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Guan L, Wang H, Chen J, Yang F, Yang J, Li J, Jin L. Isolation and Identification of Culturable Bacteria from South China Seawater and Preliminary Screening of Marine Biocontrol Bacteria. Microorganisms 2023; 11:2933. [PMID: 38138077 PMCID: PMC10746102 DOI: 10.3390/microorganisms11122933] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Revised: 11/29/2023] [Accepted: 11/30/2023] [Indexed: 12/24/2023] Open
Abstract
Marine microorganisms have evolved special metabolic pathways to produce numerous bioactive substances with novel structures and unique functions. This study analyzed the diversity of culturable bacteria in marine water samples from the South China Sea and screened the isolated bacteria with pathogenic fungi. A total of 200 culturable strains of 72 different bacteria were obtained from 56 water samples from the South China Sea. They belonged to three phyla and four classes, namely Gammaproteobacteria, Alphaproteobacteria, Bacilli and Actinomycetia. Bacilli was the dominant class, comprising up to 59.72%, followed by Gammaproteobacteria (20.83%). Bacillus, Pseudomonas, Paenibacillus and Rhizobium were the most dominant genera. Among these strains, HY-88 and HY-91 encoding BamC, FenB and PKSI genes were selected and identified as Bacillus subtilis. The respective inhibition rates of the HY-88 caused by plate confrontation against Magnaporthe grisea, Fusarium oxysporum, Botrytis cinerea, anthrax and Botrytis cinerea were 90.91%, 54.29%, 52.17% and 51.72%, in comparison with HY-91 86.36%, 48.57%, 47.83% and 34.48%. In addition, the supernatant of HY-88 showed a lesion inhibition rate of 74.5%, which was significantly higher than HY-91 (60.55%). In addition, HY-88 and HY-91 showed strong antifungal activity to Colletotrichum viniferum on detached Shine Muscat grapes. Tolerance tests showed that the HY-88 and HY-91 grew at 10-40 °C, 7-10% NaCl and pH 3-11. HY-88 and HY-91 could inhibit various fungal plant diseases, which lays a foundation for the development of new biopesticides.
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Affiliation(s)
- Limei Guan
- Institute of Biological Resources, Jiangxi Academy of Sciences, Nanchang 330029, China; (L.G.); (J.C.); (F.Y.); (J.Y.); (J.L.)
| | - Hongxiu Wang
- Institute of Microbiology, Jiangxi Academy of Sciences, Nanchang 330029, China;
| | - Junhui Chen
- Institute of Biological Resources, Jiangxi Academy of Sciences, Nanchang 330029, China; (L.G.); (J.C.); (F.Y.); (J.Y.); (J.L.)
| | - Feiying Yang
- Institute of Biological Resources, Jiangxi Academy of Sciences, Nanchang 330029, China; (L.G.); (J.C.); (F.Y.); (J.Y.); (J.L.)
| | - Jian Yang
- Institute of Biological Resources, Jiangxi Academy of Sciences, Nanchang 330029, China; (L.G.); (J.C.); (F.Y.); (J.Y.); (J.L.)
| | - Jianghuai Li
- Institute of Biological Resources, Jiangxi Academy of Sciences, Nanchang 330029, China; (L.G.); (J.C.); (F.Y.); (J.Y.); (J.L.)
| | - Liang Jin
- Institute of Biological Resources, Jiangxi Academy of Sciences, Nanchang 330029, China; (L.G.); (J.C.); (F.Y.); (J.Y.); (J.L.)
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Bhagat NR, Chauhan P, Verma P, Mishra A, Bharti VK. High-altitude and low-altitude adapted chicken gut-microbes have different functional diversity. Sci Rep 2023; 13:20856. [PMID: 38012260 PMCID: PMC10682461 DOI: 10.1038/s41598-023-48147-9] [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: 07/11/2023] [Accepted: 11/22/2023] [Indexed: 11/29/2023] Open
Abstract
Recently, there has been considerable interest in the functions of gut microbiota in broiler chickens in relation to their use as feed additives. However, the gut-microbiota of chickens reared at different altitudes are not well documented for their potential role in adapting to prevailing conditions and functional changes. In this context, the present study investigates the functional diversity of gut-microbes in high-altitude (HACh) and low-altitude adapted chickens (LACh), assessing their substrate utilization profile through Biolog Ecoplates technology. This will help in the identification of potential microbes or their synthesized metabolites, which could be beneficial for the host or industrial applications. Results revealed that among the 31 different types of studied substrates, only polymers, carbohydrates, carboxylic acids, and amine-based substrates utilization varied significantly (p < 0.05) among the chickens reared at two different altitudes where gut-microbes of LACh utilized a broad range of substrates than the HACh. Further, diversity indices (Shannon and MacIntosh) analysis in LACh samples showed significant (p < 0.05) higher richness and evenness of microbes as compared to the HACh samples. However, no significant difference was observed in the Simpson diversity index in gut microbes of lowversus high-altitude chickens. In addition, the Principal Component Analysis elucidated variation in substrate preferences of gut-microbes, where 13 and 8 carbon substrates were found to constitute PC1 and PC2, respectively, where γ-aminobutyric acid, D-glucosaminic acid, i-erythritol and tween 40 were the most relevant substrates that had a major effect on PC1, however, alpha-ketobutyric acid and glycyl-L-glutamic acid affected PC2. Hence, this study concludes that the gut-microbes of high and low-altitudes adapted chickens use different carbon substrates so that they could play a vital role in the health and immunity of an animal host based on their geographical location. Consequently, this study substantiates the difference in the substrate utilization and functional diversity of the microbial flora in chickens reared at high and low altitudes due to altitudinal changes.
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Affiliation(s)
- Neha Rani Bhagat
- DRDO-Defence Institute of High-Altitude Research (DIHAR), Ministry of Defence, Leh, 194101, UT Ladakh, India
- Department of Microbiology, Panjab University, Chandigarh, India
| | - Priyanka Chauhan
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
- School of Sciences, P. P. Savani University, NH-8, GETCO, Near Biltech, Kosamba, Surat, 394125, India
| | - Pratibha Verma
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
- Division of Microbial Technology, CSIR-National Botanical Research Institute, Lucknow, 226001, Uttar Pradesh, India
| | - Aradhana Mishra
- Division of Microbial Technology, CSIR-National Botanical Research Institute, Lucknow, 226001, Uttar Pradesh, India
| | - Vijay K Bharti
- DRDO-Defence Institute of High-Altitude Research (DIHAR), Ministry of Defence, Leh, 194101, UT Ladakh, India.
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El-Malah SS, Rasool K, Jabbar KA, Sohail MU, Baalousha HM, Mahmoud KA. Marine Bacterial Community Structures of Selected Coastal Seawater and Sediment Sites in Qatar. Microorganisms 2023; 11:2827. [PMID: 38137970 PMCID: PMC10745943 DOI: 10.3390/microorganisms11122827] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2023] [Revised: 11/09/2023] [Accepted: 11/12/2023] [Indexed: 12/24/2023] Open
Abstract
Severe environmental conditions can have a diverse impact on marine microorganisms, including bacteria. This can have an inevitable impact on the biofouling of membrane-based desalination plants. In this work, we have utilized indicator bacteria such as total coliform, fecal coliform, and Pseudomonas aeruginosa, as well as 16S rRNA sequencing, to investigate the impact of environmental conditions and spatial variations on the diversity of bacterial communities in the coastal waters and sediments from selected sites in Qatar. The concentration levels of indicator bacteria were affected by increasing temperatures and pH, and by decreasing salinity of seawater samples. Diversity indices and the molecular phylogeny demonstrated that Proteobacteria, Bacteroidetes, and Cyanobacteria were the dominant phyla in all locations. The most abundant operational taxonomic units (OTUs) at the family level were from Flavobacteriaceae (27.07%, 4.31%) and Rhodobacteraceae (22.51%, 9.86%) in seawater and sediment, respectively. Alphaproteobacteria (33.87%, 16.82%), Flavobacteria (30.68%, 5.84%), and Gammaproteobacteria (20.35%, 12.45%) were abundant at the species level in both seawater and sediment, while Clostridia (13.72%) was abundant in sediment only. The results suggest that sediment can act as a reservoir for indicator bacteria, with higher diversity and lower abundance compared to seawater.
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Affiliation(s)
- Shimaa S. El-Malah
- Qatar Environment and Energy Research Institute (QEERI), Hamad Bin Khalifa University, Qatar Foundation, Doha P.O. Box 34110, Qatar; (S.S.E.-M.); (K.R.); (K.A.J.)
| | - Kashif Rasool
- Qatar Environment and Energy Research Institute (QEERI), Hamad Bin Khalifa University, Qatar Foundation, Doha P.O. Box 34110, Qatar; (S.S.E.-M.); (K.R.); (K.A.J.)
| | - Khadeeja Abdul Jabbar
- Qatar Environment and Energy Research Institute (QEERI), Hamad Bin Khalifa University, Qatar Foundation, Doha P.O. Box 34110, Qatar; (S.S.E.-M.); (K.R.); (K.A.J.)
| | | | - Husam Musa Baalousha
- Department of Geosciences, College of Petroleum Engineering and Geosciences, King Fahd University of Petroleum and Minerals (KFUPM), Dhahran 31261, Saudi Arabia;
| | - Khaled A. Mahmoud
- Qatar Environment and Energy Research Institute (QEERI), Hamad Bin Khalifa University, Qatar Foundation, Doha P.O. Box 34110, Qatar; (S.S.E.-M.); (K.R.); (K.A.J.)
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Kumar M, Chaudhary DR, Jha B. Surface-associated bacterial assemblages on marine anthropogenic litter in the intertidal zone of the Arabian Sea, India. MARINE POLLUTION BULLETIN 2023; 193:115211. [PMID: 37392592 DOI: 10.1016/j.marpolbul.2023.115211] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Revised: 06/01/2023] [Accepted: 06/20/2023] [Indexed: 07/03/2023]
Abstract
Anthropogenic marine litter (mainly plastic pollution) is a serious concern globally. The interactions between terrestrial and marine ecosystems lead to the accumulation of marine litter in the intertidal zone. The biofilm-forming bacteria tend to colonize on surfaces of marine litter which are composed of diverse bacteria and are less studied. The present study investigated the bacterial community composition using both culturable and non-culturable (Next-generation sequencing (NGS)) approaches associated with the marine litter (polyethylene (PE), styrofoam (SF) and fabric (FB)) at three distinct locations (Alang, Diu and Sikka) of the Arabian Sea, Gujarat, India. Predominant bacteria observed using culturable and NGS techniques belonged to Proteobacteria phyla. Alphaproteobacteria class dominated on polyethylene and styrofoam surfaces in the culturable fraction among the sites while the Bacillus dominated fabric surfaces. In the metagenomics fraction, Gammaproteobacteria dominated the surfaces except for PE and SF surfaces from Sikka and Diu, respectively. The PE surface at Sikka was dominated by Fusobacteriia while SF surface from Diu was dominated by Alphaproteobacteria. Both culture-dependent and NGS approaches identified hydrocarbon-degrading bacteria as well as pathogenic bacteria on the surfaces. The outcome of the present study illustrates diverse bacterial assemblages which occur on marine litter and increases our understanding of the plastisphere community.
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Affiliation(s)
- Madhav Kumar
- CSIR - Central Salt and Marine Chemicals Research Institute, G. B. Marg, Bhavnagar, Gujarat 364002, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Doongar R Chaudhary
- CSIR - Central Salt and Marine Chemicals Research Institute, G. B. Marg, Bhavnagar, Gujarat 364002, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India.
| | - Bhavanath Jha
- CSIR - Central Salt and Marine Chemicals Research Institute, G. B. Marg, Bhavnagar, Gujarat 364002, India.
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Vijayan J, Nathan VK, Ammini P, Ammanamveetil AMH. Bacterial diversity in the aquatic system in India based on metagenome analysis-a critical review. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2023; 30:28383-28406. [PMID: 36680718 PMCID: PMC9862233 DOI: 10.1007/s11356-023-25195-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Accepted: 01/04/2023] [Indexed: 04/16/2023]
Abstract
Microbial analysis has become one of the most critical areas in aquatic ecology and a crucial component for assessing the contribution of microbes in food web dynamics and biogeochemical processes. Initial research was focused on estimating the abundance and distribution of the microbes using microscopy and culture-based analysis, which are undoubtedly complex tasks. Over the past few decades, microbiologists have endeavored to apply and extend molecular techniques to address pertinent questions related to the function and metabolism of microbes in aquatic ecology. Metagenomics analysis has revolutionized aquatic ecology studies involving the investigation of the genome of a mixed community of organisms in an ecosystem to identify microorganisms, their functionality, and the discovery of novel proteins. This review discusses the metagenomics analysis of bacterial diversity in and around different aquatic systems in India.
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Affiliation(s)
- Jasna Vijayan
- Department of Marine Biology, Microbiology and Biochemistry, School of Marine Sciences, Cochin University of Science and Technology, Cochin, 682 016, Kerala, India.
| | - Vinod Kumar Nathan
- School of Chemical and Biotechnology, Sastra Deemed University, Tirumalaisamudram, Thanjavur, 613401, Tamilnadu, India
| | - Parvathi Ammini
- Department of Biotechnology, Cochin University of Science and Technology, Cochin, 682022, Kerala, India
| | - Abdulla Mohamed Hatha Ammanamveetil
- Department of Marine Biology, Microbiology and Biochemistry, School of Marine Sciences, Cochin University of Science and Technology, Cochin, 682 016, Kerala, India
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Thakur M, Verma V, Chandel A, Kumar R, Sharma T, Kumar A, Bhardwaj S, Kumar R, Bhargava B. Lemon grass essential oil improves Gladiolus grandiflorus postharvest life by modulating water relations, microbial growth, biochemical activity, and gene expression. Sci Rep 2023; 13:2630. [PMID: 36788264 PMCID: PMC9929329 DOI: 10.1038/s41598-023-28829-0] [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: 06/30/2022] [Accepted: 01/25/2023] [Indexed: 02/16/2023] Open
Abstract
Gladiolus (Gladiolus grandiflorus Andrews) is a high-valued bulbous cut flower. However, the shorter postharvest life of the gladiolus, limits its marketing and commercial value. In the present investigation, the effect of lemon grass (LG) essential oil as an antimicrobial agent was studied towards increasing the vase life of gladiolus. The results revealed that as compared to control (distilled water), treatment with a lower concentration of 5 µL L-1 LG essential oil prolonged the vase life of gladiolus up to 11 days (d). Scanning Electron Microscope (SEM) observation indicated that the sample treated with 5 µL L-1 LG essential oil showed intact vasculature, suggesting reduced microbial blockage at the stem end which was further corroborated by microbial count. Biochemical analysis suggested an increased level of total soluble sugars, carotenoid content, lower MDA accumulation, and higher activity of antioxidant enzymes in LG treated flowers. Moreover, transcripts levels of genes associated with senescence viz., GgCyP1 and GgERS1a were downregulated, while expression of GDAD1 and antioxidant genes such as GgP5C5, GgPOD 1, GgMnSOD, and GgCAT1 were upregulated in LG treated cut spikes as compared to control. Among various treatments we have concluded that, the vase life of the gladiolus cut spike was improved along with the relative fresh flower weight and diameter of flower at the lower dose of 5 µL L-1 LG oil in the vase solution. Thus, LG oil as an eco-friendly agent has the potential to extend the postharvest life of cut flowers.
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Affiliation(s)
- Meenakshi Thakur
- grid.417640.00000 0004 0500 553XFloriculture Laboratory, Agrotechnology Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur, India
| | - Vipasha Verma
- grid.417640.00000 0004 0500 553XFloriculture Laboratory, Agrotechnology Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur, India
| | - Anjali Chandel
- grid.417640.00000 0004 0500 553XFloriculture Laboratory, Agrotechnology Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur, India ,grid.469887.c0000 0004 7744 2771Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh 201002 India
| | - Raghawendra Kumar
- grid.417640.00000 0004 0500 553XFloriculture Laboratory, Agrotechnology Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur, India
| | - Tanvi Sharma
- grid.469887.c0000 0004 7744 2771Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh 201002 India
| | - Akhil Kumar
- grid.417640.00000 0004 0500 553XFloriculture Laboratory, Agrotechnology Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur, India
| | - Sonali Bhardwaj
- grid.417640.00000 0004 0500 553XFloriculture Laboratory, Agrotechnology Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur, India
| | - Rakshak Kumar
- grid.469887.c0000 0004 7744 2771Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh 201002 India ,grid.417640.00000 0004 0500 553XBiotechnology Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur, India
| | - Bhavya Bhargava
- Floriculture Laboratory, Agrotechnology Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur, India. .,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh, 201002, India.
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Anand KP, Suthindhiran K. Microbial signature and biosynthetic gene cluster profiling of poly extremophilic marine actinobacteria isolated from Vhan Island, Tamil Nadu, India. GENE REPORTS 2023. [DOI: 10.1016/j.genrep.2023.101742] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
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Wang F, Zhang Y, Jing H, Liu H. Spatial variation and metabolic diversity of microbial communities in the surface sediments of the Mariana Trench. Front Microbiol 2022; 13:1051999. [PMID: 36545198 PMCID: PMC9760864 DOI: 10.3389/fmicb.2022.1051999] [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: 09/23/2022] [Accepted: 10/31/2022] [Indexed: 12/12/2022] Open
Abstract
Mariana Trench represents the deepest and one of least explored biosphere on Earth, and its carbon sources include euphotic sinking, lateral transportation and diffusion from underlying crust, etc. By far the spatial variation of microbial community with associated organic carbon degradation potential in the surface sediments of the Mariana Trench were still largely unknown. Based on the high-throughput 16S rRNA amplicon sequencing, significantly different microbial community structure was overserved between the shallow (<10,000 m) and deep stations (>10,000 m), which could be explained by spatial variation of Chloroflexi, Proteobacteria and Crenarchaeota, with sampling depth and total organic carbon (TOC) content as the environmental driving forces. During the 109-day incubation with Biolog EcoPlate™ microplate, polymers and carbohydrates were preferentially used, followed by amino acids and carboxylic acids, and microbial metabolic diversity was significantly different between the shallow and deep stations. The metabolic diversity of microorganisms at most shallow stations was significantly lower than that at deep stations. This could potentially be attributed the metabolic capabilities of different microbial groups with varied ecological niches, and reflected the initial preference of carbon source by the nature microbes as well. Our study obtained a rough assessment of physiological and taxonomic characteristics of the trench sediment microbial community with polyphasic approaches. Distinct microbial structure and potential carbon metabolic functions in different sampling depths might led to the differentiation of ecological niches, which enable various microorganisms to make full use of the limited resources in the deep sea, and provided a research basis for further exploration of the carbon cycle in different deep-sea regions.
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Affiliation(s)
- Fangzhou Wang
- CAS Key Lab for Experimental Study Under Deep-Sea Extreme Conditions, Institute of Deep-Sea Science and Engineering, Chinese Academy of Sciences, Sanya, China,University of Chinese Academy of Sciences, Beijing, China
| | - Yue Zhang
- CAS Key Lab for Experimental Study Under Deep-Sea Extreme Conditions, Institute of Deep-Sea Science and Engineering, Chinese Academy of Sciences, Sanya, China
| | - Hongmei Jing
- CAS Key Lab for Experimental Study Under Deep-Sea Extreme Conditions, Institute of Deep-Sea Science and Engineering, Chinese Academy of Sciences, Sanya, China,HKUST-CAS Sanya Joint Laboratory of Marine Science Research, Chinese Academy of Sciences, Sanya, China,Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, China,*Correspondence: Hongmei Jing,
| | - Hao Liu
- CAS Key Lab for Experimental Study Under Deep-Sea Extreme Conditions, Institute of Deep-Sea Science and Engineering, Chinese Academy of Sciences, Sanya, China
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Kumar M, Kumar R, Chaudhary DR, Jha B. An appraisal of early stage biofilm-forming bacterial community assemblage and diversity in the Arabian Sea, India. MARINE POLLUTION BULLETIN 2022; 180:113732. [PMID: 35594757 DOI: 10.1016/j.marpolbul.2022.113732] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/19/2022] [Revised: 05/01/2022] [Accepted: 05/02/2022] [Indexed: 06/15/2023]
Abstract
The community composition and distribution of early-stage (24 h) biofilm-forming bacteria on two different surfaces (glass slide and polystyrene plastic slide) at three different locations (Diu, Alang and Sikka) were studied using a culture-dependent and next-generation sequencing (NGS) approach in the Arabian Sea, Gujarat, India. The most dominant phyla observed using the NGS approach were the Proteobacteria among the sampling sites. Gammaproteobacteria class dominated both the surfaces among the sites and accounted for 46.7% to 89.2% of total abundance. The culture-dependent analysis showed Proteobacteria and Firmicutes as the dominant phyla on the surfaces within the sampling sites. During the initial colonization, hydrocarbon-degrading bacterial strains have also attached to the surfaces. The outcome of this study would be of great importance for targeting the early stage biofilm-forming and hydrocarbon-degrading bacterial isolates may help to degrade plastic in the marine environment.
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Affiliation(s)
- Madhav Kumar
- CSIR - Central Salt and Marine Chemicals Research Institute, G. B. Bhavnagar, Gujarat 364 002, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad- 201002, India
| | - Raghawendra Kumar
- CSIR - Central Salt and Marine Chemicals Research Institute, G. B. Bhavnagar, Gujarat 364 002, India
| | - Doongar R Chaudhary
- CSIR - Central Salt and Marine Chemicals Research Institute, G. B. Bhavnagar, Gujarat 364 002, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad- 201002, India.
| | - Bhavanath Jha
- CSIR - Central Salt and Marine Chemicals Research Institute, G. B. Bhavnagar, Gujarat 364 002, India.
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Vijayan J, Ammini P, Nathan VK. Diversity pattern of marine culturable heterotrophic bacteria in a region with coexisting upwelling and mud banks in the southeastern Arabian Sea. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2022; 29:3967-3982. [PMID: 34398377 DOI: 10.1007/s11356-021-15772-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Accepted: 07/29/2021] [Indexed: 06/13/2023]
Abstract
Mud banks and upwelling are two important oceanographic features occurring along the southwest coast of India during the southwest monsoon period. The study region, Alappuzha lying on the southwest coast of India, is unique due to the co-existence of upwelling and mud banks during the monsoon (MON) season. Water samples were collected from three stations, M1, M2, and M3, from April to September 2014, at weekly/biweekly intervals to determine the total bacterial abundance, viable prokaryotic counts, and total plate counts, along with measurements on physico-chemical parameters. For determining the heterotrophic culturable bacterial diversity, water samples were collected during two seasons, monsoon and pre-monsoon (PRM), from three stations. Water samples were inoculated into two non-selective broths for enrichment, DNA was extracted, and next-generation sequencing analysis was performed using Illumina Miseq sequencing. The sequence analysis revealed that dominant communities were Proteobacteria, followed by Firmicutes and Fusobacteria. Proportions of Fusobacteria increased during monsoon and proportions of Firmicutes were high in premonsoon season. Among Proteobacteria, Gammaproteobacteri is presented more than 99% of all the classes, irrespective of seasons. Vibrio was the most dominant genus during both seasons. The presence of anaerobic genera such as Propionigenium and Cetobacterium at all the stations during MON indicated the presence of upwelled waters. The genus Stenotrophomonas was observed in the M2 station alone. This study provides an overview of the culturable heterotrophic bacterial communities in a region in the southeastern Arabian Sea with coexisting mud banks and upwelling. The results of this study were compared with a published report on culture-independent bacterial diversity (from environmental DNA) from the same region. The study demonstrates that the use of culture media underrepresented the phylogenetic diversity and selectively enriched the class Gammaproteobacteria alone.
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Affiliation(s)
- Jasna Vijayan
- National Institute of Oceanography-CSIR, Regional Center, Dr. Salim Ali Road, Kochi, Kerala, 682018, India
| | - Parvathi Ammini
- National Institute of Oceanography-CSIR, Regional Center, Dr. Salim Ali Road, Kochi, Kerala, 682018, India.
- Department of Biotechnology, Cochin University of Science and Technology, Kochi, Kerala, 682022, India.
| | - Vinod Kumar Nathan
- National Institute of Oceanography-CSIR, Regional Center, Dr. Salim Ali Road, Kochi, Kerala, 682018, India
- School of Chemical and Biotechnology, Sastra Deemed University Tirumalaisamudram, Thanjavur, Tamilnadu, 613401, India
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Gurunathan R, Rathinam AJ, Hwang JS, Dahms HU. Shallow Hydrothermal Vent Bacteria and Their Secondary Metabolites with a Particular Focus on Bacillus. Mar Drugs 2021; 19:681. [PMID: 34940680 PMCID: PMC8704404 DOI: 10.3390/md19120681] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Revised: 11/25/2021] [Accepted: 11/26/2021] [Indexed: 11/21/2022] Open
Abstract
Extreme environments are hostile for most organisms, but such habitats represent suitable settings to be inhabited by specialized microorganisms. A marine shallow-water hydrothermal vent field is located offshore in northeast Taiwan, near the shallow shore of the southeast of Kueishantao Island (121°55' E, 24°50' N). Research on extremophilic microorganisms makes use of the biotechnological potential associated with such microorganisms and their cellular products. With the notion that extremophiles are capable of surviving in extreme environments, it is assumed that their metabolites are adapted to function optimally under such conditions. As extremophiles, they need specific culture conditions, and only a fraction of species from the original samples are recovered in culture. We used different non-selective and selective media to isolate bacterial species associated with the hydrothermal vent crab Xenograpsus testudinatus and the sediments of its habitat. The highest number of colonies was obtained from Zobell marine agar plates with an overall number of 29 genetically distinct isolates. 16sRNA gene sequencing using the Sanger sequencing method revealed that most of the bacterial species belonged to the phylum Firmicutes and the class Bacilli. The present study indicates that hydrothermal vent bacteria and their secondary metabolites may play an important role for the reconstruction of the evolutionary history of the phylum Procaryota.
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Grants
- MOST 107-2621-M-019-001, MOST 108-2621-M-019-003, MOST 109-2621-M-019-002 and MOST 110-2621-M-019-001 Ministry of Science and Technology, Taiwan.
- 109J13801-51, 110J13801-51 Center of Excellence for Ocean Engineering, NTOU, Taiwan.
- MOST 107-2621-M-037-001, MOST 108-2621-M-037-001, and MOST 109-2621-M-037-001 Ministry of Science and Technology, Taiwan.
- KMU-TC108A01 and KMU-TC108A02 Kaohsiung Medical University Research Center, Taiwan.
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Affiliation(s)
- Revathi Gurunathan
- Department of Medicinal and Applied Chemistry, Kaohsiung Medical University, Kaohsiung 80708, Taiwan;
- Department of Biomedical Science and Environmental Biology, Kaohsiung Medical University, Kaohsiung 80708, Taiwan
| | - Arthur James Rathinam
- Department of Marine Science, Bharathidasan University, Tiruchirapalli 620024, India
| | - Jiang-Shiou Hwang
- Institute of Marine Biology, National Taiwan Ocean University, Keelung 20224, Taiwan
- Center of Excellence for Ocean Engineering, National Taiwan Ocean University, Keelung 20224, Taiwan
- Center of Excellence for the Oceans, National Taiwan Ocean University, Keelung 20224, Taiwan
| | - Hans-Uwe Dahms
- Department of Biomedical Science and Environmental Biology, Kaohsiung Medical University, Kaohsiung 80708, Taiwan
- Research Center for Environmental Medicine, Kaohsiung Medical University, Kaohsiung 80708, Taiwan
- Department of Marine Biotechnology and Resources, National Sun Yat-Sen University, Kaohsiung 80424, Taiwan
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12
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Garlapati D, Kumar BC, Muthukumar C, Madeswaran P, Ramu K, Murthy MVR. Assessing the in situ bacterial diversity and composition at anthropogenically active sites using the environmental DNA (eDNA). MARINE POLLUTION BULLETIN 2021; 170:112593. [PMID: 34126444 DOI: 10.1016/j.marpolbul.2021.112593] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Revised: 05/28/2021] [Accepted: 05/30/2021] [Indexed: 06/12/2023]
Abstract
In this study, we identified the in situ bacterial groups and their community structure in coastal waters influenced by anthropogenic inputs. The use of environmental DNA (eDNA) and high throughput sequencing (HTS) were employed to derive accurate and reliable information on bacterial abundance. The V3 and V4 hypervariable regions of the 16S rRNA gene were amplified and the sequences were clustered into operational taxonomic units to analyze the site-specific variations in community composition. The percentage composition within the bacterial orders varied significantly among nearshore anthropogenic hotspots and offshore (5 km) samples. The microbial network constructed taking the bacterial abundance as nodes displayed strong positive and negative correlations within the bacterial families. Overall, the use of eDNA coupled with HTS is an incredible means for monitoring and assessing the abundance of bacterial communities and also serves as a biomonitoring tool to understand the degree of anthropogenic contamination in coastal waters.
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Affiliation(s)
- Deviram Garlapati
- National Centre for Coastal Research, Ministry of Earth Sciences (MoES), Government of India, Chennai 600100, India.
| | - B Charan Kumar
- National Centre for Coastal Research, Ministry of Earth Sciences (MoES), Government of India, Chennai 600100, India
| | - C Muthukumar
- National Centre for Coastal Research, Ministry of Earth Sciences (MoES), Government of India, Chennai 600100, India
| | - P Madeswaran
- National Centre for Coastal Research, Ministry of Earth Sciences (MoES), Government of India, Chennai 600100, India
| | - K Ramu
- National Centre for Coastal Research, Ministry of Earth Sciences (MoES), Government of India, Chennai 600100, India
| | - M V Ramana Murthy
- National Centre for Coastal Research, Ministry of Earth Sciences (MoES), Government of India, Chennai 600100, India
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13
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Kumar R, Pandit P, Kumar D, Patel Z, Pandya L, Kumar M, Joshi C, Joshi M. Landfill microbiome harbour plastic degrading genes: A metagenomic study of solid waste dumping site of Gujarat, India. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 779:146184. [PMID: 33752005 DOI: 10.1016/j.scitotenv.2021.146184] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Revised: 02/22/2021] [Accepted: 02/24/2021] [Indexed: 05/21/2023]
Abstract
Globally, environmental pollution by plastic waste has become a severe ecological and social problem worldwide. The present study aimed to analyse the bacterial community structure and functional potential of the landfill site using high throughput shotgun metagenomic approach to understand plastic degrading capabilities present in the municipal solid waste (MSW) dumping site. In this study, soil, leachate and compost samples were collected from various locations (height and depth) of the Pirana landfill site in Ahmedabad city Gujarat, India. In total 30 phyla, 58 class, 125 order, 278 families, 793 genera, and 2468 species were predicted. The most dominant phyla detected were Proteobacteria, Bacteroidetes, Firmicutes, and Actinobacteria in the soil and compost samples. Whereas, in leachate samples, the predominant phyla belonged to Firmicutes (54.24%) followed by Actinobacteria (43.67%) and Proteobacteria (1.02%). The functional profiling revealed the presence of enzymatic groups and pathways involved in biodegradation of xenobiotics. The results also demonstrated the presence of potential genes that is associated with the biodegradation of different types of plastics such as polyethylene (PE), polyethylene terephthalate (PET), and polystyrene (PS). Present study extablishes the relationship between microbial community structure and rich sources of gene pool, which are actively involved in biodegradation of plastic waste in landfill sites.
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Affiliation(s)
- Raghawendra Kumar
- Gujarat Biotechnology Research Centre, Gandhinagar, Gujarat 382011, India
| | - Priti Pandit
- Gujarat Biotechnology Research Centre, Gandhinagar, Gujarat 382011, India
| | - Dinesh Kumar
- Gujarat Biotechnology Research Centre, Gandhinagar, Gujarat 382011, India
| | - Zarna Patel
- Gujarat Biotechnology Research Centre, Gandhinagar, Gujarat 382011, India
| | - Labdhi Pandya
- Gujarat Biotechnology Research Centre, Gandhinagar, Gujarat 382011, India
| | - Manish Kumar
- Discipline of Earth Sciences, Indian Institute of Technology Gandhinagar, Gujarat 382355, India.
| | - Chaitanya Joshi
- Gujarat Biotechnology Research Centre, Gandhinagar, Gujarat 382011, India
| | - Madhvi Joshi
- Gujarat Biotechnology Research Centre, Gandhinagar, Gujarat 382011, India.
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14
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Li N, Chen X, Zhao H, Tang J, Jiang G, Li Z, Li X, Chen S, Zou S, Dong K, Xu Q. Spatial distribution and functional profile of the bacterial community in response to eutrophication in the subtropical Beibu Gulf, China. MARINE POLLUTION BULLETIN 2020; 161:111742. [PMID: 33075697 DOI: 10.1016/j.marpolbul.2020.111742] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Revised: 09/25/2020] [Accepted: 10/04/2020] [Indexed: 05/25/2023]
Abstract
In this study, we investigated the specific bacterial distribution and the response of bacterial communities to shifts in environmental factors in the subtropical Beibu Gulf, southern China. The abundances of Actinobacteria, Bacilli, Planctomycetia, Thermoleophilia, Anaerolineae, and Synechococcophycideae were significantly higher in high eutrophic samples than in medium eutrophic and oligotrophic samples. Bacterial alpha-diversity was found greater in high eutrophication samples than in the other samples. Besides, Ponticaulis koreensis, Nautella italic, Anaerospora hongkongensis, Candidatus Aquiluna rubra, and Roseovarius pacificus were sensitive to trophic variation and thus could be used as eco-markers. In addition, the relative abundances of functional genes involving carbohydrate and amino acid metabolism were very high among the samples. We also found temperature, Chl-a, TDN and NO3- were the main environmental drivers of bacterial community structure. Overall, this study provides new insight into the composition of bacterial community and function response to gradients of eutrophication in Beibu Gulf.
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Affiliation(s)
- Nan Li
- Key laboratory of Ministry of Education for Environment Change and Resources Use in Beibu Gulf, Guangxi Key Laboratory of Earth Surface Processes and Intelligent Simulation, Nanning Normal University, 175 East Mingxiu Road, Nanning 530001, Guangxi, People's Republic of China
| | - Xing Chen
- Key laboratory of Ministry of Education for Environment Change and Resources Use in Beibu Gulf, Guangxi Key Laboratory of Earth Surface Processes and Intelligent Simulation, Nanning Normal University, 175 East Mingxiu Road, Nanning 530001, Guangxi, People's Republic of China; College of Life Science and Technology, Guangxi University, 100 Daxue Road, Nanning 530004, Guangxi, People's Republic of China
| | - Huaxian Zhao
- Key laboratory of Ministry of Education for Environment Change and Resources Use in Beibu Gulf, Guangxi Key Laboratory of Earth Surface Processes and Intelligent Simulation, Nanning Normal University, 175 East Mingxiu Road, Nanning 530001, Guangxi, People's Republic of China
| | - Jinli Tang
- Key laboratory of Ministry of Education for Environment Change and Resources Use in Beibu Gulf, Guangxi Key Laboratory of Earth Surface Processes and Intelligent Simulation, Nanning Normal University, 175 East Mingxiu Road, Nanning 530001, Guangxi, People's Republic of China
| | - Gonglingxia Jiang
- Key laboratory of Ministry of Education for Environment Change and Resources Use in Beibu Gulf, Guangxi Key Laboratory of Earth Surface Processes and Intelligent Simulation, Nanning Normal University, 175 East Mingxiu Road, Nanning 530001, Guangxi, People's Republic of China
| | - Zhuoting Li
- Key laboratory of Ministry of Education for Environment Change and Resources Use in Beibu Gulf, Guangxi Key Laboratory of Earth Surface Processes and Intelligent Simulation, Nanning Normal University, 175 East Mingxiu Road, Nanning 530001, Guangxi, People's Republic of China
| | - Xiaoli Li
- Key laboratory of Ministry of Education for Environment Change and Resources Use in Beibu Gulf, Guangxi Key Laboratory of Earth Surface Processes and Intelligent Simulation, Nanning Normal University, 175 East Mingxiu Road, Nanning 530001, Guangxi, People's Republic of China
| | - Si Chen
- College of Life Science and Technology, Guangxi University, 100 Daxue Road, Nanning 530004, Guangxi, People's Republic of China
| | - Shuqi Zou
- Department of biological sciences, Kyonggi University, 154-42, Gwanggyosan-ro, Yeongtong-gu, Suwon-si, Gyeonggi-do 16227, South Korea
| | - Ke Dong
- Department of biological sciences, Kyonggi University, 154-42, Gwanggyosan-ro, Yeongtong-gu, Suwon-si, Gyeonggi-do 16227, South Korea
| | - Qiangsheng Xu
- Key laboratory of Ministry of Education for Environment Change and Resources Use in Beibu Gulf, Guangxi Key Laboratory of Earth Surface Processes and Intelligent Simulation, Nanning Normal University, 175 East Mingxiu Road, Nanning 530001, Guangxi, People's Republic of China.
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15
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Raiyani NM, Singh SP. Taxonomic and functional profiling of the microbial communities of Arabian Sea: A metagenomics approach. Genomics 2020; 112:4361-4369. [PMID: 32712295 DOI: 10.1016/j.ygeno.2020.07.024] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2019] [Revised: 04/13/2020] [Accepted: 07/11/2020] [Indexed: 01/08/2023]
Affiliation(s)
- Nirali M Raiyani
- UGC-CAS Department of Biosciences, Saurashtra University, Rajkot 360 005, Gujarat, India
| | - Satya P Singh
- UGC-CAS Department of Biosciences, Saurashtra University, Rajkot 360 005, Gujarat, India.
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16
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Chen W, Yin S, Wu A, Wang L, Chen X. Bioleaching of copper sulfides using mixed microorganisms and its community structure succession in the presence of seawater. BIORESOURCE TECHNOLOGY 2020; 297:122453. [PMID: 31787510 DOI: 10.1016/j.biortech.2019.122453] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/15/2019] [Revised: 11/17/2019] [Accepted: 11/18/2019] [Indexed: 06/10/2023]
Abstract
The bacterial diversity and dynamics in the leaching solution were analyzed during bioleaching of low-grade copper sulfide ore in the presence of seawater in this study. The results indicated a promoting response of appropriate-proportion seawater to bioleaching with improved copper recoveries. A maximum of 84.70% copper recovery was obtained in the presence of 20.00% seawater in contrast to only 72.49% in its absence. The experiments verified that seawater owned a great influence on Attached bacteria and bacterial species. 16S rDNA analysis illustrated that bacterial species decreased distinctly in the presence of seawater. Little difference between blank sample (no seawater) and sample adding 20.00% seawater was indicated by beta diversity index. Bacteria (including Acidithiobacillus ferrooxidans, Sphingomonas leidyi and Lactobacillus acetotolerans) were influenced significantly after adding seawater. Acidithiobacillus ferrooxidans accounted for the highest proportion of the community whether seawater was added or not during bioleaching.
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Affiliation(s)
- Wei Chen
- Key Laboratory of Ministry of Education for High-Efficient Mining and Safety of Metal, University of Science and Technology Beijing, Beijing 100083, China; School of Civil and Resource Engineering, University of Science and Technology Beijing, Beijing 100083, China
| | - Shenghua Yin
- Key Laboratory of Ministry of Education for High-Efficient Mining and Safety of Metal, University of Science and Technology Beijing, Beijing 100083, China; School of Civil and Resource Engineering, University of Science and Technology Beijing, Beijing 100083, China.
| | - Aixiang Wu
- Key Laboratory of Ministry of Education for High-Efficient Mining and Safety of Metal, University of Science and Technology Beijing, Beijing 100083, China; School of Civil and Resource Engineering, University of Science and Technology Beijing, Beijing 100083, China
| | - Leiming Wang
- School of Civil and Resource Engineering, University of Science and Technology Beijing, Beijing 100083, China
| | - Xun Chen
- School of Civil and Resource Engineering, University of Science and Technology Beijing, Beijing 100083, China
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