Potential sulfur metabolisms and associated bacteria within anoxic surface sediment from saline meromictic Lake Kaiike (Japan)

The effects of light and of added electron donors and sulfur compounds on sulfur metabolisms in the microbial mat dilutions from the saline meromictic Lake Kaiike were investigated. Sulfide concentrations in the mat dilution without any electron donor gradually increased by approximately 0.6-1 mM in the dark. Additions of lactate, acetate, H(2)/CO(2), propionate and iso-butylate stimulated sulfide production, whereas benzoate did not, indicating the limitation of sulfate reduction by available electron donor concentrations. More sulfide was produced, without a decrease of sulfate, in an elemental sulfur-amended dilution than in a non-amended control. In contrast, the addition of a high concentration of sulfide slowed down sulfide production. After enrichment under various conditions, microbial communities in the dilutions were characterized by a denaturing gradient gel electrophoresis of PCR-amplified 16S rRNA gene and sequencing. As a result, microorganisms affiliated with mesophilic sulfate-reducing bacteria group within the Deltaproteobacteria and the Epsilonproteobacteria were mainly enriched by the addition of electrons used in this study, suggesting that these microorganisms might play an important role in sulfur metabolisms within the surficial sediment of Lake Kaiike.     

东海表层沉积物纯培养与非培养细菌多样性

于2011年7月采集了浙江舟山沿岸海底沉积物样品(122°10′41″E,29°49′7″N),通过埋片原位观察、荧光显微计数、纯培养菌分离以及非培养细菌构建克隆文库的方法,分析和研究了东海表层沉积物细菌群落结构及其多样性.埋片原位观察和荧光显微计数法的结果表明:沉积物样品中细菌的细胞数量为(9.30±3.44)×107 cells/g;通过分离纯化共获得313株细菌,分属于20个属,4种培养基对细菌的分离效果依次为RO＞M l＞Zobell 2216＞MR2A;常规形态学与生理生化鉴定结果显示芽孢杆菌属(Bacillus)和海球菌属(Marinococcus)从数量和种类上皆为优势菌属,分别占分离菌株总数的21.08％和17.25％;对73株典型海洋细菌进行16S rDNA分子鉴定发现,厚壁菌门(57.5％)、γ-变形杆菌纲(32.9％)、黄杆菌纲(4.1％)和放线菌纲(5.5％)等为主要类群.非培养细菌克隆文库序列分析发现:细菌克隆子主要属于厚壁菌门和变形杆菌门,而芽孢杆菌纲和γ-变形杆菌纲是上述两个门的优势类群.综合纯培养与非培养数据得出东海海域表层沉积物细菌多样性丰富,具有进一步开发研究的价值.     

Comparison of bacteria from deep subsurface sediment and adjacent groundwater

Samples of groundwater and the enclosing sediments were compared for densities of bacteria using direct (acridine orange direct staining) and viable (growth on 1% PTYG medium) count methodology. Sediments to a depth of 550 m were collected from boreholes at three sites on the Savannah River Site near Aiken, South Carolina, using techniques to insure a minimum of surface contamination. Clusters of wells screened at discreet intervals were established at each site. Bacterial densities in sediment were higher, by both direct and viable count, than in groundwater samples. Differences between direct and viable counts were much greater for groundwater samples than for sediment samples. Densities of bacteria in sediment ranged from less than 1.00×10⁶ bacteria/g dry weight (gdw) up to 5.01 ×10⁸ bacteria/gdw for direct counts, while viable counts were less than 1.00×10³ CFU/gdw to 4.07×10⁷ CFU/gdw. Bacteria densities in groundwater were 1.00×10³–6.31×10⁴ bacteria/ml and 5.75–4.57×10² CFU/ml for direct and viable counts, respectively. Isolates from sediment were also found to assimilate a wider variety of carbon compounds than groundwater bacteria. The data suggest that oligotrophic aquifer sediments have unique and dense bacterial communities that are attached and not reflected in groundwater found in the strata. Effective in situ bioremediation of contaimination in these aquifers may require sampling and characterization of sediment communities.     

Diversity and antagonistic potential of bacteria associated with bryophytes from nutrient-poor habitats of the Baltic Sea Coast

Very little is known about the interaction of bryophytes with bacteria. Therefore, we analyzed bacteria associated with three bryophyte species, Tortula ruralis, Aulacomnium palustre, and Sphagnum rubellum, which represent typical moss species of three nutrient-poor plant communities at the southern Baltic Sea coast in Germany. By use of two cultivation-independent techniques, denaturing gradient gel electrophoresis and single-strand conformation polymorphism analysis of the 16S ribosomal DNA, a high degree of moss specificity was found for associated bacterial communities. This specificity could be further evidenced by a cultivation-dependent approach for the following parameters: (i) plate counts of bacteria on R2A medium, (ii) proportion of antagonistic isolates, (iii) antagonistic activity as well as spectrum against pathogens, and (iv) diversity and richness of antagonistic isolates. The proportion of isolates with antagonistic activity against the pathogenic model fungus Verticillium dahliae was highest for S. rubellum (31%), followed by A. palustre (17%) and T. ruralis (5%). A high percentage (99%) of moss-associated antagonistic bacteria produced antifungal compounds. The high recovery of antagonistic isolates strongly suggests that bryophytes represent an ecological niche which harbors a diverse and hitherto largely uncharacterized microbial population with yet unknown and untapped potential biotechnological applications, e.g., for biological control of plant pathogens.     

Evaluation of petroleum-degrading potential of bacteria from water and sediment.

Bacteria from water and sediment of an oil-polluted harbor were examined for ability to degrade petroleum. Water samples contained a greater variety of bacterial species capable of degrading petroleum than sediment. Cultures from both water and sediment contained Pseudomonas and Acinetobacter spp. Bacteria present in the water samples produced significantly greater degradation of 2-,3-,4-, and 5-ring cycloalkanes and mono-, di-, tri-, tetra-, and pentaaromatics compared with bacteria in sediment samples.     

Phylogenetic diversity of sediment bacteria in the northern Bering Sea

The bacterial diversity in sediments from the northern Bering Sea was investigated by culture-independent approaches. Community fingerprint analysis by polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE) revealed that sediment at two deep stations (DBSE and DBS1, >400 m in depth) harbored a bacterial community distinct from the sediments collected at shallow stations (<150 m in depth) on the continental shelf. Three 16S rRNA gene clone libraries for sediments collected from shallow to deep water stations (NEC5, DBSE and DBS1, respectively) were established. Sediment collected at the deepest station DBS1 showed the highest diversity index value. Sequences fell into 19 major lineages of the domain Bacteria: Alpha-, Beta-, Gamma-, Delta- and Epsilonproteobacteria, Bacteroidetes, Acidobacteria, Actinobacteria, Firmicutes, Planctomycetes, Nitrospirae, Verrucomicrobia, Chloroflexi, Chlorobi, Spirochaetes, Cyanobacteria (or chloroplasts), and candidate divisions OP8, TM6, and WS3. A small fraction of retrieved sequences (1.8%) did not fall into any taxonomic division. Deltaproteobacteria (30%) was the dominant phylum in the three libraries, followed by Gammaproteobacteria (21%) and Acidobacteria (16%). The percentages of cloned sequences with the highest similarity to reported sequences below 97 and 93% were 48.1 and 24.3%, respectively. A large number of phylotypes affiliated with bacteria that play important roles in the carbon, sulfur, and nitrogen cycles suggest an important link of bacteria to the matter cycling in these subarctic sediments.     

Diversity and biotechnological potential of culturable bacteria from Brazilian mangrove sediment

Mangrove ecosystems are environments subject to substantial degradation by anthropogenic activities. Its location, in coastal area, interfacing the continents and the oceans makes it substantially important in the prospection for biotechnological applications. In this study, we assessed the diversity of culturable bacteria present over the seasons at two depths (0–10 and 30–40 cm) in a mangrove sediment and in a transect area from the land to the sea. In total, 238 bacteria were isolated, characterized by Amplified Ribosomal DNA Restriction Analysis (ARDRA) and further identified, by Fatty Acid Methyl Esther (FAME-MIDI), into the orders of Vibrionales, Actinomycetales and Bacillales. Also the ability of the isolates in producing economically important enzymes (amylases, proteases, esterases and lipases) was evaluated and the order Vibrionales was the main enzymatic source.     

Phylogenetic diversity of sediment bacteria from the southern Cretan margin,Eastern Mediterranean Sea

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: 2670–3603 m), 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 520 m), 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.     

The antioxidant potential of dominant macroalgae species from the Sea of Japan

The range of variation in the key components of enzymatic and low-molecular-weight antioxidant systems (AOSs) is determined for 17 dominant species of macroalgae from the Sea of Japan waters that are exposed to minimal anthropogenic pressure, during the period of their active vegetative growth. The maximum activity of superoxide dismutase, glutathione reductase, ascorbate peroxidase, and the highest content of glutathione and carotenoids are observed in members of the phylum Chlorophyta. The studied algae display a wide phenotypic variability in terms of catalase activity and ascorbate abundance in their tissues. Differences between species in the constitutive capacity of AOS are found within the systematic phyla. It is shown for the first time that warm-water algae of temperate latitudes have a lower content of low-molecular-weight antioxidants and a higher activity of key antioxidant enzymes compared to those recorded for cold-temperate species.     

Organomercurial-volatilizing bacteria in the mercury-polluted sediment of Minamata Bay, Japan

A total of 4,604 bacterial strains isolated from the sediments of Minamata Bay and nearby low-level-mercury stations (control stations) were screened for the ability to volatilize mercury from inorganic and organic mercurial compounds. The strains that volatilize mercury from several kinds of organomercurials were found only in the sediments of Minamata Bay.     

Diatoms from surface sediments of Amurskiy Bay,Sea of Japan

The results of a study of diatoms from surface sediments (0–1 cm) of Amurskiy Bay are presented for the first time. The specific composition (221 species and intraspecific taxa) and ecological structure of the diatom flora were determined. The diatom species composition of phytoplankton, periphyton, and surface sediments is compared.     

Organomercurial-volatilizing bacteria in the mercury-polluted sediment of Minamata Bay, Japan.

A total of 4,604 bacterial strains isolated from the sediments of Minamata Bay and nearby low-level-mercury stations (control stations) were screened for the ability to volatilize mercury from inorganic and organic mercurial compounds. The strains that volatilize mercury from several kinds of organomercurials were found only in the sediments of Minamata Bay.     

Antimicrobial activity of surface attached marine bacteria in biofilms

Relatively little is known about the microbial ecology of biofilm communities or the diversity of antimicrobial molecules that they produce to regulate these communities. This study tested whether the production of antimicrobial activity in biofilm cultures is enhanced towards competing bacteria found in those biofilms. First, the production of antimicrobial activity of marine bacteria grown in biofilms was tested. Fourteen of the 105 marine isolates tested were found to produce antimicrobial factors when grown in biofilms. The antimicrobial activity produced by these isolates in biofilms was more potent and inhibited a broader range of target bacteria grown in biofilms compared to shaken liquid cultures. In a separate experiment, we found that cultivation in biofilms containing produced metabolites from an ‘inducer’ bacterium stimulated the production of antimicrobial molecules by ‘producer’ bacteria that were active against the ‘inducer’ bacterium. Overall, the study suggests that surface attached marine bacteria can target their antimicrobial activity towards competing bacteria in biofilms.     

Isolation and partial characterization of bacteria with potential antimicrobial activity from the Caspian Sea

Due to the constant increasing of bacterial resistance against known antibiotics, it is now necessary to find new sources of antimicrobials including the marine environment. The aim of this study was to evaluate antimicrobial activity of bacterial strains isolated from different coastal regions of the Caspian Sea and to provide phylogenetic analyses of antibiotic producing strains. Water samples collected from the Caspian Sea were serially diluted and plated on selective media. Isolates were tested against a panel of reference strains (Streptococcus pyogenes, Staphylococcus aureus, Escherichia coli, and Pseudomonas aeruginosa) by microbial antagonism and disc diffusion assay. Unweighted Pair Group Method with Arithmetic Mean (UPGMA) method was also employed to produce a phylogenetic tree based on 16S rDNA sequences. Amongst 162 isolates, 8 strains (4.93%) showed antibacterial activity. Isolated bacteria displayed more activity against gram-positive bacteria than gram-negative bacteria. Moreover, the 16S sequences obtained for the 8 selected strains were compared using a BLAST algorithm and allowed us to determine the strains genus as followed: Bacillus (RS28, RS54, RS56, RS82, RS116, and NS53), Brevundimonas (RS32), and Arthrobacter (NS25). The findings of the present study recommend that culturally marine bacteria collected from the Caspian Sea might be a potent source of novel bioactive compounds such as antibiotics.     

Application of antisera raised against sulfate-reducing bacteria for indirect immunofluorescent detection of immunoreactive bacteria in sediment from the German Baltic Sea.

Polyclonal rabbit antisera raised against sulfate-reducing bacteria (SRB) could detect several distinct populations of bacteria in sediment from the German Baltic Sea. The depth distribution of immunoreactive bacteria was determined by an indirect immunofluorescence filter method. Anti-Desulfovibrio desulfuricans DSM 1926 serum showed maximum bacterial numbers at a depth of 18 cm, with a concentration of 60 x 10(6) cells cm-3. With anti-Desulfovibrio baculatus DSM 2555 serum, counts were highest at the same depth, approaching 0.7 x 10(6) cells cm-3. Other significantly smaller populations were observed. Anti-SRBStrain 1 (lactate,vibrio) maxima were at 0 to 4 cm and at 17 to 18 cm. Anti-SRBStrain 2 (lactate,vibrio) serum showed several local maxima. Anti-SRBStrain 3 (lactate,oval) serum detected one single peak at a depth of 10 to 12 cm. Also determined were rates of sulfate reduction, total bacterial counts by acridine orange staining, and the viable counts by dilution series on anaerobic lactate medium. The total bacterial counts were highest (180 x 10(6) cells cm-3) at 3 to 4 cm and dropped to 24 x 10(6) cells cm-3 at 10 to 11 cm but showed additional local maxima reaching 140 x 10(6) cells cm-3 at a depth of 17 to 18 cm. Viable counts probable number) were above 10(5) CFU cm-3 at 0 to 3.6 cm but remained below 10(3) CFU at 7.2 to 18 cm. The sulfate reduction rate was maximal (107 nmol cm-3 day-1) at a depth of 1 to 2 cm, dropped to 10 nmol cm-3 day-1 at 12 to 13 cm, and reached 38 nmol cm-3 day-1 at 17 to 18 cm.     

A new lineage of halophilic, wall-less, contractile bacteria from a brine-filled deep of the Red Sea

A novel strictly anaerobic bacterium designated strain SSD-17B(T) was isolated from the hypersaline brine-sediment interface of the Shaban Deep, Red Sea. Cells were pleomorphic but usually consisted of a central coccoid body with one or two "tentacle-like" protrusions. These protrusions actively alternated between a straight, relaxed form and a contracted, corkscrew-like one. A peptidoglycan layer was not detected by electron microscopy. The organism forms "fried-egg"-like colonies on MM-X medium. The organism is strictly anaerobic and halophilic and has an optimum temperature for growth of about 30 to 37 degrees C and an optimum pH of about 7. Nitrate and nitrite are reduced; lactate is a fermentation product. The fatty acid profile is dominated by straight saturated and unsaturated chain compounds. Menaquinone 4 is the major respiratory quinone. Phylogenetic analysis demonstrated strain SSD-17B(T) represents a novel and distinct lineage within the radiation of the domain Bacteria. The branching position of strain SSD-17B(T) was equidistant to the taxa considered to be representative lineages of the phyla Firmicutes and Tenericutes (with its sole class Mollicutes). The phenotypic and phylogenetic data clearly show the distinctiveness of this unusual bacterium, and we therefore propose that strain SSD-17B(T) (= DSM 18853 = JCM 14575) represents a new genus and a new species, for which we recommend the name Haloplasma contractile gen. nov., sp. nov. We are also of the opinion that the organism represents a new order-level taxon, for which we propose the name Haloplasmatales.     

Distribution and characteristics of Bacillus bacteria associated with hydrobionts and the waters of the Peter the Great Bay, Sea of Japan

Bacilli of the species Bacillus subtilis, B. pumilus, B. mycoides, B. marinus and B. licheniformis (a total of 53 strains) were isolated from 15 invertebrate species and the water of the Vostok Bay, Peter the Great Bay, Sea of Japan. Bacilli were most often isolated from bivalves (22.7%) and sea cucumbers (18.9%); they occurred less frequently in sea urchins and starfish (13.2 and 7.5%, respectively). Most of bacilli strains were isolated from invertebrates inhabiting silted sediments. No Bacillus spp. strains were isolated from invertebrates inhabiting stony and sandy environments. The species diversity of bacilli isolated from marine objects under study was low. Almost all bacterial isolates were resistant to lincomycin. Unlike B. pumilus, B. subtilis isolates were mostly resistant to benzylpenicillin and ampicillin. Antibiotic sensitivity of B. licheniformis strains was variable (two strains were resistant to benzylpenicillin and oxacillin, while one was sensitive). A significant fraction of isolated bacilli contained pigments. Pigmented strains were more often isolated from seawater samples, while colorless ones predominated within hydrobionts. B. subtilis colonies had the broadest range of colors. In the Bacillus strains obtained, DNase, RNase, phosphatase, elastolytic, chitinase, and agarolytic activity was detected. Bacilli strains with hydrolytic activity occurred in invertebrates more often than in seawater.     

Calcareous nannofossil surface sediment assemblages from the Sicily Channel (central Mediterranean Sea): Palaeoceanographic implications

Quantitative analysis of 67 calcareous nannofossil assemblages from surface sediments recovered in a wide area across the Sicily Channel has been carried out in order to improve the interpretation of palaeontological data based on this planktonic group in a key area for Mediterranean palaeoceanographic studies. The investigation focused on three case studies that demonstrate the high potentiality of such a combined approach, taking into account the recent distribution of taxa or groups of taxa on the sea floor and the palaeontological record. The distribution of reworked specimens over the northern Sicily Channel sea floor validates the role of southern Sicily as a source region for reworked nannofossils and the role of rivers as their carrier. Eustatic sea-level fluctuations can be considered to be the main factor that influenced the abundance variations in sedimentary sequences of this area. The distribution of Florisphaera profunda can be explained in terms of topography (positive correlation) and mesoscale oceanographic circulation. In particular, its significant anti-correlation to the amount of chlorophyll-A deduced by satellite imagery validates the use of this species as a proxy for palaeoproductivity reconstructions. Finally, high abundance values of G. oceanica are confined to the westernmost part of the Sicily Channel, coinciding with a water mass salinity minimum. In particular, abundances of up to about 10% were observed in the westernmost part of the African Margin, suggesting the importance of the Atlantic Tunisian Current, whose activity is more pronounced in winter. The comparison of data of this species between 135 and 110 kyr BP, inside and outside the Channel, led us to deduce that the physical transport in almost unmodified waters of Atlantic origin might be the most important factor for its significant occurrence.     

Antimicrobial activity of marine bacteria associated with sponges from the waters off the coast of South East India

Seventy-five marine bacterial strains associated with four species of sponges (Echinodictyum sp., Spongia sp., Sigmadocia fibulatus and Mycale mannarensis) were isolated from the Tuticorin coast, Gulf of Mannar region. The agar-overlay method was used to screen for antibiotic production by these strains against four bacteria, viz., Bacillus subtilis, Escherichia coli, Vibrio parahaemolyticus, and Vibrio harveyi and one fungal pathogen, viz., Candida albicans. Twenty-one per cent of the bacterial strains were found to be antibiotic producers and their activities ranged from broad spectral to species specific. A strain coded SC3 was found to be highly potent and was mass cultured. The ethyl acetate extract of the culture broth was further fractionated by reverse phase HPLC and the active fraction identified. In addition, SC3 was subjected to morphological and physiological characterization. The results of the tests showed SC3 to be a Gram-positive rod, sporulating, motile, catalase and oxidase positive. Phylogenetic analysis based on comparative analysis of sequenced 16s rRNA of the active strains indicated a preponderance of bacteria belonging to Vibrio and Bacillus genera with 95-99% sequence similarities. To our knowledge this is the first report on phylogenetic identification of antibiotic producing bacteria associated with sponges from Indian waters.