51
|
Needham DM, Chow CET, Cram JA, Sachdeva R, Parada A, Fuhrman JA. Short-term observations of marine bacterial and viral communities: patterns, connections and resilience. ISME JOURNAL 2013; 7:1274-85. [PMID: 23446831 DOI: 10.1038/ismej.2013.19] [Citation(s) in RCA: 100] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Observation of short-term temporal variation in bacterial and viral communities is important for understanding patterns of aquatic microbial diversity. We collected surface seawater once daily for 38 consecutive days with seven more samples interspersed over 40 more days at one location ∼2 km from Santa Catalina Island, California. Bacterial communities were analyzed by automated ribosomal intergenic spacer analysis (ARISA) and viral communities were analyzed by terminal restriction fragment length polymorphism (TRFLP) of the conserved T4-like myoviral gene encoding the major capsid protein (g23). Common bacterial and viral taxa were consistently dominant, and relatively few displayed dramatic increases/decreases or 'boom/bust' patterns that might be expected from dynamic predator-prey interactions. Association network analysis showed most significant covariations (associations) occurred among bacterial taxa or among viral taxa and there were several modular (highly-interconnected) associations (P≤0.005). Associations observed between bacteria and viruses (P≤0.005) occurred with a median time lag of 2 days. Regression of all pairwise Bray-Curtis similarities between samples indicated a rate of bacterial community change that slows from 2.1%-0.18% per day over a week to 2 months; the rate stays around 0.4% per day for viruses. Our interpretation is that, over the scale of days, individual bacterial and viral OTUs can be dynamic and patterned; resulting in statistical associations regarded as potential ecological interactions. However, over the scale of weeks, average bacterial community variation is slower, suggesting that there is strong community-level ecological resilience, that is, a tendency to converge towards a 'mean' microbial community set by longer-term controlling factors.
Collapse
Affiliation(s)
- David M Needham
- University of Southern California, Department of Biological Sciences, Los Angeles, CA 90089, USA.
| | | | | | | | | | | |
Collapse
|
52
|
Sun W, Peng C, Zhao Y, Li Z. Functional gene-guided discovery of type II polyketides from culturable actinomycetes associated with soft coral Scleronephthya sp. PLoS One 2012; 7:e42847. [PMID: 22880121 PMCID: PMC3413676 DOI: 10.1371/journal.pone.0042847] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2012] [Accepted: 07/12/2012] [Indexed: 12/05/2022] Open
Abstract
Compared with the actinomycetes in stone corals, the phylogenetic diversity of soft coral-associated culturable actinomycetes is essentially unexplored. Meanwhile, the knowledge of the natural products from coral-associated actinomycetes is very limited. In this study, thirty-two strains were isolated from the tissue of the soft coral Scleronephthya sp. in the East China Sea, which were grouped into eight genera by 16S rDNA phylogenetic analysis: Micromonospora, Gordonia, Mycobacterium, Nocardioides, Streptomyces, Cellulomonas, Dietzia and Rhodococcus. 6 Micromonospora strains and 4 Streptomyces strains were found to be with the potential for producing aromatic polyketides based on the analysis of KSα (ketoacyl-synthase) gene in the PKS II (type II polyketides synthase) gene cluster. Among the 6 Micromonospora strains, angucycline cyclase gene was amplified in 2 strains (A5-1 and A6-2), suggesting their potential in synthesizing angucyclines e.g. jadomycin. Under the guidance of functional gene prediction, one jadomycin B analogue (7b, 13-dihydro-7-O-methyl jadomycin B) was detected in the fermentation broth of Micromonospora sp. strain A5-1. This study highlights the phylogenetically diverse culturable actinomycetes associated with the tissue of soft coral Scleronephthya sp. and the potential of coral-derived actinomycetes especially Micromonospora in producing aromatic polyketides.
Collapse
Affiliation(s)
- Wei Sun
- Marine Biotechnology Laboratory, State Key Laboratory of Microbial Metabolism & School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, People's Republic of China
| | - Chongsheng Peng
- School of Pharmacy, Shanghai Jiao Tong University, Shanghai, People's Republic of China
| | - Yunyu Zhao
- School of Pharmacy, Shanghai Jiao Tong University, Shanghai, People's Republic of China
| | - Zhiyong Li
- Marine Biotechnology Laboratory, State Key Laboratory of Microbial Metabolism & School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, People's Republic of China
- * E-mail:
| |
Collapse
|
53
|
Ling J, Dong JD, Wang YS, Zhang YY, Deng C, Lin L, Wu ML, Sun FL. Spatial variation of bacterial community structure of the Northern South China Sea in relation to water chemistry. ECOTOXICOLOGY (LONDON, ENGLAND) 2012; 21:1669-1679. [PMID: 22707093 DOI: 10.1007/s10646-012-0941-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 05/24/2012] [Indexed: 06/01/2023]
Abstract
Spatial distribution, diversity and composition of bacterial communities of the northern South China Sea (SCS) surface water and the relationship with the in situ environmental chemistry were investigated. Polymerase chain reaction denaturing gradient gel electrophoresis (PCR-DGGE) was used to investigate the bacterial community structure. The DGGE gel showed that each sample harbored a distinct bacterial community structure and spatial variations of bacterial community composition among all samples were obviously. A total of 17 intensive bands were excised and the sequence analysis of these DGGE bands revealed that Proteobacteria were the dominant bacterial group of surface water in the north part of SCS. Results of the taxonomic analysis showed that the communities consisted of Proteobacteria (α-subdivision, β-subdivision, γ-subdivision), Actinobacteria, Cyanobacteria, Bacteroidetes and Firmicutes. Unweighted pair group method with arithmetic averages clustering of the sampling stations indicated that all stations were classified mainly based on geographical proximity. Canonical correspondence analysis (CCA) was employed to further investigate the relationships between DGGE band pattern and the environmental variables and the first two CCA ordination axes suggested that the structure of the bacterial community was significantly correlated with the variables of nitrate (F = 1.24, P < 0.05).
Collapse
Affiliation(s)
- Juan Ling
- State Key Laboratory of Tropical Oceanography, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China
| | | | | | | | | | | | | | | |
Collapse
|
54
|
Subramani R, Aalbersberg W. Marine actinomycetes: an ongoing source of novel bioactive metabolites. Microbiol Res 2012; 167:571-80. [PMID: 22796410 DOI: 10.1016/j.micres.2012.06.005] [Citation(s) in RCA: 210] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2011] [Revised: 05/15/2012] [Accepted: 06/23/2012] [Indexed: 11/16/2022]
Abstract
Actinomycetes are virtually unlimited sources of novel compounds with many therapeutic applications and hold a prominent position due to their diversity and proven ability to produce novel bioactive compounds. There are more than 22,000 known microbial secondary metabolites, 70% of which are produced by actinomycetes, 20% from fungi, 7% from Bacillus spp. and 1-2% by other bacteria. Among the actinomycetes, streptomycetes group are considered economically important because out of the approximately more than 10,000 known antibiotics, 50-55% are produced by this genus. The ecological role of actinomycetes in the marine ecosystem is largely neglected and various assumptions meant there was little incentive to isolate marine strains for search and discovery of new drugs. The search for and discovery of rare and new actinomycetes is of significant interest to drug discovery due to a growing need for the development of new and potent therapeutic agents. Modern molecular technologies are adding strength to the target-directed search for detection and isolation of bioactive actinomycetes, and continued development of improved cultivation methods and molecular technologies for accessing the marine environment promises to provide access to this significant new source of chemical diversity with novel/rare actinomycetes including new species of previously reported actinomycetes.
Collapse
Affiliation(s)
- Ramesh Subramani
- Centre for Drug Discovery and Conservation, Institute of Applied Sciences, The University of the South Pacific, Laucala Campus, Suva, Fiji.
| | | |
Collapse
|
55
|
Biodiscovery from rare actinomycetes: an eco-taxonomical perspective. Appl Microbiol Biotechnol 2012; 93:1843-52. [DOI: 10.1007/s00253-012-3898-2] [Citation(s) in RCA: 60] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2011] [Revised: 01/07/2012] [Accepted: 01/09/2012] [Indexed: 11/25/2022]
|
56
|
ISHINO RYOTA, IEHATA SHUNPEI, NAKANO MIYO, TANAKA REIJI, YOSHIMATSU TAKAO, MAEDA HIROTO. Bacterial Diversity Associated with the Rotifer Brachionus plicatilis sp. Complex Determined by Culture-Dependent and -Independent Methods. Biocontrol Sci 2012; 17:51-6. [DOI: 10.4265/bio.17.51] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/01/2022]
|
57
|
Spatial heterogeneity of bacterial community structure in the sediments of the Pearl River estuary. Biologia (Bratisl) 2011. [DOI: 10.2478/s11756-011-0066-6] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
|
58
|
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]
|
59
|
|
60
|
Streptomyces tateyamensis sp. nov., Streptomyces marinus sp. nov. and Streptomyces haliclonae sp. nov., isolated from the marine sponge Haliclona sp. Int J Syst Evol Microbiol 2010; 60:2775-2779. [DOI: 10.1099/ijs.0.019869-0] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Three Gram-positive, NaCl-requiring actinobacteria were isolated from a marine sponge, Haliclona sp., collected from the coast of Tateyama City, Japan. Comparison of 16S rRNA gene sequences indicated that these strains represent novel members of the genus Streptomyces, exhibiting low 16S rRNA gene sequence similarities of 98.3–97.4 % with recognized members of the genus. The cell hydrolysates contained the LL-isomer of diaminopimelic acid and the predominant quinones were MK-9 (H6 and/or H8). The DNA G+C contents were in the range 72–75 mol%. A polyphasic study of the strains and comparison of the characters with related species of the genus show that these strains represent three novel species of the genus Streptomyces. Therefore, the names Streptomyces tateyamensis sp. nov., Streptomyces haliclonae sp. nov. and Streptomyces marinus sp. nov. are proposed for strains Sp080513SC-30T (=NBRC 105048T =DSM 41969T), Sp080513SC-31T (=NBRC 105049T =DSM 41970T) and Sp080513GE-26T (=NBRC 105047T =DSM 41968T), respectively.
Collapse
|
61
|
Ashforth EJ, Fu C, Liu X, Dai H, Song F, Guo H, Zhang L. Bioprospecting for antituberculosis leads from microbial metabolites. Nat Prod Rep 2010; 27:1709-19. [PMID: 20922218 DOI: 10.1039/c0np00008f] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Elizabeth Jane Ashforth
- Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, People's Republic of China
| | | | | | | | | | | | | |
Collapse
|
62
|
Wang G, Dai S, Chen M, Wu H, Xie L, Luo X, Li X. Two diketopiperazine cyclo(pro-phe) isomers from marine bacteria Bacillus subtilis sp. 13-2. Chem Nat Compd 2010. [DOI: 10.1007/s10600-010-9680-8] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
|
63
|
|
64
|
Sun W, Dai S, Jiang S, Wang G, Liu G, Wu H, Li X. Culture-dependent and culture-independent diversity of Actinobacteria associated with the marine sponge Hymeniacidon perleve from the South China Sea. Antonie van Leeuwenhoek 2010; 98:65-75. [PMID: 20383659 DOI: 10.1007/s10482-010-9430-8] [Citation(s) in RCA: 60] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2009] [Accepted: 03/12/2010] [Indexed: 11/27/2022]
Abstract
In this report, the diversity of Actinobacteria associated with the marine sponge Hymeniacidon perleve collected from a remote island of the South China Sea was investigated employing classical cultivation and characterization, 16S rDNA library construction, 16S rDNA-restriction fragment length polymorphism (rDNA-RFLP) and phylogenetic analysis. A total of 184 strains were isolated using seven different media and 24 isolates were selected according to their morphological characteristics for phylogenetic analysis on the basis of their 16S rRNA gene sequences. Results showed that the 24 isolates were assigned to six genera including Salinispora, Gordonia, Mycobacterium, Nocardia, Rhodococcus and Streptomyces. This is the first report that Salinispora is present in a marine sponge from the South China Sea. Subsequently, 26 rDNA clones were selected from 191 clones in an Actinobacteria-specific 16S rDNA library of the H. perleve sample, using the RFLP technique for sequencing and phylogenetic analysis. In total, 26 phylotypes were clustered in eight known genera of Actinobacteria including Mycobacterium, Amycolatopsis, Arthrobacter, Brevibacterium, Microlunatus, Nocardioides, Pseudonocardia and Streptomyces. This study contributes to our understanding of actinobacterial diversity in the marine sponge H. perleve from the South China Sea.
Collapse
Affiliation(s)
- Wei Sun
- Key Laboratory of Marine Bio-resources Sustainable Utilization (LMB-CAS), Guangdong Key Laboratory of Marine Materia Medica, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, People's Republic of China
| | | | | | | | | | | | | |
Collapse
|
65
|
Diversity, Salt Requirement, and Antibiotic Production of Actinobacteria Isolated from Marine Sponges. ACTA ACUST UNITED AC 2010. [DOI: 10.3209/saj.saj240101] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
|
66
|
Philosof A, Sabehi G, Béjà O. Comparative analyses of actinobacterial genomic fragments from Lake Kinneret. Environ Microbiol 2009; 11:3189-200. [DOI: 10.1111/j.1462-2920.2009.02024.x] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
|
67
|
JBIR-31, a new teleocidin analog, produced by salt-requiring Streptomyces sp. NBRC 105896 isolated from a marine sponge. J Antibiot (Tokyo) 2009; 63:33-6. [DOI: 10.1038/ja.2009.113] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
|
68
|
Zhao XQ, Li WJ, Jiao WC, Li Y, Yuan WJ, Zhang YQ, Klenk HP, Suh JW, Bai FW. Streptomyces xinghaiensis sp. nov., isolated from marine sediment. Int J Syst Evol Microbiol 2009; 59:2870-4. [PMID: 19628610 DOI: 10.1099/ijs.0.009878-0] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022] Open
Abstract
A novel actinomycete, strain S187(T), was isolated from a marine sediment sample collected from Xinghai Bay, Dalian, China. Growth occurred on ISP medium 2 containing 0-9 % NaCl and at pH 6.0-9.0 and 10-45 degrees C. The cell wall of strain S187(T) contained the isomer ll-diaminopimelic acid as the diagnostic diamino acid. The predominant menaquinones were MK-9(H(6)) (40.8 %), MK-9(H(8)) (38.2 %) and MK-9(H(2)) (8.8 %). The major fatty acids were iso-C(16 : 0) (29.6 %), anteiso-C(15 : 0) (14.0 %) and anteiso-C(17 : 0) (11.6 %). Cells contained phosphatidylethanolamine, phosphatidylinositol, phosphatidylglycerol, phosphatidylinositol mannosides and one unknown phospholipid. The G+C content of the genomic DNA was 72.01 mol%. The 16S rRNA gene sequence of the isolate had similarities of 98.1 and 97.5 % with those of Streptomyces flavofuscus NRRL B-8036(T) (=DSM 41426(T)) and Streptomyces albiaxialis DSM 41799(T), respectively, showing that the novel strain should be assigned to the genus Streptomyces. DNA-DNA hybridizations with the two above-mentioned Streptomyces species showed 31.4 and 46.9 % relatedness, respectively. Moreover, the three strains differed in some physiological and biochemical properties. Thus, on the basis of phenotypic and genotypic analyses, it is proposed that strain S187(T) represents a novel species of the genus Streptomyces, for which the name Streptomyces xinghaiensis sp. nov. is proposed; the type strain is S187(T) (=NRRL B-24674(T)=CCTCC AA 208049(T)=KCTC 19546(T)).
Collapse
Affiliation(s)
- Xin-Qing Zhao
- Department of Bioscience and Bioengineering, Dalian University of Technology, Dalian 116024, People's Republic of China
| | | | | | | | | | | | | | | | | |
Collapse
|
69
|
Olano C, Méndez C, Salas JA. Antitumor compounds from marine actinomycetes. Mar Drugs 2009; 7:210-48. [PMID: 19597582 PMCID: PMC2707044 DOI: 10.3390/md7020210] [Citation(s) in RCA: 215] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2009] [Revised: 06/08/2009] [Accepted: 06/11/2009] [Indexed: 11/16/2022] Open
Abstract
Chemotherapy is one of the main treatments used to combat cancer. A great number of antitumor compounds are natural products or their derivatives, mainly produced by microorganisms. In particular, actinomycetes are the producers of a large number of natural products with different biological activities, including antitumor properties. These antitumor compounds belong to several structural classes such as anthracyclines, enediynes, indolocarbazoles, isoprenoides, macrolides, non-ribosomal peptides and others, and they exert antitumor activity by inducing apoptosis through DNA cleavage mediated by topoisomerase I or II inhibition, mitochondria permeabilization, inhibition of key enzymes involved in signal transduction like proteases, or cellular metabolism and in some cases by inhibiting tumor-induced angiogenesis. Marine organisms have attracted special attention in the last years for their ability to produce interesting pharmacological lead compounds.
Collapse
Affiliation(s)
- Carlos Olano
- Departamento de Biología Funcional e Instituto Universitario de Oncología del Principado de Asturias (I.U.O.P.A), Universidad de Oviedo, 33006 Oviedo, Spain; E-Mails:
(C.O.);
(C.M.)
| | - Carmen Méndez
- Departamento de Biología Funcional e Instituto Universitario de Oncología del Principado de Asturias (I.U.O.P.A), Universidad de Oviedo, 33006 Oviedo, Spain; E-Mails:
(C.O.);
(C.M.)
| | - José A. Salas
- Departamento de Biología Funcional e Instituto Universitario de Oncología del Principado de Asturias (I.U.O.P.A), Universidad de Oviedo, 33006 Oviedo, Spain; E-Mails:
(C.O.);
(C.M.)
| |
Collapse
|
70
|
Wu J, Guan T, Jiang H, Zhi X, Tang S, Dong H, Zhang L, Li W. Diversity of Actinobacterial community in saline sediments from Yunnan and Xinjiang, China. Extremophiles 2009; 13:623-32. [PMID: 19504229 DOI: 10.1007/s00792-009-0245-3] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2008] [Accepted: 03/31/2009] [Indexed: 10/20/2022]
Abstract
The diversity and community structures of actinobacteria in saline sediments collected from Yunnan and Xinjiang Provinces, China, were investigated with cultivation and 16S rRNA gene analysis. A total of 163 actinobacterial isolates were obtained, and they were affiliated with the order Actinomycetales (distributed into five suborders: Streptosporangineae, Micrococcineae, Streptomycineae, Pseudonocardineae, and Glycomycineae). A total of 748 actinobacterial 16S rRNA gene clones were examined, and they could be classified into Actinomycetales, Acidimicrobiales, and unclassified actinobacteria. The Actinomycetales sequences were distributed into nine suborders: Streptosporangineae, Glycomycineae, Micromonosporineae, Pseudonocardineae, Corynebacterineae, Frankineae, Propionibacterineae, Streptomycineae, and Micrococcineae. The unclassified actinobacteria contained three new clusters at the level of subclass or order. Our 16S rRNA gene phylogenetic data indicated that actinobacterial communities were very diverse in the investigated saline sediments (salinity 0.4-11.6%) and some actinobacterial members may be halotolerant or halophilic. The actinobacterial community structures in the saline sediments were different from those in marine and freshwater environments. Our data have implications for a better understanding of the distribution of Actinobacteria in saline environments.
Collapse
Affiliation(s)
- Jinyuan Wu
- Yunnan Institute of Microbiology, Yunnan University, Kunming, China.
| | | | | | | | | | | | | | | |
Collapse
|
71
|
Zhao XQ, Jiao WC, Jiang B, Yuan WJ, Yang TH, Hao S. Screening and identification of actinobacteria from marine sediments: Investigation of potential producers for antimicrobial agents and type I polyketides. World J Microbiol Biotechnol 2009. [DOI: 10.1007/s11274-009-9964-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
|
72
|
Polymenakou PN, Lampadariou N, Mandalakis M, Tselepides A. Phylogenetic diversity of sediment bacteria from the southern Cretan margin, Eastern Mediterranean Sea. Syst Appl Microbiol 2008; 32:17-26. [PMID: 19058941 DOI: 10.1016/j.syapm.2008.09.006] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2008] [Revised: 09/04/2008] [Accepted: 09/05/2008] [Indexed: 10/21/2022]
Abstract
This study is the first culture-independent report on the regional variability of bacterial diversity in oxic sediments from the unexplored southern Cretan margin (SCM). Three main deep basins (water column depths: 2670-3603m), located at the mouth of two submarine canyons (Samaria Gorge and Paximades Channel) and an adjacent slope system, as well as two shallow upper-slope stations (water column depths: 215 and 520m), were sampled. A total of 454 clones were sequenced and the bacterial richness, estimated through five clone libraries using rarefaction analysis, ranged from 71 to 296 unique phylotypes. The average sequence identity of the retrieved Cretan margin sequences compared to the >1,000,000 known rRNA sequences was only 93.5%. A diverse range of prokaryotes was found in the sediments, which were represented by 15 different taxonomic groups at the phylum level. The phylogenetic analysis revealed that these new sequences grouped with the phyla Acidobacteria, Planctomycetes, Actinobacteria, Gamma-, Alpha- and Delta-proteobacteria. Only a few bacterial clones were affiliated with Chloroflexi, Bacteroidetes, Firmicutes, Gemmatimonadetes, Verrucomicrobia, Nitrospirae, Beta-proteobacteria, Lentisphaerae and Dictyoglomi. A large fraction of the retrieved sequences (12%) did not fall into any taxonomic division previously characterized by molecular criteria, whereas four novel division-level lineages, termed candidate division SCMs, were identified. Bacterial community composition demonstrated significant differences in comparison to previous phylogenetic studies. This divergence was mainly triggered by the dominance of Acidobacteria and Actinobacteria and reflected a bacterial community different from that currently known for oxic and pristine marine sediments.
Collapse
Affiliation(s)
- Paraskevi N Polymenakou
- Hellenic Centre for Marine Research, Institute of Marine Biology and Genetics, Gournes Pediados, P.O. Box 2214, GR-710 03 Heraklion, Crete, Greece.
| | | | | | | |
Collapse
|
73
|
Genetic characterisation of endophytic actinobacteria isolated from the medicinal plants in Sichuan. ANN MICROBIOL 2008. [DOI: 10.1007/bf03175563] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022] Open
|
74
|
Solanki R, Khanna M, Lal R. Bioactive compounds from marine actinomycetes. Indian J Microbiol 2008; 48:410-31. [PMID: 23100742 PMCID: PMC3476783 DOI: 10.1007/s12088-008-0052-z] [Citation(s) in RCA: 116] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2007] [Accepted: 06/12/2008] [Indexed: 11/28/2022] Open
Abstract
Actinomycetes are one of the most efficient groups of secondary metabolite producers and are very important from an industrial point of view. Among its various genera, Streptomyces, Saccharopolyspora, Amycolatopsis, Micromonospora and Actinoplanes are the major producers of commercially important biomolecules. Several species have been isolated and screened from the soil in the past decades. Consequently the chance of isolating a novel actinomycete strain from a terrestrial habitat, which would produce new biologically active metabolites, has reduced. The most relevant reason for discovering novel secondary metabolites is to circumvent the problem of resistant pathogens, which are no longer susceptible to the currently used drugs. Existence of actinomycetes has been reported in the hitherto untapped marine ecosystem. Marine actinomycetes are efficient producers of new secondary metabolites that show a range of biological activities including antibacterial, antifungal, anticancer, insecticidal and enzyme inhibition. Bioactive compounds from marine actinomycetes possess distinct chemical structures that may form the basis for synthesis of new drugs that could be used to combat resistant pathogens.
Collapse
Affiliation(s)
- Renu Solanki
- Acharya Narendra Dev College, University of Delhi, Govindpuri, Kalkaji, New Delhi, 110 019 India
| | - Monisha Khanna
- Acharya Narendra Dev College, University of Delhi, Govindpuri, Kalkaji, New Delhi, 110 019 India
| | - Rup Lal
- Molecular Biology Lab, Department of Zoology, University of Delhi, Delhi, 110 007 India
| |
Collapse
|
75
|
Yoshida A, Seo Y, Suzuki S, Nishino T, Kobayashi T, Hamada-Sato N, Kogure K, Imada C. Actinomycetal community structures in seawater and freshwater examined by DGGE analysis of 16S rRNA gene fragments. MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2008; 10:554-563. [PMID: 18418650 DOI: 10.1007/s10126-008-9092-y] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/11/2007] [Revised: 03/02/2008] [Accepted: 03/02/2008] [Indexed: 05/26/2023]
Abstract
The actinomycetal community structures in marine and freshwater environments (the Pacific Ocean, East China Sea, Tokyo Bay, and Arakawa River) were investigated by a culture-independent molecular method to clarify spatial and seasonal distributions. Deoxyribonucleic acid (DNA) was extracted from environmental water samples, and a community analysis was carried out on polymerase chain reaction-amplified 16S ribosomal DNA. The amplified DNA fragments were analyzed by denaturing gradient gel electrophoresis (DGGE) and nonmetric multidimensional scaling analysis, followed by sequencing analysis. The actinomycetal community structures were different at each station in the Pacific Ocean, the East China Sea, Tokyo Bay, and Arakawa River, and different populations predominated in each area. There were vertical variations in actinomycetal communities in the Pacific Ocean and East China Sea between the surface and 100-m depth, but communities were similar from 200- to 1,000-m depths. There were also distinct seasonal variations in communities in Tokyo Bay. Phylogenetic analysis of DNA fragments recovered from DGGE bands revealed that most of the predominant actinomycetal strains were uncultured and were quite different from well known culturable strains, such as the Streptomyces, Micromonospora, Microbispora, Salinispora, and Actinoplanes groups. These results suggest that the marine environment is an attractive target for discovering new actinomycetal populations producing bioactive compounds and that sampling depth and season are important considerations for isolating various populations effectively.
Collapse
Affiliation(s)
- Akihiro Yoshida
- Graduate School of Marine Science and Technology, Tokyo University of Marine Science and Technology, 4-5-7, Konan, Minato-ku, Tokyo 108-8477, Japan.
| | | | | | | | | | | | | | | |
Collapse
|
76
|
Mitra A, Santra SC, Mukherjee J. Distribution of actinomycetes, their antagonistic behaviour and the physico-chemical characteristics of the world's largest tidal mangrove forest. Appl Microbiol Biotechnol 2008; 80:685-95. [PMID: 18679673 DOI: 10.1007/s00253-008-1626-8] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2008] [Revised: 07/14/2008] [Accepted: 07/15/2008] [Indexed: 12/01/2022]
Abstract
We examined the relationship between distribution of actinomycetes and antagonistic behaviour with the physico-chemical characteristics of the Sundarbans, off the Bay of Bengal, India. Soil/sediment samples were collected from three regions: near to the sea, intertidal regions and mangrove forests. For the enumeration of actinomycetes, four treatments combining dilution with distilled or sea water with or without heating followed by plating onto starch-casein, glycerol-arginine and starch-nitrate media were done. Dilution with seawater, heating and plating onto starch-casein yielded maximum number of actinomycetes. The highest number of actinomycetes was isolated from an intertidal region having alluvial soil and the lowest from a site containing sandy sediments. Antimicrobial activity was dependent upon seawater. Antimicrobial score of an actinomycetes strain was calculated allotting maximum points to the isolate showing activity against all the test bacteria, next lower point to the isolate showing activity against one less the total and so on. The antagonistic potential (AP) of a sampling site was the ratio of total antimicrobial score of the isolates and their number. The high AP sites were influenced by tides, while the low AP sites were not. Pearson's correlation between soil chemical parameters and microbiological parameters revealed soil nitrogen as the key factor determining the antagonistic activity.
Collapse
Affiliation(s)
- Anindita Mitra
- School of Environmental Studies, Jadavpur University, Kolkata, 700 032, India
| | | | | |
Collapse
|
77
|
Jensen PR, Lauro FM. An assessment of actinobacterial diversity in the marine environment. Antonie van Leeuwenhoek 2008; 94:51-62. [PMID: 18500568 DOI: 10.1007/s10482-008-9239-x] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/02/2008] [Accepted: 03/07/2008] [Indexed: 10/22/2022]
Abstract
The 16S rRNA gene sequence diversity within the Phylum Actinobacteria was assessed from four sources: PCR-generated V6 sequence tags derived from seawater samples, metagenomic data from the Global Ocean Sampling (GOS) expedition, marine-derived sequences maintained in the Ribosomal Database Project (RDP), and select cultured strains for which sequence data is not yet available in the RDP. This meta-analysis revealed remarkable levels of phylogenetic diversity and confirms the existence of major, deeply rooted, and as of yet uncharacterized lineages within the phylum. A dramatic incongruence among cultured strains and those detected using culture-independent techniques was also revealed. Redundancy among the actinobacteria detected using culture-independent techniques suggests that greater sequence coverage or improved DNA extraction efficiencies may be required to detect the rare phylotypes that can be readily cultured from marine samples. Conversely, new strategies need to be developed for the cultivation of frequently observed but yet to be cultured marine actinobacteria.
Collapse
Affiliation(s)
- Paul R Jensen
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA 92093, USA.
| | | |
Collapse
|
78
|
Manipulating and understanding antibiotic production in Streptomyces coelicolor A3(2) with decoy oligonucleotides. Proc Natl Acad Sci U S A 2008; 105:1020-5. [PMID: 18187578 DOI: 10.1073/pnas.0710724105] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
We have adapted and extended the decoy oligonucleotide technique for use in prokaryotes. To identify cis-acting regulatory elements within a promoter, we developed a DNase I/T7 exonuclease footprinting technique and applied it to actII-orf4 from Streptomyces coelicolor A3(2), which encodes the pathway-specific activator for production of the antibiotic actinorhodin. Our in vivo mapping data allowed us to create decoy oligonucleotides incorporating the identified regulatory elements and to test whether their introduction into S. coelicolor affected antibiotic production. We mapped the promoter region when in a transcriptionally inactive state before the onset of actinorhodin production with the aim of designing decoy oligonucleotides capable of interfering with potential repressor binding and so stimulate actinorhodin production. Mapping identified five candidates for decoy oligonucleotides, and these were tested in a plate-based assay to rapidly validate their activity. A transfection protocol was developed for liquid cultures that enabled efficient uptake of decoys, and quantitative real-time PCR demonstrated decoy persistence for >70 h. Measurement of the effects on growth, expression of actII-orf4, and antibiotic production demonstrated that one of the decoys, in concordance with the plate assay, was more efficacious than the others in increasing actinorhodin production. Two of the identified regulatory elements occurred upstream of gene SCO5812, deletion of which reduced actinorhodin production, confirming that experimental analysis of regulatory motifs can provide new insights into factors influencing antibiotic production in streptomycetes.
Collapse
|
79
|
Piao Z, Yang L, Zhao L, Yin S. Actinobacterial community structure in soils receiving long-term organic and inorganic amendments. Appl Environ Microbiol 2008; 74:526-30. [PMID: 17933943 PMCID: PMC2223251 DOI: 10.1128/aem.00843-07] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2007] [Accepted: 10/01/2007] [Indexed: 11/20/2022] Open
Abstract
The impact of long-term organic and inorganic amendments on the actinobacterial community in soils was studied. Denaturing gradient gel electrophoresis patterns based on the V3 region of 16S rRNA suggested that there was no significant difference between the communities occurring in the different amendments. However, analysis of the clone libraries of the actinobacterial communities by the use of multiple statistical approaches showed that these communities were significantly different from each other. Results showed that long-term organic and inorganic soil amendments did not significantly alter the overall phylogenetic diversity of the actinobacterial communities but did significantly change the community structure.
Collapse
Affiliation(s)
- Zhe Piao
- Institute of Soil Science, Chinese Academy of Sciences, 71 Beijing East Road, Nanjing 210008, China
| | | | | | | |
Collapse
|
80
|
Isolation of New Polyketide Synthase Gene Fragments and a Partial Gene Cluster from East China Sea and Function Analysis of a New Acyltransfrase. Appl Biochem Biotechnol 2007; 149:67-78. [DOI: 10.1007/s12010-007-8053-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2007] [Accepted: 09/07/2007] [Indexed: 10/22/2022]
|
81
|
Bull AT, Stach JE. Marine actinobacteria: new opportunities for natural product search and discovery. Trends Microbiol 2007; 15:491-9. [DOI: 10.1016/j.tim.2007.10.004] [Citation(s) in RCA: 282] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2007] [Revised: 08/09/2007] [Accepted: 10/25/2007] [Indexed: 11/15/2022]
|
82
|
Jensen SI, Kühl M, Priemé A. Different bacterial communities associated with the roots and bulk sediment of the seagrass Zostera marina. FEMS Microbiol Ecol 2007; 62:108-17. [PMID: 17825072 DOI: 10.1111/j.1574-6941.2007.00373.x] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
The bacterial community of Zostera marina-inhabited bulk sediment vs. root-associated bacteria was investigated by terminal restriction fragment length polymorphism and sequencing, and the spatial extension of the oxygen loss from roots was determined by oxygen microsensors. Extensive oxygen loss was found in the tip region of the youngest roots, and most of the rhizoplane of Z. marina roots was thus anoxic. A significant difference between the bacterial communities associated with the roots and bulk sediment was found. No significant differences were found between differently aged root-bundles. Terminal restriction fragments (TRFs) assigned to sulfate-reducing Deltaproteobacteria showed a relative mean distribution of 12% and 23% of the PCR-amplified bacterial community in the bulk-sediment at the two sites, but only contributed <2% to the root-associated communities. TRFs assigned to Epsilonproteobacteria showed a relative mean distribution of between 5% and 11% in the root-associated communities of the youngest root bundle, in contrast to the bulk-sediment where this TRF only contributed <1.3%. TRFs assigned to Actinobacteria and Gammaproteobacteria also seemed important first root-colonizers, whereas TRFs assigned to Deltaproteobacteria became increasingly important in the root-associated community of the older root bundles. The presence of the roots thus apparently selects for a distinct bacterial community, stimulating the growth of potential symbiotic Epsilon- and Gammaproteobacteria and/or inhibiting the growth of sulfate-reducing Deltaproteobacteria.
Collapse
Affiliation(s)
- Sheila Ingemann Jensen
- Marine Biological Laboratory, Department of Biology, University of Copenhagen, Helsingør, Denmark.
| | | | | |
Collapse
|
83
|
Lam KS. New aspects of natural products in drug discovery. Trends Microbiol 2007; 15:279-89. [PMID: 17433686 DOI: 10.1016/j.tim.2007.04.001] [Citation(s) in RCA: 330] [Impact Index Per Article: 19.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2006] [Revised: 03/26/2007] [Accepted: 04/02/2007] [Indexed: 11/20/2022]
Abstract
During the past 15 years, most large pharmaceutical companies have decreased the screening of natural products for drug discovery in favor of synthetic compound libraries. Main reasons for this include the incompatibility of natural product libraries with high-throughput screening and the marginal improvement in core technologies for natural product screening in the late 1980s and early 1990 s. Recently, the development of new technologies has revolutionized the screening of natural products. Applying these technologies compensates for the inherent limitations of natural products and offers a unique opportunity to re-establish natural products as a major source for drug discovery. Examples of these new advances and technologies are described in this review.
Collapse
Affiliation(s)
- Kin S Lam
- Nereus Pharmaceuticals Inc., 10480 Wateridge Circle, San Diego, CA 92121, USA.
| |
Collapse
|
84
|
Fenical W, Jensen PR. Developing a new resource for drug discovery: marine actinomycete bacteria. Nat Chem Biol 2006; 2:666-73. [PMID: 17108984 DOI: 10.1038/nchembio841] [Citation(s) in RCA: 615] [Impact Index Per Article: 34.2] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- William Fenical
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California-San Diego, La Jolla, CA 92093-0204, USA.
| | | |
Collapse
|