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Kalaitzidou MP, Alvanou MV, Papageorgiou KV, Lattos A, Sofia M, Kritas SK, Petridou E, Giantsis IA. Pollution Indicators and HAB-Associated Halophilic Bacteria Alongside Harmful Cyanobacteria in the Largest Mussel Cultivation Area in Greece. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2022; 19:ijerph19095285. [PMID: 35564680 PMCID: PMC9104808 DOI: 10.3390/ijerph19095285] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Revised: 04/21/2022] [Accepted: 04/25/2022] [Indexed: 12/16/2022]
Abstract
Taking into consideration the essential contribution of Mytilus galloprovincialis farming, it is of rising importance to add knowledge regarding bacterial species occurrence in water samples from aquaculture zones from the point of view of both the organism and public health. In the present study, we investigated the bacterial community existing in water samples from six Mytilus galloprovincialis aquaculture areas in the Thermaikos gulf, northern Greece, that may provoke toxicity in aquatic organisms and humans and may indicate environmental pollution in mussel production as well as algal blooms. Bacterial species were identified molecularly by sequencing of a partial 16s rRNA segment and were analyzed phylogenetically for the confirmation of the bacterial taxonomy. The results obtained revealed the presence of four bacterial genera (Halomonas sp., Planococcus sp., Sulfitobacter sp., and Synechocystis sp.). Members of the Halomonas and Sulfitobacter genera have been isolated from highly polluted sites, Planococcus bacteria have been identified in samples derived directly from plastic debris, and Synechocystis bacteria are in line with microcystin detection. In this context, the monitoring of the bacteria community in mussel aquaculture water samples from the Thermaikos gulf, the largest mussel cultivation area in Greece, represents an indicator of water pollution, microplastics presence, algal blooms, and toxin presence.
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Affiliation(s)
- Maria P. Kalaitzidou
- National Reference Laboratory for Marine Biotoxins, Department of Food Microbiology, Biochemical Control, Residues, Marine Biotoxins and Other Water Toxins, Directorate of Veterinary Center of Thessaloniki, Ministry of Rural Development and Food, 54627 Thessaloniki, Greece;
| | - Maria V. Alvanou
- Department of Animal Science, Faculty of Agricultural Sciences, University of Western Macedonia, 53100 Florina, Greece; (M.V.A.); (A.L.)
| | - Konstantinos V. Papageorgiou
- 3rd Military Veterinary Hospital, General Staff, Hellenic Ministry of Defense, 15th Km Thessaloniki-Vasilika, 57001 Thessaloniki, Greece;
| | - Athanasios Lattos
- Department of Animal Science, Faculty of Agricultural Sciences, University of Western Macedonia, 53100 Florina, Greece; (M.V.A.); (A.L.)
| | - Marina Sofia
- Faculty of Veterinary Science, University of Thessaly, 43100 Karditsa, Greece;
| | - Spyridon K. Kritas
- Laboratory of Microbiology and Infectious Diseases, School of Veterinary Medicine, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece; (S.K.K.); (E.P.)
| | - Evanthia Petridou
- Laboratory of Microbiology and Infectious Diseases, School of Veterinary Medicine, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece; (S.K.K.); (E.P.)
| | - Ioannis A. Giantsis
- Department of Animal Science, Faculty of Agricultural Sciences, University of Western Macedonia, 53100 Florina, Greece; (M.V.A.); (A.L.)
- Correspondence:
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2
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Torres-Beltrán M, Vargas-Gastélum L, Magdaleno-Moncayo D, Riquelme M, Herguera-García JC, Prieto-Davó A, Lago-Lestón A. The metabolic core of the prokaryotic community from deep-sea sediments of the southern Gulf of Mexico shows different functional signatures between the continental slope and abyssal plain. PeerJ 2021; 9:e12474. [PMID: 34993013 PMCID: PMC8679910 DOI: 10.7717/peerj.12474] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Accepted: 10/20/2021] [Indexed: 11/20/2022] Open
Abstract
Marine sediments harbor an outstanding level of microbial diversity supporting diverse metabolic activities. Sediments in the Gulf of Mexico (GoM) are subjected to anthropic stressors including oil pollution with potential effects on microbial community structure and function that impact biogeochemical cycling. We used metagenomic analyses to provide significant insight into the potential metabolic capacity of the microbial community in Southern GoM deep sediments. We identified genes for hydrocarbon, nitrogen and sulfur metabolism mostly affiliated with Alpha and Betaproteobacteria, Acidobacteria, Chloroflexi and Firmicutes, in relation to the use of alternative carbon and energy sources to thrive under limiting growth conditions, and metabolic strategies to cope with environmental stressors. In addition, results show amino acids metabolism could be associated with sulfur metabolism carried out by Acidobacteria, Chloroflexi and Firmicutes, and may play a crucial role as a central carbon source to favor bacterial growth. We identified the tricarboxylic acid cycle (TCA) and aspartate, glutamate, glyoxylate and leucine degradation pathways, as part of the core carbon metabolism across samples. Further, microbial communities from the continental slope and abyssal plain show differential metabolic capacities to cope with environmental stressors such as oxidative stress and carbon limiting growth conditions, respectively. This research combined taxonomic and functional information of the microbial community from Southern GoM sediments to provide fundamental knowledge that links the prokaryotic structure to its potential function and which can be used as a baseline for future studies to model microbial community responses to environmental perturbations, as well as to develop more accurate mitigation and conservation strategies.
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Affiliation(s)
- Mónica Torres-Beltrán
- Departamento de Innovación Biomédica, Centro de Investigación Científica y de Educación Superior de Ensenada, Ensenada, Baja California, Mexico
| | - Lluvia Vargas-Gastélum
- Departamento de Microbiología, Centro de Investigación Científica y de Educación Superior de Ensenada, Ensenada, Baja California, Mexico
| | - Dante Magdaleno-Moncayo
- Facultad de Ingeniería, Arquitectura y Diseño, Universidad Autónoma de Baja California, Ensenada, Baja California, Mexico
| | - Meritxell Riquelme
- Departamento de Microbiología, Centro de Investigación Científica y de Educación Superior de Ensenada, Ensenada, Baja California, Mexico
| | - Juan Carlos Herguera-García
- Departamento de Ecología Marina, Centro de Investigación Científica y de Educación Superior de Ensenada, Ensenada, Baja California, Mexico
| | - Alejandra Prieto-Davó
- Facultad de Química, Universidad Nacional Autónoma de México, Sisal, Yucatán, Mexico
| | - Asunción Lago-Lestón
- Departamento de Innovación Biomédica, Centro de Investigación Científica y de Educación Superior de Ensenada, Ensenada, Baja California, Mexico
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3
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Bacterial community structure and functional profiling of high Arctic fjord sediments. World J Microbiol Biotechnol 2021; 37:133. [PMID: 34255189 DOI: 10.1007/s11274-021-03098-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Accepted: 06/23/2021] [Indexed: 10/20/2022]
Abstract
Kongsfjorden, an Arctic fjord is significantly affected by the glacier melt and Atlantification, both the processes driven by accelerated warming in the Arctic. This has lead to changes in primary production, carbon pool and microbial communities, especially that in the sediment. In this study, we have examined the bacterial community structure of surface (0-2 cm) and subsurface (3-9 cm) sediments of Kongsfjorden using the high throughput sequencing analysis. Results revealed that bacterial community structure of Kongsfjorden sediments were dominated by phylum Proteobacteria followed by Bacteroidetes and Epsilonbacteraeota. While α- and γ-Proteobacterial class were dominant in surface sediments; δ-Proteobacteria were found to be predominant in subsurface sediments. The bacterial community structure in the surface and subsurface sediments showed significant variations (p ≤ 0.05). Total organic carbon could be one of the major parameters controlling the bacterial diversity in the surface and subsurface sediments. Functional prediction analysis indicated that the bacterial community could be involved in the degradation of complex organic compounds such as glycans, glycosaminoglycans, polycyclic aromatic hydrocarbons and also in the biosynthesis of secondary metabolites.
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4
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Quach NT, Dam HT, Tran DM, Vu THN, Nguyen QV, Nguyen KT, Nguyen QH, Phi CB, Le TH, Chu HH, Thuoc Doan V, Shyu DJH, Kang H, Li WJ, Phi QT. Diversity of microbial community and its metabolic potential for nitrogen and sulfur cycling in sediments of Phu Quoc island, Gulf of Thailand. Braz J Microbiol 2021; 52:1385-1395. [PMID: 33856662 DOI: 10.1007/s42770-021-00481-8] [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: 08/18/2020] [Accepted: 03/29/2021] [Indexed: 11/29/2022] Open
Abstract
Although Phu Quoc island, Gulf of Thailand possesses diverse marine and coastal ecosystems, biodiversity and metabolic capability of microbial communities remain poorly investigated. The aim of our study was to evaluate the biodiversity and metabolic potential of sediment microbial communities in Phu Quoc island. The marine sediments were collected from three different areas and analyzed by using 16S rRNA gene-based amplicon approach. A total of 1,143,939 reads were clustered at a 97% sequence similarity into 8,331 unique operational taxonomic units, representing 52 phyla. Bacteria and archaea occupied averagely around 86% and 14%, respectively, of the total prokaryotic community. Proteobacteria, Planctomycetes, Chloroflexi, and Thaumarchaeota were the dominant phyla in all sediments, which were involved in nitrogen and sulfur metabolism. Sediments harboring of higher nitrogen sources were found to coincide with increased abundance of archaeal phylum Thaumarchaeota. Predictive functional analysis showed high abundance prokaryotic genes associated with nitrogen cycling including nifA-Z, amoABC, nirA, narBIJ, napA, nxrAB, nrfA-K, nirBD, nirS, nirK, norB-Z, nlnA, ald, and ureA-J, based on taxonomic groups detected by 16S rRNA sequencing. Although the key genes involved in sulfur cycling were found to be at low to undetectable levels, the other genes encoding for sulfur-related biological processes were present, suggesting that alternative pathways may be involved in sulfur cycling at our study site. In conclusion, our study for the first time shed light on diversity of microbial communities in Phu Quoc island.
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Affiliation(s)
- Ngoc Tung Quach
- Institute of Biotechnology, Vietnam Academy of Science and Technology, Hanoi, 10000, Vietnam.,Graduate University of Science and Technology, Vietnam Academy of Science and Technology, Hanoi, 10000, Vietnam
| | - Hang Thuy Dam
- School of Biotechnology and Food Technology, Hanoi University of Science and Technology, Hanoi, 10000, Vietnam
| | - Dinh Man Tran
- Institute of Biotechnology, Vietnam Academy of Science and Technology, Hanoi, 10000, Vietnam.
| | - Thi Hanh Nguyen Vu
- Institute of Biotechnology, Vietnam Academy of Science and Technology, Hanoi, 10000, Vietnam.,Graduate University of Science and Technology, Vietnam Academy of Science and Technology, Hanoi, 10000, Vietnam
| | - Quoc Viet Nguyen
- Institute of Biotechnology, Vietnam Academy of Science and Technology, Hanoi, 10000, Vietnam
| | - Kim Thoa Nguyen
- Institute of Biotechnology, Vietnam Academy of Science and Technology, Hanoi, 10000, Vietnam
| | - Quang Huy Nguyen
- University of Science and Technology of Hanoi, Vietnam Academy of Science and Technology, Hanoi, 10000, Vietnam
| | | | - Thanh Ha Le
- School of Biotechnology and Food Technology, Hanoi University of Science and Technology, Hanoi, 10000, Vietnam
| | - Hoang Ha Chu
- Institute of Biotechnology, Vietnam Academy of Science and Technology, Hanoi, 10000, Vietnam.,Graduate University of Science and Technology, Vietnam Academy of Science and Technology, Hanoi, 10000, Vietnam
| | - Van Thuoc Doan
- Hanoi National University of Education, Hanoi, 10000, Vietnam
| | - Douglas J H Shyu
- Department of Biological Science and Technology, National Pingtung University of Science and Technology, Pingtung, 91201, Taiwan
| | - Heonjoong Kang
- School of Earth and Environmental Sciences, College of Natural Sciences, Seoul National University NS80, Seoul, 08826, Korea
| | - Wen-Jun Li
- School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, China
| | - Quyet Tien Phi
- Institute of Biotechnology, Vietnam Academy of Science and Technology, Hanoi, 10000, Vietnam. .,Graduate University of Science and Technology, Vietnam Academy of Science and Technology, Hanoi, 10000, Vietnam.
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5
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Jroundi F, Martinez-Ruiz F, Merroun ML, Gonzalez-Muñoz MT. Exploring bacterial community composition in Mediterranean deep-sea sediments and their role in heavy metal accumulation. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 712:135660. [PMID: 31791772 DOI: 10.1016/j.scitotenv.2019.135660] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/25/2019] [Revised: 11/18/2019] [Accepted: 11/19/2019] [Indexed: 06/10/2023]
Abstract
The role of microbial processes in bioaccumulation of major and trace elements has been broadly demonstrated. However, microbial communities from marine sediments have been poorly investigated to this regard. In marine environments, particularly under high anthropogenic pressure, heavy metal accumulation increases constantly, which may lead to significant environmental issues. A better knowledge of bacterial diversity and its capability to bioaccumulate metals is essential to face environmental quality assessment. The oligotrophic westernmost Mediterranean, which is highly sensitive to environmental changes and subjected to increasing anthropogenic pressure, was selected for this study. A sediment core spanning the last two millennia was sampled at two intervals, with ages corresponding to 140 (S1) and 1400 (S2) yr BP. High-throughput sequencing showed an abundance of Bacillus, Micrococcus, unclassified members of Planococcaceae, Anaerolineaceae, Planctomycetaceae, Microlunatus, and Microbacterium in both intervals, with slight differences in their abundance, along with newly detected ones in S2, i.e., Propionibacterium, Fictibacillus, Thalassobacillus, and Bacteroides. Canonical correspondence analysis (CCA) and co-occurrence patterns confirmed strong correlations among the taxa and the environmental parameters, suggesting either shared and preferred environmental conditions, or the performance of functions similar to or complementary to each other. These results were further confirmed using culture-dependent methods. The diversity of the culturable bacterial community revealed a predominance of Bacillus, and Micrococcus or Kocuria. The interaction of these bacterial communities with selected heavy metals (Cu, Cr, Zn and Pb) was also investigated, and their capacity of bioaccumulating metals within the cells and/or in the extracellular polymeric substances (EPS) is demonstrated. Interestingly, biomineralization of Pb resulted in the precipitation of Pb phosphates (pyromorphite). Our study supports that remnants of marine bacterial communities can survive in deep-sea sediments over thousands of years. This is extremely important in terms of bioremediation, in particular when considering possible environmentally friendly strategies to bioremediate inorganic contaminants.
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Affiliation(s)
- Fadwa Jroundi
- Department of Microbiology, Faculty of Science, University of Granada, Avda. Fuentenueva s/n, 18071 Granada, Spain.
| | - Francisca Martinez-Ruiz
- Instituto Andaluz de Ciencias de la Tierra (CSIC-UGR), Av. de las Palmeras 4, 18100 (Armilla) Granada, Spain.
| | - Mohamed L Merroun
- Department of Microbiology, Faculty of Science, University of Granada, Avda. Fuentenueva s/n, 18071 Granada, Spain.
| | - María Teresa Gonzalez-Muñoz
- Department of Microbiology, Faculty of Science, University of Granada, Avda. Fuentenueva s/n, 18071 Granada, Spain.
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6
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Kapili BJ, Barnett SE, Buckley DH, Dekas AE. Evidence for phylogenetically and catabolically diverse active diazotrophs in deep-sea sediment. ISME JOURNAL 2020; 14:971-983. [PMID: 31907368 PMCID: PMC7082343 DOI: 10.1038/s41396-019-0584-8] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/25/2019] [Revised: 12/16/2019] [Accepted: 12/19/2019] [Indexed: 12/18/2022]
Abstract
Diazotrophic microorganisms regulate marine productivity by alleviating nitrogen limitation. However, we know little about the identity and activity of diazotrophs in deep-sea sediments, a habitat covering nearly two-thirds of the planet. Here, we identify candidate diazotrophs from Pacific Ocean sediments collected at 2893 m water depth using 15N-DNA stable isotope probing and a novel pipeline for nifH sequence analysis. Together, these approaches detect an unexpectedly diverse assemblage of active diazotrophs, including members of the Acidobacteria, Firmicutes, Nitrospirae, Gammaproteobacteria, and Deltaproteobacteria. Deltaproteobacteria, predominately members of the Desulfobacterales and Desulfuromonadales, are the most abundant diazotrophs detected, and display the most microdiversity of associated nifH sequences. Some of the detected lineages, including those within the Acidobacteria, have not previously been shown to fix nitrogen. The diazotrophs appear catabolically diverse, with the potential for using oxygen, nitrogen, iron, sulfur, and carbon as terminal electron acceptors. Therefore, benthic diazotrophy may persist throughout a range of geochemical conditions and provide a stable source of fixed nitrogen over geologic timescales. Our results suggest that nitrogen-fixing communities in deep-sea sediments are phylogenetically and catabolically diverse, and open a new line of inquiry into the ecology and biogeochemical impacts of deep-sea microorganisms.
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Affiliation(s)
- Bennett J Kapili
- Department of Earth System Science, Stanford University, Stanford, CA, 94305, USA.
| | - Samuel E Barnett
- School of Integrative Plant Science, Cornell University, Ithaca, NY, 14853, USA
| | - Daniel H Buckley
- School of Integrative Plant Science, Cornell University, Ithaca, NY, 14853, USA
| | - Anne E Dekas
- Department of Earth System Science, Stanford University, Stanford, CA, 94305, USA.
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7
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Delacuvellerie A, Cyriaque V, Gobert S, Benali S, Wattiez R. The plastisphere in marine ecosystem hosts potential specific microbial degraders including Alcanivorax borkumensis as a key player for the low-density polyethylene degradation. JOURNAL OF HAZARDOUS MATERIALS 2019; 380:120899. [PMID: 31326835 DOI: 10.1016/j.jhazmat.2019.120899] [Citation(s) in RCA: 142] [Impact Index Per Article: 28.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/25/2018] [Revised: 07/12/2019] [Accepted: 07/13/2019] [Indexed: 05/20/2023]
Abstract
Most plastics are released to the environment in landfills and around 32% end up in the sea, inducing large ecological and health impacts. The plastics constitute a physical substrate and potential carbon source for microorganisms. The present study compares the structures of bacterial communities from floating plastics, sediment-associated plastics and sediments from the Mediterranean Sea. The 16S rRNA microbiome profiles of surface and sediment plastic-associated microbial biofilms from the same geographic location differ significantly, with the omnipresence of Bacteroidetes and Gammaproteobacteria. Our research confirmed that plastisphere hosts microbial communities were environmental distinct niche. In parallel, this study used environmental samples to investigate the enrichment of potential plastic-degrading bacteria with Low Density PolyEthylene (LDPE), PolyEthylene Terephthalate (PET) and PolyStyrene (PS) plastics as the sole carbon source. In this context, we showed that the bacterial community composition is clearly plastic nature dependent. Hydrocarbon-degrading bacteria such as Alcanivorax, Marinobacter and Arenibacter genera are enriched with LDPE and PET, implying that these bacteria are potential players in plastic degradation. Finally, our data showed for the first time the ability of Alcanivorax borkumensis to form thick biofilms specifically on LDPE and to degrade this petroleum-based plastic.
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Affiliation(s)
- Alice Delacuvellerie
- Proteomics and Microbiology Department, University of Mons, 20 place du Parc, 7000 Mons, Belgium
| | - Valentine Cyriaque
- Proteomics and Microbiology Department, University of Mons, 20 place du Parc, 7000 Mons, Belgium
| | - Sylvie Gobert
- Oceanology Department, University of Liège, 11 Allée du 6 août, 4000 Liège, Belgium
| | - Samira Benali
- Polymer and Composite Materials Department, University of Mons, 15 Avenue Maistriau, 7000 Mons, Belgium
| | - Ruddy Wattiez
- Proteomics and Microbiology Department, University of Mons, 20 place du Parc, 7000 Mons, Belgium.
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8
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Zhuang M, Sanganyado E, Li P, Liu W. Distribution of microbial communities in metal-contaminated nearshore sediment from Eastern Guangdong, China. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2019; 250:482-492. [PMID: 31026695 DOI: 10.1016/j.envpol.2019.04.041] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/14/2019] [Revised: 03/22/2019] [Accepted: 04/08/2019] [Indexed: 06/09/2023]
Abstract
Nearshore environments are a critical transitional zone that connects the marine and terrestrial/freshwater ecosystems. The release of anthropogenic chemicals into nearshore ecosystems pose a human and environmental health risk. We investigated the microbial diversity, abundance and function in metal-contaminated sediments collected from the Rongjiang, Hanjiang and Lianjiang River estuaries and adjacent coastal areas using high throughput sequencing. The concentration of nutrients (NO3-N, NO2-N, NH4-N, PO4-P) and metal (Cu, Zn, Cd, Pb, As, Hg) contaminants were higher at the mouth of the rivers compared to the coastal lines, and this was confirmed using cluster analysis. Estimates obtained using geoaccumulation index showed that about 38.9% of the sites were contaminated with Pb and the pollution load index showed that sediment from the mouth of Hanjiang River Estuary was moderately polluted with metals. In the nearshore sediment samples collected, Proteobacteria, Bacteroidetes, Planctomycetes, Chloroflexi, Acidobacteria were the dominant phylum with relative abundances of 46.6%, 8.05%, 6.47%, 5.26%, and 4.59%, respectively. There was no significant correlation between environmental variables and microbial abundance and diversity except for total organic carbon (TOC) (diversity; r = 0.569, p < 0.05) and Cr (diversity; r = 0.581, p < 0.05). At phyla level, Nitrospirae had a significant negative correlation with all metals except Cr, while OD1 had a significant positive correlation with all the metals. Overall, changes in nearshore sediment microbial communities by environmental factors were observed, and these may affect biogeochemical cycling.
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Affiliation(s)
- Mei Zhuang
- Marine Biology Institute, Shantou University, Shantou, Guangdong Province, China
| | - Edmond Sanganyado
- Marine Biology Institute, Shantou University, Shantou, Guangdong Province, China
| | - Ping Li
- Marine Biology Institute, Shantou University, Shantou, Guangdong Province, China
| | - Wenhua Liu
- Marine Biology Institute, Shantou University, Shantou, Guangdong Province, China.
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Dominance of Wolbachia sp. in the deep-sea sediment bacterial metataxonomic sequencing analysis in the Bay of Bengal, Indian Ocean. Genomics 2019; 112:1030-1041. [PMID: 31229556 DOI: 10.1016/j.ygeno.2019.06.019] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2018] [Revised: 05/24/2019] [Accepted: 06/17/2019] [Indexed: 11/23/2022]
Abstract
The Bay of Bengal, located in the north-eastern part of the Indian Ocean is world's largest bay occupying an area of ~8,39,000 mile2. The variability in bacterial community structure and function in sediment ecosystems of the Bay of Bengal is examined by Illumina high-throughput metagenomic sequencing. Of five metataxonomics data sets presented, two (SD1 and SD2) were from stations close to the shore and three (SD4, SD5, and SD6) were from the deep-sea (~3000 m depth). Phylum Proteobacteria (90.27 to 92.52%) dominated the deep-sea samples, whereas phylum Firmicutes (65.35 to 90.98%) dominated the coastal samples. Comparative analysis showed that coastal and deep-sea sediments showed distinct microbial communities. Wolbachia species, belonging to class Alphaproteobacteria was the most dominant species in the deep-sea sediments. The gene functions of bacterial communities were predicted for deep-sea and coastal sediment ecosystems. The results indicated that deep-sea sediment bacterial communities were involved in metabolic activities like dehalogenation and sulphide oxidation.
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10
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van de Kamp J, Hook SE, Williams A, Tanner JE, Bodrossy L. Baseline characterization of aerobic hydrocarbon degrading microbial communities in deep-sea sediments of the Great Australian Bight, Australia. Environ Microbiol 2019; 21:1782-1797. [PMID: 30761716 DOI: 10.1111/1462-2920.14559] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2018] [Revised: 01/28/2019] [Accepted: 02/07/2019] [Indexed: 11/30/2022]
Abstract
Exploratory drilling for deep-sea oil and gas resources is planned for the Great Australian Bight (GAB). There is scant knowledge of the region's benthic ecosystems and no baseline information of the region's indigenous oil degrading bacteria. To address this knowledge gap, we used next generation sequencing (NGS) of three marker genes (alkB, c23o and pmoA) to detect and characterize the microbial communities capable of aerobic hydrocarbon degradation. Unique, highly novel microbial communities capable of degrading hydrocarbons occur in surface sediments at depths between 200 and 2800 m. Clustering at 97% demonstrated differences in community structure with depth, changing most markedly between 400 and 1000 m depth on the continental slope, and identified putative functional 'ecotypes' related to depth. Observed differences in community structure showed strong correlations with temperature, other physicochemical properties of the overlying water column and are further modulated by differences in sediment grain size. This study provides important baseline data on hydrocarbon degrading microbial communities prior to the start of petroleum resource extraction. Our data will inform future ecological monitoring of the GAB deep-sea ecosystem.
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Affiliation(s)
- Jodie van de Kamp
- Oceans and Atmosphere, Commonwealth Scientific and Industrial Research Organisation, Hobart, Tasmania, 7000, Australia
| | - Sharon E Hook
- Oceans and Atmosphere, Commonwealth Scientific and Industrial Research Organisation, Lucas Heights, New South Wales, 2234, Australia
| | - Alan Williams
- Oceans and Atmosphere, Commonwealth Scientific and Industrial Research Organisation, Hobart, Tasmania, 7000, Australia
| | - Jason E Tanner
- Aquatic Sciences, South Australian Research and Development Institute, West Beach, South Australia, 5024, Australia
| | - Levente Bodrossy
- Oceans and Atmosphere, Commonwealth Scientific and Industrial Research Organisation, Hobart, Tasmania, 7000, Australia
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11
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Mandalakis M, Gavriilidou A, Polymenakou PN, Christakis CA, Nomikou P, Medvecký M, Kilias SP, Kentouri M, Kotoulas G, Magoulas A. Microbial strains isolated from CO 2-venting Kolumbo submarine volcano show enhanced co-tolerance to acidity and antibiotics. MARINE ENVIRONMENTAL RESEARCH 2019; 144:102-110. [PMID: 30654982 DOI: 10.1016/j.marenvres.2019.01.002] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/29/2018] [Revised: 12/31/2018] [Accepted: 01/03/2019] [Indexed: 06/09/2023]
Abstract
As ocean acidification intensifies, there is growing global concern about the impacts that future pH levels are likely to have on marine life and ecosystems. By analogy, a steep decrease of seawater pH with depth is encountered inside the Kolumbo submarine volcano (northeast Santorini) as a result of natural CO2 venting, making this system ideal for ocean acidification research. Here, we investigated whether the increase of acidity towards deeper layers of Kolumbo crater had any effect on relevant phenotypic traits of bacterial isolates. A total of 31 Pseudomonas strains were isolated from both surface- (SSL) and deep-seawater layers (DSL), with the latter presenting a significantly higher acid tolerance. In particular, the DSL strains were able to cope with H+ levels that were 18 times higher. Similarly, the DSL isolates exhibited a significantly higher tolerance than SSL strains against six commonly used antibiotics and As(III). More importantly, a significant positive correlation was revealed between antibiotics and acid tolerance across the entire set of SSL and DSL isolates. Our findings imply that Pseudomonas species with higher resilience to antibiotics could be favored by the prospect of acidifying oceans. Further studies are required to determine if this feature is universal across marine bacteria and to assess potential ecological impacts.
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Affiliation(s)
- Manolis Mandalakis
- Institute of Marine Biology, Biotechnology and Aquaculture, Hellenic Centre for Marine Research, 71500, Heraklion, Greece.
| | - Asimenia Gavriilidou
- Institute of Marine Biology, Biotechnology and Aquaculture, Hellenic Centre for Marine Research, 71500, Heraklion, Greece
| | - Paraskevi N Polymenakou
- Institute of Marine Biology, Biotechnology and Aquaculture, Hellenic Centre for Marine Research, 71500, Heraklion, Greece
| | - Christos A Christakis
- Institute of Marine Biology, Biotechnology and Aquaculture, Hellenic Centre for Marine Research, 71500, Heraklion, Greece
| | - Paraskevi Nomikou
- Faculty of Geology and Geoenvironment, National and Kapodistrian University of Athens, Panepistimioupoli Zographou, 15784, Athens, Greece
| | - Matej Medvecký
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, 61137, Brno, Czech Republic; Veterinary Research Institute, 62100, Brno, Czech Republic
| | - Stephanos P Kilias
- Faculty of Geology and Geoenvironment, National and Kapodistrian University of Athens, Panepistimioupoli Zographou, 15784, Athens, Greece
| | - Maroudio Kentouri
- Department of Biology, University of Crete, 70013, Heraklion, Greece
| | - Georgios Kotoulas
- Institute of Marine Biology, Biotechnology and Aquaculture, Hellenic Centre for Marine Research, 71500, Heraklion, Greece
| | - Antonios Magoulas
- Institute of Marine Biology, Biotechnology and Aquaculture, Hellenic Centre for Marine Research, 71500, Heraklion, Greece
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12
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Wang S, Yu M, Wei J, Huang M, Shi X, Chen H. Microbial community composition and diversity in the Indian Ocean deep sea REY-rich muds. PLoS One 2018; 13:e0208230. [PMID: 30557300 PMCID: PMC6296507 DOI: 10.1371/journal.pone.0208230] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2017] [Accepted: 11/14/2018] [Indexed: 01/22/2023] Open
Abstract
Studies about the composition and diversity of microbial community in the Rare Earth Elements-rich muds are limited. In this research, we conducted a characterization for the composition and diversity of bacterial and archaeal communities from rare earth elements-rich gravity core sediment at approximately 4800 meters deep in the Indian Ocean by Illumina high-throughput sequencing targeting 16S rRNA genes. The results showed that the most abundant bacteria were Proteobacteria, followed by Firmicutes and Actinobacteria. Amongst Proteobacteria, Gammaproteobacteria are present in all sections of this sediment core accounted for a particularly large proportion of bacterial sequences. Candidatus Nitrosopumilus, with a higher relative abundance in our samples, belongs to Thaumarchaeota. This is the first report on the composition and diversity of rare earth elements-rich muds microbial communities in the Indian Ocean deep sea.
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Affiliation(s)
- Shuyan Wang
- Key Lab of Marine Bioactive Substances of SOA, The First Institute of Oceanography, Qingdao, China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
- Qingdao Key Lab of Marine Natural Products R&D, Qingdao, China
| | - Miao Yu
- Laboratory for Marine Geology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Jiaqiang Wei
- Key Lab of Marine Bioactive Substances of SOA, The First Institute of Oceanography, Qingdao, China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
- Qingdao Key Lab of Marine Natural Products R&D, Qingdao, China
| | - Mu Huang
- Laboratory for Marine Geology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Xuefa Shi
- Laboratory for Marine Geology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Hao Chen
- Key Lab of Marine Bioactive Substances of SOA, The First Institute of Oceanography, Qingdao, China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
- Qingdao Key Lab of Marine Natural Products R&D, Qingdao, China
- * E-mail:
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13
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Johny TK, Saidumohamed BE, Sasidharan RS, Bhat SG. Inferences of gut bacterial diversity from next-generation sequencing of 16S rDNA in deep sea blind ray - Benthobatis moresbyi. ACTA ACUST UNITED AC 2018. [DOI: 10.1016/j.egg.2018.07.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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14
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Edrada-Ebel R, Ævarsson A, Polymenakou P, Hentschel U, Carettoni D, Day J, Green D, Hreggviðsson GÓ, Harvey L, McNeil B. SeaBioTech: From Seabed to Test-Bed: Harvesting the Potential of Marine Biodiversity for Industrial Biotechnology. GRAND CHALLENGES IN MARINE BIOTECHNOLOGY 2018. [DOI: 10.1007/978-3-319-69075-9_12] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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15
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Hornick KM, Buschmann AH. Insights into the diversity and metabolic function of bacterial communities in sediments from Chilean salmon aquaculture sites. ANN MICROBIOL 2017. [DOI: 10.1007/s13213-017-1317-8] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
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16
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Rivas-Marín E, Devos DP. The Paradigms They Are a-Changin': past, present and future of PVC bacteria research. Antonie van Leeuwenhoek 2017; 111:785-799. [PMID: 29058138 PMCID: PMC5945725 DOI: 10.1007/s10482-017-0962-z] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/16/2017] [Accepted: 10/10/2017] [Indexed: 11/22/2022]
Abstract
These are exciting times for PVC researchers! The PVC superphylum is composed of the bacterial phyla Planctomycetes, Verrucomicrobia, Chlamydiae (those three founders giving it its name), Lentisphaerae and Kirimatiellaeota as well as some uncultured candidate phyla, such as the Candidatus Omnitrophica (previously known as OP3). Despite early debates, most of the disagreements that surround this group of bacteria have been recently resolved. In this article, we review the history of the study of PVC bacteria, with a particular focus on the misinterpretations that emerged early in the field and their resolution. We begin with a historical perspective that describes the relevant facts of PVC research from the early times when they were not yet termed PVC. Those were controversial times and we refer to them as the “discovery age” of the field. We continue by describing new discoveries due to novel techniques and data that combined with the reinterpretations of old ones have contributed to solve most of the discordances and we refer to these times as the “illumination age” of PVC research. We follow by arguing that we are just entering the “golden age” of PVC research and that the future of this growing community is looking bright. We finish by suggesting a few of the directions that PVC researches might take in the future.
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Affiliation(s)
- Elena Rivas-Marín
- Centro Andaluz de Biología del Desarrollo (CABD)-CSIC, University Pablo de Olavide, Carretera Utrera, km 1, 41013, Seville, Spain
| | - Damien P Devos
- Centro Andaluz de Biología del Desarrollo (CABD)-CSIC, University Pablo de Olavide, Carretera Utrera, km 1, 41013, Seville, Spain.
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17
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Li Y, Wu C, Zhou M, Wang ET, Zhang Z, Liu W, Ning J, Xie Z. Diversity of Cultivable Protease-Producing Bacteria in Laizhou Bay Sediments, Bohai Sea, China. Front Microbiol 2017; 8:405. [PMID: 28360893 PMCID: PMC5352678 DOI: 10.3389/fmicb.2017.00405] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2016] [Accepted: 02/27/2017] [Indexed: 11/13/2022] Open
Abstract
Protease-producing bacteria are widespread in ocean sediments and play important roles in degrading sedimentary nitrogenous organic materials. However, the diversity of the bacteria and the proteases involved in such processes remain largely unknown especially for communities in enclosed sea bays. Here, we investigated the diversity of the extracellular protease-producing bacteria and their protease types in Laizhou Bay. A total of 121 bacterial isolates were obtained from sediment samples in 7 sites and their protease types were characterized. The abundance of cultivable protease-producing bacteria was about 104 CFU g-1 of sediment. Phylogenetic analysis based on 16S rRNA gene sequences suggest that the isolates belonged to 17 genera from 4 phyla including Firmicutes, Actinobacteria, Proteobacteria and Bacteroidetes, and mainly dominated by the genera Pseudoalteromonas (40.5%), Bacillus (36.3%), and Photobacterium (5.8%). The diversity and community structure varied among different sampling sites but no significant correlation was observed with soil sediment's characteristics. Enzyme activity and inhibition tests further revealed that all isolates secreted proteases that were inhibited by serine and/or metalloprotease inhibitors, and a smaller proportion was inhibited by inhibitors of cysteine and/or aspartic proteases. Furthermore, all isolates effectively degraded casein and/or gelatin with only a few that could hydrolyze elastin, suggesting that the bacteria were producing different kinds of serine proteases or metalloproteases. This study provided novel insights on the community structure of cultivable protease-producing bacteria near the Yellow River estuary of an enclosed sea bay.
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Affiliation(s)
- Yan Li
- Key Laboratory of Coastal Biology and Utilization, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences Yantai, China
| | - Chaoya Wu
- Key Laboratory of Coastal Biology and Utilization, Yantai Institute of Coastal Zone Research, Chinese Academy of SciencesYantai, China; School of Chemical and Biological Engineering, Lanzhou Jiaotong UniversityLanzhou, China
| | - Mingyang Zhou
- School of Chemistry and Pharmaceutical Engineering, Qilu University of Technology Jinan, China
| | - En Tao Wang
- Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional Mexico City, Mexico
| | - Zhenpeng Zhang
- Key Laboratory of Coastal Biology and Utilization, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences Yantai, China
| | - Wei Liu
- Key Laboratory of Coastal Biology and Utilization, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences Yantai, China
| | - Jicai Ning
- Key Laboratory of Coastal Biology and Utilization, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences Yantai, China
| | - Zhihong Xie
- Key Laboratory of Coastal Biology and Utilization, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences Yantai, China
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18
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Fehr AGJ, Ruetten M, Seth-Smith HMB, Nufer L, Voegtlin A, Lehner A, Greub G, Crosier PS, Neuhauss SCF, Vaughan L. A Zebrafish Model for Chlamydia Infection with the Obligate Intracellular Pathogen Waddlia chondrophila. Front Microbiol 2016; 7:1829. [PMID: 27917158 PMCID: PMC5114312 DOI: 10.3389/fmicb.2016.01829] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2016] [Accepted: 11/01/2016] [Indexed: 01/22/2023] Open
Abstract
Obligate intracellular chlamydial bacteria of the Planctomycetes-Verrucomicrobia-Chlamydiae (PVC) superphylum are important pathogens of terrestrial and marine vertebrates, yet many features of their pathogenesis and host specificity are still unknown. This is particularly true for families such as the Waddliacea which, in addition to epithelia, cellular targets for nearly all Chlamydia, can infect and replicate in macrophages, an important arm of the innate immune system or in their free-living amoebal counterparts. An ideal pathogen model system should include both host and pathogen, which led us to develop the first larval zebrafish model for chlamydial infections with Waddlia chondrophila. By varying the means and sites of application, epithelial cells of the swim bladder, endothelial cells of the vasculature and phagocytosing cells of the innate immune system became preferred targets for infection in zebrafish larvae. Through the use of transgenic zebrafish, we could observe recruitment of neutrophils to the infection site and demonstrate for the first time that W. chondrophila is taken up and replicates in these phagocytic cells and not only in macrophages. Furthermore, we present evidence that myeloid differentiation factor 88 (MyD88) mediated signaling plays a role in the innate immune reaction to W. chondrophila, eventually by Toll-like receptor (TLRs) recognition. Infected larvae with depleted levels of MyD88 showed a higher infection load and a lower survival rate compared to control fish. This work presents a new and potentially powerful non-mammalian experimental model to study the pathology of chlamydial virulence in vivo and opens up new possibilities for investigation of other members of the PVC superphylum.
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Affiliation(s)
- Alexander G J Fehr
- Vetsuisse Faculty, Institute for Veterinary Pathology, University of Zurich Zurich, Switzerland
| | - Maja Ruetten
- Vetsuisse Faculty, Institute for Veterinary Pathology, University of Zurich Zurich, Switzerland
| | - Helena M B Seth-Smith
- Vetsuisse Faculty, Institute for Veterinary Pathology, University of ZurichZurich, Switzerland; Functional Genomics Center Zurich, Molecular and Life Sciences, University of ZurichZurich, Switzerland
| | - Lisbeth Nufer
- Vetsuisse Faculty, Institute for Veterinary Pathology, University of Zurich Zurich, Switzerland
| | - Andrea Voegtlin
- Vetsuisse Faculty, Institute of Veterinary Bacteriology, University of Zurich Zurich, Switzerland
| | - Angelika Lehner
- Vetsuisse Faculty, Institute for Food Safety and Hygiene, University of Zurich Zurich, Switzerland
| | - Gilbert Greub
- Institute of Microbiology, University Hospital Center and University of Lausanne Lausanne, Switzerland
| | - Philip S Crosier
- Department of Molecular Medicine and Pathology, School of Medical Sciences, University of Auckland Auckland, New Zealand
| | | | - Lloyd Vaughan
- Vetsuisse Faculty, Institute for Veterinary Pathology, University of Zurich Zurich, Switzerland
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19
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Crespo-Medina M, Bowles MW, Samarkin VA, Hunter KS, Joye SB. Microbial diversity and activity in seafloor brine lake sediments (Alaminos Canyon block 601, Gulf of Mexico). GEOBIOLOGY 2016; 14:483-498. [PMID: 27444236 DOI: 10.1111/gbi.12185] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/25/2015] [Accepted: 03/07/2016] [Indexed: 06/06/2023]
Abstract
The microbial communities thriving in deep-sea brines are sustained largely by energy rich substrates supplied through active seepage. Geochemical, microbial activity, and microbial community composition data from different habitats at a Gulf of Mexico brine lake in Alaminos Canyon revealed habitat-linked variability in geochemistry that in turn drove patterns in microbial community composition and activity. The bottom of the brine lake was the most geochemically extreme (highest salinity and nutrient concentrations) habitat and its microbial community exhibited the highest diversity and richness indices. The habitat at the upper halocline of the lake hosted the highest rates of sulfate reduction and methane oxidation, and the largest inventories of dissolved inorganic carbon, particulate organic carbon, and hydrogen sulfide. Statistical analyses indicated a significant positive correlation between the bacterial and archaeal diversity in the bottom brine sample and NH4+ inventories. Other environmental factors with positive correlation with microbial diversity indices were DOC, H2 S, and DIC concentrations. The geochemical regime of different sites within this deep seafloor extreme environment exerts a clear selective force on microbial communities and on patterns of microbial activity.
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Affiliation(s)
- M Crespo-Medina
- Department of Marine Sciences, University of Georgia, Athens, GA, USA
| | - M W Bowles
- Department of Marine Sciences, University of Georgia, Athens, GA, USA
| | - V A Samarkin
- Department of Marine Sciences, University of Georgia, Athens, GA, USA
| | - K S Hunter
- Department of Marine Sciences, University of Georgia, Athens, GA, USA
| | - S B Joye
- Department of Marine Sciences, University of Georgia, Athens, GA, USA
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20
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Jokanović S, Huter A, Orlić S. Bacterial Diversity of the Boka Kotorska Bay. THE HANDBOOK OF ENVIRONMENTAL CHEMISTRY 2016. [DOI: 10.1007/698_2016_32] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/11/2023]
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21
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Yoo AY, Park JK. Isolation and characterization of a serine protease-producing marine bacterium Marinomonas arctica PT-1. Bioprocess Biosyst Eng 2015; 39:307-14. [DOI: 10.1007/s00449-015-1514-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2015] [Accepted: 11/24/2015] [Indexed: 10/22/2022]
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22
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Polymenakou PN, Christakis CA, Mandalakis M, Oulas A. Pyrosequencing analysis of microbial communities reveals dominant cosmopolitan phylotypes in deep-sea sediments of the eastern Mediterranean Sea. Res Microbiol 2015; 166:448-457. [PMID: 25908548 DOI: 10.1016/j.resmic.2015.03.005] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2014] [Revised: 01/22/2015] [Accepted: 03/23/2015] [Indexed: 10/23/2022]
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23
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Anders H, Power JF, MacKenzie AD, Lagutin K, Vyssotski M, Hanssen E, Moreau JW, Stott MB. Limisphaera ngatamarikiensis gen. nov., sp. nov., a thermophilic, pink-pigmented coccus isolated from subaqueous mud of a geothermal hotspring. Int J Syst Evol Microbiol 2015; 65:1114-1121. [DOI: 10.1099/ijs.0.000063] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A novel bacterial strain, NGM72.4T, was isolated from a hot spring in the Ngatamariki geothermal field, New Zealand. Phylogenetic analysis based on 16S rRNA gene sequences grouped it into the phylum
Verrucomicrobia
and class level group 3 (also known as OPB35 soil group). NGM72.4T stained Gram-negative, and was catalase- and oxidase-positive. Cells were small cocci, 0.5–0.8 µm in diameter, which were motile by means of single flagella. Transmission electron micrograph (TEM) imaging showed an unusual pirellulosome-like intracytoplasmic membrane. The peptidoglycan content was very small with only trace levels of diaminopimelic acid detected. No peptidoglycan structure was visible in TEM imaging. The predominant isoprenoid quinone was MK-7 (92 %). The major fatty acids (>15 %) were C16 : 0, anteiso-C15 : 0, iso-C16 : 0 and anteiso-C17 : 0. Major phospholipids were phosphatidylethanolamine (PE), phosphatidylmonomethylethanolamine (PMME) and cardiolipin (CL), and a novel analogous series of phospholipids where diacylglycerol was replaced with diacylserinol (sPE, sPMME, sCL). The DNA G+C content was 65.6 mol%. Cells displayed an oxidative chemoheterotrophic metabolism. NGM72.4T is a strictly aerobic thermophile (growth optimum 60–65 °C), has a slightly alkaliphilic pH growth optimum (optimum pH 8.1–8.4) and has a NaCl tolerance of up to 8 g l−1. Colonies were small, circular and pigmented pale pink. The distinct phylogenetic position and phenotypic traits of strain NGM72.4T distinguish it from all other described species of the phylum
Verrucomicrobia
and, therefore, it is considered to represent a novel species in a new genus for which we propose the name Limisphaera ngatamarikiensis gen. nov., sp. nov. The type strain is NGM72.4T ( = ICMP 20182T = DSM 27329T).
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Affiliation(s)
- Heike Anders
- Lehrstuhl für Tierhygiene, Technische Universität München, Weihenstephaner Berg 3 0D-85354, Freising, Germany
- GNS Science, Extremophile Research Group, Private Bag 2000, Taupō 3352, New Zealand
| | - Jean F. Power
- GNS Science, Extremophile Research Group, Private Bag 2000, Taupō 3352, New Zealand
| | | | - Kirill Lagutin
- Callaghan Innovation, PO Box 31310, Lower Hutt 5040, New Zealand
| | | | - Eric Hanssen
- University of Melbourne, 30 Flemington Road, Victoria 3010, Australia
| | - John W. Moreau
- University of Melbourne, 30 Flemington Road, Victoria 3010, Australia
| | - Matthew B. Stott
- GNS Science, Extremophile Research Group, Private Bag 2000, Taupō 3352, New Zealand
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24
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Spatial scales of bacterial community diversity at cold seeps (Eastern Mediterranean Sea). ISME JOURNAL 2014; 9:1306-18. [PMID: 25500510 PMCID: PMC4438319 DOI: 10.1038/ismej.2014.217] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/28/2014] [Revised: 10/09/2014] [Accepted: 10/10/2014] [Indexed: 11/08/2022]
Abstract
Cold seeps are highly productive, fragmented marine ecosystems that form at the seafloor around hydrocarbon emission pathways. The products of microbial utilization of methane and other hydrocarbons fuel rich chemosynthetic communities at these sites, with much higher respiration rates compared with the surrounding deep-sea floor. Yet little is known as to the richness, composition and spatial scaling of bacterial communities of cold seeps compared with non-seep communities. Here we assessed the bacterial diversity across nine different cold seeps in the Eastern Mediterranean deep-sea and surrounding seafloor areas. Community similarity analyses were carried out based on automated ribosomal intergenic spacer analysis (ARISA) fingerprinting and high-throughput 454 tag sequencing and were combined with in situ and ex situ geochemical analyses across spatial scales of a few tens of meters to hundreds of kilometers. Seep communities were dominated by Deltaproteobacteria, Epsilonproteobacteria and Gammaproteobacteria and shared, on average, 36% of bacterial types (ARISA OTUs (operational taxonomic units)) with communities from nearby non-seep deep-sea sediments. Bacterial communities of seeps were significantly different from those of non-seep sediments. Within cold seep regions on spatial scales of only tens to hundreds of meters, the bacterial communities differed considerably, sharing <50% of types at the ARISA OTU level. Their variations reflected differences in porewater sulfide concentrations from anaerobic degradation of hydrocarbons. This study shows that cold seep ecosystems contribute substantially to the microbial diversity of the deep-sea.
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25
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Mahmoudi N, Robeson MS, Castro HF, Fortney JL, Techtmann SM, Joyner DC, Paradis CJ, Pfiffner SM, Hazen TC. Microbial community composition and diversity in Caspian Sea sediments. FEMS Microbiol Ecol 2014; 91:1-11. [PMID: 25764536 PMCID: PMC4399438 DOI: 10.1093/femsec/fiu013] [Citation(s) in RCA: 54] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Abstract
The Caspian Sea is heavily polluted due to industrial and agricultural effluents as well as extraction of oil and gas reserves. Microbial communities can influence the fate of contaminants and nutrients. However, insight into the microbial ecology of the Caspian Sea significantly lags behind other marine systems. Here we describe microbial biomass, diversity and composition in sediments collected from three sampling stations in the Caspian Sea. Illumina sequencing of 16S rRNA genes revealed the presence of a number of known bacterial and archaeal heterotrophs suggesting that organic carbon is a primary factor shaping microbial communities. Surface sediments collected from bottom waters with low oxygen levels were dominated by Gammaproteobacteria while surface sediments collected from bottom waters under hypoxic conditions were dominated by Deltaproteobacteria, specifically sulfate-reducing bacteria. Thaumarchaeota was dominant across all surface sediments indicating that nitrogen cycling in this system is strongly influenced by ammonia-oxidizing archaea. This study provides a baseline assessment that may serve as a point of reference as this system changes or as the efficacy of new remediation efforts are implemented. This study describes microbial biomass, community composition and diversity in Caspian Sea sediments using lipid and genomic techniques.
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Affiliation(s)
- Nagissa Mahmoudi
- Department of Civil and Environmental Engineering, University of Tennessee, 37996-2313 Knoxville, TN Center for Environmental Biotechnology, University of Tennessee, 37996-1605 Knoxville, TN
| | - Michael S Robeson
- BioSciences Division, Oak Ridge National Laboratory, 37831-6038 Oak Ridge, TN
| | - Hector F Castro
- Department of Chemistry, University of Tennessee, 37996-1600 Knoxville, TN
| | - Julian L Fortney
- Department of Civil and Environmental Engineering, University of Tennessee, 37996-2313 Knoxville, TN Center for Environmental Biotechnology, University of Tennessee, 37996-1605 Knoxville, TN
| | - Stephen M Techtmann
- Department of Civil and Environmental Engineering, University of Tennessee, 37996-2313 Knoxville, TN Center for Environmental Biotechnology, University of Tennessee, 37996-1605 Knoxville, TN
| | - Dominique C Joyner
- Department of Civil and Environmental Engineering, University of Tennessee, 37996-2313 Knoxville, TN Center for Environmental Biotechnology, University of Tennessee, 37996-1605 Knoxville, TN
| | - Charles J Paradis
- Department of Earth and Planetary Sciences, University of Tennessee, 37996-1410 Knoxville, TN
| | - Susan M Pfiffner
- Center for Environmental Biotechnology, University of Tennessee, 37996-1605 Knoxville, TN
| | - Terry C Hazen
- Department of Civil and Environmental Engineering, University of Tennessee, 37996-2313 Knoxville, TN BioSciences Division, Oak Ridge National Laboratory, 37831-6038 Oak Ridge, TN Center for Environmental Biotechnology, University of Tennessee, 37996-1605 Knoxville, TN Department of Earth and Planetary Sciences, University of Tennessee, 37996-1410 Knoxville, TN Department of Microbiology, University of Tennessee, 37996-0845 Knoxville, TN
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26
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Oliveira V, Gomes NCM, Cleary DFR, Almeida A, Silva AMS, Simões MMQ, Silva H, Cunha Â. Halophyte plant colonization as a driver of the composition of bacterial communities in salt marshes chronically exposed to oil hydrocarbons. FEMS Microbiol Ecol 2014; 90:647-62. [PMID: 25204351 DOI: 10.1111/1574-6941.12425] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2014] [Revised: 08/08/2014] [Accepted: 08/31/2014] [Indexed: 12/29/2022] Open
Abstract
In this study, two molecular techniques [denaturing gradient gel electrophoresis (DGGE) and barcoded pyrosequencing] were used to evaluate the composition of bacterial communities in salt marsh microhabitats [bulk sediment and sediment surrounding the roots (rhizosphere) of Halimione portulacoides and Sarcocornia perennis ssp. perennis] that have been differentially affected by oil hydrocarbon (OH) pollution. Both DGGE and pyrosequencing revealed that bacterial composition is structured by microhabitat. Rhizosphere sediment from both plant species revealed enrichment of operational taxonomic units closely related to Acidimicrobiales, Myxococcales and Sphingomonadales. The in silico metagenome analyses suggest that homologous genes related to OH degradation appeared to be more frequent in both plant rhizospheres than in bulk sediment. In summary, this study suggests that halophyte plant colonization is an important driver of hydrocarbonoclastic bacterial community composition in estuarine environments, which can be exploited for in situ phytoremediation of OH in salt marsh environments.
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Affiliation(s)
- Vanessa Oliveira
- Department of Biology & Centre for Environmental and Marine Studies (CESAM), University of Aveiro, Campus Universitário de Santiago, Aveiro, Portugal
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27
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Diversity of marine microbes in a changing Mediterranean Sea. RENDICONTI LINCEI-SCIENZE FISICHE E NATURALI 2014. [DOI: 10.1007/s12210-014-0333-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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28
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Cruz A, Henriques I, Sousa ACA, Baptista I, Almeida A, Takahashi S, Tanabe S, Correia A, Suzuki S, Anselmo AM, Mendo S. A microcosm approach to evaluate the degradation of tributyltin (TBT) by Aeromonas molluscorum Av27 in estuarine sediments. ENVIRONMENTAL RESEARCH 2014; 132:430-437. [PMID: 24858283 DOI: 10.1016/j.envres.2014.04.031] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/28/2014] [Revised: 04/23/2014] [Accepted: 04/25/2014] [Indexed: 06/03/2023]
Abstract
Tributyltin (TBT) is a biocide extremely toxic to a wide range of organisms, which has been used for decades in antifouling paints. Despite its global ban in 2008, TBT is still a problem of great concern due to the high levels trapped in sediments. Aeromonas molluscorum Av27 is a TBT degrading bacterium that was isolated from an estuarine system. We investigated the ability and the role of this bacterium on TBT degradation in this estuarine system, using a microcosm approach in order to mimic environmental conditions. The experiment was established and followed for 150 days. Simultaneously, changes in the indigenous bacterial community structure were also investigated. The results revealed a maximum TBT degradation rate of 28% accompanied by the detection of the degradation products over time. Additionally, it was observed that TBT degradation was significantly enhanced by the presence of Av27. In addition a significantly higher TBT degradation occurred when the concentration of Av27 was higher. TBT degradation affected the bacterial community composition as revealed by the changes in the prevalence of Proteobacteria subdivisions, namely the increase of Deltaproteobacteria and the onset of Epsilonproteobacteria. However, the addition of Av27 strain did not affect the dominant phylotypes. Total bacterial number, bacterial biomass productivity, 16S rRNA gene and denaturing gradient gel electrophoresis (DGGE) analyses also indicated alterations on the bacterial community structure over time, with bacteria non-tolerant to pollutants increasing their representativeness, as, for instance, the increase of the number of Alphaproteobacteria clones from 6% in the beginning to 12% at the end of the experiment. The work herein presented confirms the potential of Av27 strain to be used in the decontamination of TBT-polluted environments.
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Affiliation(s)
- Andreia Cruz
- Departamento de Biologia & CESAM, Universidade de Aveiro, Campus Universitário de Santiago, 3810-193 Aveiro, Portugal.
| | - Isabel Henriques
- Departamento de Biologia & CESAM, Universidade de Aveiro, Campus Universitário de Santiago, 3810-193 Aveiro, Portugal
| | - Ana C A Sousa
- Departamento de Biologia & CESAM, Universidade de Aveiro, Campus Universitário de Santiago, 3810-193 Aveiro, Portugal
| | - Inês Baptista
- Departamento de Biologia & CESAM, Universidade de Aveiro, Campus Universitário de Santiago, 3810-193 Aveiro, Portugal
| | - Adelaide Almeida
- Departamento de Biologia & CESAM, Universidade de Aveiro, Campus Universitário de Santiago, 3810-193 Aveiro, Portugal
| | - Shin Takahashi
- Center for Marine Environmental Studies (CMES), Ehime University, Matsuyama 790-8577, Japan
| | - Shinsuke Tanabe
- Center for Marine Environmental Studies (CMES), Ehime University, Matsuyama 790-8577, Japan
| | - António Correia
- Departamento de Biologia & CESAM, Universidade de Aveiro, Campus Universitário de Santiago, 3810-193 Aveiro, Portugal
| | - Satoru Suzuki
- Center for Marine Environmental Studies (CMES), Ehime University, Matsuyama 790-8577, Japan
| | - Ana Maria Anselmo
- Laboratório Nacional de Energia e Geologia, Unidade de Bioenergia, Estrada da Portela, Bairro do Zambujal, Apartado 7586-Alfragide, 2610-999 Amadora, Portugal
| | - Sónia Mendo
- Departamento de Biologia & CESAM, Universidade de Aveiro, Campus Universitário de Santiago, 3810-193 Aveiro, Portugal
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Kunihiro T, Veuger B, Vasquez-Cardenas D, Pozzato L, Le Guitton M, Moriya K, Kuwae M, Omori K, Boschker HTS, van Oevelen D. Phospholipid-derived fatty acids and quinones as markers for bacterial biomass and community structure in marine sediments. PLoS One 2014; 9:e96219. [PMID: 24769853 PMCID: PMC4000199 DOI: 10.1371/journal.pone.0096219] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2013] [Accepted: 04/04/2014] [Indexed: 11/18/2022] Open
Abstract
Phospholipid-derived fatty acids (PLFA) and respiratory quinones (RQ) are microbial compounds that have been utilized as biomarkers to quantify bacterial biomass and to characterize microbial community structure in sediments, waters, and soils. While PLFAs have been widely used as quantitative bacterial biomarkers in marine sediments, applications of quinone analysis in marine sediments are very limited. In this study, we investigated the relation between both groups of bacterial biomarkers in a broad range of marine sediments from the intertidal zone to the deep sea. We found a good log-log correlation between concentrations of bacterial PLFA and RQ over several orders of magnitude. This relationship is probably due to metabolic variation in quinone concentrations in bacterial cells in different environments, whereas PLFA concentrations are relatively stable under different conditions. We also found a good agreement in the community structure classifications based on the bacterial PLFAs and RQs. These results strengthen the application of both compounds as quantitative bacterial biomarkers. Moreover, the bacterial PLFA- and RQ profiles revealed a comparable dissimilarity pattern of the sampled sediments, but with a higher level of dissimilarity for the RQs. This means that the quinone method has a higher resolution for resolving differences in bacterial community composition. Combining PLFA and quinone analysis as a complementary method is a good strategy to yield higher resolving power in bacterial community structure.
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Affiliation(s)
- Tadao Kunihiro
- Department of Ecosystem Studies, Royal Netherlands Institute of Sea Research (NIOZ), Yerseke, The Netherlands
- Department of Marine Microbiology, Royal Netherlands Institute of Sea Research (NIOZ), Yerseke, The Netherlands
- * E-mail:
| | - Bart Veuger
- Department of Ecosystem Studies, Royal Netherlands Institute of Sea Research (NIOZ), Yerseke, The Netherlands
| | - Diana Vasquez-Cardenas
- Department of Ecosystem Studies, Royal Netherlands Institute of Sea Research (NIOZ), Yerseke, The Netherlands
- Department of Marine Microbiology, Royal Netherlands Institute of Sea Research (NIOZ), Yerseke, The Netherlands
| | - Lara Pozzato
- Department of Ecosystem Studies, Royal Netherlands Institute of Sea Research (NIOZ), Yerseke, The Netherlands
| | - Marie Le Guitton
- Department of Ecosystem Studies, Royal Netherlands Institute of Sea Research (NIOZ), Yerseke, The Netherlands
| | - Kazuyoshi Moriya
- School of Natural Science & Technology, Kanazawa University, Kakuma-machi, Kanazawa, Japan
| | - Michinobu Kuwae
- Center for Marine Environmental Studies (CMES), Ehime University, Matsuyama, Ehime, Japan
| | - Koji Omori
- Center for Marine Environmental Studies (CMES), Ehime University, Matsuyama, Ehime, Japan
| | - Henricus T. S. Boschker
- Department of Marine Microbiology, Royal Netherlands Institute of Sea Research (NIOZ), Yerseke, The Netherlands
| | - Dick van Oevelen
- Department of Ecosystem Studies, Royal Netherlands Institute of Sea Research (NIOZ), Yerseke, The Netherlands
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Effect of copper exposure on bacterial community structure and function in the sediments of Jiaozhou Bay, China. World J Microbiol Biotechnol 2014; 30:2033-43. [DOI: 10.1007/s11274-014-1628-x] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2013] [Accepted: 02/24/2014] [Indexed: 11/26/2022]
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Diversity of both the cultivable protease-producing bacteria and bacterial extracellular proteases in the coastal sediments of King George Island, Antarctica. PLoS One 2013; 8:e79668. [PMID: 24223990 PMCID: PMC3817139 DOI: 10.1371/journal.pone.0079668] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2013] [Accepted: 09/23/2013] [Indexed: 11/22/2022] Open
Abstract
Protease-producing bacteria play a vital role in degrading sedimentary organic nitrogen. However, the diversity of these bacteria and their extracellular proteases in most regions remain unknown. In this paper, the diversity of the cultivable protease-producing bacteria and of bacterial extracellular proteases in the sediments of Maxwell Bay, King George Island, Antarctica was investigated. The cultivable protease-producing bacteria reached 105 cells/g in all 8 sediment samples. The cultivated protease-producing bacteria were mainly affiliated with the phyla Actinobacteria, Firmicutes, Bacteroidetes, and Proteobacteria, and the predominant genera were Bacillus (22.9%), Flavobacterium (21.0%) and Lacinutrix (16.2%). Among these strains, Pseudoalteromonas and Flavobacteria showed relatively high protease production. Inhibitor analysis showed that nearly all the extracellular proteases from the bacteria were serine proteases or metalloproteases. These results begin to address the diversity of protease-producing bacteria and bacterial extracellular proteases in the sediments of the Antarctic Sea.
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Li J, Li F, Yu S, Qin S, Wang G. Impacts of mariculture on the diversity of bacterial communities within intertidal sediments in the Northeast of China. MICROBIAL ECOLOGY 2013; 66:861-870. [PMID: 23963221 DOI: 10.1007/s00248-013-0272-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/01/2013] [Accepted: 07/24/2013] [Indexed: 06/02/2023]
Abstract
Mariculture is one of the major seafood supplies worldwide and has caused serious environmental concerns on the coastal zone. Its rapid development has been shown to disrupt the sediment ecosystems and thus influence the benthic bacterial communities. Bacterial diversity and community structure within both adjacent farms and non-cultured zones intertidal sediments along the coasts of Qinhuangdao and Dalian, China, were investigated using full-length 16S rRNA gene-based T-RFLP analyses and clone library construction. Richness and Shannon-Wiener index were significantly increased at sites adjacent the mariculture farm with mean values of 29 and 2.97 from peak profiles of T-RFLP result. Clustering analyses suggested that impacts of mariculture on bacterial diversity of sediment were significantly larger than those resulted from temporal and spatial scales. Upon comparisons of RFLP patterns from 602 clones from libraries of the selected five samples, 137 OTUs were retrieved. Members of γ- and δ-Proteobacteria, Bacilli, Flavobacteria, and Actinobacteria were recorded in all libraries. In addition, γ-Proteobacteria were dominant in all samples (21.7~45.0 %). Redundancy analysis revealed that the distribution of bacterial composition seemed to be determined by the variables of salinity, PO4 (3-)-P, NH4 (+)-N, and Chlorophyll a content. The phyla of γ-Proteobacteria, Clostridia, Flavobacteria, Bacilli, and Planctomycetes were principal components to contribute to the bacterial differences of clone libraries. Our finding demonstrated that these phyla could display variations of bacterial composition linked to environmental disturbance resulted from mariculture.
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Affiliation(s)
- Jialin Li
- Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, 264003, China
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Zhu D, Tanabe SH, Yang C, Zhang W, Sun J. Bacterial community composition of South China Sea sediments through pyrosequencing-based analysis of 16S rRNA genes. PLoS One 2013; 8:e78501. [PMID: 24205246 PMCID: PMC3804488 DOI: 10.1371/journal.pone.0078501] [Citation(s) in RCA: 61] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2013] [Accepted: 09/14/2013] [Indexed: 01/12/2023] Open
Abstract
Background Subseafloor sediments accumulate large amounts of organic and inorganic materials that contain a highly diverse microbial ecosystem. The aim of this study was to survey the bacterial community of subseafloor sediments from the South China Sea. Methodology/Principal Findings Pyrosequencing of over 265,000 amplicons of the V3 hypervariable region of the 16S ribosomal RNA gene was performed on 16 sediment samples collected from multiple locations in the northern region of the South China Sea from depths ranging from 35 to 4000 m. A total of 9,726 operational taxonomic units (OTUs; between 695 and 2819 unique OTUs per sample) at 97% sequence similarity level were generated. In total, 40 bacterial phyla including 22 formally described phyla and 18 candidate phyla, with Proteobacteria, Firmicutes, Planctomycetes, Actinobacteria and Chloroflexi being most diverse, were identified. The most abundant phylotype, accounting for 42.6% of all sequences, belonged to Gammaproteobacteria, which possessed absolute predominance in the samples analyzed. Among the 18 candidate phyla, 12 were found for the first time in the South China Sea. Conclusions This study provided a novel insight into the composition of bacterial communities of the South China Sea subseafloor. Furthermore, abundances and community similarity analysis showed that the compositions of the bacterial communities are very similar at phylum level at different depths from 35-4000 m.
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Affiliation(s)
- Daochen Zhu
- School of Environmental Engineering, Jiangsu University, Zhenjiang, Jiangsu, China
- State Key Laboratory of Applied Microbiology in South China (Ministry-Guangdong Province Jointly Breeding Base), Guangdong Institute of Microbiology, Guangzhou, China
- * E-mail: (DZ); (WZ)
| | - Shoko-Hosoi Tanabe
- School of Environmental Science, University of Shiga Prefecture, Hikone, Shiga, Japan
| | - Chong Yang
- Department of R&D, Zhenjiang Bio-innova Biotech Co, Ltd., Zhenjiang, Jiangsu, China
| | - Weimin Zhang
- State Key Laboratory of Applied Microbiology in South China (Ministry-Guangdong Province Jointly Breeding Base), Guangdong Institute of Microbiology, Guangzhou, China
- * E-mail: (DZ); (WZ)
| | - Jianzhong Sun
- School of Environmental Engineering, Jiangsu University, Zhenjiang, Jiangsu, China
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Luna GM, Corinaldesi C, Rastelli E, Danovaro R. Patterns and drivers of bacterial α- and β-diversity across vertical profiles from surface to subsurface sediments. ENVIRONMENTAL MICROBIOLOGY REPORTS 2013; 5:731-739. [PMID: 24115624 DOI: 10.1111/1758-2229.12075] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2013] [Accepted: 06/08/2013] [Indexed: 06/02/2023]
Abstract
We investigated the patterns and drivers of bacterial α- and β-diversity, along with viral and prokaryotic abundance and the carbon production rates, in marine surface and subsurface sediments (down to 1 m depth) in two habitats: vegetated sediments (seagrass meadow) and non-vegetated sediments. Prokaryotic abundance and production decreased with depth in the sediment, but cell-specific production rates and the virus-to-prokaryote ratio increased, highlighting unexpectedly high activity in the subsurface. The highest diversity was observed in vegetated sediments. Bacterial β-diversity between sediment horizons was high, and only a minor number of taxa was shared between surface and subsurface layers. Viruses significantly contributed to explain α- and β-diversity patterns. Despite potential limitations due to the only use of fingerprinting techniques, this study indicates that the coastal subsurface host highly active and diversified bacterial assemblages, that subsurface cells are more active than expected and that viruses promote β-diversity and stimulate bacterial metabolism in subsurface layers. The limited number of taxa shared between habitats, and between surface and subsurface sediment horizons, suggests that future investigations of the shallow subsurface will provide insights into the census of bacterial diversity, and the comprehension of the patterns and drivers of prokaryotic diversity in marine ecosystems.
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Affiliation(s)
- Gian Marco Luna
- Institute of Marine Sciences (CNR - ISMAR), National Research Council, Castello 2737/f, Arsenale - Tesa 104, 30122, Venezia, Italy
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Krett G, Vágány V, Makk J, Jáger K, Reskóné MN, Márialigeti K, Borsodi AK. Phylogenetic diversity of bacterial communities inhabiting the sediment of Lake Hévíz - a comparison of cultivation and cloning. Acta Microbiol Immunol Hung 2013; 60:211-35. [PMID: 23827752 DOI: 10.1556/amicr.60.2013.2.11] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Lake Hévíz is the largest natural warm water lake of Europe. The curative mud of the lake comprises volcanic and marsh components although their species composition is hardly known yet. The aim of the present study was to gain information about the distribution and species diversity of bacterial communities inhabiting the sediment of Lake Hévíz using cultivation-based and molecular cloning methods. Samples from two depths and locations were taken in 2004 and 2007. Representatives of the altogether 255 bacterial isolates were affiliated with the phyla Firmicutes, Actinobacteria, Proteobacteria and Bacteroidetes. The most abundant groups belonged to the genus Bacillus (Firmicutes). Many of Lake Hévíz isolates showed the highest sequence similarity to bacteria known to be plant associated or members of normal human microbiota as well as participating in decomposition of highly resistant organic materials. In the three clone libraries, phylotypes belonging to altogether different phyla (Firmicutes, Actinobacteria, Proteobacteria, Bacteroidetes, Cyanobacteria, Chlorobi, Chloroflexi, Deferribacteres, Nitrospirae, Spirochaetes and Verrucomicrobia) were revealed from which members of Gammaproteobacteria and Cyanobacteria proved to be the most abundant. Regardless of the sampling times and methodology used, high spatial heterogeneities of bacterial community structures were characteristic of the sediment of Lake Hévíz.
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Affiliation(s)
- Gergely Krett
- Eötvös Loránd University, Department of Microbiology, H-1117 Budapest, Pázmány P. sétány 1/C, Hungary
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Garcias-Bonet N, Arrieta JM, de Santana CN, Duarte CM, Marbà N. Endophytic bacterial community of a Mediterranean marine angiosperm (Posidonia oceanica). Front Microbiol 2012; 3:342. [PMID: 23049528 PMCID: PMC3448135 DOI: 10.3389/fmicb.2012.00342] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2012] [Accepted: 09/04/2012] [Indexed: 11/24/2022] Open
Abstract
Bacterial endophytes are crucial for the survival of many terrestrial plants, but little is known about the presence and importance of bacterial endophytes of marine plants. We conducted a survey of the endophytic bacterial community of the long-living Mediterranean marine angiosperm Posidonia oceanica in surface-sterilized tissues (roots, rhizomes, and leaves) by Denaturing Gradient Gel Electrophoresis (DGGE). A total of 26 Posidonia oceanica meadows around the Balearic Islands were sampled, and the band patterns obtained for each meadow were compared for the three sampled tissues. Endophytic bacterial sequences were detected in most of the samples analyzed. A total of 34 OTUs (Operational Taxonomic Units) were detected. The main OTUs of endophytic bacteria present in P. oceanica tissues belonged primarily to Proteobacteria (α, γ, and δ subclasses) and Bacteroidetes. The OTUs found in roots significantly differed from those of rhizomes and leaves. Moreover, some OTUs were found to be associated to each type of tissue. Bipartite network analysis revealed differences in the bacterial endophyte communities present on different islands. The results of this study provide a pioneering step toward the characterization of the endophytic bacterial community associated with tissues of a marine angiosperm and reveal the presence of bacterial endophytes that differed among locations and tissue types.
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Akoumianaki I, Nomaki H, Pachiadaki M, Kormas KA, Kitazato H, Tokuyama H. Low bacterial diversity and high labile organic matter concentrations in the sediments of the Medee deep-sea hypersaline anoxic basin. Microbes Environ 2012; 27:504-8. [PMID: 22504432 PMCID: PMC4103561 DOI: 10.1264/jsme2.me12045] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Studies in the center and margin of the Medee Basin, a Mediterranean deep-sea hypersaline anoxic basin, and at a reference site during Penelope cruise (2007), revealed the existence of a 7 m-thick halocline, with high salinity (328 psu), and high sedimentary organic carbon and biopolymer concentrations. The 194 16S rRNA sequences retrieved were grouped into 118 unique phylotypes. Pseudomonas gessardii, dominated in the center, while 33 phylotypes were detected at the margin and 73 at the reference site. The study suggested conditions hostile to bacteria in the sediments of the Medee Basin and preservation of sedimentary labile organic matter.
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Affiliation(s)
- Ioanna Akoumianaki
- Institute of Oceanography, Hellenic Centre for Marine Research, Anavissos 19013, Attiki, Greece
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38
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Bellou N, Papathanassiou E, Dobretsov S, Lykousis V, Colijn F. The effect of substratum type, orientation and depth on the development of bacterial deep-sea biofilm communities grown on artificial substrata deployed in the Eastern Mediterranean. BIOFOULING 2012; 28:199-213. [PMID: 22352335 DOI: 10.1080/08927014.2012.662675] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
An increasing number of deep-sea studies have highlighted the importance of deep-sea biofouling, especially in relation to the protection of deep-sea instruments. In this study, the microbial communities developed on different substrata (titanium, aluminum, limestone, shale and neutrino telescope glass) exposed for 155 days at different depths (1500 m, 2500 m, 3500 m and 4500 m) and positions (vertical and horizontal) in the Eastern Mediterranean Deep Sea were compared. Replicated biofilm samples were analyzed using a Terminal Restriction Fragment Length Polymorphisms (T-RFLP) method. The restriction enzymes CfoI and RsaI produced similar total numbers (94, 93) of different T-RFLP peaks (T-RFs) along the vertical transect. In contrast, the mean total T-RF number between each sample according to substratum type and depth was higher in more samples when CfoI was used. The total species richness (S) of the bacterial communities differed significantly between the substrata, and depended on the orientation of each substratum within one depth and throughout the water column (ANOVA). T-RFLP analyses using the Jaccard similarity index showed that within one depth layer, the composition of microbial communities on different substrata was different and highly altered among communities developed on the same substratum but exposed to fouling at different depths. Based on Multidimensional Scaling Analyses (MDS), the study suggests that depth plays an important role in the composition of deep-sea biofouling communities, while substratum type and orientation of substrata throughout the water column are less important. To the authors' knowledge, this is the first study of biofilm development in deep waters, in relation to the effects of substratum type, orientation and depth.
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Affiliation(s)
- Nikoleta Bellou
- Hellenic Centre for Marine Research, Institute of Oceanography, Athens, Greece.
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Liao L, Xu XW, Jiang XW, Wang CS, Zhang DS, Ni JY, Wu M. Microbial diversity in deep-sea sediment from the cobalt-rich crust deposit region in the Pacific Ocean. FEMS Microbiol Ecol 2011; 78:565-85. [DOI: 10.1111/j.1574-6941.2011.01186.x] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2010] [Revised: 07/04/2011] [Accepted: 08/14/2011] [Indexed: 11/26/2022] Open
Affiliation(s)
- Li Liao
- College of Life Sciences; Zhejiang University; Hangzhou; China
| | | | - Xia-Wei Jiang
- College of Life Sciences; Zhejiang University; Hangzhou; China
| | | | | | | | - Min Wu
- College of Life Sciences; Zhejiang University; Hangzhou; China
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40
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Orcutt BN, Sylvan JB, Knab NJ, Edwards KJ. Microbial ecology of the dark ocean above, at, and below the seafloor. Microbiol Mol Biol Rev 2011; 75:361-422. [PMID: 21646433 PMCID: PMC3122624 DOI: 10.1128/mmbr.00039-10] [Citation(s) in RCA: 324] [Impact Index Per Article: 24.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
The majority of life on Earth--notably, microbial life--occurs in places that do not receive sunlight, with the habitats of the oceans being the largest of these reservoirs. Sunlight penetrates only a few tens to hundreds of meters into the ocean, resulting in large-scale microbial ecosystems that function in the dark. Our knowledge of microbial processes in the dark ocean-the aphotic pelagic ocean, sediments, oceanic crust, hydrothermal vents, etc.-has increased substantially in recent decades. Studies that try to decipher the activity of microorganisms in the dark ocean, where we cannot easily observe them, are yielding paradigm-shifting discoveries that are fundamentally changing our understanding of the role of the dark ocean in the global Earth system and its biogeochemical cycles. New generations of researchers and experimental tools have emerged, in the last decade in particular, owing to dedicated research programs to explore the dark ocean biosphere. This review focuses on our current understanding of microbiology in the dark ocean, outlining salient features of various habitats and discussing known and still unexplored types of microbial metabolism and their consequences in global biogeochemical cycling. We also focus on patterns of microbial diversity in the dark ocean and on processes and communities that are characteristic of the different habitats.
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Affiliation(s)
- Beth N. Orcutt
- Center for Geomicrobiology, Aarhus University, 8000 Aarhus, Denmark
- Marine Environmental Biology Section, Department of Biological Sciences, University of Southern California, Los Angeles, California 90089
| | - Jason B. Sylvan
- Marine Environmental Biology Section, Department of Biological Sciences, University of Southern California, Los Angeles, California 90089
| | - Nina J. Knab
- Marine Environmental Biology Section, Department of Biological Sciences, University of Southern California, Los Angeles, California 90089
| | - Katrina J. Edwards
- Marine Environmental Biology Section, Department of Biological Sciences, University of Southern California, Los Angeles, California 90089
- Department of Earth Sciences, University of Southern California, Los Angeles, California 90089
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Divya B, Parvathi A, Loka Bharathi PA, Nair S. 16S rRNA-based bacterial diversity in the organic-rich sediments underlying oxygen-deficient waters of the eastern Arabian Sea. World J Microbiol Biotechnol 2011. [DOI: 10.1007/s11274-011-0760-0] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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42
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Zeng Y, Zou Y, Chen B, Grebmeier JM, Li H, Yu Y, Zheng T. Phylogenetic diversity of sediment bacteria in the northern Bering Sea. Polar Biol 2011. [DOI: 10.1007/s00300-010-0947-0] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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43
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Kang YJ, Cheng J, Mei LJ, Hu J, Piao Z, Yin SX. Multiple copies of 16S rRNA gene affect the restriction patterns and DGGE profile revealed by analysis of genome database. Microbiology (Reading) 2010. [DOI: 10.1134/s0026261710050103] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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Comparative analysis of acidobacterial genomic fragments from terrestrial and aquatic metagenomic libraries, with emphasis on acidobacteria subdivision 6. Appl Environ Microbiol 2010; 76:6769-77. [PMID: 20729323 DOI: 10.1128/aem.00343-10] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The bacterial phylum Acidobacteria has a widespread distribution and is one of the most common and diverse phyla in soil habitats. However, members of this phylum have often been recalcitrant to cultivation methods, hampering the study of this presumably important bacterial group. In this study, we used a cultivation-independent metagenomic approach to recover genomic information from soilborne members of this phylum. A soil metagenomic fosmid library was screened by PCR targeting acidobacterial 16S rRNA genes, facilitating the recovery of 17 positive clones. Recovered inserts appeared to originate from a range of Acidobacteria subdivisions, with dominance of subdivision 6 (10 clones). Upon full-length insert sequencing, gene annotation identified a total of 350 open reading frames (ORFs), representing a broad range of functions. Remarkably, six inserts from subdivision 6 contained a region of gene synteny, containing genes involved in purine de novo biosynthesis and encoding tRNA synthetase and conserved hypothetical proteins. Similar genomic regions had previously been observed in several environmental clones recovered from soil and marine sediments, facilitating comparisons with respect to gene organization and evolution. Comparative analyses revealed a general dichotomy between marine and terrestrial genes in both phylogeny and G+C content. Although the significance of this homologous gene cluster across subdivision 6 members is not known, it appears to be a common feature within a large percentage of all acidobacterial genomic fragments recovered from both of these environments.
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Danovaro R, Company JB, Corinaldesi C, D'Onghia G, Galil B, Gambi C, Gooday AJ, Lampadariou N, Luna GM, Morigi C, Olu K, Polymenakou P, Ramirez-Llodra E, Sabbatini A, Sardà F, Sibuet M, Tselepides A. Deep-sea biodiversity in the Mediterranean Sea: the known, the unknown, and the unknowable. PLoS One 2010; 5:e11832. [PMID: 20689848 PMCID: PMC2914020 DOI: 10.1371/journal.pone.0011832] [Citation(s) in RCA: 113] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2010] [Accepted: 05/28/2010] [Indexed: 11/28/2022] Open
Abstract
Deep-sea ecosystems represent the largest biome of the global biosphere, but
knowledge of their biodiversity is still scant. The Mediterranean basin has been
proposed as a hot spot of terrestrial and coastal marine biodiversity but has
been supposed to be impoverished of deep-sea species richness. We summarized all
available information on benthic biodiversity (Prokaryotes, Foraminifera,
Meiofauna, Macrofauna, and Megafauna) in different deep-sea ecosystems of the
Mediterranean Sea (200 to more than 4,000 m depth), including open slopes, deep
basins, canyons, cold seeps, seamounts, deep-water corals and deep-hypersaline
anoxic basins and analyzed overall longitudinal and bathymetric patterns. We
show that in contrast to what was expected from the sharp decrease in organic
carbon fluxes and reduced faunal abundance, the deep-sea biodiversity of both
the eastern and the western basins of the Mediterranean Sea is similarly high.
All of the biodiversity components, except Bacteria and Archaea, displayed a
decreasing pattern with increasing water depth, but to a different extent for
each component. Unlike patterns observed for faunal abundance, highest negative
values of the slopes of the biodiversity patterns were observed for Meiofauna,
followed by Macrofauna and Megafauna. Comparison of the biodiversity associated
with open slopes, deep basins, canyons, and deep-water corals showed that the
deep basins were the least diverse. Rarefaction curves allowed us to estimate
the expected number of species for each benthic component in different
bathymetric ranges. A large fraction of exclusive species was associated with
each specific habitat or ecosystem. Thus, each deep-sea ecosystem contributes
significantly to overall biodiversity. From theoretical extrapolations we
estimate that the overall deep-sea Mediterranean biodiversity (excluding
prokaryotes) reaches approximately 2805 species of which about 66% is
still undiscovered. Among the biotic components investigated (Prokaryotes
excluded), most of the unknown species are within the phylum Nematoda, followed
by Foraminifera, but an important fraction of macrofaunal and megafaunal species
also remains unknown. Data reported here provide new insights into the patterns
of biodiversity in the deep-sea Mediterranean and new clues for future
investigations aimed at identifying the factors controlling and threatening
deep-sea biodiversity.
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Affiliation(s)
- Roberto Danovaro
- Dipartimento Scienze del Mare, Università Politecnica delle Marche, Ancona, Italy.
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Comparative metagenomics of bathypelagic plankton and bottom sediment from the Sea of Marmara. ISME JOURNAL 2010; 5:285-304. [PMID: 20668488 DOI: 10.1038/ismej.2010.113] [Citation(s) in RCA: 97] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
To extend comparative metagenomic analyses of the deep-sea, we produced metagenomic data by direct 454 pyrosequencing from bathypelagic plankton (1000 m depth) and bottom sediment of the Sea of Marmara, the gateway between the Eastern Mediterranean and the Black Seas. Data from small subunit ribosomal RNA (SSU rRNA) gene libraries and direct pyrosequencing of the same samples indicated that Gamma- and Alpha-proteobacteria, followed by Bacteroidetes, dominated the bacterial fraction in Marmara deep-sea plankton, whereas Planctomycetes, Delta- and Gamma-proteobacteria were the most abundant groups in high bacterial-diversity sediment. Group I Crenarchaeota/Thaumarchaeota dominated the archaeal plankton fraction, although group II and III Euryarchaeota were also present. Eukaryotes were highly diverse in SSU rRNA gene libraries, with group I (Duboscquellida) and II (Syndiniales) alveolates and Radiozoa dominating plankton, and Opisthokonta and Alveolates, sediment. However, eukaryotic sequences were scarce in pyrosequence data. Archaeal amo genes were abundant in plankton, suggesting that Marmara planktonic Thaumarchaeota are ammonia oxidizers. Genes involved in sulfate reduction, carbon monoxide oxidation, anammox and sulfatases were over-represented in sediment. Genome recruitment analyses showed that Alteromonas macleodii 'surface ecotype', Pelagibacter ubique and Nitrosopumilus maritimus were highly represented in 1000 m-deep plankton. A comparative analysis of Marmara metagenomes with ALOHA deep-sea and surface plankton, whale carcasses, Peru subsurface sediment and soil metagenomes clustered deep-sea Marmara plankton with deep-ALOHA plankton and whale carcasses, likely because of the suboxic conditions in the deep Marmara water column. The Marmara sediment clustered with the soil metagenome, highlighting the common ecological role of both types of microbial communities in the degradation of organic matter and the completion of biogeochemical cycles.
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Waddell EJ, Elliott TJ, Sani RK, Vahrenkamp JM, Roggenthen WM, Anderson CM, Bang SS. Phylogenetic evidence of noteworthy microflora from the subsurface of the former Homestake gold mine, Lead, South Dakota. ENVIRONMENTAL TECHNOLOGY 2010; 31:979-991. [PMID: 20662386 PMCID: PMC3565620 DOI: 10.1080/09593331003789511] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
Molecular characterization of subsurface microbial communities in the former Homestake gold mine, South Dakota, was carried out by 16S rDNA sequence analysis using a water sample and a weathered soil-like sample. Geochemical analyses indicated that both samples were high in sulphur, rich in nitrogen and salt, but with significantly different metal concentrations. Microbial diversity comparisons unexpectedly revealed three distinct operational taxonomic units (OTUs) belonging to the archaeal phylum Thaumarchaeota, typically identified from marine environments, and one OTU belonging to a potentially novel phylum that fell sister to Thaumarchaeota. To our knowledge this is only the second report of Thaumarchaeota in a terrestrial environment. The majority of the clones from Archaea sequence libraries fell into two closely related OTUs and were grouped most closely to an ammonia-oxidizing, carbon-fixing and halophilic thaumarchaeote genus, Nitrosopumilus. The two samples showed neither Euryarchaeota nor Crenarchaeota members that have often been identified from other subsurface terrestrial ecosystems. Bacteria OTUs containing the highest percentage of sequences were related to sulphur-oxidizing bacteria of the orders Chromatiales and Thiotrichales. Community members of Bacteria from individual Homestake ecosystems were heterogeneous and distinctive to each community, with unique phylotypes identified within each sample.
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Affiliation(s)
- Evan J. Waddell
- Department of Chemical and Biological Engineering, South Dakota School of Mines and Technology, Rapid City, SD 57701
| | - Terran J. Elliott
- Department of Chemical and Biological Engineering, South Dakota School of Mines and Technology, Rapid City, SD 57701
| | - Rajesh K. Sani
- Department of Chemical and Biological Engineering, South Dakota School of Mines and Technology, Rapid City, SD 57701
| | | | - William M. Roggenthen
- Department of Geology and Geological Engineering, South Dakota School of Mines and Technology, Rapid City, SD 57701
| | | | - Sookie S. Bang
- Department of Chemical and Biological Engineering, South Dakota School of Mines and Technology, Rapid City, SD 57701
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Ghosh A, Dey N, Bera A, Tiwari A, Sathyaniranjan KB, Chakrabarti K, Chattopadhyay D. Culture independent molecular analysis of bacterial communities in the mangrove sediment of Sundarban, India. SALINE SYSTEMS 2010; 6:1. [PMID: 20163727 PMCID: PMC2837041 DOI: 10.1186/1746-1448-6-1] [Citation(s) in RCA: 99] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/29/2009] [Accepted: 02/17/2010] [Indexed: 11/29/2022]
Abstract
Background Sundarban is the world's largest coastal sediment comprising of mangrove forest which covers about one million hectares in the south-eastern parts of India and southern parts of Bangladesh. The microbial diversity in this sediment is largely unknown till date. In the present study an attempt has been made to understand the microbial diversity in this sediment using a cultivation-independent molecular approach. Results Two 16 S rRNA gene libraries were constructed and partial sequencing of the selected clones was carried out to identify bacterial strains present in the sediment. Phylogenetic analysis of partially sequenced 16 S rRNA gene sequences revealed the diversity of bacterial strains in the Sundarban sediment. At least 8 different bacterial phyla were detected. The major divisions of detected bacterial phyla were Proteobacteria (alpha, beta, gamma, and delta), Flexibacteria (CFB group), Actinobacteria, Acidobacteria, Chloroflexi, Firmicutes, Planctomycetes and Gammatimonadates. Conclusion The gammaproteobacteria were found to be the most abundant bacterial group in Sundarban sediment. Many clones showed similarity with previously reported bacterial lineages recovered from various marine sediments. The present study indicates a probable hydrocarbon and oil contamination in this sediment. In the present study, a number of clones were identified that have shown similarity with bacterial clones or isolates responsible for the maintenance of the S-cycle in the saline environment.
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Affiliation(s)
- Abhrajyoti Ghosh
- Department of Biochemistry and Department of Biotechnology, University of Calcutta, 35, Ballygunge Circular Road, Kolkata- 700019, West Bengal, India.,Current address: Max Planck Research Group "Molecular Biology of Archaea", Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch-Strasse, D-35043 Marburg, Germany
| | - Nirmalya Dey
- Department of Biochemistry and Department of Biotechnology, University of Calcutta, 35, Ballygunge Circular Road, Kolkata- 700019, West Bengal, India.,Current address: Division of Nephrology Department of Medicine, 7703 Floyd Curl Drive, University of Texas Health Science Center at San Antonio, San Antonio, Texas 78229 3900, USA
| | - Amit Bera
- Department of Biochemistry and Department of Biotechnology, University of Calcutta, 35, Ballygunge Circular Road, Kolkata- 700019, West Bengal, India
| | - Amit Tiwari
- Department of Biochemistry and Department of Biotechnology, University of Calcutta, 35, Ballygunge Circular Road, Kolkata- 700019, West Bengal, India.,Current address: Institute of Molecular Cancer Research, University of Zurich, 17 K 28, Winterthurerstrasse 190, Zurich-8057, Switzerland
| | - K B Sathyaniranjan
- Department of Biochemistry and Department of Biotechnology, University of Calcutta, 35, Ballygunge Circular Road, Kolkata- 700019, West Bengal, India
| | - Kalyan Chakrabarti
- Department of Agricultural Chemistry & Soil Science, Institute of Agricultural Science, University of Calcutta, 35, Ballygunge Circular Road. Kolkata- 700019, West Bengal, India
| | - Dhrubajyoti Chattopadhyay
- Department of Biochemistry and Department of Biotechnology, University of Calcutta, 35, Ballygunge Circular Road, Kolkata- 700019, West Bengal, India
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Bacterial diversity and biogeography in deep-sea surface sediments of the South Atlantic Ocean. ISME JOURNAL 2009; 4:159-70. [PMID: 19829317 DOI: 10.1038/ismej.2009.106] [Citation(s) in RCA: 170] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Microbial biogeographic patterns in the deep sea depend on the ability of microorganisms to disperse. One possible limitation to microbial dispersal may be the Walvis Ridge that separates the Antarctic Lower Circumpolar Deep Water from the North Atlantic Deep Water. We examined bacterial communities in three basins of the eastern South Atlantic Ocean to determine diversity and biogeography of bacterial communities in deep-sea surface sediments. The analysis of 16S ribosomal RNA (rRNA) gene clone libraries in each basin revealed a high diversity, representing 521 phylotypes with 98% identity in 1051 sequences. Phylotypes affiliated with Gammaproteobacteria, Deltaproteobacteria and Acidobacteria were present in all three basins. The distribution of these shared phylotypes seemed to be influenced neither by the Walvis Ridge nor by different deep water masses, suggesting a high dispersal capability, as also indicated by low distance-decay relationships. However, the total bacterial diversity showed significant differences between the basins, based on 16S rRNA gene sequences as well as on terminal restriction fragment length polymorphism fingerprints. Noticeably, both geographic distance and environmental heterogeneity influenced bacterial diversity at intermediate (10-3000 km) and large scales (>3000 km), indicating a complex interplay of local contemporary environmental effects and dispersal limitation.
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Zhou MY, Chen XL, Zhao HL, Dang HY, Luan XW, Zhang XY, He HL, Zhou BC, Zhang YZ. Diversity of both the cultivable protease-producing bacteria and their extracellular proteases in the sediments of the South China sea. MICROBIAL ECOLOGY 2009; 58:582-590. [PMID: 19301066 DOI: 10.1007/s00248-009-9506-z] [Citation(s) in RCA: 67] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/10/2008] [Accepted: 02/22/2009] [Indexed: 05/27/2023]
Abstract
Protease-producing bacteria are known to play an important role in degrading sedimentary particular organic nitrogen, and yet, their diversity and extracellular proteases remain largely unknown. In this paper, the diversity of the cultivable protease-producing bacteria and their extracellular proteases in the sediments of the South China Sea was investigated. The richness of the cultivable protease-producing bacteria reached 10(6) cells/g in all sediment samples. Analysis of the 16S rRNA gene sequences revealed that the predominant cultivated protease-producing bacteria are Gammaproteobacteria affiliated with the genera Pseudoalteromonas, Alteromonas, Marinobacter, Idiomarina, Halomonas, Vibrio, Shewanella, Pseudomonas, and Rheinheimera, with Alteromonas (34.6%) and Pseudoalteromonas (28.2%) as the predominant groups. Inhibitor analysis showed that nearly all the extracellular proteases from the bacteria are serine proteases or metalloproteases. Moreover, these proteases have different hydrolytic ability to different proteins, reflecting they may belong to different kinds of serine proteases or metalloproteases. To our knowledge, this study represents the first report of the diversity of bacterial proteases in deep-sea sediments.
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Affiliation(s)
- Ming-Yang Zhou
- State Key Lab of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Jinan 250100, People's Republic of China
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