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Ray K, Basak SK, Giri CK, Kotal HN, Mandal A, Chatterjee K, Saha S, Biswas B, Mondal S, Das I, Ghosh A, Bhadury P, Joshi R. Ecological restoration at pilot-scale employing site-specific rationales for small-patch degraded mangroves in Indian Sundarbans. Sci Rep 2024; 14:12952. [PMID: 38839775 PMCID: PMC11153218 DOI: 10.1038/s41598-024-63281-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Accepted: 05/27/2024] [Indexed: 06/07/2024] Open
Abstract
To date, degraded mangrove ecosystem restoration accomplished worldwide primarily aligns towards rehabilitation with monotypic plantations, while ecological restoration principles are rarely followed in these interventions. However, researchers admit that most of these initiatives' success rate is not appreciable often. An integrative framework of ecological restoration for degraded mangroves where site-specific observations could be scientifically rationalized, with co-located reference pristine mangroves as the target ecosystem to achieve is currently distinctively lacking. Through this experimental scale study, we studied the suitability of site-specific strategies to ecologically restore degraded mangrove patches vis-à-vis the conventional mono-species plantations in a highly vulnerable mangrove ecosystem in Indian Sundarbans. This comprehensive restoration framework was trialed in small discrete degraded mangrove patches spanning ~ 65 ha. Site-specific key restoration components applied are statistically validated through RDA analyses and Bayesian t-tests. 25 quantifiable metrics evaluate the restoration success of a ~ 3 ha degraded mangrove patch with Ridgeline distribution, Kolmogorov-Smirnov (K-S) tests, and Mahalanobis Distance (D2) measure to prove the site's near-equivalence to pristine reference in multiple ecosystem attributes. This restoration intervention irrevocably establishes the greater potential of this framework in the recovery of ecosystem functions and self-sustenance compared to that of predominant monoculture practices for vulnerable mangroves.
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Affiliation(s)
- Krishna Ray
- Environmental Biotechnology Group, Department of Botany, West Bengal State University, Berunanpukuria, Malikapur, Barasat, Kolkata, 700126, India.
| | - Sandip Kumar Basak
- Sarat Centenary College, Dhaniakhali, Hooghly, West Bengal, 712302, India.
| | - Chayan Kumar Giri
- Environmental Biotechnology Group, Department of Botany, West Bengal State University, Berunanpukuria, Malikapur, Barasat, Kolkata, 700126, India
| | - Hemendra Nath Kotal
- Environmental Biotechnology Group, Department of Botany, West Bengal State University, Berunanpukuria, Malikapur, Barasat, Kolkata, 700126, India
| | - Anup Mandal
- Environmental Biotechnology Group, Department of Botany, West Bengal State University, Berunanpukuria, Malikapur, Barasat, Kolkata, 700126, India
| | - Kiranmoy Chatterjee
- Department of Statistics, Bidhannagar College, Salt Lake City, Sector 1, Block EB, Kolkata, 700064, India
| | - Subhajit Saha
- Environmental Biotechnology Group, Department of Botany, West Bengal State University, Berunanpukuria, Malikapur, Barasat, Kolkata, 700126, India
| | - Biswajit Biswas
- Environmental Biotechnology Group, Department of Botany, West Bengal State University, Berunanpukuria, Malikapur, Barasat, Kolkata, 700126, India
| | - Sumana Mondal
- Environmental Biotechnology Group, Department of Botany, West Bengal State University, Berunanpukuria, Malikapur, Barasat, Kolkata, 700126, India
| | - Ipsita Das
- Environmental Biotechnology Group, Department of Botany, West Bengal State University, Berunanpukuria, Malikapur, Barasat, Kolkata, 700126, India
| | - Anwesha Ghosh
- Centre for Climate and Environmental Studies, Indian Institute of Science Education and Research Kolkata, Mohanpur, Nadia, West Bengal, 741246, India
| | - Punyasloke Bhadury
- Integrative Taxonomy and Microbial Ecology Research Group, Department of Biological Sciences, Indian Institute of Science Education and Research Kolkata, Mohanpur, Nadia, West Bengal, 741246, India
| | - Rahul Joshi
- Zoological Survey of India (ZSI), Prani Vigyan Bhawan, Block M, New Alipore, Kolkata, 700053, India
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Tiwari ON, Bobby MN, Kondi V, Halder G, Kargarzadeh H, Ikbal AMA, Bhunia B, Thomas S, Efferth T, Chattopadhyay D, Palit P. Comprehensive review on recent trends and perspectives of natural exo-polysaccharides: Pioneering nano-biotechnological tools. Int J Biol Macromol 2024; 265:130747. [PMID: 38479657 DOI: 10.1016/j.ijbiomac.2024.130747] [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: 09/03/2023] [Revised: 02/22/2024] [Accepted: 03/07/2024] [Indexed: 04/18/2024]
Abstract
Exopolysaccharides (EPSs), originating from various microbes, and mushrooms, excel in their conventional role in bioremediation to showcase diverse applications emphasizing nanobiotechnology including nano-drug carriers, nano-excipients, medication and/or cell encapsulation, gene delivery, tissue engineering, diagnostics, and associated treatments. Acknowledged for contributions to adsorption, nutrition, and biomedicine, EPSs are emerging as appealing alternatives to traditional polymers, for biodegradability and biocompatibility. This article shifts away from the conventional utility to delve deeply into the expansive landscape of EPS applications, particularly highlighting their integration into cutting-edge nanobiotechnological methods. Exploring EPS synthesis, extraction, composition, and properties, the discussion emphasizes their structural diversity with molecular weight and heteropolymer compositions. Their role as raw materials for value-added products takes center stage, with critical insights into recent applications in nanobiotechnology. The multifaceted potential, biological relevance, and commercial applicability of EPSs in contemporary research and industry align with the nanotechnological advancements coupled with biotechnological nano-cleansing agents are highlighted. EPS-based nanostructures for biological applications have a bright future ahead of them. Providing crucial information for present and future practices, this review sheds light on how eco-friendly EPSs derived from microbial biomass of terrestrial and aquatic environments can be used to better understand contemporary nanobiotechnology for the benefit of society.
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Affiliation(s)
- Onkar Nath Tiwari
- Centre for Conservation and Utilization of Blue Green Algae, Division of Microbiology, ICAR-Indian Agricultural Research Institute, New Delhi 110012, India.
| | - Md Nazneen Bobby
- Department of Biotechnology, Vignan's Foundation for Science, Technology & Research, Vadlamudi, Andhra Pradesh 522213, India
| | - Vanitha Kondi
- Department of Pharmaceutics, Vishnu Institute of Pharmaceutical Education and Research, Narsapur, Medak 502313, Telangana, India
| | - Gopinath Halder
- Department of Chemical Engineering, National Institute of Technology Durgapur, West Bengal 713209, India
| | - Hanieh Kargarzadeh
- Center of Molecular and Macromolecular Studies, Polish Academy of Sciences, Seinkiewicza 112, 90-363 Lodz, Poland
| | - Abu Md Ashif Ikbal
- Department of Pharmaceutical Sciences, Drug Discovery Research Laboratory, Assam University, Silchar 788011, India
| | - Biswanath Bhunia
- Department of Bio Engineering, National Institute of Technology Agartala, Jirania 799046, India
| | - Sabu Thomas
- School of Nanoscience and Nanotechnology, Mahatma Gandhi University, Priyadarshini Hills, Athirampuzha, Kerala, 686560, India; Department of Chemical Sciences, University of Johannesburg, P.O. Box, 17011, Doornfontein, 2028, Johannesburg, South Africa
| | - Thomas Efferth
- Department of Pharmaceutical Biology, Institute of Pharmaceutical and Biomedical Sciences, University of Mainz, Staudinger Weg 5, 55128 Mainz, Germany
| | - Debprasad Chattopadhyay
- ICMR-National Institute of Traditional Medicine, Nehru Nagar, Belagavi 590010, India; School of Life Sciences, Swami Vivekananda University, Barrackpore, Kolkata 700102, India
| | - Partha Palit
- Department of Pharmaceutical Sciences, Drug Discovery Research Laboratory, Assam University, Silchar 788011, India.
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Hutchings B, López-Legentil S, Stefaniak LM, Nydam M, Erwin PM. Distinct microbial communities in an ascidian-crustacean symbiosis. ENVIRONMENTAL MICROBIOLOGY REPORTS 2024; 16:e13242. [PMID: 38383831 PMCID: PMC10881349 DOI: 10.1111/1758-2229.13242] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Accepted: 02/01/2024] [Indexed: 02/23/2024]
Abstract
Ascidians are marine invertebrates known to occasionally host symbiotic crustaceans. Although the microbiomes of both ascidians and free-living crustaceans have been characterized, there is no documentation of microbial communities in an ascidian-crustacean symbiosis. Samples of the solitary ascidian Ascidia sydneiensis and ambient seawater were collected in Belize. Four symbiotic amphipod crustaceans were retrieved from the branchial sac of the animal, and their microbiomes were compared with those from their ascidian host (tunic and branchial sac compartments) and seawater. Microbiome richness and diversity differed significantly between sample types, with amphipod microbiomes exhibiting significantly lower diversity than tunic and ambient seawater samples. Microbiome composition also differed significantly between sample types and among all pairwise comparisons, except for branchial sac and amphipod microbiomes. Differential operational taxonomic unit (OTU) analyses revealed that only 3 out of 2553 OTUs had significantly different relative abundances in amphipods compared with ascidian branchial sacs, whereas 72 OTUs differed between amphipod and tunic and 315 between amphipod and seawater samples. Thus, different body compartments of A. sydneiensis hosted distinct microbiomes, and symbiotic amphipods contained microbiomes resembling the region they inhabit (i.e., the branchial sac), suggesting that environmental filtering and co-evolutionary processes are determinants of microbiome composition within ascidian-crustacean symbioses.
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Affiliation(s)
- Brenna Hutchings
- Department of Biology & Marine Biology, and Center for Marine Science, University of North Carolina Wilmington, Wilmington, North Carolina, USA
| | - Susanna López-Legentil
- Department of Biology & Marine Biology, and Center for Marine Science, University of North Carolina Wilmington, Wilmington, North Carolina, USA
| | - Lauren M Stefaniak
- Department of Marine Science, Coastal Carolina University, Conway, South Carolina, USA
| | - Marie Nydam
- Department of Biology, SOKA University of America, Aliso Viejo, California, USA
| | - Patrick M Erwin
- Department of Biology & Marine Biology, and Center for Marine Science, University of North Carolina Wilmington, Wilmington, North Carolina, USA
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Bo X, Zhao Y, Qin F, Wu F, Tan M, Ju S, Song Z, Li W, He F, Wei Y, Xu H, Huang X. Cytotoxic metabolites from the mangrove endophytic fungus Aspergillus sp. GXNU QG1a. Nat Prod Res 2024:1-8. [PMID: 38226421 DOI: 10.1080/14786419.2024.2303601] [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: 11/30/2023] [Accepted: 01/02/2024] [Indexed: 01/17/2024]
Abstract
A new benzoquinone, guxiumasperone A (1), and a new diisoprenyl-cyclohexene-type meroterpenoids, biscognienyne M (2), along with four known diisoprenyl-cyclohexene analogues was isolated from the mangrove endophytic fungus Aspergillus QG1a. Their structures were determined by extensive spectral analysis of 1D and 2D NMR, HR-ESI- MS, and X-ray crystallography. Compound 1 was deduced by a single-crystal X-ray diffraction analysis, and the absolute configuration of 2 was further unequivocally elucidated by comparing the experimental electronic circular dichroism (ECD) data with calculated ECD spectra. Compounds 1 and 2 showed significant cytotoxic activity against selected tumour cells. Particularly, compound 2 exhibited strong activity against A2780 cancer cells with an IC50 value of 6.8 μM.
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Affiliation(s)
- Xianglong Bo
- State Key Laboratory for Chemistry and Molecular Engineering of Medicinal Resources, College of Chemistry and Pharmaceutical Sciences, Guangxi Normal University, Guilin, P.R. China
| | - Yufei Zhao
- State Key Laboratory for Chemistry and Molecular Engineering of Medicinal Resources, College of Chemistry and Pharmaceutical Sciences, Guangxi Normal University, Guilin, P.R. China
| | - Feng Qin
- State Key Laboratory for Chemistry and Molecular Engineering of Medicinal Resources, College of Chemistry and Pharmaceutical Sciences, Guangxi Normal University, Guilin, P.R. China
| | - Furong Wu
- State Key Laboratory for Chemistry and Molecular Engineering of Medicinal Resources, College of Chemistry and Pharmaceutical Sciences, Guangxi Normal University, Guilin, P.R. China
| | - Meijing Tan
- State Key Laboratory for Chemistry and Molecular Engineering of Medicinal Resources, College of Chemistry and Pharmaceutical Sciences, Guangxi Normal University, Guilin, P.R. China
| | - Shichao Ju
- State Key Laboratory for Chemistry and Molecular Engineering of Medicinal Resources, College of Chemistry and Pharmaceutical Sciences, Guangxi Normal University, Guilin, P.R. China
| | - Zishuo Song
- State Key Laboratory for Chemistry and Molecular Engineering of Medicinal Resources, College of Chemistry and Pharmaceutical Sciences, Guangxi Normal University, Guilin, P.R. China
| | - Wenjun Li
- State Key Laboratory for Chemistry and Molecular Engineering of Medicinal Resources, College of Chemistry and Pharmaceutical Sciences, Guangxi Normal University, Guilin, P.R. China
| | - Fan He
- State Key Laboratory for Chemistry and Molecular Engineering of Medicinal Resources, College of Chemistry and Pharmaceutical Sciences, Guangxi Normal University, Guilin, P.R. China
| | - Youquan Wei
- State Key Laboratory for Chemistry and Molecular Engineering of Medicinal Resources, College of Chemistry and Pharmaceutical Sciences, Guangxi Normal University, Guilin, P.R. China
| | - Hua Xu
- State Key Laboratory for Chemistry and Molecular Engineering of Medicinal Resources, College of Chemistry and Pharmaceutical Sciences, Guangxi Normal University, Guilin, P.R. China
| | - Xishan Huang
- State Key Laboratory for Chemistry and Molecular Engineering of Medicinal Resources, College of Chemistry and Pharmaceutical Sciences, Guangxi Normal University, Guilin, P.R. China
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Sui J, He X, Yi G, Zhou L, Liu S, Chen Q, Xiao X, Wu J. Diversity and structure of the root-associated bacterial microbiomes of four mangrove tree species, revealed by high-throughput sequencing. PeerJ 2023; 11:e16156. [PMID: 37810771 PMCID: PMC10559887 DOI: 10.7717/peerj.16156] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Accepted: 08/31/2023] [Indexed: 10/10/2023] Open
Abstract
Background Root-associated microbes of the mangrove trees play important roles in protecting and maintaining mangrove ecosystems. At present, most of our understanding of mangrove root-related microbial diversity is obtained from specific mangrove species in selected geographic regions. Relatively little is known about the composition of the bacterial microbiota existing in disparate mangrove species microenvironments, particularly the relationship among different mangrove species in tropical environments. Methods We collected the root, rhizosphere soil, and non-rhizosphere soil of four mangrove trees (Acanthus ilicifolius, Bruguiera gymnorrhiza, Clerodendrum inerme, and Lumnitzera racemosa) and detected the 16S rRNA gene by a conventional PCR. We performed high throughput sequencing using Illumina Novaseq 6000 platform (2 × 250 paired ends) to investigate the bacterial communities related with the different mangrove species. Results We analyzed the bacterial diversity and composition related to the diverse ecological niches of mangrove species. Our data confirmed distinct distribution patterns of bacterial communities in the three rhizocompartments of the four mangrove species. Microbiome composition varied with compartments and host mangrove species. The bacterial communities between the endosphere and the other two compartments were distinctly diverse independent of mangrove species. The large degree of overlap in critical community members of the same rhizocompartment across distinct mangrove species was found at the phylum level. Furthermore, this is the first report of Acidothermus found in mangrove environments. In conclusion, understanding the complicated host-microbe associations in different mangrove species could lay the foundation for the exploitation of the microbial resource and the production of secondary metabolites.
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Affiliation(s)
- Jinlei Sui
- Public Research Center, Hainan Medical College, Haikou, China
| | - Xiaowen He
- Public Research Center, Hainan Medical College, Haikou, China
| | - Guohui Yi
- Public Research Center, Hainan Medical College, Haikou, China
| | - Limin Zhou
- Public Research Center, Hainan Medical College, Haikou, China
| | - Shunqing Liu
- Public Research Center, Hainan Medical College, Haikou, China
| | - Qianqian Chen
- Public Research Center, Hainan Medical College, Haikou, China
| | - Xiaohu Xiao
- Rubber Research Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
| | - Jinyan Wu
- Public Research Center, Hainan Medical College, Haikou, China
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Skariah S, Abdul-Majid S, Hay AG, Acharya A, Kano N, Al-Ishaq RK, de Figueiredo P, Han A, Guzman A, Dargham SR, Sameer S, Kim GE, Khan S, Pillai P, Sultan AA. Soil Properties Correlate with Microbial Community Structure in Qatari Arid Soils. Microbiol Spectr 2023; 11:e0346222. [PMID: 36847511 PMCID: PMC10100838 DOI: 10.1128/spectrum.03462-22] [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: 08/30/2022] [Accepted: 02/05/2023] [Indexed: 03/01/2023] Open
Abstract
This is the first detailed characterization of the microbiota and chemistry of different arid habitats from the State of Qatar. Analysis of bacterial 16S rRNA gene sequences showed that in aggregate, the dominant microbial phyla were Actinobacteria (32.3%), Proteobacteria (24.8%), Firmicutes (20.7%), Bacteroidetes (6.3%), and Chloroflexi (3.6%), though individual soils varied widely in the relative abundances of these and other phyla. Alpha diversity measured using feature richness (operational taxonomic units [OTUs]), Shannon's entropy, and Faith's phylogenetic diversity (PD) varied significantly between habitats (P = 0.016, P = 0.016, and P = 0.015, respectively). Sand, clay, and silt were significantly correlated with microbial diversity. Highly significant negative correlations were also seen at the class level between both classes Actinobacteria and Thermoleophilia (phylum Actinobacteria) and total sodium (R = -0.82 and P = 0.001 and R = -0.86, P = 0.000, respectively) and slowly available sodium (R = -0.81 and P = 0.001 and R = -0.8 and P = 0.002, respectively). Additionally, class Actinobacteria also showed significant negative correlation with sodium/calcium ratio (R = -0.81 and P = 0.001). More work is needed to understand if there is a causal relationship between these soil chemical parameters and the relative abundances of these bacteria. IMPORTANCE Soil microbes perform a multitude of essential biological functions, including organic matter decomposition, nutrient cycling, and soil structure preservation. Qatar is one of the most hostile and fragile arid environments on earth and is expected to face a disproportionate impact of climate change in the coming years. Thus, it is critical to establish a baseline understanding of microbial community composition and to assess how soil edaphic factors correlate with microbial community composition in this region. Although some previous studies have quantified culturable microbes in specific Qatari habitats, this approach has serious limitations, as in environmental samples, approximately only 0.5% of cells are culturable. Hence, this method vastly underestimates natural diversity within these habitats. Our study is the first to systematically characterize the chemistry and total microbiota associated with different habitats present in the State of Qatar.
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Affiliation(s)
- Sini Skariah
- Department of Microbiology and Immunology, Weill Cornell Medicine—Qatar, Cornell University, Qatar Foundation—Education City, Doha, Qatar
| | - Sara Abdul-Majid
- Department of Microbiology and Immunology, Weill Cornell Medicine—Qatar, Cornell University, Qatar Foundation—Education City, Doha, Qatar
| | - Anthony G. Hay
- Department of Microbiology, Cornell University, Ithaca, New York, USA
| | - Anushree Acharya
- Department of Microbiology and Immunology, Weill Cornell Medicine—Qatar, Cornell University, Qatar Foundation—Education City, Doha, Qatar
| | - Noora Kano
- Department of Microbiology and Immunology, Weill Cornell Medicine—Qatar, Cornell University, Qatar Foundation—Education City, Doha, Qatar
| | - Raghad Khalid Al-Ishaq
- Department of Microbiology and Immunology, Weill Cornell Medicine—Qatar, Cornell University, Qatar Foundation—Education City, Doha, Qatar
| | - Paul de Figueiredo
- Department of Microbial Pathogenesis and Immunology, College of Medicine, Texas A&M Health Science Center, Texas A&M University, Bryan, Texas, USA
- Department of Veterinary Pathobiology, Texas A&M University, College Station, Texas, USA
| | - Arum Han
- Department of Electrical and Computer Engineering, Texas A&M University, Texas, USA
- Department of Biomedical Engineering, Texas A&M University, Texas, USA
| | - Adrian Guzman
- Department of Electrical and Computer Engineering, Texas A&M University, Texas, USA
- Department of Biomedical Engineering, Texas A&M University, Texas, USA
| | - Soha Roger Dargham
- Biostatistics, Epidemiology, & Biomathematics Research Core, Weill Cornell Medicine—Qatar, Cornell University, Qatar Foundation—Education City, Doha, Qatar
| | - Saad Sameer
- Department of Microbiology and Immunology, Weill Cornell Medicine—Qatar, Cornell University, Qatar Foundation—Education City, Doha, Qatar
| | - Gi Eun Kim
- Department of Microbiology and Immunology, Weill Cornell Medicine—Qatar, Cornell University, Qatar Foundation—Education City, Doha, Qatar
| | - Sabiha Khan
- Department of Microbiology and Immunology, Weill Cornell Medicine—Qatar, Cornell University, Qatar Foundation—Education City, Doha, Qatar
| | - Priyamvada Pillai
- Department of Microbiology and Immunology, Weill Cornell Medicine—Qatar, Cornell University, Qatar Foundation—Education City, Doha, Qatar
| | - Ali A. Sultan
- Department of Microbiology and Immunology, Weill Cornell Medicine—Qatar, Cornell University, Qatar Foundation—Education City, Doha, Qatar
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Chatterjee S, Das S. Whole-genome sequencing of biofilm-forming and chromium-resistant mangrove fungus Aspergillus niger BSC-1. World J Microbiol Biotechnol 2022; 39:55. [PMID: 36565384 DOI: 10.1007/s11274-022-03497-w] [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: 09/29/2022] [Accepted: 12/13/2022] [Indexed: 12/25/2022]
Abstract
Filamentous fungus Aspergillus niger has gained significant industrial and ecological value due to its great potential in enzymatic activities. The present study reports the complete genome sequence of A. niger BSC-1 which was isolated from Indian Sundarban mangrove ecosystem. The study revealed that the genome of A. niger BSC-1 was 35.1 Mbp assembled in 40 scaffolds with 49.2% GC content. A total of 10,709 genes were reported out of which 10,535 genes were predicted for encoding the proteins. BUSCO assessment showed 98.6% of genome completeness indicating high quality genome sequencing. The genome sequencing of A. niger BSC-1 revealed the presence of rodA and exgA genes for initial adhesion to surface and Ags genes for matrix formation, during biofilm growth. OrthoVenn2 analysis revealed that A.niger BSC-1 shared 9552 gene clusters with the reference strain A. niger CBS554.65. Semi-quantitative RT-PCR analysis unveiled the role of Ags1 and P-type ATPase in fungal biofilm formation and chromium (Cr) resistance, respectively. During biofilm growth the expression of Ags1 significantly (P < 0.0001; two-way ANOVA followed by Sidak's multiple comparisons test) increased with respect to planktonic culture revealing the possible involvement of Ags1 in biofilm matrix formation. Expression of P-type ATPase gene was significantly upregulated (P < 0.0001; one-way ANOVA followed by Dunnett's multiple comparisons test) with the increasing chromium concentration in the fungal culture. Besides, several other genes encoding metalloprotease, copper and zinc binding proteins, and NADH-dependent oxidoreductase were also found in the genome of A. niger BSC-1. These proteins are also involved in heavy metal tolerance and nanofabrication indicating that this filamentous fungus A. niger BSC-1 could be potentially utilized for chromium detoxification through biofilm or nanobiremediation.
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Affiliation(s)
- Shreosi Chatterjee
- Laboratory of Environmental Microbiology and Ecology (LEnME), Department of Life Science, National Institute of Technology, Rourkela, 769 008, Odisha, India
| | - Surajit Das
- Laboratory of Environmental Microbiology and Ecology (LEnME), Department of Life Science, National Institute of Technology, Rourkela, 769 008, Odisha, India.
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Scherer BP, Mason OU, Mast AR. Bacterial communities vary across populations and tissue type in red mangroves (Rhizophora mangle, Rhizophoraceae) along an expanding front. FEMS Microbiol Ecol 2022; 98:6840209. [PMID: 36413458 DOI: 10.1093/femsec/fiac139] [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: 01/24/2022] [Revised: 11/07/2022] [Accepted: 11/18/2022] [Indexed: 11/23/2022] Open
Abstract
Plant-associated microbial communities may be important sources of functional diversity and genetic variation that influence host evolution. Bacteria provide benefits for their hosts, yet in most plant systems we know little about their taxonomic composition or variation across tissues and host range. Red Mangrove (Rhizophora mangle L.) is a vital coastal plant species that is currently expanding poleward and with it, perhaps, its microbiome. We explored variability in bacterial communities across tissues, individuals, and populations. We collected samples from six sample types from 5 to 10 individuals at each of three populations and used 16S rRNA gene (iTag) sequencing to describe their bacterial communities. Core community members and dominant bacterial classes were determined for each sample type. Pairwise PERMANOVA of Bray-Curtis dissimilarity and Indicator Species Analysis revealed significant differences in bacterial communities between sample types and populations. We described the previously unexplored microbiome of the reproductive tissues of R. mangle. Populations and most sample types were associated with distinct communities. Bacterial communities associated with R. mangle are influenced by host geography and sample type. Our study provides a foundation for future work exploring the functional roles of these microbes and their relevance to biogeochemical cycling.
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Affiliation(s)
- Brendan P Scherer
- Florida State University, 319 Stadium Drive, Tallahassee, FL 32304, United States
| | - Olivia U Mason
- Department of Earth, Ocean and Atmospheric Sciences, Florida State University, 1011 Academic Way, Tallahassee, FL 32304, United States
| | - Austin R Mast
- Department of Biological Sciences, Florida State University, 319 Stadium Drive, Tallahassee, FL 32304, United States
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Okeke ES, Okoye CO, Chidike Ezeorba TP, Mao G, Chen Y, Xu H, Song C, Feng W, Wu X. Emerging bio-dispersant and bioremediation technologies as environmentally friendly management responses toward marine oil spill: A comprehensive review. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2022; 322:116123. [PMID: 36063698 DOI: 10.1016/j.jenvman.2022.116123] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Revised: 08/13/2022] [Accepted: 08/25/2022] [Indexed: 06/15/2023]
Abstract
Marine oil spills emanating from wells, pipelines, freighters, tankers, and storage facilities draw public attention and necessitate quick and environmentally friendly response measures. It is sometimes feasible to contain the oil with booms and collect it with skimmers or burn it, but this is impracticable in many circumstances, and all that can be done without causing further environmental damage is adopting natural attenuation, particularly through microbial biodegradation. Biodegradation can be aided by carefully supplying biologically accessible nitrogen and phosphorus to alleviate some of the microbial growth constraints at the shoreline. This review discussed the characteristics of oil spills, origin, ecotoxicology, health impact of marine oils spills, and responses, including the variety of remedies and responses to oil spills using biological techniques. The different bioremediation and bio-dispersant treatment technologies are then described, with a focus on the use of green surfactants and their advances, benefits/drawbacks. These technologies were thoroughly explained, with a timeline of research and recent studies. Finally, the hurdles that persist as a result of spills are explored, as well as the measures that must be taken and the potential for the development of existing treatment technologies, all of which must be linked to the application of integrated procedures.
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Affiliation(s)
- Emmanuel Sunday Okeke
- Institute of Environmental Health and Ecological Security, School of Environment and Safety Engineering, Jiangsu University, Zhenjiang, 212013, PR China; Department of Biochemistry, Faculty of Biological Sciences, University of Nigeria, Nsukka, 41000, Nsukka Enugu State, Nigeria; Natural Science Unit, SGS, University of Nigeria, Nsukka, 41000, Nsukka Enugu State, Nigeria
| | - Charles Obinwanne Okoye
- Department of Zoology and Environmental Biology, Faculty of Biological Sciences, University of Nigeria, Nsukka, 41000, Nsukka Enugu State, Nigeria; Biofuel Institute, School of Environment and Safety Engineering, Jiangsu University, Zhenjiang, 212013, PR China
| | - Timothy Prince Chidike Ezeorba
- Department of Biochemistry, Faculty of Biological Sciences, University of Nigeria, Nsukka, 41000, Nsukka Enugu State, Nigeria
| | - Guanghua Mao
- Institute of Environmental Health and Ecological Security, School of Environment and Safety Engineering, Jiangsu University, Zhenjiang, 212013, PR China
| | - Yao Chen
- Institute of Environmental Health and Ecological Security, School of Environment and Safety Engineering, Jiangsu University, Zhenjiang, 212013, PR China
| | - Hai Xu
- Institute of Environmental Health and Ecological Security, School of Environment and Safety Engineering, Jiangsu University, Zhenjiang, 212013, PR China
| | - Chang Song
- Institute of Environmental Health and Ecological Security, School of Environment and Safety Engineering, Jiangsu University, Zhenjiang, 212013, PR China
| | - Weiwei Feng
- Institute of Environmental Health and Ecological Security, School of Environment and Safety Engineering, Jiangsu University, Zhenjiang, 212013, PR China.
| | - Xiangyang Wu
- Institute of Environmental Health and Ecological Security, School of Environment and Safety Engineering, Jiangsu University, Zhenjiang, 212013, PR China.
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10
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Quintero IJ, Castillo AM, Mejía LC. Diversity and Taxonomy of Soil Bacterial Communities in Urban and Rural Mangrove Forests of the Panama Bay. Microorganisms 2022; 10:microorganisms10112191. [PMID: 36363784 PMCID: PMC9697262 DOI: 10.3390/microorganisms10112191] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Revised: 10/26/2022] [Accepted: 10/27/2022] [Indexed: 11/09/2022] Open
Abstract
Mangrove ecosystems are threatened worldwide by a wide range of factors including climate change, coastal development, and pollution. The effects of these factors on soil bacterial communities of Neotropical mangroves and their temporal dynamics is largely undocumented. Here we compared the diversity and taxonomic composition of bacterial communities in the soil of two mangrove forest sites of the Panama Bay: Juan Diaz (JD), an urban mangrove forest in Panama City surrounded by urban development, with occurrence of five mangrove species, and polluted with solid waste and sewage; and Bayano (B), a rural mangrove forest without urban development, without solid waste pollution, and with the presence of two mangrove species. Massive amplicon sequencing of the V4 region of the 16S rRNA gene and community analyses were implemented. In total, 20,691 bacterial amplicon sequence variants were identified, and the bacterial community was more diverse in the rural mangrove forest based on Faith’s phylogenetic diversity index. The three dominant phyla of bacteria found and shared between the two sites were Proteobacteria, Desulfobacterota, and Chloroflexi. The ammonia oxidizing archaea class Nitrosphaeria was found among the top 10 most abundant. Dominant genera of bacteria that occurred in the two mangrove sites were: BD2-11_terrestrial_group (Gemmatimonadota), EPR3968-O8a-Bc78 (Gammaproteobacteria), Salinimicrobium (Bacteroidetes), Sulfurovum (Campylobacteria), and Woeseia (Gammaproteobacteria) of which the first three and Methyloceanibacter had increased in relative abundance in the transition from rainy to dry to rainy season in the urban mangrove forest. Altogether, our study suggests that factors such as urban development, vegetation composition, pollution, and seasonal changes may cause shifts in bacterial diversity and relative abundance of specific taxa in mangrove soils. In particular, taxa with roles in biogeochemical cycles of carbon, nitrogen, sulfur, and phosphorus, and on rhizosphere taxa, could be important for mangrove plant resilience to environmental stress.
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Affiliation(s)
- Indira J. Quintero
- Centro de Biodiversidad y Descubrimiento de Drogas, Instituto de Investigaciones Científicas y Servicios de Alta Tecnología (INDICASAT-AIP) Clayton, Panamá 0843, Panama
- Programa de Maestría en Ciencias Biológicas, Universidad de Panamá, Panamá 0824, Panama
| | - Anakena M. Castillo
- Centro de Biodiversidad y Descubrimiento de Drogas, Instituto de Investigaciones Científicas y Servicios de Alta Tecnología (INDICASAT-AIP) Clayton, Panamá 0843, Panama
- Departamento de Investigación en Entomología Médica, Instituto Conmemorativo Gorgas de Estudios de la Salud (ICGES), Panamá 0816, Panama
| | - Luis C. Mejía
- Centro de Biodiversidad y Descubrimiento de Drogas, Instituto de Investigaciones Científicas y Servicios de Alta Tecnología (INDICASAT-AIP) Clayton, Panamá 0843, Panama
- Smithsonian Tropical Research Institute, Panamá 0843, Panama
- Departamento de Genética y Biología Molecular, Universidad de Panamá, Panamá 0824, Panama
- Correspondence: ; Tel.: +507-517-0700
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11
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Palit K, Rath S, Chatterjee S, Das S. Microbial diversity and ecological interactions of microorganisms in the mangrove ecosystem: Threats, vulnerability, and adaptations. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2022; 29:32467-32512. [PMID: 35182344 DOI: 10.1007/s11356-022-19048-7] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2021] [Accepted: 01/31/2022] [Indexed: 06/14/2023]
Abstract
Mangroves are among the world's most productive ecosystems and a part of the "blue carbon" sink. They act as a connection between the terrestrial and marine ecosystems, providing habitat to countless organisms. Among these, microorganisms (e.g., bacteria, archaea, fungi, phytoplankton, and protozoa) play a crucial role in this ecosystem. Microbial cycling of major nutrients (carbon, nitrogen, phosphorus, and sulfur) helps maintain the high productivity of this ecosystem. However, mangrove ecosystems are being disturbed by the increasing concentration of greenhouse gases within the atmosphere. Both the anthropogenic and natural factors contribute to the upsurge of greenhouse gas concentration, resulting in global warming. Changing climate due to global warming and the increasing rate of human interferences such as pollution and deforestation are significant concerns for the mangrove ecosystem. Mangroves are susceptible to such environmental perturbations. Global warming, human interventions, and its consequences are destroying the ecosystem, and the dreadful impacts are experienced worldwide. Therefore, the conservation of mangrove ecosystems is necessary for protecting them from the changing environment-a step toward preserving the globe for better living. This review highlights the importance of mangroves and their microbial components on a global scale and the degree of vulnerability of the ecosystems toward anthropic and climate change factors. The future scenario of the mangrove ecosystem and the resilience of plants and microbes have also been discussed.
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Affiliation(s)
- Krishna Palit
- Laboratory of Environmental Microbiology and Ecology (LEnME), Department of Life Science, National Institute of Technology, Rourkela, 769008, Odisha, India
| | - Sonalin Rath
- Laboratory of Environmental Microbiology and Ecology (LEnME), Department of Life Science, National Institute of Technology, Rourkela, 769008, Odisha, India
| | - Shreosi Chatterjee
- Laboratory of Environmental Microbiology and Ecology (LEnME), Department of Life Science, National Institute of Technology, Rourkela, 769008, Odisha, India
| | - Surajit Das
- Laboratory of Environmental Microbiology and Ecology (LEnME), Department of Life Science, National Institute of Technology, Rourkela, 769008, Odisha, India.
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12
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Thomson T, Ellis JI, Fusi M, Prinz N, Bennett-Smith MF, Aylagas E, Carvalho S, Jones BH. The Right Place at the Right Time: Seasonal Variation of Bacterial Communities in Arid Avicennia marina Soils in the Red Sea Is Specific to Its Position in the Intertidal. Front Ecol Evol 2022. [DOI: 10.3389/fevo.2022.845611] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Mangrove forests play an important role in facilitating biogeochemical pathways and cycling acting as blue carbon sinks. These services are primarily regulated by the activity of the soil microbiome. However, there is still limited research into spatial and temporal variation patterns of bacterial community assemblages in mangrove soils. This study investigated important ecological scales of microprocesses that govern microbial communities in an arid mangrove ecosystem. Shifts in microbial community composition were influenced by fluctuations in environmental factors within the mangrove forests of the Red Sea influenced by seasonal changes in sea level. Notably, in summer microbial communities in shrub sites differed significantly from the fringe and the winter samples, with lower alpha diversity yet a higher dominance of specialized species capable of surviving in extreme conditions. The onset of dispersal limitation and heterogenous selection and the reduction of drift are likely the main forces shaping community assemblages. Specifically, in summer lower mean tidal levels eliminate tidal inundation creating a harsh high salinity and high temperature environment with no tidal connection thereby influencing the onset of dispersal limitation. An increased understanding of the spatial and temporal variation of bacterial communities is critical when assessing delivery of ecosystem services and their role in soil biogeochemical processes.
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13
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Zhang X, Liu S, Jiang Z, Wu Y, Huang X. Gradient of microbial communities around seagrass roots was mediated by sediment grain size. Ecosphere 2022. [DOI: 10.1002/ecs2.3942] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Affiliation(s)
- Xia Zhang
- Key Laboratory of Tropical Marine Bio‐resources and Ecology South China Sea Institute of Oceanology, Chinese Academy of Sciences Guangzhou China
- Southern Marine Science and Engineering Guangdong Laboratory Guangzhou China
| | - Songlin Liu
- Key Laboratory of Tropical Marine Bio‐resources and Ecology South China Sea Institute of Oceanology, Chinese Academy of Sciences Guangzhou China
- Southern Marine Science and Engineering Guangdong Laboratory Guangzhou China
- Key Laboratory of Tropical Marine Biotechnology of Hainan Province Sanya Institute of Oceanology, SCSIO Sanya China
| | - Zhijian Jiang
- Key Laboratory of Tropical Marine Bio‐resources and Ecology South China Sea Institute of Oceanology, Chinese Academy of Sciences Guangzhou China
- Southern Marine Science and Engineering Guangdong Laboratory Guangzhou China
| | - Yunchao Wu
- Key Laboratory of Tropical Marine Bio‐resources and Ecology South China Sea Institute of Oceanology, Chinese Academy of Sciences Guangzhou China
- Southern Marine Science and Engineering Guangdong Laboratory Guangzhou China
| | - Xiaoping Huang
- Key Laboratory of Tropical Marine Bio‐resources and Ecology South China Sea Institute of Oceanology, Chinese Academy of Sciences Guangzhou China
- Southern Marine Science and Engineering Guangdong Laboratory Guangzhou China
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14
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Fiard M, Cuny P, Sylvi L, Hubas C, Jézéquel R, Lamy D, Walcker R, El Houssainy A, Heimbürger-Boavida LE, Robinet T, Bihannic I, Gilbert F, Michaud E, Dirberg G, Militon C. Mangrove microbiota along the urban-to-rural gradient of the Cayenne estuary (French Guiana, South America): Drivers and potential bioindicators. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 807:150667. [PMID: 34599952 DOI: 10.1016/j.scitotenv.2021.150667] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Revised: 09/13/2021] [Accepted: 09/25/2021] [Indexed: 06/13/2023]
Abstract
The microbial communities inhabiting the Atlantic-East Pacific (AEP) mangroves have been poorly studied, and mostly comprise chronically polluted mangroves. In this study, we characterized changes in the structure and diversity of microbial communities of mangroves along the urban-to-rural gradient of the Cayenne estuary (French Guiana, South America) that experience low human impact. The microbial communities were assigned into 50 phyla. Proteobacteria, Chloroflexi, Acidobacteria, Bacteroidetes, and Planctomycetes were the most abundant taxa. The environmental determinants found to significantly correlated to the microbial communities at these mangroves were granulometry, dieldrin concentration, pH, and total carbon (TC) content. Furthermore, a precise analysis of the sediment highlights the existence of three types of anthropogenic pressure among the stations: (i) organic matter (OM) enrichment due to the proximity to the city and its wastewater treatment plant, (ii) dieldrin contamination, and (iii) naphthalene contamination. These forms of weak anthropogenic pressure seemed to impact the bacterial population size and microbial assemblages. A decrease in Bathyarchaeota, "Candidatus Nitrosopumilus", and Nitrospira genera was observed in mangroves subjected to OM enrichment. Mangroves polluted with organic contaminants were enriched in Desulfobacteraceae, Desulfarculaceae, and Acanthopleuribacteraceae (with dieldrin or polychlorobiphenyl contamination), and Chitinophagaceae and Geobacteraceae (with naphthalene contamination). These findings provide insights into the main environmental factors shaping microbial communities of mangroves in the AEP that experience low human impact and allow for the identification of several potential microbial bioindicators of weak anthropogenic pressure.
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Affiliation(s)
- Maud Fiard
- Aix Marseille Univ., Université de Toulon, CNRS, IRD, MIO, 13288 Marseille, France.
| | - Philippe Cuny
- Aix Marseille Univ., Université de Toulon, CNRS, IRD, MIO, 13288 Marseille, France.
| | - Léa Sylvi
- Aix Marseille Univ., Université de Toulon, CNRS, IRD, MIO, 13288 Marseille, France.
| | - Cédric Hubas
- Biologie des Organismes et Ecosystèmes Aquatiques (UMR 8067 BOREA) Muséum National D'Histoire Naturelle, CNRS, Sorbonne Université, IRD, UCN, UA, Station Marine de Concarneau, 29900 Concarneau, France.
| | | | - Dominique Lamy
- Biologie des Organismes et Ecosystèmes Aquatiques (UMR 8067 BOREA) Muséum National D'Histoire Naturelle, CNRS, Sorbonne Université, IRD, UCN, UA, Rue Buffon, 75005 Paris, France; Institute of Ecology and Environmental Sciences of Paris (iEES-Paris), Sorbonne Université, Univ Paris Est Créteil, IRD, CNRS, INRA, 4 place Jussieu, 75005 Paris, France.
| | - Romain Walcker
- Laboratoire Ecologie Fonctionnelle et Environnement, Université de Toulouse, CNRS, Toulouse, France.
| | - Amonda El Houssainy
- Aix Marseille Univ., Université de Toulon, CNRS, IRD, MIO, 13288 Marseille, France.
| | | | - Tony Robinet
- Biologie des Organismes et Ecosystèmes Aquatiques (UMR 8067 BOREA) Muséum National D'Histoire Naturelle, CNRS, Sorbonne Université, IRD, UCN, UA, Station Marine de Concarneau, 29900 Concarneau, France.
| | | | - Franck Gilbert
- Laboratoire Ecologie Fonctionnelle et Environnement, Université de Toulouse, CNRS, Toulouse, France.
| | - Emma Michaud
- Univ Brest, CNRS, IRD, Ifremer, LEMAR, 29280 Plouzané, France.
| | - Guillaume Dirberg
- Biologie des Organismes et Ecosystèmes Aquatiques (UMR 8067 BOREA) Muséum National D'Histoire Naturelle, CNRS, Sorbonne Université, IRD, UCN, UA, Rue Buffon, 75005 Paris, France.
| | - Cécile Militon
- Aix Marseille Univ., Université de Toulon, CNRS, IRD, MIO, 13288 Marseille, France.
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15
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Mai Z, Ye M, Wang Y, Foong SY, Wang L, Sun F, Cheng H. Characteristics of Microbial Community and Function With the Succession of Mangroves. Front Microbiol 2021; 12:764974. [PMID: 34950118 PMCID: PMC8689078 DOI: 10.3389/fmicb.2021.764974] [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: 08/26/2021] [Accepted: 11/05/2021] [Indexed: 12/02/2022] Open
Abstract
In this study, 16S high-throughput and metagenomic sequencing analyses were employed to explore the changes in microbial community and function with the succession of mangroves (Sonneratia alba, Rhizophora apiculata, and Bruguiera parviflora) along the Merbok river estuary in Malaysia. The sediments of the three mangroves harbored their own unique dominant microbial taxa, whereas R. apiculata exhibited the highest microbial diversity. In general, Gammaproteobacteria, Actinobacteria, Alphaproteobacteria, Deltaproteobacteria, and Anaerolineae were the dominant microbial classes, but their abundances varied significantly among the three mangroves. Principal coordinates and redundancy analyses revealed that the specificity of the microbial community was highly correlated with mangrove populations and environmental factors. The results further showed that R. apiculata exhibited the highest carbon-related metabolism, coinciding with the highest organic carbon and microbial diversity. In addition, specific microbial taxa, such as Desulfobacterales and Rhizobiales, contributed the highest functional activities related to carbon metabolism, prokaryote carbon fixation, and methane metabolism. The present results provide a comprehensive understanding of the adaptations and functions of microbes in relation to environmental transition and mangrove succession in intertidal regions. High microbial diversity and carbon metabolism in R. apiculata might in turn facilitate and maintain the formation of climax mangroves in the middle region of the Merbok river estuary.
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Affiliation(s)
- Zhimao Mai
- State Key Laboratory of Tropical Oceanography, Key Laboratory of Tropical Marine Bio-Resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China.,Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China
| | - Mai Ye
- State Key Laboratory of Tropical Oceanography, Key Laboratory of Tropical Marine Bio-Resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China.,Guangdong Provincial Academy of Environmental Science, Guangzhou, China
| | - Youshao Wang
- State Key Laboratory of Tropical Oceanography, Key Laboratory of Tropical Marine Bio-Resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China.,Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China
| | - Swee Yeok Foong
- School of Biological Sciences, Universiti Sains Malaysia, Penang, Malaysia
| | - Lin Wang
- State Key Laboratory of Tropical Oceanography, Key Laboratory of Tropical Marine Bio-Resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China.,Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China
| | - Fulin Sun
- State Key Laboratory of Tropical Oceanography, Key Laboratory of Tropical Marine Bio-Resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China.,Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China.,Daya Bay Marine Biology Research Station, Chinese Academy of Sciences, Shenzhen, China
| | - Hao Cheng
- State Key Laboratory of Tropical Oceanography, Key Laboratory of Tropical Marine Bio-Resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China.,Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China
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16
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Tong T, Li R, Chai M, Wang Q, Yang Y, Xie S. Metagenomic analysis of microbial communities continuously exposed to Bisphenol A in mangrove rhizosphere and non-rhizosphere soils. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 792:148486. [PMID: 34465064 DOI: 10.1016/j.scitotenv.2021.148486] [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: 04/05/2021] [Revised: 05/31/2021] [Accepted: 06/12/2021] [Indexed: 06/13/2023]
Abstract
Bisphenol A (BPA) is widely distributed in littoral zones and may cause adverse impacts on mangrove ecosystem. Biodegradation and phytoremediation are two primary processes for BPA dissipation in mangrove soils. However, the rhizosphere effects of different mangrove species on BPA elimination are still unresolved. In this study, three typical mangrove seedlings, namely Avicennia marina, Bruguiera gymnorrhiza (L.) and Aegiceras corniculatum, were cultivated in soil microcosms for four months and then subjected to 28-day continuous BPA amendment. Un-planted soil microcosms (as control) were also set up. The BPA residual rates and root exudates were monitored, and the metabolic pathways as well as functional microbial communities were also investigated to decipher the rhizosphere effects based on metagenomic analysis. The BPA residual rates in all planted soils were significantly lower than that in un-planted soil on day 7. Both plantation and BPA dosage had significant effects on bacterial abundance. A distinct separation of microbial structure was found between planted and un-planted soil microcosms. Genera Pseudomonas and Lutibacter got enriched with BPA addition and may play important roles in BPA biodegradation. The shifts in bacterial community structure upon BPA addition were different among the microcosms with different mangrove species. Genus Novosphingobium increased in Avicennia marina and Bruguiera gymnorrhiza (L.) rhizosphere soils but decreased in Aegiceras corniculatum rhizosphere soil. Based on KEGG annotation and binning analysis, the proposal of BPA degradation pathways and the quantification of relevant functional genes were achieved. The roles of Pseudomonas and Novosphingobium may differ in lower BPA degradation pathways. The quantity variation patterns of functional genes during the 28-day BPA amendment were different among soil microcosms and bacterial genera.
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Affiliation(s)
- Tianli Tong
- State Key Joint Laboratory of Environmental Simulation and Pollution Control, College of Environmental Sciences and Engineering, Peking University, Beijing 100871, China
| | - Ruili Li
- School of Environmental and Energy, Shenzhen Graduate School of Peking University, Shenzhen 518055, Guangdong, China.
| | - Minwei Chai
- School of Environmental and Energy, Shenzhen Graduate School of Peking University, Shenzhen 518055, Guangdong, China
| | - Qian Wang
- School of Environmental and Energy, Shenzhen Graduate School of Peking University, Shenzhen 518055, Guangdong, China
| | - Yuyin Yang
- State Key Joint Laboratory of Environmental Simulation and Pollution Control, College of Environmental Sciences and Engineering, Peking University, Beijing 100871, China
| | - Shuguang Xie
- State Key Joint Laboratory of Environmental Simulation and Pollution Control, College of Environmental Sciences and Engineering, Peking University, Beijing 100871, China; School of Environmental and Energy, Shenzhen Graduate School of Peking University, Shenzhen 518055, Guangdong, China.
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17
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Diversity and abundance of diazotrophic communities of seagrass Halophila ovalis based on genomic and transcript level in Daya Bay, South China Sea. Arch Microbiol 2021; 203:5577-5589. [PMID: 34436633 DOI: 10.1007/s00203-021-02544-8] [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: 06/09/2021] [Revised: 08/16/2021] [Accepted: 08/17/2021] [Indexed: 10/20/2022]
Abstract
Seagrass ecosystems are among the most productive marine ecosystems, and diazotrophic communities play a crucial role in sustaining the productivity and stability of such ecosystems by introducing fixed nitrogen. However, information concerning both total and active diazotrophic groups existing in different compartments of seagrass is lacking. This study comprehensively investigated the diversity, structure, and abundance of diazotrophic communities in different parts of the seagrass Halophila ovalis at the DNA and RNA level from clone libraries and real-time quantitative PCR. Our results indicated that nearly one-third of existing nitrogen-fixing bacteria were active, and their abundance might be controlled by nitrogen to phosphorus ratio (N:P). Deltaproteobacteria and Gammaproteobacteria were dominant groups among the total and active diazotrophic communities in all samples. These two groups accounted for 82.21% and 70.96% at the DNA and RNA levels, respectively. The genus Pseudomonas and sulfate-reducing bacteria (genera: Desulfosarcina, Desulfobulbus, Desulfocapsa, and Desulfopila) constituted the significant fraction of nitrogen-fixing bacteria in the seagrass ecosystem, playing an additional role in denitrification and sulfate reduction, respectively. Moreover, the abundance of the nitrogenase gene, nifH, was highest in seawater and lowest in rhizosphere sediments from all samples. This study highlighted the role of diazotropic communities in the subtropical seagrass ecosystem.
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18
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Composition and Activity of N2-Fixing Microorganisms in Mangrove Forest Soils. FORESTS 2021. [DOI: 10.3390/f12070822] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Mangrove forests are considered to be a highly productive ecosystem, but they are also generally nitrogen (N)-limited. Thus, soil N2 fixation can be important for the stability of both mangrove ecosystem functions and upland N supply. This study evaluates the N2 fixation activity and composition of relevant microorganisms in two coastal mangrove forests—the Guandu mangrove in an upstream estuary and the Bali mangrove in a downstream estuary—using the acetylene reduction method, real-time polymerase chain reaction, and next-generation sequencing. The results demonstrated that ambient nitrogenase activity was higher in downstream mangrove forests (13.2–15.6 nmol h−1 g−1 soil) than in upstream mangrove forests (0.2–1.4 nmol h−1 g−1 soil). However, both the maximum potential nitrogenase activity and nitrogenase gene (nifH gene) copy number were found to be higher in the upstream than in the downstream mangrove forests, implying that the nitrogenase activity and diazotrophic abundance may not necessarily be positively correlated. In addition, amended MoO4 (which inhibits the activity of sulfate-reducing bacteria in N2-fixation) yielded low nitrogenase activity, and sulfate-reducing bacteria made up 20–50% of the relative diazotrophic abundance in the mangrove forests, indicating that these bacteria might be the major active diazotrophs in this environment.
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do Carmo Linhares D, Saia FT, Duarte RTD, Nakayama CR, de Melo IS, Pellizari VH. Methanotrophic Community Detected by DNA-SIP at Bertioga's Mangrove Area, Southeast Brazil. MICROBIAL ECOLOGY 2021; 81:954-964. [PMID: 33392629 DOI: 10.1007/s00248-020-01659-7] [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: 08/17/2020] [Accepted: 12/03/2020] [Indexed: 06/12/2023]
Abstract
Methanotrophic bacteria can use methane as sole carbon and energy source. Its importance in the environment is related to the mitigation of methane emissions from soil and water to the atmosphere. Brazilian mangroves are highly productive, have potential to methane production, and it is inferred that methanotrophic community is of great importance for this ecosystem. The scope of this study was to investigate the functional and taxonomic diversity of methanotrophic bacteria present in the anthropogenic impacted sediments from Bertioga´s mangrove (SP, Brazil). Sediment sample was cultivated with methane and the microbiota actively involved in methane oxidation was identified by DNA-based stable isotope probing (DNA-SIP) using methane as a labeled substrate. After 4 days (96 h) of incubation and consumption of 0.7 mmol of methane, the most active microorganisms were related to methanotrophs Methylomonas and Methylobacter as well as to methylotrophic Methylotenera, indicating a possible association of these bacterial groups within a methane-derived food chain in the Bertioga mangrove. The abundance of genera Methylomonas, able to couple methane oxidation to nitrate reduction, may indicate that under low dissolved oxygen tensions, some aerobic methanotrophs could shift to intraerobic methane oxidation to avoid oxygen starvation.
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Affiliation(s)
- Débora do Carmo Linhares
- Laboratory of Industrial Biotechnology, Institute for Technological Research of São Paulo, 05508-901, São Paulo, SP, Brazil.
- Department of Biological Oceanography, Oceanographic Institute, University of Sao Paulo, Praça do Oceanográfico, 191, 05508-120, Butantã, São Paulo-SP, Brazil.
| | - Flávia Talarico Saia
- Institute of Marine Sciences, Federal University of São Paulo, Av. Dr. Carvalho de Mendonça, 144, Encruzilhada, Santos, SP, 11070-102, Brazil
| | - Rubens Tadeu Delgado Duarte
- Laboratory of Molecular Ecology and Extremophiles, Department of Microbiology, Immunology and Parasitology, Federal University of Santa Catarina, Florianópolis, SC, 88040-900, Brazil
| | - Cristina Rossi Nakayama
- Institute of Environmental, Chemical and Pharmaceutical Sciences, Federal University of São Paulo, Rua São Nicolau, 210, Diadema, SP, 09913-030, Brazil
| | | | - Vivian Helena Pellizari
- Department of Biological Oceanography, Oceanographic Institute, University of Sao Paulo, Praça do Oceanográfico, 191, 05508-120, Butantã, São Paulo-SP, Brazil
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20
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Louvado A, Coelho FJRC, Palma M, Tavares LC, Ozorio ROA, Magnoni L, Viegas I, Gomes NCM. Effect of glycerol feed-supplementation on seabass metabolism and gut microbiota. Appl Microbiol Biotechnol 2020; 104:8439-8453. [PMID: 32845369 DOI: 10.1007/s00253-020-10809-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2020] [Revised: 07/20/2020] [Accepted: 08/02/2020] [Indexed: 12/22/2022]
Abstract
Dietary glycerol supplementation in aquaculture feed is seen as an alternative and inexpensive way to fuel fish metabolism, attenuate metabolic utilization of dietary proteins and, subsequently, reduce nitrogen excretion. In this study, we evaluated the impact of dietary glycerol supplementation on nitrogen excretion of European seabass (Dicentrarchus labrax) and its effects on metabolite profile and bacterial community composition of gut digesta. These effects were evaluated in a 60-day trial with fish fed diets supplemented with 2.5% or 5% (w/w) refined glycerol and without glycerol supplementation. Nuclear magnetic resonance spectroscopy and high-throughput 16S rRNA gene sequencing were used to characterize the effects of glycerol supplementation on digesta metabolite and bacterial community composition of 6-h postprandial fish. Our results showed that ammonia excretion was not altered by dietary glycerol supplementation, and the highest glycerol dosage was associated with significant increases in amino acids and a decrease of ergogenic creatine in digesta metabolome. Concomitantly, significant decreases in putative amino acid degradation pathways were detected in the predicted metagenome analysis, suggesting a metabolic shift. Taxon-specific analysis revealed significant increases in abundance of some specific genera (e.g., Burkholderia and Vibrio) and bacterial diversity. Overall, our results indicate glycerol supplementation may decrease amino acid catabolism without adversely affecting fish gut bacterial communities.Key points• Glycerol can be an inexpensive and energetic alternative in fish feed formulations.• Glycerol did not affect nitrogen excretion and gut bacteriome composition.• Glycerol reduced uptake of amino acids and increased uptake of ergogenic creatine.• Glycerol reduced putative amino acid degradation pathways in predicted metagenome.
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Affiliation(s)
- A Louvado
- Department of Biology & CESAM, University of Aveiro, 3810-193, Aveiro, Portugal
| | - F J R C Coelho
- Department of Biology & CESAM, University of Aveiro, 3810-193, Aveiro, Portugal
| | - M Palma
- University of Coimbra, Centre for Functional Ecology, Department of Life Sciences, 3000-456, Coimbra, Portugal
| | - L C Tavares
- Centre for Neuroscience and Cell Biology, University of Coimbra, 3004-517, Coimbra, Portugal
| | - R O A Ozorio
- Interdisciplinary Centre of Marine and Environmental Research (CIIMAR), University of Porto, Matosinhos, Portugal
| | - L Magnoni
- Interdisciplinary Centre of Marine and Environmental Research (CIIMAR), University of Porto, Matosinhos, Portugal
| | - I Viegas
- University of Coimbra, Centre for Functional Ecology, Department of Life Sciences, 3000-456, Coimbra, Portugal.,Centre for Neuroscience and Cell Biology, University of Coimbra, 3004-517, Coimbra, Portugal
| | - N C M Gomes
- Department of Biology & CESAM, University of Aveiro, 3810-193, Aveiro, Portugal.
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21
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Oliveira V, Martins P, Marques B, Cleary DFR, Lillebø AI, Calado R. Aquaponics using a fish farm effluent shifts bacterial communities profile in halophytes rhizosphere and endosphere. Sci Rep 2020; 10:10023. [PMID: 32572050 PMCID: PMC7308282 DOI: 10.1038/s41598-020-66093-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2018] [Accepted: 05/11/2020] [Indexed: 11/28/2022] Open
Abstract
The intensification of marine aquaculture raises multiple sustainability issues, namely the handling of nutrient-rich effluents that can adversely impact ecosystems. As integrated multi-trophic aquaculture (IMTA) gains momentum, the use of halophyte plants to phytoremediate aquaculture effluents has received growing attention, particularly in aquaponics. It is, therefore, important to obtain a more in-depth knowledge of the microbial communities present in the root systems of these plants, both in their natural environment (sediment) and in aquaponics, in order to understand their nutrient removal potential. The present study used denaturing gradient gel electrophoresis (DGGE) and barcoded pyrosequencing to assess the bacterial community present in the endosphere and rhizosphere of three halophyte plants: Halimione portulacoides, Salicornia ramosissima and Sarcocornia perennis. Species-specific effects were recorded in the profile and diversity of the bacterial communities present in halophyte roots, with significant differences also recorded for the same halophyte species grown in contrasting environments (sediment vs. aquaponics). In aquaponics the most abundant groups belonged to the orders Rhodocyclales, Campylobacterales, Rhodobacterales and Desulfobacterales, while in the natural environment (sediment) the most abundant groups belonged to the orders Rhizobiales, Sphingomonadales and Alteromonadales. An overall enrichment in bacterial taxa involved in nutrient cycling was recorded in the roots of halophytes grown in aquaponics (such as Denitromonas, Mesorhizobium, Colwellia, Dokdonella and Arcobacter), thereby highlighting their potential to reduce the nutrient loads from aquaculture effluents.
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Affiliation(s)
- Vanessa Oliveira
- CESAM - Centre for Environmental and Marine Studies, Departament of Biology, University of Aveiro, Campus Universitário de Santiago, 3810-193, Aveiro, Portugal
| | - Patrícia Martins
- ECOMARE, CESAM - Centre for Environmental and Marine Studies, Departament of Biology, University of Aveiro, Campus Universitário de Santiago, 3810-193, Aveiro, Portugal
| | - Bruna Marques
- ECOMARE, CESAM - Centre for Environmental and Marine Studies, Departament of Biology, University of Aveiro, Campus Universitário de Santiago, 3810-193, Aveiro, Portugal
| | - Daniel F R Cleary
- CESAM - Centre for Environmental and Marine Studies, Departament of Biology, University of Aveiro, Campus Universitário de Santiago, 3810-193, Aveiro, Portugal
| | - Ana I Lillebø
- ECOMARE, CESAM - Centre for Environmental and Marine Studies, Departament of Biology, University of Aveiro, Campus Universitário de Santiago, 3810-193, Aveiro, Portugal.
| | - Ricardo Calado
- ECOMARE, CESAM - Centre for Environmental and Marine Studies, Departament of Biology, University of Aveiro, Campus Universitário de Santiago, 3810-193, Aveiro, Portugal.
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22
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Biogeochemical Processes of C and N in the Soil of Mangrove Forest Ecosystems. FORESTS 2020. [DOI: 10.3390/f11050492] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The mangrove forest provides various ecosystem services in tropical and subtropical regions. Many of these services are driven by the biogeochemical cycles of C and N, and soil is the major reservoir for these chemical elements. These cycles may be influenced by the changing climate. The high plant biomass in mangrove forests makes these forests an important sink for blue C storage. However, anaerobic soil conditions may also turn mangrove forests into an environmentally detrimental producer of greenhouse gases (such as CH4 and N2O), especially as air temperatures increase. In addition, the changing environmental factors associated with climate change may also influence the N cycles and change the patterns of N2 fixation, dissimilatory nitrate reduction to ammonium, and denitrification processes. This review summarizes the biogeochemical processes of C and N cycles in mangrove forest soils based on recently published studies, and how these processes may respond to climate change, with the aim of predicting the impacts of climate change on the mangrove forest ecosystem.
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23
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Zhang X, Zhao C, Yu S, Jiang Z, Liu S, Wu Y, Huang X. Rhizosphere Microbial Community Structure Is Selected by Habitat but Not Plant Species in Two Tropical Seagrass Beds. Front Microbiol 2020; 11:161. [PMID: 32194512 PMCID: PMC7065525 DOI: 10.3389/fmicb.2020.00161] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2019] [Accepted: 01/22/2020] [Indexed: 11/19/2022] Open
Abstract
Rhizosphere bacterial community structures and their determining drivers have been studied in a variety of marine and freshwater ecosystems for a range of plant species. However, there is still limited information about the influence of habitat on microbial communities in seagrass beds. This study aimed to determine which factors (habitat and plant species) have crucial roles on the rhizospheric bacteria associated with two tropical seagrass species (Thalassia hemprichii and Enhalus acoroides) that are dominant at Xincun Bay and Tanmen Harbor in Hainan Island, South China. Using Illumina HiSeq sequencing, we observed substantial differences in the bacterial richness, diversity, and relative abundances of taxa between the two habitats, which were characterized differently in sediment type and nutrient status. Rhizospheric bacteria from sandy sediment at the eutrophic Xincun Bay were dominated by Desulfobacteraceae and Helicobacteraceae, which are primarily involved in sulfate cycling, whereas rhizosphere microbes from the reef flat at oligotrophic Tanmen Harbor were dominated by Vibrionaceae and Woeseiaceae, which may play important roles in nitrogen and carbon fixing. Additionally, we speculated that host-specific effects of these two seagrass species may be covered under nutrient-rich conditions and in mixed community patches, emphasizing the importance of the nutrient status of the sediment and vegetation composition of the patches. In addition, our study confirmed that Proteobacteria was more adapted to the rhizosphere environment than to low-carbon conditions that occurred in bulk sediment, which was primarily dominated by well-known fermentative bacteria in the phylum Firmicutes.
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Affiliation(s)
- Xia Zhang
- Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China.,Innovation Academy of South China Sea Ecology and Environmental Engineering, Chinese Academy of Sciences, Guangzhou, China
| | - Chunyu Zhao
- Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China.,Innovation Academy of South China Sea Ecology and Environmental Engineering, Chinese Academy of Sciences, Guangzhou, China
| | - Shuo Yu
- Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China.,Innovation Academy of South China Sea Ecology and Environmental Engineering, Chinese Academy of Sciences, Guangzhou, China
| | - Zhijian Jiang
- Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China.,Innovation Academy of South China Sea Ecology and Environmental Engineering, Chinese Academy of Sciences, Guangzhou, China
| | - Songlin Liu
- Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China.,Innovation Academy of South China Sea Ecology and Environmental Engineering, Chinese Academy of Sciences, Guangzhou, China
| | - Yunchao Wu
- Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China.,Innovation Academy of South China Sea Ecology and Environmental Engineering, Chinese Academy of Sciences, Guangzhou, China
| | - Xiaoping Huang
- Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China.,Innovation Academy of South China Sea Ecology and Environmental Engineering, Chinese Academy of Sciences, Guangzhou, China.,University of Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing, China
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24
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Inoue T, Shimono A, Akaji Y, Baba S, Takenaka A, Tuck Chan H. Mangrove-diazotroph relationships at the root, tree and forest scales: diazotrophic communities create high soil nitrogenase activities in Rhizophora stylosa rhizospheres. ANNALS OF BOTANY 2020; 125:131-144. [PMID: 31678987 PMCID: PMC7145623 DOI: 10.1093/aob/mcz164] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2019] [Accepted: 10/14/2019] [Indexed: 06/01/2023]
Abstract
BACKGROUND AND AIMS The tidal flats on which mangrove plants grow tend to have low soil nitrogen contents because nitrogen-containing litter is repeatedly washed offshore by ebb tides. Under such circumstances, it is unclear how mangrove plants acquire the nitrogen required to support their vigorous growth. In the present work, chemical and biological characteristics of diazotrophy around mangrove plant roots were surveyed under natural conditions to elucidate mangrove-diazotroph relationships. METHODS Soil nitrogenase activity of a representative mangrove plant, Rhizophora stylosa, which has a broad geographical distribution, was measured using the acetylene reduction assay at forest, tree and prop root scales. In addition, diazotrophic community composition was compared between rhizosphere and bulk soil based on sequencing of nifH genes. KEY RESULTS Soil nitrogenase activity was high near prop roots, and this pattern was enhanced as soil live root content increased. At the forest scale, we observed high soil nitrogenase activity (acetylene-reducing activity) inside the forest (the highest value was 90.9 µmol C2H2 min-1 cm-3, average 46.8 ± 18.2 µmol C2H2 min-1 cm-3). Rates decreased sharply from the forest to the tidal flat (range 1.2-22.2 µmol C2H2 min-1 cm-3, average 7.9 ± 4.5 µmol C2H2 min-1 cm-3). The nifH operational taxonomic unit composition differed significantly among forest and tree rhizospheres and the bulk soil (P < 0.0001). CONCLUSIONS Our results suggest that the accumulation of diazotrophs around R. stylosa mangrove trees enhances the supply of biologically fixed nitrogen to the mangrove roots. This supply is especially important when the soil naturally contains little nitrogen. This nitrogen acquisition system may be a key process that explains the high productivity of mangrove ecosystems.
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Affiliation(s)
- Tomomi Inoue
- National Institute for Environmental Studies, Onogawa Tsukuba, Ibaraki, Japan
| | - Ayako Shimono
- Toho University, Department of Biology, Faculty of Science, Miyama, Funabashi, Chiba, Japan
| | - Yasuaki Akaji
- National Institute for Environmental Studies, Onogawa Tsukuba, Ibaraki, Japan
| | - Shigeyuki Baba
- International Society for Mangrove Ecosystems, University of the Ryukyus, Nishihara, Okinawa, Japan
| | - Akio Takenaka
- National Institute for Environmental Studies, Onogawa Tsukuba, Ibaraki, Japan
| | - Hung Tuck Chan
- International Society for Mangrove Ecosystems, University of the Ryukyus, Nishihara, Okinawa, Japan
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25
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Sam Kamaleson A, Gonsalves MJ, Nazareth DR. Interactions of sulfur and methane-oxidizing bacteria in tropical estuarine sediments. ENVIRONMENTAL MONITORING AND ASSESSMENT 2019; 191:496. [PMID: 31312943 DOI: 10.1007/s10661-019-7616-8] [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: 12/06/2018] [Accepted: 06/24/2019] [Indexed: 06/10/2023]
Abstract
The bacterial oxidation of sulfur and methane is central to the biogeochemical processes in sediments such as the tropical mangrove sediments. However, there is a lacuna of information on the seasonal interactions including the influence of monsoons which is a major driver of seasonal change, on sulfur-oxidizing bacteria (SOB) and methane-oxidizing bacteria (MOB), their activity and the environmental variables. To understand these interactions, the analysis was carried out on sediment samples that were sampled monthly for a year from Chorao mangrove, Goa, southwest coast of India. SOB (3.8×105CFU g-1) and MOB (0.90×105CFU g-1) had maximum average abundance in the surface sediments in the post-monsoon and monsoon season, respectively. The mean sulfur-oxidation activity (SOA) of 2.63 mM day-1 and methane-oxidation activity (MOA) of 110.94 mM day-1 were highest in surface sediments during the post-monsoon season. Generally, the activity of SOB and MOB in surface sediments of post-monsoon was 2.2 times(×) and 2.8× respectively higher than that in the monsoon season. Among the environmental parameters analyzed, protein and sulfide concentrations significantly (p < 0.001) influenced SOA and MOA, respectively. There was a significant difference in SOA (p < 0.003) and MOA (p < 0.036) in surface sediments between the monsoon and the post-monsoon season. During the monsoon season, when the system is a sink of terrestrial/anthropogenic material, the interrelationship of SOB with MOA (r = 0.617, p < 0.001) and SOB with SOA (r = 0.489, p < 0.05) aids in maintaining the homeostasis of the system.
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Affiliation(s)
- A Sam Kamaleson
- CSIR-National Institute of Oceanography, Dona Paula, Goa, 403004, India
- Bharathidasan University, Tiruchirappalli, Tamil Nadu, India
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26
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Louvado A, Coelho FJRC, Oliveira V, Gomes H, Cleary DFR, Simões MMQ, Cunha A, Gomes NCM. Microcosm evaluation of the impact of oil contamination and chemical dispersant addition on bacterial communities and sediment remediation of an estuarine port environment. J Appl Microbiol 2019; 127:134-149. [PMID: 30907485 DOI: 10.1111/jam.14261] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Revised: 02/26/2019] [Accepted: 03/04/2019] [Indexed: 01/21/2023]
Abstract
AIM To evaluate the interactive effects of oil contamination and chemical dispersant application on bacterial composition and sediment remediation of an estuarine port environment. METHODS AND RESULTS A multifactorial controlled microcosm experiment was set up using sediment cores retrieved from an estuarine port area located at Ria de Aveiro lagoon (Aveiro, Portugal). An oil spill with and without chemical dispersant addition was simulated. Sediment oil hydrocarbon concentrations and benthic bacterial community structure were evaluated by GC-MS and 16S rRNA high-throughput sequencing respectively. Although initially (first 10 days) chemical dispersion of oil enhanced the concentrations of the heavier polycyclic aromatic hydrocarbons and of the C22 -C30 alkane group, with time (21 days), no significant differences in hydrocarbon concentrations were detected among treatments. Moreover, no significant changes were detected in the structure of sediment bacterial communities, which mainly consisted of operational taxonomic units related to hydrocarbon-contaminated marine environments. We hypothesize that the environmental background of the sampling site preconditioned the communities' response to additional contamination. CONCLUSION This experimental microcosm study showed that the chemical dispersion of oil did not influence sediment remediation or bacterial community composition. SIGNIFICANCE AND IMPACT OF THE STUDY Our study showed that chemical dispersion of oil may not improve the remediation of port sediments. Further studies are needed to investigate the impact of chemical dispersants in combination with bioremediation strategies on the process of sediment remediation in port areas.
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Affiliation(s)
- A Louvado
- Department of Biology & CESAM, University of Aveiro, Aveiro, Portugal
| | - F J R C Coelho
- Department of Biology & CESAM, University of Aveiro, Aveiro, Portugal
| | - V Oliveira
- Department of Biology & CESAM, University of Aveiro, Aveiro, Portugal
| | - H Gomes
- Department of Biology & CESAM, University of Aveiro, Aveiro, Portugal
| | - D F R Cleary
- Department of Biology & CESAM, University of Aveiro, Aveiro, Portugal
| | - M M Q Simões
- Department of Chemistry & QOPNA, University of Aveiro, Aveiro, Portugal
| | - A Cunha
- Department of Biology & CESAM, University of Aveiro, Aveiro, Portugal
| | - N C M Gomes
- Department of Biology & CESAM, University of Aveiro, Aveiro, Portugal
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27
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Duarte LN, Coelho FJRC, Oliveira V, Cleary DFR, Martins P, Gomes NCM. Characterization of bacterioplankton communities from a hatchery recirculating aquaculture system (RAS) for juvenile sole (Solea senegalensis) production. PLoS One 2019; 14:e0211209. [PMID: 30682196 PMCID: PMC6347143 DOI: 10.1371/journal.pone.0211209] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2018] [Accepted: 01/09/2019] [Indexed: 12/18/2022] Open
Abstract
There is a growing consensus that future technological developments of aquaculture systems should account for the structure and function of microbial communities in the whole system and not only in fish guts. In this study, we aimed to investigate the composition of bacterioplankton communities of a hatchery recirculating aquaculture system (RAS) used for the production of Senegalese sole (Solea senegalensis) juveniles. To this end, we used a 16S rRNA gene based denaturing gradient gel electrophoresis (DGGE) and pyrosequencing analyses to characterize the bacterioplankton communities of the RAS and its water supply. Overall, the most abundant orders were Alteromonadales, Rhodobacterales, Oceanospirillales, Vibrionales, Flavobacteriales, Lactobacillales, Thiotrichales, Burkholderiales and Bdellovibrionales. Although we found a clear distinction between the RAS and the water supply bacterioplankton communities, most of the abundant OTUs (≥50 sequences) in the hatchery RAS were also present in the water supply. These included OTUs related to Pseudoalteromonas genus and the Roseobacter clade, which are known to comprise bacterial members with activity against Vibrio fish pathogens. Overall, in contrast to previous findings for sole grow-out RAS, our results suggest that the water supply may influence the bacterioplankton community structure of sole hatchery RAS. Further studies are needed to investigate the effect of aquaculture practices on RAS bacterioplankton communities and identification of the key drivers of their structure and diversity.
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Affiliation(s)
- Letícia N. Duarte
- Department of Biology & CESAM, University of Aveiro, Aveiro, Portugal
| | | | - Vanessa Oliveira
- Department of Biology & CESAM, University of Aveiro, Aveiro, Portugal
| | | | - Patrícia Martins
- Department of Biology & CESAM, University of Aveiro, Aveiro, Portugal
| | - Newton C. M. Gomes
- Department of Biology & CESAM, University of Aveiro, Aveiro, Portugal
- * E-mail:
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28
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Louvado A, Coelho FJRC, Gomes H, Cleary DFR, Cunha Â, Gomes NCM. Independent and interactive effects of reduced seawater pH and oil contamination on subsurface sediment bacterial communities. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2018; 25:32756-32766. [PMID: 30244446 DOI: 10.1007/s11356-018-3214-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/23/2018] [Accepted: 09/12/2018] [Indexed: 06/08/2023]
Abstract
Ocean acidification may exacerbate the environmental impact of oil hydrocarbon pollution by disrupting the core composition of the superficial (0-1 cm) benthic bacterial communities. However, at the subsurface sediments (approximately 5 cm below sea floor), the local biochemical characteristics and the superjacent sediment barrier may buffer these environmental changes. In this study, we used a microcosm experimental approach to access the independent and interactive effects of reduced seawater pH and oil contamination on the composition of subsurface benthic bacterial communities, at two time points, by 16S rRNA gene-based high-throughput sequencing. An in-depth taxa-specific variance analysis revealed that the independent effects of reduced seawater pH and oil contamination were significant predictors of changes in the relative abundance of some specific bacterial groups (e.g., Firmicutes, Rhizobiales, and Desulfobulbaceae). However, our results indicated that the overall microbial community structure was not affected by independent and interactive effects of reduced pH and oil contamination. This study provides evidence that bacterial communities inhabiting subsurface sediment may be less susceptible to the effects of oil contamination in a scenario of reduced seawater pH.
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Affiliation(s)
- António Louvado
- Department of Biology & CESAM, University of Aveiro, Campus de Santiago, 3810-193, Aveiro, Portugal
| | - Francisco J R C Coelho
- Department of Biology & CESAM, University of Aveiro, Campus de Santiago, 3810-193, Aveiro, Portugal
| | - Hélder Gomes
- Department of Biology & CESAM, University of Aveiro, Campus de Santiago, 3810-193, Aveiro, Portugal
| | - Daniel F R Cleary
- Department of Biology & CESAM, University of Aveiro, Campus de Santiago, 3810-193, Aveiro, Portugal
| | - Ângela Cunha
- Department of Biology & CESAM, University of Aveiro, Campus de Santiago, 3810-193, Aveiro, Portugal
| | - Newton C M Gomes
- Department of Biology & CESAM, University of Aveiro, Campus de Santiago, 3810-193, Aveiro, Portugal.
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29
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Priya G, Lau NS, Furusawa G, Dinesh B, Foong SY, Amirul AAA. Metagenomic insights into the phylogenetic and functional profiles of soil microbiome from a managed mangrove in Malaysia. ACTA ACUST UNITED AC 2018. [DOI: 10.1016/j.aggene.2018.07.001] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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30
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Shiau YJ, Cai Y, Lin YT, Jia Z, Chiu CY. Community Structure of Active Aerobic Methanotrophs in Red Mangrove (Kandelia obovata) Soils Under Different Frequency of Tides. MICROBIAL ECOLOGY 2018; 75:761-770. [PMID: 29022063 DOI: 10.1007/s00248-017-1080-1] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/11/2017] [Accepted: 09/22/2017] [Indexed: 06/07/2023]
Abstract
Methanotrophs are important microbial communities in coastal ecosystems. They reduce CH4 emission in situ, which is influenced by soil conditions. This study aimed to understand the differences in active aerobic methanotrophic communities in mangrove forest soils experiencing different inundation frequency, i.e., in soils from tidal mangroves, distributed at lower elevations, and from dwarf mangroves, distributed at higher elevations. Labeling of pmoA gene of active methanotrophs using DNA-based stable isotope probing (DNA-SIP) revealed that methanotrophic activity was higher in the dwarf mangrove soils than in the tidal mangrove soils, possibly because of the more aerobic soil conditions. Methanotrophs affiliated with the cluster deep-sea-5 belonging to type Ib methanotrophs were the most dominant methanotrophs in the fresh mangrove soils, whereas type II methanotrophs also appeared in the fresh dwarf mangrove soils. Furthermore, Methylobacter and Methylosarcina were the most important active methanotrophs in the dwarf mangrove soils, whereas Methylomonas and Methylosarcina were more active in the tidal mangrove soils. High-throughput sequencing of the 16S ribosomal RNA (rRNA) gene also confirmed similar differences in methanotrophic communities at the different locations. However, several unclassified methanotrophic bacteria were found by 16S rRNA MiSeq sequencing in both fresh and incubated mangrove soils, implying that methanotrophic communities in mangrove forests may significantly differ from the methanotrophic communities documented in previous studies. Overall, this study showed the feasibility of 13CH4 DNA-SIP to study the active methanotrophic communities in mangrove forest soils and revealed differences in the methanotrophic community structure between coastal mangrove forests experiencing different tide frequencies.
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Affiliation(s)
- Yo-Jin Shiau
- Biodiversity Research Center, Academia Sinica, No. 128, Academia Road Section II, Nangang, Taipei, 11529, Taiwan
| | - Yuanfeng Cai
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Science, No. 71 East Beijing Road, Nanjing, 210008, People's Republic of China
| | - Yu-Te Lin
- Biodiversity Research Center, Academia Sinica, No. 128, Academia Road Section II, Nangang, Taipei, 11529, Taiwan
| | - Zhongjun Jia
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Science, No. 71 East Beijing Road, Nanjing, 210008, People's Republic of China.
| | - Chih-Yu Chiu
- Biodiversity Research Center, Academia Sinica, No. 128, Academia Road Section II, Nangang, Taipei, 11529, Taiwan.
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31
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Martin BC, Gleeson D, Statton J, Siebers AR, Grierson P, Ryan MH, Kendrick GA. Low Light Availability Alters Root Exudation and Reduces Putative Beneficial Microorganisms in Seagrass Roots. Front Microbiol 2018; 8:2667. [PMID: 29375529 PMCID: PMC5768916 DOI: 10.3389/fmicb.2017.02667] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2017] [Accepted: 12/21/2017] [Indexed: 01/05/2023] Open
Abstract
Seagrass roots host a diverse microbiome that is critical for plant growth and health. Composition of microbial communities can be regulated in part by root exudates, but the specifics of these interactions in seagrass rhizospheres are still largely unknown. As light availability controls primary productivity, reduced light may impact root exudation and consequently the composition of the root microbiome. Hence, we analyzed the influence of light availability on root exudation and community structure of the root microbiome of three co-occurring seagrass species, Halophila ovalis, Halodule uninervis and Cymodocea serrulata. Plants were grown under four light treatments in mesocosms for 2 weeks; control (100% surface irradiance (SI), medium (40% SI), low (20% SI) and fluctuating light (10 days 20% and 4 days 100%). 16S rDNA amplicon sequencing revealed that microbial diversity, composition and predicted function were strongly influenced by the presence of seagrass roots, such that root microbiomes were unique to each seagrass species. Reduced light availability altered seagrass root exudation, as characterized using fluorescence spectroscopy, and altered the composition of seagrass root microbiomes with a reduction in abundance of potentially beneficial microorganisms. Overall, this study highlights the potential for above-ground light reduction to invoke a cascade of changes from alterations in root exudation to a reduction in putative beneficial microorganisms and, ultimately, confirms the importance of the seagrass root environment - a critical, but often overlooked space.
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Affiliation(s)
- Belinda C. Martin
- School of Biological Sciences, The University of Western Australia, Crawley, WA, Australia
- UWA Oceans Institute, The University of Western Australia, Crawley, WA, Australia
| | - Deirdre Gleeson
- School of Agriculture and Environment, The University of Western Australia, Crawley, WA, Australia
| | - John Statton
- School of Biological Sciences, The University of Western Australia, Crawley, WA, Australia
- UWA Oceans Institute, The University of Western Australia, Crawley, WA, Australia
- Western Australian Marine Science Institution, Perth, WA, Australia
| | - Andre R. Siebers
- School of Biological Sciences, The University of Western Australia, Crawley, WA, Australia
| | - Pauline Grierson
- School of Biological Sciences, The University of Western Australia, Crawley, WA, Australia
- West Australian Biogeochemistry Centre, School of Biological Sciences, The University of Western Australia, Crawley, WA, Australia
| | - Megan H. Ryan
- School of Agriculture and Environment, The University of Western Australia, Crawley, WA, Australia
| | - Gary A. Kendrick
- School of Biological Sciences, The University of Western Australia, Crawley, WA, Australia
- UWA Oceans Institute, The University of Western Australia, Crawley, WA, Australia
- Western Australian Marine Science Institution, Perth, WA, Australia
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32
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Coelho FJRC, Cleary DFR, Gomes NCM, Pólonia ARM, Huang YM, Liu LL, de Voogd NJ. Sponge Prokaryote Communities in Taiwanese Coral Reef and Shallow Hydrothermal Vent Ecosystems. MICROBIAL ECOLOGY 2018; 75:239-254. [PMID: 28699015 DOI: 10.1007/s00248-017-1023-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/12/2017] [Accepted: 06/15/2017] [Indexed: 06/07/2023]
Abstract
Previously, it was believed that the prokaryote communities of typical 'low-microbial abundance' (LMA) or 'non-symbiont harboring' sponges were merely subsets of the prokaryote plankton community. Recent research has, however, shown that these sponges are dominated by particular clades of Proteobacteria or Cyanobacteria. Here, we expand on this research and assess the composition and putative functional profiles of prokaryotic communities from LMA sponges collected in two ecosystems (coral reef and hydrothermal vent) from vicinal islands of Taiwan with distinct physicochemical conditions. Six sponge species identified as Acanthella cavernosa (Bubarida), Echinodictyum asperum, Ptilocaulis spiculifer (Axinellida), Jaspis splendens (Tetractinellida), Stylissa carteri (Scopalinida) and Suberites sp. (Suberitida) were sampled in coral reefs in the Penghu archipelago. One sponge species provisionally identified as Hymeniacidon novo spec. (Suberitida) was sampled in hydrothermal vent habitat. Each sponge was dominated by a limited set of operational taxonomic units which were similar to sequences from organisms previously obtained from other LMA sponges. There was a distinct bacterial community between sponges collected in coral reef and in hydrothermal vents. The putative functional profile revealed that the prokaryote community from sponges collected in hydrothermal vents was significantly enriched for pathways related to DNA replication and repair.
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Affiliation(s)
- F J R C Coelho
- Department of Biology & CESAM, University of Aveiro, Campus de Santiago, 3810-193, Aveiro, Portugal
| | - D F R Cleary
- Department of Biology & CESAM, University of Aveiro, Campus de Santiago, 3810-193, Aveiro, Portugal
| | - N C M Gomes
- Department of Biology & CESAM, University of Aveiro, Campus de Santiago, 3810-193, Aveiro, Portugal
| | - A R M Pólonia
- Department of Biology & CESAM, University of Aveiro, Campus de Santiago, 3810-193, Aveiro, Portugal
- Center for Neuroscience and Cell Biology, University of Coimbra, 3004-504, Coimbra, Portugal
| | - Y M Huang
- Department of Marine Recreation, National Penghu University of Science and Technology, Penghu, Taiwan
- Naturalis Biodiversity Center, Leiden, the Netherlands
| | - L-L Liu
- Department of Oceanography, National Sun Yet-Sen University, Kaohsiung, Taiwan
| | - N J de Voogd
- Naturalis Biodiversity Center, Leiden, the Netherlands.
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33
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Cleary DFR, Polónia ARM, de Voogd NJ. Prokaryote composition and predicted metagenomic content of two Cinachyrella Morphospecies and water from West Papuan Marine Lakes. FEMS Microbiol Ecol 2017; 94:4693832. [DOI: 10.1093/femsec/fix175] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2017] [Accepted: 12/03/2017] [Indexed: 01/08/2023] Open
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Xu Y, He Y, Tang X, Brookes PC, Xu J. Reconstruction of microbial community structures as evidences for soil redox coupled reductive dechlorination of PCP in a mangrove soil. THE SCIENCE OF THE TOTAL ENVIRONMENT 2017; 596-597:147-157. [PMID: 28431359 DOI: 10.1016/j.scitotenv.2017.04.073] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/28/2017] [Revised: 04/07/2017] [Accepted: 04/09/2017] [Indexed: 05/26/2023]
Abstract
The aim was to investigate the influence of pentachlorophenol (PCP) on the soil microbial communities and the coupled mechanism between PCP reductive dechlorination and soil redox under anaerobic condition. Accordingly, a slurry incubation experiment was carried out in which bacterial and archaeal communities were detected by MiSeq amplicon sequencing. The original microbial community balance was gradually disrupted and new microbial structure was reconstructed subsequently through self-regulation and acclimation during PCP transformation, coupling with the changes of soil biogeochemical redox dynamics. The phylum Bacteroidetes predominated during the earlier PCP dechlorination period and then was progressively replaced by Proteobacteria and Firmicutes groups when PCP was mostly transformed into 2,3,4,5-TeCP and 3,4,5-TCP. Heatmap and hierarchical cluster analysis revealed the Clostridium-like, Geobacter-like and Dehalococcoides-like organisms enriched concurrently during PCP reductive dechlorination processes. The relative abundance changes of the redox-active microorganisms, together with their relevance to the corresponding biogeochemical redox processes, showed that PCP dechlorination, Fe(III) and SO42- reduction, as well as methanogenesis were coupled terminal electron accepting processes. The combined analysis of the microbial function, the affinity for substrates (H2 and acetate) and the sensitivity for PCP toxicity by microorganisms might explain why electron transport chain has changed in soil biogeochemical redox process. Our study offers a comprehensive description of the impact of PCP on the soil microbial community structures, which could be very useful for understanding the regulation of soil nutrient and energy transfer during biogeochemical cycling processes in soils with significant inputs of exogenous pollutants.
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Affiliation(s)
- Yan Xu
- Institute of Soil and Water Resources and Environmental Science, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China; Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, Hangzhou 310058, China
| | - Yan He
- Institute of Soil and Water Resources and Environmental Science, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China; Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, Hangzhou 310058, China.
| | - Xianjin Tang
- Institute of Soil and Water Resources and Environmental Science, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China; Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, Hangzhou 310058, China
| | - Philip C Brookes
- Institute of Soil and Water Resources and Environmental Science, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China; Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, Hangzhou 310058, China
| | - Jianming Xu
- Institute of Soil and Water Resources and Environmental Science, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China; Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, Hangzhou 310058, China
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Díez-Méndez A, Rivas R. Improvement of saffron production using Curtobacterium herbarum as a bioinoculant under greenhouse conditions. AIMS Microbiol 2017; 3:354-364. [PMID: 31294166 PMCID: PMC6604984 DOI: 10.3934/microbiol.2017.3.354] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2017] [Accepted: 05/16/2017] [Indexed: 11/18/2022] Open
Abstract
Plant Growth Promoting Rhizobacteria (PGPR) are natural soil bacteria which establish a beneficial relationship with their host. This microbiota community exists in the rhizosphere and inside plant tissues and stimulates plant growth by a variety of direct or indirect mechanisms. These bacterial plant promoters are frequently present in different environments, and are associated with many plant species, both wild and agricultural. Saffron is the dried stigmas of Crocus sativus (L.) and is the most expensive spice in the world. Remarkably, saffron cultivation and collection is carried out by hand and does not involve the use of machines. Additionally, 150 flowers are needed to produce one gram of dried stigmas. Hence, a slight increase in the size of the saffron filaments per plant would result in a significant increase in the production of this spice. In this study, we report the improved production of saffron using Curtobacterium herbarum Cs10, isolated from Crocus seronitus subs clusii, as a bioinoculant. The bacterial strain was selected owing to its multifunctional ability to produce siderophores, solubilize phosphate and to produce plant growth hormones like IAA. Furthermore, the isolate was tested on saffron producing plants under greenhouse conditions. The results indicate that Curtobacterium herbarum Cs10 improves the number of flowers and significantly enhances the length of the saffron filaments and overall saffron production compared to the control treated plants.
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Affiliation(s)
- Alexandra Díez-Méndez
- Department of Microbiology and Genetics, Edificio Departamental de Biología, Universidad de Salamanca, (USAL) Dres. de la Reina s/n, 37007, Salamanca, Spain.,Instituto Hispano Luso de Investigaciones Agrarias (CIALE), Salamanca, Spain
| | - Raul Rivas
- Department of Microbiology and Genetics, Edificio Departamental de Biología, Universidad de Salamanca, (USAL) Dres. de la Reina s/n, 37007, Salamanca, Spain.,Instituto Hispano Luso de Investigaciones Agrarias (CIALE), Salamanca, Spain.,Associated Unit USAL-CSIC (IRNASA), Salamanca, Spain
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Ettinger CL, Voerman SE, Lang JM, Stachowicz JJ, Eisen JA. Microbial communities in sediment from Zostera marina patches, but not the Z. marina leaf or root microbiomes, vary in relation to distance from patch edge. PeerJ 2017; 5:e3246. [PMID: 28462046 PMCID: PMC5410140 DOI: 10.7717/peerj.3246] [Citation(s) in RCA: 58] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2017] [Accepted: 03/29/2017] [Indexed: 12/31/2022] Open
Abstract
Background Zostera marina (also known as eelgrass) is a foundation species in coastal and marine ecosystems worldwide and is a model for studies of seagrasses (a paraphyletic group in the order Alismatales) that include all the known fully submerged marine angiosperms. In recent years, there has been a growing appreciation of the potential importance of the microbial communities (i.e., microbiomes) associated with various plant species. Here we report a study of variation in Z. marina microbiomes from a field site in Bodega Bay, CA. Methods We characterized and then compared the microbial communities of root, leaf and sediment samples (using 16S ribosomal RNA gene PCR and sequencing) and associated environmental parameters from the inside, edge and outside of a single subtidal Z. marina patch. Multiple comparative approaches were used to examine associations between microbiome features (e.g., diversity, taxonomic composition) and environmental parameters and to compare sample types and sites. Results Microbial communities differed significantly between sample types (root, leaf and sediment) and in sediments from different sites (inside, edge, outside). Carbon:Nitrogen ratio and eelgrass density were both significantly correlated to sediment community composition. Enrichment of certain taxonomic groups in each sample type was detected and analyzed in regard to possible functional implications (especially regarding sulfur metabolism). Discussion Our results are mostly consistent with prior work on seagrass associated microbiomes with a few differences and additional findings. From a functional point of view, the most significant finding is that many of the taxa that differ significantly between sample types and sites are closely related to ones commonly associated with various aspects of sulfur and nitrogen metabolism. Though not a traditional model organism, we believe that Z. marina can become a model for studies of marine plant-microbiome interactions.
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Affiliation(s)
| | - Sofie E Voerman
- Climate Change Cluster, University of Technology Sydney, Sydney, Australia.,School of Life Sciences, University of Technology Sydney, Sydney, Australia
| | - Jenna M Lang
- Genome Center, University of California, Davis, CA, United States.,Trace Genomics, San Francisco, CA, United States
| | - John J Stachowicz
- Department of Evolution and Ecology, University of California, Davis, CA, United States
| | - Jonathan A Eisen
- Genome Center, University of California, Davis, CA, United States.,Department of Evolution and Ecology, University of California, Davis, CA, United States.,Department of Medical Microbiology and Immunology, University of California, Davis, Davis, CA, United States
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Ullah R, Yasir M, Khan I, Bibi F, Sohrab SS, Al-Ansari A, Al-Abbasi F, Al-Sofyani AA, Daur I, Lee SW, Azhar EI. Comparative bacterial community analysis in relatively pristine and anthropogenically influenced mangrove ecosystems on the Red Sea. Can J Microbiol 2017; 63:649-660. [PMID: 28376307 DOI: 10.1139/cjm-2016-0587] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Mangrove habitats are ecologically important ecosystems that are under severe pressure worldwide because of environmental changes and human activities. In this study, 16S rRNA gene amplicon deep-sequencing was used to compare bacterial communities in Red Sea mangrove ecosystems at anthropogenically influenced coastal sites with those at a relatively pristine island site. In total, 32 phyla were identified from the mangrove rhizospheres, with Proteobacteria predominating at each of the studied sites; however, the relative abundance was significantly decreased at the coastal sites (Mastorah, MG-MS; Ar-Rayis, MG-AR) compared with the pristine island site near Dhahban (MG-DBI). The phyla Actinobacteria, Firmicutes, Acidobacteria, Chloroflexi, Spirochetes, and Planctomycetes were present at a relative abundance of >1% at the MG-MS and MG-AR sites, but their concentration was <1% at the MG-DBI site. A total of 1659 operational taxonomic units (OTUs) were identified at the species level, and approximately 945 OTUs were shared across the different sampling sites. Multivariate principal coordinate data analysis separated the MG-DBI site from the MG-AR and MG-MS cluster. Specific bacterial taxa were enriched at each location, and in particular, the genera Pseudoalteromonas and Cobetia were predominantly identified in the MG-DBI site compared with the anthropogenically influenced coastal sites.
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Affiliation(s)
- Riaz Ullah
- a Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia.,b Biochemistry Department, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Muhammad Yasir
- a Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Imran Khan
- a Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia.,b Biochemistry Department, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Fehmida Bibi
- a Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Sayed Sartaj Sohrab
- a Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Ahmed Al-Ansari
- c Department of Environmental Sciences, Faculty of Meteorology, Environment and Arid Land Agriculture, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Fahad Al-Abbasi
- b Biochemistry Department, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Abdulmohsin A Al-Sofyani
- d Marine Biology Department, Faculty of Marine Science, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Ihsanullah Daur
- e Department of Arid Land Agriculture, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Seon-Woo Lee
- f Department of Applied Biology, Dong-A University, Busan 49315, Republic of Korea
| | - Esam I Azhar
- a Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia.,g Medical Laboratory Technology Department, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
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Preisner EC, Fichot EB, Norman RS. Microbial Mat Compositional and Functional Sensitivity to Environmental Disturbance. Front Microbiol 2016; 7:1632. [PMID: 27799927 PMCID: PMC5066559 DOI: 10.3389/fmicb.2016.01632] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2016] [Accepted: 09/30/2016] [Indexed: 11/13/2022] Open
Abstract
The ability of ecosystems to adapt to environmental perturbations depends on the duration and intensity of change and the overall biological diversity of the system. While studies have indicated that rare microbial taxa may provide a biological reservoir that supports long-term ecosystem stability, how this dynamic population is influenced by environmental parameters remains unclear. In this study, a microbial mat ecosystem located on San Salvador Island, The Bahamas was used as a model to examine how environmental disturbance affects the protein synthesis potential (PSP) of rare and abundant archaeal and bacterial communities and how these changes impact potential biogeochemical processes. This ecosystem experienced a large shift in salinity (230 to 65 g kg-1) during 2011-2012 following the landfall of Hurricane Irene on San Salvador Island. High throughput sequencing and analysis of 16S rRNA and rRNA genes from samples before and after the pulse disturbance showed significant changes in the diversity and PSP of abundant and rare taxa, suggesting overall compositional and functional sensitivity to environmental change. In both archaeal and bacterial communities, while the majority of taxa showed low PSP across conditions, the overall community PSP increased post-disturbance, with significant shifts occurring among abundant and rare taxa across and within phyla. Broadly, following the post-disturbance reduction in salinity, taxa within Halobacteria decreased while those within Crenarchaeota, Thaumarchaeota, Thermoplasmata, Cyanobacteria, and Proteobacteria, increased in abundance and PSP. Quantitative PCR of genes and transcripts involved in nitrogen and sulfur cycling showed concomitant shifts in biogeochemical cycling potential. Post-disturbance conditions increased the expression of genes involved in N-fixation, nitrification, denitrification, and sulfate reduction. Together, our findings show complex community adaptation to environmental change and help elucidate factors connecting disturbance, biodiversity, and ecosystem function that may enhance ecosystem models.
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Affiliation(s)
| | | | - Robert S. Norman
- Department of Environmental Health Sciences, University of South Carolina, ColumbiaSC, USA
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Wu P, Xiong X, Xu Z, Lu C, Cheng H, Lyu X, Zhang J, He W, Deng W, Lyu Y, Lou Q, Hong Y, Fang H. Bacterial Communities in the Rhizospheres of Three Mangrove Tree Species from Beilun Estuary, China. PLoS One 2016; 11:e0164082. [PMID: 27695084 PMCID: PMC5047532 DOI: 10.1371/journal.pone.0164082] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2016] [Accepted: 09/19/2016] [Indexed: 01/28/2023] Open
Abstract
The bacterial communities played important roles in the high productivity mangrove ecosystem. In this study, we investigated the vertical distributions of rhizosphere bacteria from three mangrove species (Bruguiera gymnorrhiza, Kandelia candel and Aegiceras corniculatum) in Beilun Estuary, China using high throughput DNA pyrosequencing of the 16S rRNA gene. Phylogenetic analysis showed that bacterial communities from mangrove rhizosphere sediments were dominated by Proteobacteria (mostly Deltaproteobacteria and Gammaproteobacteria), followed by Chloroflexi, Bacteroidetes, Planctomycetes and Acidobacteria. However, the ANOVA analysis on Shannon and Chao1 indices indicated that bacterial communities among sediments of the three mangrove species varied more strongly than the sampling depths. In addition, the PCA result demonstrated that the bacterial communities could be separated into three groups according to the mangrove species. Moreover, the dominated orders Rhodospirillales, GCA004 and envOPS12 were significantly different among sediments of the three mangrove species. The results of this study provided valuable information about the distribution feature of rhizosphere bacteria from Chinese mangrove plants and shed insights into biogeochemical transformations driven by bacteria in rhizosphere sediments.
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Affiliation(s)
- Peng Wu
- South China Sea Environmental Monitoring Center, State Oceanic Administration, Guangzhou, China
| | - Xiaofei Xiong
- South China Sea Environmental Monitoring Center, State Oceanic Administration, Guangzhou, China
| | - Zhanzhou Xu
- South China Sea Environmental Monitoring Center, State Oceanic Administration, Guangzhou, China
| | - Chuqian Lu
- South China Sea Environmental Monitoring Center, State Oceanic Administration, Guangzhou, China
| | - Hao Cheng
- State Key Laboratory of Tropical Oceanography, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China
| | - Xiangli Lyu
- South China Sea Environmental Monitoring Center, State Oceanic Administration, Guangzhou, China
| | - Jinghuai Zhang
- South China Sea Environmental Monitoring Center, State Oceanic Administration, Guangzhou, China
| | - Wei He
- South China Sea Environmental Monitoring Center, State Oceanic Administration, Guangzhou, China
| | - Wei Deng
- South China Sea Environmental Monitoring Center, State Oceanic Administration, Guangzhou, China
| | - Yihua Lyu
- South China Sea Environmental Monitoring Center, State Oceanic Administration, Guangzhou, China
| | - Quansheng Lou
- South China Sea Environmental Monitoring Center, State Oceanic Administration, Guangzhou, China
| | - Yiguo Hong
- State Key Laboratory of Tropical Oceanography, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China
- * E-mail: (YH); (HF)
| | - Hongda Fang
- South China Sea Environmental Monitoring Center, State Oceanic Administration, Guangzhou, China
- * E-mail: (YH); (HF)
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40
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Comparison of archaeal and bacterial communities in two sponge species and seawater from an Indonesian coral reef environment. Mar Genomics 2016; 29:69-80. [DOI: 10.1016/j.margen.2016.04.014] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2016] [Revised: 04/28/2016] [Accepted: 04/28/2016] [Indexed: 12/17/2022]
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Cleary DFR, Polónia ARM, Sousa AI, Lillebø AI, Queiroga H, Gomes NCM. Temporal dynamics of sediment bacterial communities in monospecific stands of Juncus maritimus and Spartina maritima. PLANT BIOLOGY (STUTTGART, GERMANY) 2016; 18:824-834. [PMID: 27061465 DOI: 10.1111/plb.12459] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2015] [Accepted: 04/05/2016] [Indexed: 06/05/2023]
Abstract
In the present study, we used 16S rRNA barcoded pyrosequencing to investigate to what extent monospecific stands of different salt marsh plant species (Juncus maritimus and Spartina maritima), sampling site and temporal variation affect sediment bacterial communities. We also used a bioinformatics tool, PICRUSt, to predict metagenome gene functional content. Our results showed that bacterial community composition from monospecific stands of both plant species varied temporally, but both host plant species maintained compositionally distinct communities of bacteria. Juncus sediment was characterised by higher abundances of Alphaproteobacteria, Myxococcales, Rhodospirillales, NB1-j and Ignavibacteriales, while Spartina sediment was characterised by higher abundances of Anaerolineae, Synechococcophycidae, Desulfobacterales, SHA-20 and Rhodobacterales. The differences in composition and higher taxon abundance between the sediment bacterial communities of stands of both plant species may be expected to affect overall metabolic diversity. In line with this expectation, there were also differences in the predicted enrichment of selected metabolic pathways. In particular, bacterial communities of Juncus sediment were predicted to be enriched for pathways related to the degradation of various (xenobiotic) compounds. Bacterial communities of Spartina sediment in turn were predicted to be enriched for pathways related to the biosynthesis of various bioactive compounds. Our study highlights the differences in composition and predicted functions of sediment-associated bacterial communities from two different salt marsh plant species. Loss of salt marsh habitat may thus be expected to both adversely affect microbial diversity and ecosystem functioning and have consequences for environmental processes such as nutrient cycling and pollutant remediation.
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Affiliation(s)
- D F R Cleary
- Departamento de Biologia, CESAM - Centro de Estudos do Ambiente e do Mar, Universidade de Aveiro, Aveiro, Portugal
| | - A R M Polónia
- Departamento de Biologia, CESAM - Centro de Estudos do Ambiente e do Mar, Universidade de Aveiro, Aveiro, Portugal
| | - A I Sousa
- Departamento de Biologia, CESAM - Centro de Estudos do Ambiente e do Mar, Universidade de Aveiro, Aveiro, Portugal
| | - A I Lillebø
- Departamento de Biologia, CESAM - Centro de Estudos do Ambiente e do Mar, Universidade de Aveiro, Aveiro, Portugal
| | - H Queiroga
- Departamento de Biologia, CESAM - Centro de Estudos do Ambiente e do Mar, Universidade de Aveiro, Aveiro, Portugal
| | - N C M Gomes
- Departamento de Biologia, CESAM - Centro de Estudos do Ambiente e do Mar, Universidade de Aveiro, Aveiro, Portugal
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Cleary DFR, Becking LE, Polónia ARM, Freitas RM, Gomes NCM. Jellyfish-associated bacterial communities and bacterioplankton in Indonesian Marine lakes. FEMS Microbiol Ecol 2016; 92:fiw064. [PMID: 27004797 DOI: 10.1093/femsec/fiw064] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/15/2016] [Indexed: 01/08/2023] Open
Abstract
In the present study, we compared communities of bacteria in two jellyfish species (the 'golden' jellyfish Mastigias cf.papua and the box jellyfish Tripedalia cf.cystophora) and water in three marine lakes located in the Berau region of northeastern Borneo, Indonesia. Jellyfish-associated bacterial communities were compositionally distinct and less diverse than bacterioplankton communities. Alphaproteobacteria, Gammaproteobacteria, Synechococcophycidae and Flavobacteriia were the most abundant classes in water. Jellyfish-associated bacterial communities were dominated by OTUs assigned to the Gammaproteobacteria (family Endozoicimonaceae), Mollicutes, Spirochaetes and Alphaproteobacteria (orders Kiloniellales and Rhodobacterales). Mollicutes were mainly restricted to Mastigias whereas Spirochaetes and the order Kiloniellales were most abundant in Tripedalia hosts. The most abundant OTU overall in jellyfish hosts was assigned to the family Endozoicimonaceae and was highly similar to organisms in Genbank obtained from various hosts including an octocoral, bivalve and fish species. Other abundant OTUs included an OTU assigned to the order Entomoplasmatales and mainly found in Mastigias hosts and OTUs assigned to the Spirochaetes and order Kiloniellales and mainly found in Tripedalia hosts. The low sequence similarity of the Entomoplasmatales OTU to sequences in Genbank suggests that it may be a novel lineage inhabiting Mastigias and possibly restricted to marine lakes.
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Affiliation(s)
- Daniel F R Cleary
- Department of Biology, CESAM, Universidade de Aveiro, Campus Universitário de Santiago, 3810-193 Aveiro, Portugal
| | - Leontine E Becking
- Department of Marine Zoology, Naturalis Biodiversity Center, Darwinweg 2, 2333 CR Leiden, the Netherlands Wageningen University and Research Centre, Marine Animal Ecology Group, PO Box 338, 6700 AH Wageningen, the Netherlands Department of Environmental Science, Policy, and Management, University of California Berkeley, 130 Mulford Hall, Berkeley CA 94720-3114, USA
| | - Ana R M Polónia
- Department of Biology, CESAM, Universidade de Aveiro, Campus Universitário de Santiago, 3810-193 Aveiro, Portugal
| | - Rossana M Freitas
- Department of Biology, CESAM, Universidade de Aveiro, Campus Universitário de Santiago, 3810-193 Aveiro, Portugal
| | - Newton C M Gomes
- Department of Biology, CESAM, Universidade de Aveiro, Campus Universitário de Santiago, 3810-193 Aveiro, Portugal
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Distinct Habitats Select Particular Bacterial Communities in Mangrove Sediments. Int J Microbiol 2016; 2016:3435809. [PMID: 26989418 PMCID: PMC4773542 DOI: 10.1155/2016/3435809] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2015] [Revised: 01/09/2016] [Accepted: 01/27/2016] [Indexed: 11/18/2022] Open
Abstract
We investigated the relationship among environmental variables, composition, and structure of bacterial communities in different habitats in a mangrove located nearby to an oil exploitation area, aiming to retrieve the natural pattern of bacterial communities in this ecosystem. The T-RFLP analysis showed a high diversity of bacterial populations and an increase in the bacterial richness from habitats closer to the sea and without vegetation (S1) to habitats covered by Avicennia schaueriana (S2) and Rhizophora mangle (S3). Environmental variables in S1 and S2 were more similar than in S3; however, when comparing the bacterial compositions, S2 and S3 shared more OTUs between them, suggesting that the presence of vegetation is an important factor in shaping these bacterial communities. In silico analyses of the fragments revealed a high diversity of the class Gammaproteobacteria in the 3 sites, although in general they presented quite different bacterial composition, which is probably shaped by the specificities of each habitat. This study shows that microhabitats inside of a mangrove ecosystem harbor diverse and distinct microbiota, reinforcing the need to conserve these ecosystems as a whole.
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Abstract
Mangroves are unique, and endangered, coastal ecosystems that play a vital role in the tropical and subtropical environments. A comprehensive description of the microbial communities in these ecosystems is currently lacking, and additional studies are required to have a complete understanding of the functioning and resilience of mangroves worldwide. In this work, we carried out a metagenomic study by comparing the microbial community of mangrove sediment with the rhizosphere microbiome of Avicennia marina, in northern Red Sea mangroves, along the coast of Saudi Arabia. Our results revealed that rhizosphere samples presented similar profiles at the taxonomic and functional levels and differentiated from the microbiome of bulk soil controls. Overall, samples showed predominance by Proteobacteria, Bacteroidetes and Firmicutes, with high abundance of sulfate reducers and methanogens, although specific groups were selectively enriched in the rhizosphere. Functional analysis showed significant enrichment in 'metabolism of aromatic compounds', 'mobile genetic elements', 'potassium metabolism' and 'pathways that utilize osmolytes' in the rhizosphere microbiomes. To our knowledge, this is the first metagenomic study on the microbiome of mangroves in the Red Sea, and the first application of unbiased 454-pyrosequencing to study the rhizosphere microbiome associated with A. marina. Our results provide the first insights into the range of functions and microbial diversity in the rhizosphere and soil sediments of gray mangrove (A. marina) in the Red Sea.
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Pyrosequencing-Based Seasonal Observation of Prokaryotic Diversity in Pneumatophore-Associated Soil of Avicennia marina. Curr Microbiol 2015; 72:68-74. [DOI: 10.1007/s00284-015-0920-9] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2015] [Accepted: 09/09/2015] [Indexed: 02/02/2023]
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Azman AS, Othman I, Velu SS, Chan KG, Lee LH. Mangrove rare actinobacteria: taxonomy, natural compound, and discovery of bioactivity. Front Microbiol 2015; 6:856. [PMID: 26347734 PMCID: PMC4542535 DOI: 10.3389/fmicb.2015.00856] [Citation(s) in RCA: 79] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2015] [Accepted: 08/06/2015] [Indexed: 11/13/2022] Open
Abstract
Actinobacteria are one of the most important and efficient groups of natural metabolite producers. The genus Streptomyces have been recognized as prolific producers of useful natural compounds as they produced more than half of the naturally-occurring antibiotics isolated to-date and continue as the primary source of new bioactive compounds. Lately, Streptomyces groups isolated from different environments produced the same types of compound, possibly due to frequent genetic exchanges between species. As a result, there is a dramatic increase in demand to look for new compounds which have pharmacological properties from another group of Actinobacteria, known as rare actinobacteria; which is isolated from special environments such as mangrove. Recently, mangrove ecosystem is becoming a hot spot for studies of bioactivities and the discovery of natural products. Many novel compounds discovered from the novel rare actinobacteria have been proven as potential new drugs in medical and pharmaceutical industries such as antibiotics, antimicrobials, antibacterials, anticancer, and antifungals. This review article highlights the latest studies on the discovery of natural compounds from the novel mangrove rare actinobacteria and provides insight on the impact of these findings.
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Affiliation(s)
- Adzzie-Shazleen Azman
- Jeffrey Cheah School of Medicine and Health Sciences, Monash University Sunway Campus Selangor, Malaysia
| | - Iekhsan Othman
- Jeffrey Cheah School of Medicine and Health Sciences, Monash University Sunway Campus Selangor, Malaysia
| | - Saraswati S Velu
- Jeffrey Cheah School of Medicine and Health Sciences, Monash University Sunway Campus Selangor, Malaysia
| | - Kok-Gan Chan
- Division of Genetics and Molecular Biology, Faculty of Science, Institute of Biological Sciences, University of Malaya Kuala Lumpur, Malaysia
| | - Learn-Han Lee
- Jeffrey Cheah School of Medicine and Health Sciences, Monash University Sunway Campus Selangor, Malaysia
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Viswanath G, Jegan S, Baskaran V, Kathiravan R, Prabavathy VR. Diversity and N-acyl-homoserine lactone production by Gammaproteobacteria associated with Avicennia marina rhizosphere of South Indian mangroves. Syst Appl Microbiol 2015; 38:340-5. [DOI: 10.1016/j.syapm.2015.03.008] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2014] [Revised: 03/14/2015] [Accepted: 03/31/2015] [Indexed: 01/25/2023]
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Coelho FJRC, Cleary DFR, Rocha RJM, Calado R, Castanheira JM, Rocha SM, Silva AMS, Simões MMQ, Oliveira V, Lillebø AI, Almeida A, Cunha Â, Lopes I, Ribeiro R, Moreira-Santos M, Marques CR, Costa R, Pereira R, Gomes NCM. Unraveling the interactive effects of climate change and oil contamination on laboratory-simulated estuarine benthic communities. GLOBAL CHANGE BIOLOGY 2015; 21:1871-1886. [PMID: 25382269 DOI: 10.1111/gcb.12801] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/22/2014] [Accepted: 10/28/2014] [Indexed: 06/04/2023]
Abstract
There is growing concern that modifications to the global environment such as ocean acidification and increased ultraviolet radiation may interact with anthropogenic pollutants to adversely affect the future marine environment. Despite this, little is known about the nature of the potential risks posed by such interactions. Here, we performed a multifactorial microcosm experiment to assess the impact of ocean acidification, ultraviolet B (UV-B) radiation and oil hydrocarbon contamination on sediment chemistry, the microbial community (composition and function) and biochemical marker response of selected indicator species. We found that increased ocean acidification and oil contamination in the absence of UV-B will significantly alter bacterial composition by, among other things, greatly reducing the relative abundance of Desulfobacterales, known to be important oil hydrocarbon degraders. Along with changes in bacterial composition, we identified concomitant shifts in the composition of oil hydrocarbons in the sediment and an increase in oxidative stress effects on our indicator species. Interestingly, our study identifies UV-B as a critical component in the interaction between these factors, as its presence alleviates harmful effects caused by the combination of reduced pH and oil pollution. The model system used here shows that the interactive effect of reduced pH and oil contamination can adversely affect the structure and functioning of sediment benthic communities, with the potential to exacerbate the toxicity of oil hydrocarbons in marine ecosystems.
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Affiliation(s)
- Francisco J R C Coelho
- Department of Biology & CESAM, University of Aveiro, Campus de Santiago, 3810-193, Aveiro, Portugal
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Pegoraro N, Calado R, Duarte LN, Manco SC, Fernandes FJ, Polónia ARM, Cleary DFR, Gomes NCM. Molecular analysis of skin bacterial assemblages from codfish and pollock after dry-salted fish production. J Food Prot 2015; 78:983-9. [PMID: 25951394 DOI: 10.4315/0362-028x.jfp-14-390] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Dry-salted codfish and pollock are commercially important food products with a relatively long shelf life. To date, bacterial assemblages present in these products that are relevant for food safety have been monitored using only classical molecular and/or cultivation methods. The present study employed a rapid and accurate identification method involving PCR with denaturing gradient gel electrophoresis and pyrosequencing to characterize the bacterial assemblages in the skin of three closely related fishes: Gadus morhua, Gadus macrocephalus, and Theragra chalcogramma. This methodology can be crucial for timely identification of food spoilage, hazard analysis, and monitoring of critical control points during food production. Although all specimens were processed in the same factory, there were significant compositional differences in their skin bacterial communities. In general, the bacterial community was dominated by gram-negative species of the Gammaproteobacteria. Pyrosequencing yielded 90, 69, and 245 operational taxonomic units associated with G. morhua, G. macrocephalus, and T. chalcogramma, respectively. The most dominant operational taxonomic units were assigned in order to Pseudomonas sp., Serratia marcescens, Salinisphaera sp., and Psychrobacter pulmonis. Spoilage and pathogenic bacterial groups were detected in all the studied salted gadoid samples.
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Affiliation(s)
- Natália Pegoraro
- Department of Biology, CESAM, University of Aveiro, Campus Universitário de Santiago, 3810-193 Aveiro, Portugal
| | - Ricardo Calado
- Department of Biology, CESAM, University of Aveiro, Campus Universitário de Santiago, 3810-193 Aveiro, Portugal
| | - Letícia N Duarte
- Department of Biology, CESAM, University of Aveiro, Campus Universitário de Santiago, 3810-193 Aveiro, Portugal
| | - Sónia C Manco
- Department of Biology, CESAM, University of Aveiro, Campus Universitário de Santiago, 3810-193 Aveiro, Portugal
| | - Fernando J Fernandes
- Department of Biology, CESAM, University of Aveiro, Campus Universitário de Santiago, 3810-193 Aveiro, Portugal
| | - Ana R M Polónia
- Department of Biology, CESAM, University of Aveiro, Campus Universitário de Santiago, 3810-193 Aveiro, Portugal
| | - Daniel F R Cleary
- Department of Biology, CESAM, University of Aveiro, Campus Universitário de Santiago, 3810-193 Aveiro, Portugal
| | - Newton C M Gomes
- Department of Biology, CESAM, University of Aveiro, Campus Universitário de Santiago, 3810-193 Aveiro, Portugal.
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Oliveira V, Gomes NCM, Almeida A, Silva AMS, Silva H, Cunha Â. Microbe-assisted phytoremediation of hydrocarbons in estuarine environments. MICROBIAL ECOLOGY 2015; 69:1-12. [PMID: 25001506 DOI: 10.1007/s00248-014-0455-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/13/2014] [Accepted: 06/23/2014] [Indexed: 06/03/2023]
Abstract
Estuaries are sinks for various anthropogenic contaminants, such as petroleum hydrocarbons, giving rise to significant environmental concern. The demand for organisms and processes capable of degrading pollutants in a clean, effective, and less expensive process is of great importance. Phytoremedition approaches involving plant/bacteria interactions have been explored as an alternative, and halophyte vegetation has potential for use in phytoremedition of hydrocarbon contamination. Studies with plant species potentially suitable for microbe-assisted phytoremediation are widely represented in scientific literature. However, the in-depth understanding of the biological processes associated with the re-introduction of indigenous bacteria and plants and their performance in the degradation of hydrocarbons is still the limiting step for the application of these bioremediation solutions in a field context. The intent of the present review is to summarize the sources and effects of hydrocarbon contamination in estuarine environments, the strategies currently available for bioremediation (potential and limitations), and the perspectives of the use of halophyte plants in microbe-assisted phytoremediation approaches.
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Affiliation(s)
- Vanessa Oliveira
- Centre for Environmental and Marine Studies (CESAM) and Department of Biology, University of Aveiro, Campus Universitário de Santiago, 3810-193, Aveiro, Portugal
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