Chondroitinase-Producing Bacteria in Natural Habitats

A search was undertaken for bacteria which degrade chondroitin sulfate in nature and to find bacteria with a usefully high rate of chondroitinase (ChSase) productivity. First, 253 ChSase-producing bacteria were obtained from aquatic and land environments in Japan by aerobic and anaerobic screening methods. Identification according to Bergey's Manual of Determinative Bacteriology or Bain and Shewan (1968) permitted assignment of the majority of the isolates to seven genera, Aeromonas, Vibrio, Flavobacterium, Beneckea, Proteus, Micrococcus, and Arthrobacter. Next, ChSase productivities of all the isolates were compared with those of two established ChSase-producing stock strains, Proteus vulgaris NCTC 4636 and Flavobacterium heparinum ATCC 13125. As a result, special attention was given to production by a strain of Aeromonas sp. of large quantities of extracellular ChSase-AC. None of the isolates from the current study displayed significant ChSase-ABC productivity. Finally, ChSase-AC was prepared from the culture fluid of the Aeromonas strain by fractional precipitation with ammonium sulfate, chromatography on phospho-cellulose and diethylaminoethyl-cellulose, and gel filtration on Sephadex G-200. It was concluded that the Aeromonas strain may represent a profitable source of the enzyme ChSase-AC.     

Aerobic Anoxygenic Photosynthesis in Roseobacter Clade Bacteria from Diverse Marine Habitats

The marine Roseobacter clade comprises several genera of marine bacteria related to the uncultured SAR83 cluster, the second most abundant marine picoplankton lineage. Cultivated representatives of this clade are physiologically heterogeneous, and only some have the capability for aerobic anoxygenic photosynthesis, a process of potentially great ecological importance in the world's oceans. In an attempt to correlate phylogeny with ecology, we investigated the diversity of Roseobacter clade strains from various marine habitats (water samples, biofilms, laminariae, diatoms, and dinoflagellate cultures) by using the 16S rRNA gene as a phylogenetic marker gene. The potential for aerobic anoxygenic photosynthesis was determined on the genetic level by PCR amplification and sequencing of the pufLM genes of the bacterial photosynthesis reaction center and on the physiological level by detection of bacteriochlorophyll (Bchl) a. A collection of ca. 1,000 marine isolates was screened for members of the marine Roseobacter clade by 16S rRNA gene-directed multiplex PCR and sequencing. The 42 Roseobacter clade isolates found tended to form habitat-specific subclusters. The pufLM genes were detected in two groups of strains from dinoflagellate cultures but in none of the other Roseobacter clade isolates. Strains within the first group (the DFL-12 cluster) also synthesized Bchl a. Strains within the second group (the DFL-35 cluster) formed a new species of Roseovarius and did not produce Bchl a under the conditions investigated here, thus demonstrating the importance of genetic methods for screening of cultivation-dependent metabolic traits. The pufL genes of the dinoflagellate isolates were phylogenetically closely related to pufL genes from Betaproteobacteria, confirming similar previous observations which have been interpreted as indications of gene transfer events.     

Isolation of Broad-Host-Range Replicons from Marine Sediment Bacteria

Naturally occurring plasmids isolated from heterotrophic bacterial isolates originating from coastal California marine sediments were characterized by analyzing their incompatibility and replication properties. Previously, we reported on the lack of DNA homology between plasmids from the culturable bacterial population of marine sediments and the replicon probes specific for a number of well-characterized incompatibility and replication groups (P. A. Sobecky, T. J. Mincer, M. C. Chang, and D. R. Helinski, Appl. Environ. Microbiol. 63:888–895, 1997). In the present study we isolated 1.8- to 2.3-kb fragments that contain functional replication origins from one relatively large (30-kb) and three small (<10-kb) naturally occurring plasmids present in different marine isolates. 16S rRNA sequence analyses indicated that the four plasmid-bearing marine isolates belonged to the α and γ subclasses of the class Proteobacteria. Three of the marine sediment isolates are related to the γ-3 subclass organisms Vibrio splendidus and Vibrio fischeri, while the fourth isolate may be related to Roseobacter litoralis. Sequence analysis of the plasmid replication regions revealed the presence of features common to replication origins of well-characterized plasmids from clinical bacterial isolates, suggesting that there may be similar mechanisms for plasmid replication initiation in the indigenous plasmids of gram-negative marine sediment bacteria. In addition to replication in Escherichia coli DH5α and C2110, the host ranges of the plasmid replicons, designated repSD41, repSD121, repSD164, and repSD172, extended to marine species belonging to the genera Achromobacter, Pseudomonas, Serratia, and Vibrio. While sequence analysis of repSD41 and repSD121 revealed considerable stretches of homology between the two fragments, these regions do not display incompatibility properties against each other. The replication origin repSD41 was detected in 5% of the culturable plasmid-bearing marine sediment bacterial isolates, whereas the replication origins repSD164 and repSD172 were not detected in any plasmid-bearing bacteria other than the parental isolates. Microbial community DNA extracted from samples collected in November 1995 and June 1997 and amplified by PCR yielded positive signals when they were hybridized with probes specific for repSD41 and repSD172 replication sequences. In contrast, replication sequences specific for repSD164 were not detected in the DNA extracted from marine sediment microbial communities.  The maintenance and horizontal transfer of extrachromosomal elements provide one mechanism by which microbial communities can rapidly adapt to changes in environmental conditions. This adaptation can be in the form of plasmid rearrangements and duplications (18, 40), a change in the plasmid copy number (40, 54), or lateral or horizontal movement of plasmids within bacterial populations. An example demonstrating the importance of plasmid-mediated genetic adaptation in natural microbial communities, likely caused by lateral transfer, is the increased frequencies (2- to 10-fold) of catabolic plasmids reported in bacterial isolates obtained from polluted marine and freshwater environments compared to isolates from nonpolluted or less impacted ecosystems (8, 23, 43). Plasmids also play a major role in promoting the widespread distribution of antibiotic resistance genes attributed to the intense and increased use of antibiotics (42).The ability of plasmids to self-transfer or to be mobilized by transfer-proficient plasmids and the ability to replicate in different bacterial hosts are key factors in the spread of plasmid-encoded genes within microbial communities. Plasmids which are considered to have broad host ranges in nature have the potential to significantly affect the microbial community structure and function due to their ability to replicate and be maintained in members of distantly related genera. Thus, to better understand gene flux in natural systems and hence the potential role of plasmids in promoting horizontal transfer within microbial communities, knowledge of the distribution, diversity, and host ranges of naturally occurring plasmids is necessary.At present, most indigenous plasmids from marine and freshwater systems have been only partially characterized with respect to host range, replication mechanisms, incompatibility groups, and conjugal abilities. Plasmids containing similar or related replication systems are considered incompatible if they cannot coexist in a host cell (12, 41). This trait has facilitated the grouping of plasmids from gram-negative bacteria, mainly members of the family Enterobacteriaceae, into more than 30 different incompatibility groups (3). While molecularly based plasmid classification or replicon typing by using DNA sequences of replication origins and incompatibility loci of well-characterized plasmids has been useful in classifying plasmids from bacterial isolates of medical importance (9, 10, 14), plasmids from various marine microbial communities, including sediments, biofilms, bulk water, and the marine air-water interface, have been recently shown to contain incompatibility and replication regions unrelated to those currently defined (11, 53).The present study was undertaken to characterize, at the molecular level, the replication and incompatibility loci of naturally occurring plasmids isolated from gram-negative marine heterotrophs for use as replicon probes to classify and type, at the molecular level, plasmids present in bacterial populations of marine sediments. Replication origins were obtained from plasmids ranging in size from 6 to 30 kb isolated from culturable bacteria of coastal California marine sediments (53). Phylogenetic analysis indicated that the plasmids were initially isolated from bacteria belonging to the α and γ-3 subclasses of the class Proteobacteria. Although a sequence and hybridization analysis of the replication origins from the marine plasmids confirmed the lack of homology with previously described plasmids, the replication regions contained features commonly found in previously characterized plasmid replication origins. The replication origins of the naturally occurring plasmids appear to have a broad host range, as indicated by their ability to replicate in members of diverse gram-negative marine genera. In addition to molecular characterization of the indigenous plasmids, the persistence of the replicons in marine sediment bacterial populations was determined by PCR amplification of microbial community DNA extracted on different dates and examined for the presence of homologous plasmid replication sequences.     

北极海泥菌群的分离鉴定及生物学特性的初步研究

对从北极冰川海面下1500-4000m处的海泥样品中分离的8株冷适应细菌进行了生理特征和分子生物学研究。其中5株嗜冷菌、3株耐冷菌,利用16SrDNA通用引物对5株嗜冷菌基因组DNA进行扩增,测序得到其部分16SrDNA序列。经Blast调出与菌株16SrDNA同源的序列,按照Neighbor-Joining方法构建16SrDNA系统发育树。对8株细菌进行酶检测试验,结果表明其中有部分细菌产低温酶:N014产淀粉酶,R151产明胶酶,P371产纤维素酶。研究结果为进一步开发利用冷适应微生物产物提供参考依据。     

The Ability of Saprotrophic Bacteria Isolated from Natural Habitats to Lyse Yeasts

More than 600 bacterial strains isolated from different horizons of steppe biogeocenoses and zoogenous loci (diplopod intestines and feces) were tested for the ability to lyse yeast cell walls. About half of the strains that were isolated from biotopes with active degradation of plant debris (steppe litters and diplopod intestines and feces) were found to possess yeast-lytic activity. Most of the yeast-lytic strains belonged to the genera Streptomyces, Promicromonospora, Oerskovia, and Agromyces. The yeast-lytic activity of actinobacteria from the genera Agromyces, Mycobacterium, and Micrococcus has not previously been reported.     

Isolation and Characterization of Methanesulfonic Acid-Degrading Bacteria from the Marine Environment

Two methylotrophic bacterial strains, TR3 and PSCH4, capable of growth on methanesulfonic acid as the sole carbon source were isolated from the marine environment. Methanesulfonic acid metabolism in these strains was initiated by an inducible NADH-dependent monooxygenase, which cleaved methanesulfonic acid into formaldehyde and sulfite. The presence of hydroxypyruvate reductase and the absence of ribulose monophosphate-dependent hexulose monophosphate synthase indicated the presence of the serine pathway for formaldehyde assimilation. Cell suspensions of bacteria grown on methanesulfonic acid completely oxidized methanesulfonic acid to carbon dioxide and sulfite with a methanesulfonic acid/oxygen stoichiometry of 1.0:2.0. Oxygen electrode-substrate studies indicated the dissimilation of formaldehyde to formate and carbon dioxide for energy generation. Carbon dioxide was not fixed by ribulose bisphosphate carboxylase. It was shown that methanol is not an intermediate in methanesulfonic acid metabolism, although these strains grew on methanol and other one-carbon compounds, as well as a variety of heterotrophic carbon sources. These two novel marine facultative methylotrophs have the ability to mineralize methanesulfonic acid and may play a role in the cycling of global organic sulfur.     

Medium for the Selective Isolation of Members of the Genus Pseudomonas from Natural Habitats

A new medium was developed that was superior to four others tested in selecting for members of the genus Pseudomonas.     

Method for the Isolation of Proteolytic Marine Bacteria

A two-layer plate consisting of a lower indicator layer of milk-agar and an upper nutrient agar layer was developed for isolating proteolytic marine bacteria.     

Isolation of Iodide-Oxidizing Bacteria from Iodide-Rich Natural Gas Brines and Seawaters

Iodide-oxidizing bacteria (IOB), which oxidize iodide (I⁻) to molecular iodine (I₂), were isolated from iodide-rich (63 μM to 1.2 mM) natural gas brine waters collected from several locations. Agar media containing iodide and starch were prepared, and brine waters were spread directly on the media. The IOB, which appeared as purple colonies, were obtained from 28 of the 44 brine waters. The population sizes of IOB in the brines were 10² to 10⁵ colony-forming units (CFU) mL⁻¹. However, IOB were not detected in natural seawaters and terrestrial soils (fewer than 10 CFU mL⁻¹ and 10² CFU g wet weight of soils⁻¹, respectively). Interestingly, after the enrichment with 1 mM iodide, IOB were found in 6 of the 8 seawaters with population sizes of 10³ to 10⁵ CFU mL⁻¹. 16S rDNA sequencing and phylogenetic analyses showed that the IOB strains are divided into two groups within the α-subclass of the Proteobacteria. One of the groups was phylogenetically most closely related to Roseovarius tolerans with sequence similarities between 94% and 98%. The other group was most closely related to Rhodothalassium salexigens, although the sequence similarities were relatively low (89% to 91%). The iodide-oxidizing reaction by IOB was mediated by an extracellular enzyme protein that requires oxygen. Radiotracer experiments showed that IOB produce not only I₂ but also volatile organic iodine, which were identified as diiodomethane (CH₂I₂) and chloroiodomethane (CH₂ClI). These results indicate that at least two types of IOB are distributed in the environment, and that they are preferentially isolated in environments in which iodide levels are very high. It is possible that IOB oxidize iodide in the natural environment, and they could significantly contribute to the biogeochemical cycling of iodine.     

Habitats and Distribution Patterns of Marine Luminous Bacteria in the Western Baltic Sea

Numbers of luminous bacteria were counted at three stations of the brackish water ecosystem of the western Baltic Sea from July 1985 to July 1986. Additional samples were taken during three cruises from stations at the North Atlantic Ocean, the Norwegian Sea and adjacent marine areas. — In Kiel Bight (western Baltic) values varied between 0 and 68,000 luminous cfu 1⁻¹. With exception of the coastal station a distinct seasonal distribution pattern was shown in a water depth of 20 m: high numbers found in summer were opposed to low numbers in winter, the peaks being rather high in comparison to those of other areas. Statistical analysis showed that the results of 20 m were significantly different from those of 0 and 10 m depth; however, there was no correlation with temperature and salinity. Taxonomic studies revealed that the population consisted primarily of the genus Photobacterium. — The optimum of salinity was not a brackish but a marine one and was about 30% for the majority of the strains tested. A smaller number of strains grew best at a salinity between 10 and 15%. Optima of temperature ranged from 15 to 20 °C for most of the test strains. — Taxonomic analysis was also performed with luminous strains from marine areas adjacent to the western Baltic Sea, Photobacterium being the dominant genus here, too. Luminous bacteria were also enriched from the external surface and the gut contents of whitings (Merlangius merlangus) and cods (Gadus morhua). A model is proposed which explains the distribution pattern found. According to this, the gut-dwelling luminous bacteria are transported by their hosts from the North Sea into the western Baltic Sea. Here they are released into the environment, thus inhabiting another niche.     

具有抑菌活性的海洋细菌的分离与鉴定

分离并筛选具有抑菌活性的海洋细菌对于开发和利用海洋微生物具有重要意义,该研究从6份海泥样品中共分离到78株海洋细菌,以6种细菌作为敏感指示菌,采用覆盖技术对分离菌株进行拮抗试验,17株海洋细菌具有抑菌活性,对其中2株具有较强抑菌活性的海洋细菌进行革兰氏染色,耐盐试验,运动性观察,过氧化氢酶测定,明胶液化试验,硫化氢产生试验,石蕊牛奶试验,糖类发酵,硝酸盐还原等特性分析,依据《伯杰氏细菌鉴定手册》进行分类鉴定,它们分别应归属为气单孢菌属（Aeromonas sp.）和假单孢菌属（Pseudomonas sp.）。     

Isolation of High Molecular Weight DNA from Marine Sponge Bacteria for BAC Library Construction

Metagenomics is a powerful tool for mining the genetic repositories from environmental microorganisms. Bacteria associated with marine sponges (phylum Porifera) are rich sources of biologically active natural products. However, to date, few compounds are discovered from the sponge metagenomic libraries, and the main reason might be the difficulties in recovery of high molecular weight (HMW) DNA from sponge symbionts to construct large insert libraries. Here, we describe a method to recover HMW bacterial DNA from diverse sponges with high quality for bacterial artificial chromosome (BAC) library construction. Microorganisms concentrated from sponges by differential centrifugation were embedded in agarose plugs to lyse out the HMW DNA for recovery. DNA fragments over 436 kb size were recovered from three different types of sponges, Halichondria sp., Haliclona sp., and Xestospongia sp. To evaluate the recovered DNA quality, the diversity of bacterial DNA comprised in the HMW DNA derived from sponge Halichondria sp. was analyzed, and this HMW DNA sample was also cloned into a shuttle BAC vector between Escherichia coli and Streptomyces sp. The results showed that more than five types of bacterial DNA, i.e., Proteobacteria, Nitrospirae, Cyanobacteria, Planctomycetes, and unidentified bacteria, had been recovered by this method, and an average 100 kb size insert DNA in a constructed BAC library demonstrated that the recovered HMW DNA is suitable for metagenomic library construction.     

Uptake of Cyclic AMP by Natural Populations of Marine Bacteria

The major objective of this study was to describe the mechanism(s) of cyclic AMP uptake by natural populations of marine bacteria. A second objective was to determine whether this uptake could contribute to the intracellular regulatory pool of cyclic AMP. Using high-specific-activity ³²P-labeled cyclic AMP, we found several high-affinity uptake systems. The highest-affinity system had a half-saturation constant of <10 pM. This system was extremely specific for cyclic nucleotides, particularly cyclic AMP. It appeared to meet the criteria for active transport. Uptake of cyclic AMP over a wide concentration range (up to 2 μM) showed multiphasic kinetics, with half-saturation constants of 1 nM and greater. These lower-affinity systems were much less specific for cyclic nucleotides. Although much of the labeled cyclic AMP taken up by the high-affinity systems was metabolized, some remained as intact cyclic AMP within the cells during 1 h of incubation. This suggests that at least some of the bacteria use cyclic AMP dissolved in seawater to augment their intracellular pools.     

Isolation and Characterization of a GDSL Esterase from the Metagenome of a Marine Sponge-associated Bacteria

Using a metagenome library constructed from a bacterial associated with a marine sponge Hyrtios erecta, we identified a novel esterase that belongs to the SGNH hydrolase superfamily of esterases. The substrate specificity of EstHE1 was determined using p-nitrophenyl (pNP) ester (C2: acetate, C4: butylate, C6: caproate, C12: laurate, C16: palmitate). EstHE1 exhibited activity against C2 (5.6 U/mg), C4 (5.1 U/mg), and C6 (2.8 U/mg) substrates. The optimal temperature for EstHE1 esterase activity of the pNP acetate substrate was 40°C, and EstHE1 retained 60% of its enzymatic activity in the 30–50°C range. This esterase showed moderate thermostability, retaining 58% of its activity even after preincubation for 12 h at 40°C. EstHE1 also maintained activity in high concentrations of NaCl, indicating that this esterase is salt-tolerant. Thus, EstHE1 has the thermal stability and salt tolerance necessary for use as an industrial enzyme.     

Isolation and Identification of Photosynthetic Bacteria (Rhodospirillaceae) from Antarctic Marine and Freshwater Sediments

Sediment samples obtained from three freshwater lakes and off-shore coastal marine waters on Signy Island, South Orkney Islands, Antarctica have been inoculated into selective enrichment media for purple non-sulphur bacteria (Rhodospirillaceae). From the freshwater sediments strains of Rhodopseudomonas sphaeroides (1), Rhodopseudomonas palustris (1), Rhodospirillum fulvum (1), Rhodospirillum molischanum (1) and Rhodomicrobium vannielii (3) have been isolated. The only purple non-sulphur bacteria obtained from Lake 10 (Amos lake) were strains of Rhodomicrobium vannielii which were able to tolerate hydrogen sulphide (up to 0.04% w/v) found in this lake. Growth of all the other isolates is inhibited by the presence of hydrogen sulphide. Marine sediments yielded strains of Rhodopseudomonas palustris and Rhodomicrobium vannielii . All the isolates grow optimally at temperatures between 25 and 30 °C. mean generation times vary between 8 and 10.7 h depending on species. There is no evidence of cold adaptation in any of the strains studied.     

Properties of Alginate Lyases from Marine Bacteria

Alginate lyases (EC 4.2.2.3) from two marine bacteria were isolated and partially characterized. A cell-bound lyase from isolate A3 had a molecular weight of approximately 100,000 and cleaved mannuronate blocks, apparently in an exo manner. A lyase recovered from the culture medium of isolate W3 was soluble in saturated ammonium sulfate, cleaved guluronate blocks, apparently in an endo manner, and had a molecular weight of 35,000. The thiobarbiturate test and urea-polyacrylamide gel electrophoresis were used to determine substrate specificity and mode of substrate cleavage by the enzymes.     

Isolation and Analysis of Bacteria with Antimicrobial Activities from the Marine Sponge Haliclona simulans Collected from Irish Waters

Samples of the marine sponge Haliclona simulans were collected from Irish coastal waters, and bacteria were isolated from these samples. Phylogenetic analyses of the cultured isolates showed that four different bacterial phyla were represented; Bacteriodetes, Actinobacteria, Proteobacteria, and Firmicutes. The sponge bacterial isolates were assayed for the production of antimicrobial substances, and biological activities against Gram-positive and Gram-negative bacteria and fungi were demonstrated, with 50% of isolates showing antimicrobial activity against at least one of the test strains. Further testing showed that the antimicrobial activities extended to the important pathogens Pseudomonas aeruginosa, Clostridium difficile, multi-drug-resistant Staphylococcus aureus, and pathogenic yeast strains. The Actinomycetes were numerically the most abundant producers of antimicrobial activities, although activities were also noted from Bacilli and Pseudovibrio isolates. Surveys for the presence of potential antibiotic encoding polyketide synthase and nonribosomal peptide synthetase genes also revealed that genes for the biosynthesis of these secondary metabolites were present in most bacterial phyla but were particularly prevalent among the Actinobacteria and Proteobacteria. This study demonstrates that the culturable fraction of bacteria from the sponge H. simulans is diverse and appears to possess much potential as a source for the discovery of new medically relevant biological active agents.     

Isolation and Characterization of Two Groups of Novel Marine Bacteria Producing Violacein

Thirteen strains of novel marine bacteria producing a purple pigment were isolated from the Pacific coast of Japan. They were divided into two groups based on their 16S ribosomal RNA gene sequences, and both groups of bacteria belonged to the genus Pseudoalteromonas. The UV-visible spectrum of the pigment was identical to those of violacein, a pigment produced by several species of bacteria including Chromobacterium violaceum, an opportunistic pathogen. Further analysis of the chemical structure of the pigment by mass spectroscopy and nuclear magnetic resonance spectroscopy showed that the pigment was violacein. The high purity of violacein in the crude extract enabled us to employ simple and nonpolluting procedures to purify the pigment. Isolated bacteria may be useful as a C. violaceum substitute for the safe production of violacein.     

Bioactive Compounds from Marine Bacteria and Fungi

Marine bacteria and fungi are of considerable importance as new promising sources of a huge number of biologically active products. Some of these marine species live in a stressful habitat, under cold, lightless and high pressure conditions. Surprisingly, a large number of species with high diversity survive under such conditions and produce fascinating and structurally complex natural products. Up till now, only a small number of microorganisms have been investigated for bioactive metabolites, yet a huge number of active substances with some of them featuring unique structural skeletons have been isolated. This review covers new biologically active natural products published recently (2007–09) and highlights the chemical potential of marine microorganisms, with focus on bioactive products as well as on their mechanisms of action.