{"title":"破译动物粪便共堆肥的微生物组潜力和代谢谱揭示了非微生物和微生物生物刺激物的共存网络，以加强可持续农业的保守做法","authors":"Argha Chakraborty, M. K. Saroja, Sourav Garai, Sukamal Sarkar, Aiswarya Bhattacharjee, Kalyan Roy, Sanchayeeta Misra, Rupak Goswami, Sudipta Tripathi, Natesan Ravisankar, Gautam Chatterjee","doi":"10.1186/s40538-025-00765-3","DOIUrl":null,"url":null,"abstract":"<div><h3>Background</h3><p>India has a rich history of agriculture with its vast biodiversity niches and traditional soil conservation practices. More recently, there have been growing molecular insights into crop-soil management practices and their niche microbial consortia and underlying services. However, harnessing traditional innovations to conserve and promote niche-specific microbiome management in agriculture has not been explored in detail. In an earlier report, we anticipated that the oldest documented microbial technology, <i>Kunapajala</i>, has the indigenous microbiome potential that reinforces its unifying cyclical operation interlinked with agro-waste recycling and valorization to eco-friendly food production. In the present study, we aimed to elucidate the molecular signatures of the microbiome–metabolite potential in this traditional liquid manure.</p><h3>Results</h3><p>Our results showed that fish- and livestock waste-derived <i>Kunapajala</i> are dynamic sources of plant-available macronutrients, plant growth regulators, and other bio-active compounds over 90 days of incubation. Besides estimation of microbial loads and dynamics in culture-based assays, whole genome metagenome (WGMG) sequencing data confirmed that bacteria, primarily <i>Firmicutes</i> and <i>Proteobacteria</i>, constitute the dominant kingdom (> 95% of total reads), with over 30% microbial abundance as potential plant growth-promoting rhizobacteria (PGPR), notably representing <i>Clostridium</i>, <i>Corynebacterium</i>, and <i>Bacillus</i>, in 30-day fermented products. The Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway database further identifies the predominance of enzymatic regulations in carbohydrate and amino acid metabolism (> 20%), reflecting high organic matter turnover into different hydrolysates and metabolites in <i>Kunapajala</i>. To further support and validate, liquid chromatography coupled to hybrid quadrupole time-of-flight mass spectrometry (LC–QTOF-MS) based metabolite screening elucidates their potential roles in plant growth promotion and stress adaptation. We also investigate the plant biostimulant potential of <i>Kunapajala</i> and further establish its function as an organic fertilizer in a controlled pot-based assay in red amaranth. Overall, our microbiome–metabolite data highlight the dynamic co-occurrence of non-microbial and microbial biostimulants to redefine its niche compositional network and potential roles in sustainable agriculture.</p><h3>Conclusions</h3><p>Our study presents the first comprehensive microbiomes and metabolite profiling of <i>Kunapajala</i>, which could further advance and inform strategies for customized optimization of microbial consortia in agroecosystem functioning. Overall, employing metagenomic approaches to harnessing traditional organic amendments brings new molecular insights to strengthen conservative practices in sustainable agriculture.</p><h3>Graphical Abstract</h3>\n<div><figure><div><div><picture><source><img></source></picture></div></div></figure></div></div>","PeriodicalId":512,"journal":{"name":"Chemical and Biological Technologies in Agriculture","volume":"12 1","pages":""},"PeriodicalIF":5.2000,"publicationDate":"2025-04-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://chembioagro.springeropen.com/counter/pdf/10.1186/s40538-025-00765-3","citationCount":"0","resultStr":"{\"title\":\"Deciphering the microbiome potential and metabolic profiling of animal waste co-composting reveals the co-occurrence network of non-microbial and microbial biostimulants to strengthen conservative practices in sustainable agriculture\",\"authors\":\"Argha Chakraborty, M. K. Saroja, Sourav Garai, Sukamal Sarkar, Aiswarya Bhattacharjee, Kalyan Roy, Sanchayeeta Misra, Rupak Goswami, Sudipta Tripathi, Natesan Ravisankar, Gautam Chatterjee\",\"doi\":\"10.1186/s40538-025-00765-3\",\"DOIUrl\":null,\"url\":null,\"abstract\":\"<div><h3>Background</h3><p>India has a rich history of agriculture with its vast biodiversity niches and traditional soil conservation practices. More recently, there have been growing molecular insights into crop-soil management practices and their niche microbial consortia and underlying services. However, harnessing traditional innovations to conserve and promote niche-specific microbiome management in agriculture has not been explored in detail. In an earlier report, we anticipated that the oldest documented microbial technology, <i>Kunapajala</i>, has the indigenous microbiome potential that reinforces its unifying cyclical operation interlinked with agro-waste recycling and valorization to eco-friendly food production. In the present study, we aimed to elucidate the molecular signatures of the microbiome–metabolite potential in this traditional liquid manure.</p><h3>Results</h3><p>Our results showed that fish- and livestock waste-derived <i>Kunapajala</i> are dynamic sources of plant-available macronutrients, plant growth regulators, and other bio-active compounds over 90 days of incubation. Besides estimation of microbial loads and dynamics in culture-based assays, whole genome metagenome (WGMG) sequencing data confirmed that bacteria, primarily <i>Firmicutes</i> and <i>Proteobacteria</i>, constitute the dominant kingdom (> 95% of total reads), with over 30% microbial abundance as potential plant growth-promoting rhizobacteria (PGPR), notably representing <i>Clostridium</i>, <i>Corynebacterium</i>, and <i>Bacillus</i>, in 30-day fermented products. The Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway database further identifies the predominance of enzymatic regulations in carbohydrate and amino acid metabolism (> 20%), reflecting high organic matter turnover into different hydrolysates and metabolites in <i>Kunapajala</i>. To further support and validate, liquid chromatography coupled to hybrid quadrupole time-of-flight mass spectrometry (LC–QTOF-MS) based metabolite screening elucidates their potential roles in plant growth promotion and stress adaptation. We also investigate the plant biostimulant potential of <i>Kunapajala</i> and further establish its function as an organic fertilizer in a controlled pot-based assay in red amaranth. Overall, our microbiome–metabolite data highlight the dynamic co-occurrence of non-microbial and microbial biostimulants to redefine its niche compositional network and potential roles in sustainable agriculture.</p><h3>Conclusions</h3><p>Our study presents the first comprehensive microbiomes and metabolite profiling of <i>Kunapajala</i>, which could further advance and inform strategies for customized optimization of microbial consortia in agroecosystem functioning. Overall, employing metagenomic approaches to harnessing traditional organic amendments brings new molecular insights to strengthen conservative practices in sustainable agriculture.</p><h3>Graphical Abstract</h3>\\n<div><figure><div><div><picture><source><img></source></picture></div></div></figure></div></div>\",\"PeriodicalId\":512,\"journal\":{\"name\":\"Chemical and Biological Technologies in Agriculture\",\"volume\":\"12 1\",\"pages\":\"\"},\"PeriodicalIF\":5.2000,\"publicationDate\":\"2025-04-12\",\"publicationTypes\":\"Journal Article\",\"fieldsOfStudy\":null,\"isOpenAccess\":false,\"openAccessPdf\":\"https://chembioagro.springeropen.com/counter/pdf/10.1186/s40538-025-00765-3\",\"citationCount\":\"0\",\"resultStr\":null,\"platform\":\"Semanticscholar\",\"paperid\":null,\"PeriodicalName\":\"Chemical and Biological Technologies in Agriculture\",\"FirstCategoryId\":\"97\",\"ListUrlMain\":\"https://link.springer.com/article/10.1186/s40538-025-00765-3\",\"RegionNum\":2,\"RegionCategory\":\"农林科学\",\"ArticlePicture\":[],\"TitleCN\":null,\"AbstractTextCN\":null,\"PMCID\":null,\"EPubDate\":\"\",\"PubModel\":\"\",\"JCR\":\"Q1\",\"JCRName\":\"AGRICULTURE, MULTIDISCIPLINARY\",\"Score\":null,\"Total\":0}","platform":"Semanticscholar","paperid":null,"PeriodicalName":"Chemical and Biological Technologies in Agriculture","FirstCategoryId":"97","ListUrlMain":"https://link.springer.com/article/10.1186/s40538-025-00765-3","RegionNum":2,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"Q1","JCRName":"AGRICULTURE, MULTIDISCIPLINARY","Score":null,"Total":0}
Deciphering the microbiome potential and metabolic profiling of animal waste co-composting reveals the co-occurrence network of non-microbial and microbial biostimulants to strengthen conservative practices in sustainable agriculture
Background
India has a rich history of agriculture with its vast biodiversity niches and traditional soil conservation practices. More recently, there have been growing molecular insights into crop-soil management practices and their niche microbial consortia and underlying services. However, harnessing traditional innovations to conserve and promote niche-specific microbiome management in agriculture has not been explored in detail. In an earlier report, we anticipated that the oldest documented microbial technology, Kunapajala, has the indigenous microbiome potential that reinforces its unifying cyclical operation interlinked with agro-waste recycling and valorization to eco-friendly food production. In the present study, we aimed to elucidate the molecular signatures of the microbiome–metabolite potential in this traditional liquid manure.
Results
Our results showed that fish- and livestock waste-derived Kunapajala are dynamic sources of plant-available macronutrients, plant growth regulators, and other bio-active compounds over 90 days of incubation. Besides estimation of microbial loads and dynamics in culture-based assays, whole genome metagenome (WGMG) sequencing data confirmed that bacteria, primarily Firmicutes and Proteobacteria, constitute the dominant kingdom (> 95% of total reads), with over 30% microbial abundance as potential plant growth-promoting rhizobacteria (PGPR), notably representing Clostridium, Corynebacterium, and Bacillus, in 30-day fermented products. The Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway database further identifies the predominance of enzymatic regulations in carbohydrate and amino acid metabolism (> 20%), reflecting high organic matter turnover into different hydrolysates and metabolites in Kunapajala. To further support and validate, liquid chromatography coupled to hybrid quadrupole time-of-flight mass spectrometry (LC–QTOF-MS) based metabolite screening elucidates their potential roles in plant growth promotion and stress adaptation. We also investigate the plant biostimulant potential of Kunapajala and further establish its function as an organic fertilizer in a controlled pot-based assay in red amaranth. Overall, our microbiome–metabolite data highlight the dynamic co-occurrence of non-microbial and microbial biostimulants to redefine its niche compositional network and potential roles in sustainable agriculture.
Conclusions
Our study presents the first comprehensive microbiomes and metabolite profiling of Kunapajala, which could further advance and inform strategies for customized optimization of microbial consortia in agroecosystem functioning. Overall, employing metagenomic approaches to harnessing traditional organic amendments brings new molecular insights to strengthen conservative practices in sustainable agriculture.
期刊介绍：
Chemical and Biological Technologies in Agriculture is an international, interdisciplinary, peer-reviewed forum for the advancement and application to all fields of agriculture of modern chemical, biochemical and molecular technologies. The scope of this journal includes chemical and biochemical processes aimed to increase sustainable agricultural and food production, the evaluation of quality and origin of raw primary products and their transformation into foods and chemicals, as well as environmental monitoring and remediation. Of special interest are the effects of chemical and biochemical technologies, also at the nano and supramolecular scale, on the relationships between soil, plants, microorganisms and their environment, with the help of modern bioinformatics. Another special focus is the use of modern bioorganic and biological chemistry to develop new technologies for plant nutrition and bio-stimulation, advancement of biorefineries from biomasses, safe and traceable food products, carbon storage in soil and plants and restoration of contaminated soils to agriculture.
This journal presents the first opportunity to bring together researchers from a wide number of disciplines within the agricultural chemical and biological sciences, from both industry and academia. The principle aim of Chemical and Biological Technologies in Agriculture is to allow the exchange of the most advanced chemical and biochemical knowledge to develop technologies which address one of the most pressing challenges of our times - sustaining a growing world population.
Chemical and Biological Technologies in Agriculture publishes original research articles, short letters and invited reviews. Articles from scientists in industry, academia as well as private research institutes, non-governmental and environmental organizations are encouraged.
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