technology. The gene expression profile of the clay microbial community was analyzed through SEED subsystems of the MG-RAST server. Due to the unavailability of metatranscriptomic data on other therapeutic clays, Chamliyal's profile was compared to non-therapeutic soils, as well as healthy and diseased human skin microbiomes. The study identified Firmicutes, Proteobacteria, and Actinobacteria as the primary active microbial phyla in Chamliyal clay. These resemble those abundant in a healthy human skin microbiome. This is significant as lower levels of these phyla in the skin are linked to inflammatory skin conditions like psoriasis. Interestingly, pathogenic microbes actively metabolizing in the clay were absent. Importantly, 6% of the transcripts annotated to sulfur and iron metabolism, which are known to play a major role in skin disease management. This study provides the most comprehensive and a novel overview of the metatranscriptome of any of the healing clay available worldwide. The findings offer valuable insights into the clay microbiome's potential in managing skin disorders, inspiring future endeavors to harness these insights for medical applications.
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Affiliation(s)
- Sakshi Sharma
- School of Biotechnology, University of Jammu, J&K, 180006, India
| | - Monika Kumari
- School of Biotechnology, University of Jammu, J&K, 180006, India
| | - Jyoti Vakhlu
- School of Biotechnology, University of Jammu, J&K, 180006, India.
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Moreira IS. Biodegradation of Pollutants in the Environment: Omics Approaches. Int J Mol Sci 2023; 24:ijms24108815. [PMID: 37240161 DOI: 10.3390/ijms24108815] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Accepted: 05/12/2023] [Indexed: 05/28/2023] Open
Abstract
This special edition intends to highlight how omics approaches have been used in biodegradation studies to understand the mechanisms involved and improve biodegradation processes [...].
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Affiliation(s)
- Irina S Moreira
- CBQF-Centro de Biotecnologia e Química Fina, Laboratório Associado, Escola Superior de Biotecnologia, Universidade Católica Portuguesa, Rua Diogo Botelho 1327, 4169-005 Porto, Portugal
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Gautam K, Sharma P, Dwivedi S, Singh A, Gaur VK, Varjani S, Srivastava JK, Pandey A, Chang JS, Ngo HH. A review on control and abatement of soil pollution by heavy metals: Emphasis on artificial intelligence in recovery of contaminated soil. ENVIRONMENTAL RESEARCH 2023; 225:115592. [PMID: 36863654 DOI: 10.1016/j.envres.2023.115592] [Citation(s) in RCA: 18] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Revised: 02/10/2023] [Accepted: 02/27/2023] [Indexed: 06/18/2023]
Abstract
"Save Soil Save Earth" is not just a catchphrase; it is a necessity to protect soil ecosystem from the unwanted and unregulated level of xenobiotic contamination. Numerous challenges such as type, lifespan, nature of pollutants and high cost of treatment has been associated with the treatment or remediation of contaminated soil, whether it be either on-site or off-site. Due to the food chain, the health of non-target soil species as well as human health were impacted by soil contaminants, both organic and inorganic. In this review, the use of microbial omics approaches and artificial intelligence or machine learning has been comprehensively explored with recent advancements in order to identify the sources, characterize, quantify, and mitigate soil pollutants from the environment for increased sustainability. This will generate novel insights into methods for soil remediation that will reduce the time and expense of soil treatment.
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Affiliation(s)
- Krishna Gautam
- Centre for Energy and Environmental Sustainability, Lucknow, India
| | - Poonam Sharma
- Department of Bioengineering, Integral University, Lucknow, India
| | - Shreya Dwivedi
- Institute for Industrial Research & Toxicology, Ghaziabad, Lucknow, India
| | - Amarnath Singh
- Comprehensive Cancer Center, The Ohio State University and James Cancer Hospital, Columbus, OH, USA
| | - Vivek Kumar Gaur
- Centre for Energy and Environmental Sustainability, Lucknow, India; Amity Institute of Biotechnology, Amity University Uttar Pradesh, Lucknow Campus, Lucknow, India; School of Energy and Chemical Engineering, UNIST, Ulsan, 44919, Republic of Korea.
| | - Sunita Varjani
- School of Energy and Environment, City University of Hong Kong, Tat Chee Avenue, Kowloon, Hong Kong; Sustainability Cluster, School of Engineering, University of Petroleum and Energy Studies, Dehradun, 248 007, India.
| | | | - Ashok Pandey
- Centre for Energy and Environmental Sustainability, Lucknow, India; Centre for Innovation and Translational Research, CSIR-Indian Institute of Toxicology Research, Lucknow, 226 001, India; Sustainability Cluster, School of Engineering, University of Petroleum and Energy Studies, Dehradun, 248 007, India
| | - Jo-Shu Chang
- Department of Chemical Engineering, National Cheng Kung University, Tainan, Taiwan
| | - Huu Hao Ngo
- Centre for Technology in Water and Wastewater, School of Civil and Environmental, Engineering, University of Technology Sydney, Sydney, NSW, 2007, Australia
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Diwan D, Rashid MM, Vaishnav A. Current understanding of plant-microbe interaction through the lenses of multi-omics approaches and their benefits in sustainable agriculture. Microbiol Res 2022; 265:127180. [PMID: 36126490 DOI: 10.1016/j.micres.2022.127180] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Revised: 08/26/2022] [Accepted: 08/27/2022] [Indexed: 11/28/2022]
Abstract
The success of sustainable agricultural practices has now become heavily dependent on the interactions between crop plants and their associated microbiome. Continuous advancement in high throughput sequencing platforms, omics-based approaches, and gene editing technologies has remarkably accelerated this area of research. It has enabled us to characterize the interactions of plants with associated microbial communities more comprehensively and accurately. Furthermore, the genomic and post-genomic era has significantly refined our perspective toward the complex mechanisms involved in those interactions, opening new avenues for efficiently deploying the knowledge in developing sustainable agricultural practices. This review focuses on our fundamental understanding of plant-microbe interactions and the contribution of existing multi-omics approaches, including those under active development and their tremendous success in unraveling different aspects of the complex network between plant hosts and microbes. In addition, we have also discussed the importance of sustainable and eco-friendly agriculture and the associated outstanding challenges ahead.
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Affiliation(s)
- Deepti Diwan
- Washington University School of Medicine, Saint Louis, MO 63110, USA.
| | - Md Mahtab Rashid
- Department of Plant Pathology, Bihar Agricultural University, Sabour, Bhagalpur, Bihar 813210, India; Department of Mycology and Plant Pathology, Institute of Agricultural Sciences, Banaras Hindu University, Varanasi, Uttar Pradesh 221005, India
| | - Anukool Vaishnav
- Department of Biotechnology, GLA University, Mathura, Uttar Pradesh 281121, India; Department of Plant and Microbial Biology, University of Zürich, Zollikerstrasse 107, Zürich CH-8008, Switzerland; Plant-Soil Interaction Group, Agroscope (Reckenholz), Reckenholzstrasse 191, Zürich 8046, Switzerland
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