Determination of the Total Microbial Abundance in Black Sea Bottom Sediments Using Flow Cytometry

Microbiology - The known approaches to sample preparation have been improved to achieve a more complete detection of microorganisms of the Black Sea bottom sediments using flow cytometry of SYBR...     

Tube-dwelling Meiofauna in Marine Sediments

Tube-dwelling has been recognized previously as a life-style for several meiobenthic species, but behavioural observation of living specimens has rarely been reported. The extent to which tube-building and tube-dwelling occurs within meiofauna, and how they have influenced evolutionary and ecological processes as well as morphology within these organisms, is relatively unknown but potentially of great significance. In addition to direct observation of tube-building and the occurence of tubes in natural habitats, the internal anatomy associated with tube-building in two nematode species (Ptycholaimellus jacobi, P. ponticus) and one harpacticoid copepod species (Stenhelia palustris) is the focus of this study. Special attention is given to the secretory products, glands, and their association with secretory pores. Also, the role of meiobenthic tube-dwelling activities in relationship to their environment is extensive discussed.     

Biodegradation of Pyrene in Marine Beach Sediments

The potential of chitosan (0.1% dry weight equivalent) as a bioremediation additive for removal of the recalcitrant polycyclic aromatic hydrocarbon (PAH) pyrene in marine beach sediments was investigated using an open irrigation system over a 63-day period. Osmocote, a slow release fertilizer, was used as the key nutrient supplement at a concentration of 1% in sediment (dry weight equivalent). Osmocote significantly (p < .05) enhanced nutrient levels, and the metabolic activity of the indigenous microbial biomass. Both additives were comparable in stimulating pyrene biodegradation rates; with chitosan (0.062 day^?1) being slightly more effective as an amendment than Osmocote (0.051 day^?1). Loss of pyrene in a control sediment (i.e., pyrene, without additives) was 66.6% over a 63-day period. The concurrent application of additives yielded the greatest biodegradation rates (0.072day^?1), resulting in a 98.2% loss of pyrene over 63 days. The treatment of oil contaminated beach sediments with both osmocote (1%) and chitosan (0.1%) is therefore recommended as an effective treatment for the intrinsic biodegradation of recalcitrant PAHs in oil-contaminated beach sediments.     

Temporal and Spatial Abundance of Naked Amoebae (Gymnamoebae) in Marine Benthic Sediments of the Clyde Sea Area, Scotland

ABSTRACT. The abundances of benthic naked amoebae in the sediments of the Clyde Sea Area, Scotland, were studied throughout 1991. Four sites differing in sediment grain size and organic carbon content were chosen for study. Amoebae were enumerated by enrichment cultivation methods and found to be numerically important, attaining densities of up to 14,883 amoebae/cm³ on one occasion. They were most abundant, and temporally stable, in finer sediments where they averaged 2,224 cells/cm³ and lower and more variable in the sandy sediments, averaging 874 cells/cm³ throughout the year. In general, amoebae were most abundant in the surface sediment layers. Around 70 different morphotypes were recorded, and 61% of all amoebae counted were less than 10 μm in length. This is the first detailed quantitative study of benthic marine gymanamoebae and shows that naked amoebae and flagellates are numerically the dominant interstitial fauna in sediments of this area. Moreover, the gymnamoebae comprised the largest proportion of total protozoan biomass (excluding foraminiferans) and clearly need to be considered in future models of benthic carbon flow.     

Prokaryotic Diversity in Zostera noltii-Colonized Marine Sediments

The diversity of microorganisms present in a sediment colonized by the phanerogam Zostera noltii has been analyzed. Microbial DNA was extracted and used for constructing two 16S rDNA clone libraries for Bacteria and Archaea. Bacterial diversity was very high in these samples, since 57 different sequences were found among the 60 clones analyzed. Eight major lineages of the Domain Bacteria were represented in the library. The most frequently retrieved bacterial group (36% of the clones) was δ-Proteobacteria related to sulfate-reducing bacteria. The second most abundant group (27%) was γ-Proteobacteria, including five clones closely related to S-oxidizing endosymbionts. The archaeal clone library included members of Crenarchaeota and Euryarchaeota, with nine different sequences among the 15 analyzed clones, indicating less diversity when compared to the Bacteria organisms. None of these sequences was closely related to cultured Archaea organisms.     

Higher Abundance of Bacteria than of Viruses in Deep Mediterranean Sediments

The interactions between viral abundance and bacterial density, biomass, and production were investigated along a longitudinal transect consisting of nine deep-sea stations encompassing the entire Mediterranean basin. The numbers of viruses were very low (range, 3.6 × 10⁷ to 12.0 × 10⁷ viruses g⁻¹) and decreased eastward. The virus-to-bacterium ratio was always < 1.0, indicating that the deep-sea sediments of the Mediterranean Sea are the first example of a marine ecosystem not numerically dominated by viruses. The lowest virus numbers were found where the lowest bacterial metabolism and turnover rates and the largest cell size were observed, suggesting that bacterial doubling time might play an important role in benthic virus development.     

Characterization of beta-Glucosidase Activity in Intertidal Marine Sediments

Glycoside derivatives of 4-methylumbelliferone (MUF) were used to characterize the polysaccharidase enzyme systems present in sediments from an intertidal mud flat. The formation of highly fluorescent MUF on hydrolysis of the various glycosides was determined at low substrate concentrations (<1 muM) and with short incubation periods (>5 min). The hydrolysis of MUF-beta-d-glucose in sediments from depth intervals of 0 to 2 cm was insensitive to the presence of oxygen, dissolved sulfide, and iron; magnesium and calcium were stimulatory, however. A pronounced temperature optimum was observed at 40 degrees C, a salinity optimum at 30 per thousand, and a pH optimum at 8.5. Rates of hydrolysis were completely inhibited by the addition of mercuric chloride and sodium azide, but only partially inhibited by toluene and the specific beta-glucosidase inhibitor delta-1,5-gluconolactone. The response to delta-1,5-gluconolactone suggested that about 50% of the observed hydrolysis of MUF-beta-d-glucoside was due to exo- and endoglucanases. A wide variety of hydrolytic activities was observed, with at least some nonspecificity occurring in the case of MUF-beta-d-fucoside. Depth profiles indicated maximal activity in surface sediments with a rapid decline below 2 cm. MUF-glycosides provided a convenlent tool for initial analyses of the dynamics and controls of polymer hydrolysis in marine sediments.     

海洋沉积环境来源真菌次生代谢产物的研究

海洋沉积环境复杂多样,微生物往往进化形成与其环境相适应的代谢系统.真菌作为海洋沉积环境中的重要微生物,它们的次生代谢产物结构出新率高、生物活性显著,是开发海洋先导药物的新兴资源.本文综述了1995-2011年间发表的200个海洋沉积环境真菌次生代谢产物,其来源菌株广泛分布在真菌16个属,主要集中在Penicillium属(30％)、Aspergillus属(19％)、Spicaria属(18％)和Trichoderma属(13％);其结构类型包括生物碱类(86个)、萜类(42个)、聚酮类(42个)、肽类(15个)、甾体类(5个)、脑苷脂类(4个)和其他类(6个),活性研究主要集中在细胞毒性和抗菌等方面.     

Abundance and Diversity of Ammonia-Oxidizing Microorganisms in the Sediments of Jinshan Lake

Community structures of ammonia-oxidizing microorganisms were investigated using PCR primers designed to specifically target the ammonia monooxygenase α-subunit (amoA) gene in the sediment of Jinshan Lake. Relationships between the abundance and diversity of ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB), and physicochemical parameters were also explored. The AOA abundance decreased sharply from west to east; however, the AOB abundance changed slightly with AOB outnumbering AOA in two of the four sediment samples (JS), JS3 and JS4. The AOA abundance was significantly correlated with the NH₄–N, NO₃–N, and TP. No significant correlations were observed between the AOB abundance and environmental variables. AOB had a higher diversity and richness of amoA genes than AOA. Among the 76 archaeal amoA sequences retrieved, 57.89, 38.16, and 3.95 % fell within the Nitrosopumilus, Nitrososphaera, and Nitrososphaera sister clusters, respectively. The 130 bacterial amoA gene sequences obtained in this study were grouped with known AOB sequences in the Nitrosomonas and Nitrosospira genera, which occupied 72.31 % and 27.69 % of the AOB group, respectively. Compared to the other three sample sites, the AOA and AOB community compositions at JS4 showed a large difference. This work could enhance our understanding of the roles of ammonia-oxidizing microorganisms in freshwater lake environment.     

Isolation of Cellulolytic Actinomycetes from Marine Sediments

The cellulolytic activity of 36 actinomycetes strains isolated from marine sediments was investigated by the cellulose-azure method. Approximately 50% of the isolates exhibited various degrees of cellulolytic activity.     

Methane Production in Shallow-Water, Tropical Marine Sediments

The in situ production of methane was monitored in several types of tropical benthic communities. A bed of Thalassia testudinum located in Caesar Creek (Florida Keys) exhibited the highest methanogenic activity (initial rates = 1.81 to 1.86 mumol CH4/m2 per h) as compared with another seagrass (Syringodium sp., 0.15 to 0.33 mumol/m2 per h) and two coral reef environments (Hydro-Lab, 0.016 to 0.10 mumol/m2 per h; Curacao, 0.14 to 0.47 mumol/m2 per h). The results suggest that a wide variety of benthic metabolic processes (e.g., photosynthetic oxygen production) influences methane production rates.     

Abiotic Racemization Kinetics of Amino Acids in Marine Sediments

The ratios of d- versus l-amino acids can be used to infer the sources and composition of sedimentary organic matter. Such inferences, however, rely on knowing the rates at which amino acids in sedimentary organic matter racemize abiotically between the d- and the l-forms. Based on a heating experiment, we report kinetic parameters for racemization of aspartic acid, glutamic acid, serine, and alanine in bulk sediment from Aarhus Bay, Denmark, taken from the surface, 30 cm, and 340 cm depth below seafloor. Extrapolation to a typical cold deep sea sediment temperature of 3°C suggests racemization rate constants of 0.50×10⁻⁵–11×10⁻⁵ yr⁻¹. These results can be used in conjunction with measurements of sediment age to predict the ratio of d:l amino acids due solely to abiotic racemization of the source material, deviations from which can indicate the abundance and turnover of active microbial populations.     

Abundance and Biomass of Heterotrophic Flagellates, and Factors Controlling Their Abundance and Distribution in Sediments of Botany Bay

The abundance and biomass of heterotrophic flagellates were estimated monthly in sediments of Botany Bay during March 1999-February 2000. The annual abundance and biomass were in the ranges of 0.46-4.70 x 10(5) cells/cm(3) and of 0.30-8.61 micro g C/cm(3), respectively. The majority of heterotrophic flagellates (93-100%) were less than 10 mm in length and few flagellates were larger than 10 mm. Of the total microbial carbon biomass, heterotrophic flagellates made up about 5% (but at times up to 35%). The contribution of heterotrophic flagellates varied from month to month, and among the sites. The abundance of heterotrophic flagellates was negatively correlated with sediment grain size and positively correlated with the abundance of bacteria, algae (autotrophic flagellates and diatoms), and their probable grazers. A best subsets regression analysis showed that bacterial and algal abundance are the most important factors controlling the abundance of heterotrophic flagellates. When the previously reported grazing rates on bacteria were applied, heterotrophic flagellates would consume a maximum of 64% of bacterial standing stock daily in Botany Bay, suggesting that heterotrophic flagellates are important as bacterivores. However, the importance of heterotrophic flagellate grazing probably varies significantly among the sites and from month to month.     

Seasonal Rates of Methane Oxidation in Anoxic Marine Sediments

Methane concentrations and rates of methane oxidation were measured in intact sediment cores from an inshore marine sediment at Jutland, Denmark. The rates of methane oxidation, determined by the appearance of ¹⁴CO₂ from injected ¹⁴CH₄, varied with sediment depth and season. Most methane oxidation was anoxic, but oxygen may have contributed to methane oxidation at the sediment surface. Cumulative rates (0- to 12-cm depth) for methane oxidation at Kysing Fjord were 3.34, 3.48, 8.60, and 17.04 μmol m⁻² day⁻¹ for April (4°C), May (13°C), July (17°C), and August (21°C), respectively. If all of the methane was oxidized by sulfate, it would account for only 0.01 to 0.06% of the sulfate reduction. The data indicate that methane was produced, in addition to being oxidized, in the 0- to 18-cm sediment stratum.     

Nitrogen Metabolism Genes from Temperate Marine Sediments

In this study, we analysed metagenomes along with biogeochemical profiles from Skagerrak (SK) and Bothnian Bay (BB) sediments, to trace the prevailing nitrogen pathways. NO₃ ^? was present in the top 5 cm below the sediment-water interface at both sites. NH₄ ⁺ increased with depth below 5 cm where it overlapped with the NO₃ ^? zone. Steady-state modelling of NO₃ ^? and NH₄ ⁺ porewater profiles indicates zones of net nitrogen species transformations. Bacterial protease and hydratase genes appeared to make up the bulk of total ammonification genes. Genes involved in ammonia oxidation (amo, hao), denitrification (nir, nor), dissimilatory NO₃ ^? reduction to NH₄ ⁺ (nfr and otr) and in both of the latter two pathways (nar, nap) were also present. Results show ammonia-oxidizing bacteria (AOB) and ammonia-oxidizing archaea (AOA) are similarly abundant in both sediments. Also, denitrification genes appeared more abundant than DNRA genes. 16S rRNA gene analysis showed that the relative abundance of the nitrifying group Nitrosopumilales and other groups involved in nitrification and denitrification (Nitrobacter, Nitrosomonas, Nitrospira, Nitrosococcus and Nitrosomonas) appeared less abundant in SK sediments compared to BB sediments. Beggiatoa and Thiothrix 16S rRNA genes were also present, suggesting chemolithoautotrophic NO₃ ^? reduction to NO₂ ^? or NH₄ ⁺ as a possible pathway. Our results show the metabolic potential for ammonification, nitrification, DNRA and denitrification activities in North Sea and Baltic Sea sediments.     

Marine Sediments Illuminate Chlamydiae Diversity and Evolution

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Distribution of Methanogenic and Sulfate-Reducing Bacteria in Near-Shore Marine Sediments

The distribution of methanogenic and sulfate-reducing bacteria was examined in sediments from three sites off the coast of eastern Connecticut and five sites in Long Island Sound. Both bacterial groups were detected at all sites. Three distributional patterns were observed: (i) four sites exhibited methanogenic and sulfate-reducing populations which were restricted to the upper 10 to 20 cm, with a predominance of sulfate reducers; (ii) three sites in western Long Island Sound exhibited a methanogenic population most abundant in sediments deeper than those occupied by sulfate reducers; (iii) at one site that was influenced by fresh groundwater, methanogens and sulfate reducers were numerous within the same depths; however, the number of sulfate reducers varied vertically and temporally with sulfate concentrations. It was concluded that the distributions of abundant methanogenic and sulfate-reducing bacteria were mutually exclusive. Methanogenic enrichments yielded all genera of methanogens except Methanosarcina, with the methanobacteria predominating.     

Occurrence of Priming in the Degradation of Lignocellulose in Marine Sediments

More than 50% of terrestrially-derived organic carbon (terrOC) flux from the continents to the ocean is remineralised in the coastal zone despite its perceived high refractivity. The efficient degradation of terrOC in the marine environment could be fuelled by labile marine-derived material, a phenomenon known as “priming effect”, but experimental data to confirm this mechanism are lacking. We tested this hypothesis by treating coastal sediments with ¹³C-lignocellulose, as a proxy for terrOC, with and without addition of unlabelled diatom detritus that served as the priming inducer. The occurrence of priming was assessed by the difference in lignocellulose mineralisation between diatom-amended treatments and controls in aerobic sediment slurries. Priming of lignocellulose degradation was observed only at the initial stages of the experiment (day 7) and coincided with overall high microbial activity as exemplified by total CO₂ production. Lignocellulose mineralisation did not differ consistently between diatom treatments and control for the remaining experimental time (days 14–28). Based on this pattern, we hypothesize that the faster initiation of lignocellulose mineralisation in diatom-amended treatments is attributed to the decomposition of accessible polysaccharide components within the lignocellulose complex by activated diatom degraders. The fact that diatom-degraders contributed to lignocellulose degradation was also supported by the different patterns in ¹³C-enrichment of phospholipid fatty acids between treatments. Although we did not observe differences between treatments in the total quantity of respired lignocellulose at the end of the experiment, differences in timing could be important in natural ecosystems where the amount of time that a certain compound is subject to aerobic degradation before burial to deeper anoxic sediments may be limited.