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Baig U, Dahanukar N, Shintre N, Holkar K, Pund A, Lele U, Gujarathi T, Patel K, Jakati A, Singh R, Vidwans H, Tamhane V, Deshpande N, Watve M. Phylogenetic diversity and activity screening of cultivable Actinobacteria isolated from marine sponges and associated environments from the western coast of India. Access Microbiol 2021; 3:000242. [PMID: 34712902 PMCID: PMC8549387 DOI: 10.1099/acmi.0.000242] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Accepted: 06/10/2021] [Indexed: 11/19/2022] Open
Abstract
The phylogenetic diversity of cultivable actinobacteria isolated from sponges (Haliclona spp.) and associated intertidal zone environments along the northern parts of the western coast of India were studied using 16S rRNA gene sequences. A subset of randomly selected actinobacterial cultures were screened for three activities, namely predatory behaviour, antibacterial activity and enzyme inhibition. We recovered 237 isolates from the phylum Actinobacteria belonging to 19 families and 28 genera, which could be attributed to 95 putative species using maximum-likelihood partition and 100 putative species using Bayesian partition in Poisson tree processes. Although the trends in the discovery of actinobacterial genera isolated from sponges were consistent with previous studies from different study areas, we provide the first report of nine actinobacterial species from sponges. We observed widespread non-obligate epibiotic predatory behaviour in eight actinobacterial genera and we provide the first report of predatory activity in Brevibacterium, Glutamicibacter, Micromonospora, Nocardiopsis, Rhodococcus and Rothia. Sponge-associated actinobacteria showed significantly more predatory behaviour than environmental isolates. While antibacterial activity by actinobacterial isolates mainly affected Gram-positive target bacteria with little or no effect on Gram-negative bacteria, predation targeted both Gram-positive and Gram-negative prey with equal propensity. Actinobacterial isolates from both sponges and associated environments produced inhibitors of serine proteases and angiotensin-converting enzyme. Predatory behaviour was strongly associated with inhibition of trypsin and chymotrypsin. Our study suggests that the sponges and associated environments of the western coast of India are rich in actinobacterial diversity, with widespread predatory activity, antibacterial activity and production of enzyme inhibitors. Understanding the diversity and associations among various actinobacterial activities – with each other and the source of isolation – can provide new insights into marine microbial ecology and provide opportunities to isolate novel therapeutic agents.
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Affiliation(s)
- Ulfat Baig
- Indian Institute of Science Education and Research, Pune (IISER-P), Dr Homi Bhabha Road, Pashan, Pune 411008, Maharashtra, India
| | - Neelesh Dahanukar
- Indian Institute of Science Education and Research, Pune (IISER-P), Dr Homi Bhabha Road, Pashan, Pune 411008, Maharashtra, India
| | - Neha Shintre
- Department of Microbiology, M.E.S. Abasaheb Garware College, Pune 411004, Maharashtra, India
| | - Ketki Holkar
- Indian Institute of Science Education and Research, Pune (IISER-P), Dr Homi Bhabha Road, Pashan, Pune 411008, Maharashtra, India
| | - Anagha Pund
- Indian Institute of Science Education and Research, Pune (IISER-P), Dr Homi Bhabha Road, Pashan, Pune 411008, Maharashtra, India
| | - Uttara Lele
- Indian Institute of Science Education and Research, Pune (IISER-P), Dr Homi Bhabha Road, Pashan, Pune 411008, Maharashtra, India
| | - Tejal Gujarathi
- Indian Institute of Science Education and Research, Pune (IISER-P), Dr Homi Bhabha Road, Pashan, Pune 411008, Maharashtra, India
| | - Kajal Patel
- Indian Institute of Science Education and Research, Pune (IISER-P), Dr Homi Bhabha Road, Pashan, Pune 411008, Maharashtra, India
| | - Avantika Jakati
- Indian Institute of Science Education and Research, Pune (IISER-P), Dr Homi Bhabha Road, Pashan, Pune 411008, Maharashtra, India
| | - Ruby Singh
- Indian Institute of Science Education and Research, Pune (IISER-P), Dr Homi Bhabha Road, Pashan, Pune 411008, Maharashtra, India
| | - Harshada Vidwans
- Indian Institute of Science Education and Research, Pune (IISER-P), Dr Homi Bhabha Road, Pashan, Pune 411008, Maharashtra, India
| | - Vaijayanti Tamhane
- Institute of Bioinformatics and Biotechnology, Savitribai Phule Pune University, Pune 411007, Maharashtra, India
| | - Neelima Deshpande
- Department of Microbiology, M.E.S. Abasaheb Garware College, Pune 411004, Maharashtra, India
| | - Milind Watve
- Behavioural Intervention for Lifestyle Disorders (BILD) Clinic, Deenanath Mangeshkar Hospital and Research Centre, Erandwane, Pune 411004, Maharashtra, India
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Ho XY, Katermeran NP, Deignan LK, Phyo MY, Ong JFM, Goh JX, Ng JY, Tun K, Tan LT. Assessing the Diversity and Biomedical Potential of Microbes Associated With the Neptune's Cup Sponge, Cliona patera. Front Microbiol 2021; 12:631445. [PMID: 34267732 PMCID: PMC8277423 DOI: 10.3389/fmicb.2021.631445] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2020] [Accepted: 06/01/2021] [Indexed: 11/13/2022] Open
Abstract
Marine sponges are known to host a complex microbial consortium that is essential to the health and resilience of these benthic invertebrates. These sponge-associated microbes are also an important source of therapeutic agents. The Neptune's Cup sponge, Cliona patera, once believed to be extinct, was rediscovered off the southern coast of Singapore in 2011. The chance discovery of this sponge presented an opportunity to characterize the prokaryotic community of C. patera. Sponge tissue samples were collected from the inner cup, outer cup and stem of C. patera for 16S rRNA amplicon sequencing. C. patera hosted 5,222 distinct OTUs, spanning 26 bacterial phyla, and 74 bacterial classes. The bacterial phylum Proteobacteria, particularly classes Gammaproteobacteria and Alphaproteobacteria, dominated the sponge microbiome. Interestingly, the prokaryotic community structure differed significantly between the cup and stem of C. patera, suggesting that within C. patera there are distinct microenvironments. Moreover, the cup of C. patera had lower diversity and evenness as compared to the stem. Quorum sensing inhibitory (QSI) activities of selected sponge-associated marine bacteria were evaluated and their organic extracts profiled using the MS-based molecular networking platform. Of the 110 distinct marine bacterial strains isolated from sponge samples using culture-dependent methods, about 30% showed quorum sensing inhibitory activity. Preliminary identification of selected QSI active bacterial strains revealed that they belong mostly to classes Alphaproteobacteria and Bacilli. Annotation of the MS/MS molecular networkings of these QSI active organic extracts revealed diverse classes of natural products, including aromatic polyketides, siderophores, pyrrolidine derivatives, indole alkaloids, diketopiperazines, and pyrone derivatives. Moreover, potential novel compounds were detected in several strains as revealed by unique molecular families present in the molecular networks. Further research is required to determine the temporal stability of the microbiome of the host sponge, as well as mining of associated bacteria for novel QS inhibitors.
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Affiliation(s)
- Xin Yi Ho
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore
| | - Nursheena Parveen Katermeran
- Natural Sciences and Science Education, National Institute of Education, Nanyang Technological University, Singapore, Singapore
| | - Lindsey Kane Deignan
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore
| | - Ma Yadanar Phyo
- Natural Sciences and Science Education, National Institute of Education, Nanyang Technological University, Singapore, Singapore
| | - Ji Fa Marshall Ong
- Natural Sciences and Science Education, National Institute of Education, Nanyang Technological University, Singapore, Singapore
| | - Jun Xian Goh
- Natural Sciences and Science Education, National Institute of Education, Nanyang Technological University, Singapore, Singapore
| | - Juat Ying Ng
- National Parks Board, Singapore Botanic Gardens, Singapore, Singapore
| | - Karenne Tun
- National Parks Board, Singapore Botanic Gardens, Singapore, Singapore
| | - Lik Tong Tan
- Natural Sciences and Science Education, National Institute of Education, Nanyang Technological University, Singapore, Singapore
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