Distribution of Microorganisms in the Subsurface of the Manus Basin Hydrothermal Vent Field in Papua New Guinea

The distribution of microorganisms in the subsurfaces of hydrothermal vents was investigated by using subvent rock core samples. Microbial cells and ATP were detected from cores taken at depths of less than 99.4 and 44.8 m below the seafloor (mbsf), respectively. Cores from various depths were incubated anaerobically with a heterotrophic medium. Growth at 60 and 90°C was ascribed to a Geobacillus sp. in the 448.6- to 99.4-mbsf cores and a Deinococcus sp. in the 64.8- to 128.9-mbsf cores, respectively, based on the 16S ribosomal DNA analysis.     

Bradyrhizobium Populations Occur in Deep Soil under the Leguminous Tree Acacia albida

Soil cores were drilled under the leguminous tree Acacia albida growing in two different ecoclimatic zones of West Africa: the Sahelian area (100 to 500 mm of annual rainfall) and the Sudano-Guinean area (1,000 to 1,500 mm of annual rainfall). Soil samples were collected at different depths from the surface down to the water table level and analyzed for the presence of rhizobia able to nodulate A. albida. In both areas, population densities of rhizobia were substantially greater near the water table than near the surface. In the Sahelian area, rhizobia were present as deep as 34 m at a concentration of 1.3 × 10³/g of soil. In the Sudano-Guinean area, population densities at 0.5 to 4.5 m depth were higher than in the Sahelian area and, at several depths, comparable to that of temperate soils supporting legume crops (10⁴ rhizobia per g of soil). Surface and deep soil isolates from all four sites were found to be slow-growing rhizobia (Bradyrhizobium sp.). The proportion of effective isolates was almost the same within surface and deep soils.     

Persistence and efficacy of termiticides used in preconstruction treatments to soil in Mississippi

Laboratory and field studies were conducted to determine the persistence and efficacy of termiticides used as preconstruction treatments against subterranean termites. Bifenthrin (0.067%), chlorpyrifos (0.75%), and imidacloprid (0.05%) ([AI]; wt:wt) were applied to soil beneath a monolithic concrete slab at their minimum labeled rates. Soil samples were taken from three depths (0-2.5, 2.6-7.6, and 7.7-15.2 cm) at six sampling times (0, 3, 6, 9, 12 and 48 mo) from sites in Harrison and Oktibbeha counties in Mississippi. Residue analyses were conducted on the 0-2.5- and 2.6-7.5-cm depths, and bioassays were conducted using all three depths. In field studies, significant termiticide degradation occurred between sampling times 0 and 48 mo for all termiticides. At all sampling times, the top 2.5 cm of soil contained more termiticide than the other depths. Time to 50% dissipation of termiticide in the 0-2.5-cm depth was 9, 6, and 2 mo for bifenthrin, chlorpyrifos, and imidacloprid, respectively. Termite mortalities in contact bioassays remained high for bifenthrin and chlorpyrifos throughout the 48-mo sampling period; however, mortality of termites exposed to imidacloprid-treated soil dropped after the initial sampling. Termites readily penetrated all termiticide-treated soil in bioassays of 52-mm soil cores at 48 mo. Percentage of mortality in these bioassays was 15, 43, and 13 for bifenthrin, chlorpyrifos, and imidacloprid respectively.     

Microarray-based characterization of microbial community functional structure and heterogeneity in marine sediments from the Gulf of Mexico

Marine sediments of coastal margins are important sites of carbon sequestration and nitrogen cycling. To determine the metabolic potential and structure of marine sediment microbial communities, two cores were collected each from the two stations (GMT at a depth of 200 m and GMS at 800 m) in the Gulf of Mexico, and six subsamples representing different depths were analyzed from each of these two cores using functional gene arrays containing approximately 2,000 probes targeting genes involved in carbon fixation; organic carbon degradation; contaminant degradation; metal resistance; and nitrogen, sulfur, and phosphorous cycling. The geochemistry was highly variable for the sediments based on both site and depth. A total of 930 (47.1%) probes belonging to various functional gene categories showed significant hybridization with at least 1 of the 12 samples. The overall functional gene diversity of the samples from shallow depths was in general lower than those from deep depths at both stations. Also high microbial heterogeneity existed in these marine sediments. In general, the microbial community structure was more similar when the samples were spatially closer. The number of unique genes at GMT increased with depth, from 1.7% at 0.75 cm to 18.9% at 25 cm. The same trend occurred at GMS, from 1.2% at 0.25 cm to 15.2% at 16 cm. In addition, a broad diversity of geochemically important metabolic functional genes related to carbon degradation, nitrification, denitrification, nitrogen fixation, sulfur reduction, phosphorus utilization, contaminant degradation, and metal resistance were observed, implying that marine sediments could play important roles in biogeochemical cycling of carbon, nitrogen, phosphorus, sulfate, and various metals. Finally, the Mantel test revealed significant positive correlations between various specific functional genes and functional processes, and canonical correspondence analysis suggested that sediment depth, PO(4)(3-), NH(4)(+), Mn(II), porosity, and Si(OH)(4) might play major roles in shaping the microbial community structure in the marine sediments.     

Methane production in rice soil is inhibited by cyanobacteria

The present study was aimed at understanding the role of cyanobacteria and Azolla in methane production and oxidation in laboratory simulation experiments using soil samples from rice fields. All the seven cyanobacterial strains tested effected a significant decrease in the headspace concentration of methane in flooded soil, incubated under light. Synechocystis sp. was the most effective in retarding methane concentration by 10-20 fold over that in controls without cyanobacteria. The decrease in the headspace concentration of methane was negligible in nonsterile soil samples, inoculated with Synechocystis sp. and then incubated under dark. Moist soil cores (0-5 cm depth), collected from rice fields that had been treated with urea in combination with a cyanobacterial mixture, Azolla microphylla, or cyanobacterial mixture plus A. microphylla, effected distinctly more rapid decrease in the headspace concentration of methane added at 200 microl(-1) than did the soil cores from plots treated with urea alone (30, 60, 90 and 120 kg N ha(-1)), irrespective of the rate of chemical nitrogen applied to rice fields. Besides, soil cores from plots treated with urea alone at 60, 90 and 120 kg N ha(-1) oxidised methane more rapidly than did the core samples from plots treated with urea alone at 30kg N ha(-1). Cyanobacteria and A. microphylla, applied to flood water, appear to play a major role in mitigation of methane emission from rice fields-through enhanced methane oxidation.     

中亚热带杉木人工林细根生物量空间变异与取样数量估算

林木细根生物量具有一定的空间异质性,因此采用合理的细根取样策略对精确估算细根生物量十分重要。通过在福建省三明杉木人工林林内采用土钻法随机选取100个取样点,分析不同细根类型(杉木、林下植被、总细根)生物量的空间变异特征,并对细根生物量所需的取样数量进行估计。结果表明:不同细根类型单位面积生物量随径级(0—1、1—2 mm)及土层深度的增加变异增大,所需的取样数量也相应增加。Shapiro-Wilk检验表明,仅0—2 mm杉木细根和总细根单位面积生物量符合正态分布,其余各个细根类型不同径级不同土层单位面积生物量均不符合正态分布,均呈明显的右偏分布。蒙特卡罗统计模拟分析表明:在置信水平为95%、精度为80%的条件下,直径为0—1 mm、1—2 mm和0—2 mm的细根,杉木采集95、96、32个样品可以满足测定单位面积生物量的需要,林下植被分别采集98、98、63个样品可以满足测定单位面积生物量的需要,而总细根分别采集93、93、18个样品可以满足测定单位面积生物量的需要。     

Subfossil 16S rRNA Gene Sequences of Green Sulfur Bacteria in the Black Sea and Their Implications for Past Photic Zone Anoxia

The Black Sea is the largest extant anoxic water body on Earth. Its oxic-anoxic boundary is located at a depth of 100 m and is populated by a single phylotype of marine green sulfur bacteria. This organism, Chlorobium sp. strain BS-1, is extraordinarily low light adapted and can therefore serve as an indicator of deep photic zone anoxia (A. K. Manske, J. Glaeser, M. M. M. Kuypers, and J. Overmann, Appl. Environ. Microbiol. 71:8049-8060, 2005). In the present study, two sediment cores were retrieved from the bottom of the Black Sea at depths of 2,006 and 2,162 m and were analyzed for the presence of subfossil DNA sequences of BS-1 using ancient-DNA methodology. Using optimized cultivation media, viable cells of the BS-1 phylotype were detected only at the sediment surface and not in deeper layers. In contrast, green sulfur bacterial 16S rRNA gene fragments were amplified from all the sediment layers investigated, including turbidites. After separation by denaturing gradient gel electrophoresis and sequencing, 14 different sequence types were distinguished. The sequence of BS-1 represented only a minor fraction of the amplification products and was found in 6 of 22 and 4 of 26 samples from the 2,006- and 2,162-m stations, respectively. Besides the sequences of BS-1, three additional phylotypes of the marine clade of green sulfur bacteria were detected. However, the majority of sequences clustered with groups from freshwater habitats. Our results suggest that a considerable fraction of green sulfur bacterial chemofossils did not originate in a low-light marine chemocline environment and therefore were likely to have an allochthonous origin. Thus, analysis of subfossil DNA sequences permits a more differentiated interpretation and reconstruction of past environmental conditions if specific chemofossils of stenoec species, like Chlorobium sp. strain BS-1, are employed.     

Assessment of a rapid method,using soil cores,for estimating the amount and distribution of crop roots in the field

Summary A study was made of the relationship between the number of roots (N_r) observed on unit area of the freshly exposed, horizontal faces of soil cores, and the amounts of roots (per unit volume) present in the same cores. Soil cores, 7 cm diameter, were extracted to depths of 1 m from cereal crops in 1976 at three field sites located on clay soils. Sampling was either at the start of stem elongation, or at anthesis. Estimates of root length per unit soil volume (L) were derived from N_r by assuming random orientation of roots in the soil.Values of L were found to be highly correlated with the measured lengths of both the main roots (root axes) and the total roots (axes and laterals) washed from the soil at a given growth stage, for each of the soils. On average, L was 3.3 times the length of root axes washed from the soil, and was 0.42 times the length of total roots, but there was appreciable variation between different growth stages and field sites. Possible factors giving rise to differences between L and the measured lengths of roots are discussed. Estimates of root length from observation of soil cores may nonetheless provide a suitable basis for rapidly comparing therelative distribution of roots down the soil profile under field conditions.     

Poliovirus retention in 75-cm soil cores after sewage and rainwater application

The adsorption rate of a guanidine-resistant strain of poliovirus LSc 2ab was measured in Long Island soils with in situ field cores (10.1 by 75 cm). The test virus was chosen because it exhibited soil adsorption and elution characteristics of a number of non-polioviruses. After the inoculation of cores with seeded sewage effluent at a 1-cm/h infiltration rate, cores were extracted, fractionated, and analyzed for total plaque-forming units per each 5-cm fraction. The results showed that 77% of the viruses were adsorbed in the first 5 cm of soil. An additional 11% were found in the 5- to 10-cm fraction, and a total of 96% of the viruses were adsorbed by 25 cm. The remaining 4% were uniformly distributed over the next 50 cm of soil, with a minimum of 0.23% in each soil section. Few viruses (< 0.22%) were observed in core filtrates. Analysis of the viral distribution pattern in seeded cores, after an application of a single rinse of either sewage effluent or rainwater, indicated that large-scale viral mobilization was absent. However, localized areas of viral movement were noted in both of the rinsed cores, with the rainwater-rinsed cores exhibiting more expensive movement. All mobilized viruses were resorbed at lower core depths.     

Poliovirus retention in 75-cm soil cores after sewage and rainwater application.

The adsorption rate of a guanidine-resistant strain of poliovirus LSc 2ab was measured in Long Island soils with in situ field cores (10.1 by 75 cm). The test virus was chosen because it exhibited soil adsorption and elution characteristics of a number of non-polioviruses. After the inoculation of cores with seeded sewage effluent at a 1-cm/h infiltration rate, cores were extracted, fractionated, and analyzed for total plaque-forming units per each 5-cm fraction. The results showed that 77% of the viruses were adsorbed in the first 5 cm of soil. An additional 11% were found in the 5- to 10-cm fraction, and a total of 96% of the viruses were adsorbed by 25 cm. The remaining 4% were uniformly distributed over the next 50 cm of soil, with a minimum of 0.23% in each soil section. Few viruses (< 0.22%) were observed in core filtrates. Analysis of the viral distribution pattern in seeded cores, after an application of a single rinse of either sewage effluent or rainwater, indicated that large-scale viral mobilization was absent. However, localized areas of viral movement were noted in both of the rinsed cores, with the rainwater-rinsed cores exhibiting more expensive movement. All mobilized viruses were resorbed at lower core depths.     

Effects of soil amendment on gas depth profiles in soil monoliths using direct mass spectrometric measurement

Land use and agricultural practices are known to influence the source and sink concentrations of various gases, including greenhouse gases (NOx CH4 and CO2). in soils. With everincreasing production of domestic sewage sludge and the prohibition of disposal at sea, pressure on waste disposal increases. Anaerobically digested domestic sewage sludge and/or lime were applied to an upland. Scottish soil and their effects on gas depth profiles monitored as indicators of microbial processes of the soil ecosystem. The concentrations of various gases (Ar, O2. CO2, CH4, N2, NOx) were measured simultaneously at each depth using membrane inlet mass spectrometry (MIMS). This technique enables the direct measurement of multiple gas species throughout soil cores with minimal disturbance. Intact soil monoliths were collected from the sample site, following amendment, and maintained in a constant temperature, environmental growth chambers. Statistical analyses (one-way ANOVA and LSD tests) were conducted to identify the depths at which gas concentrations in amended cores were significantly different from those in control (un-amended) cores. Significant effects were observed on the concentration of CO2, CH4, NOx and N2 at certain depths. Average CH4 concentration was consistently higher (>1 microM) in the upper horizon following application of sludge and sludge and lime together. N2 and NOx concentrations were elevated in cores treated with lime by approximately 100 and 32 microM. respectively, in much of the upper horizon. CO2 concentration increased above control mean values, at certain depths, following application of either sludge or lime. Some explanation for the changes in soil gas concentration was provided by reference to the microorganism assemblages and the gases associated with biochemistry of nitrification, denitrification, methane oxidation and methanogenesis.     

Isolation of a bacterium assimilating (R)-3-chloro-1,2-propanediol and production of (S)-3-chloro-1,2-propanediol using microbial resolution

A bacterium capable of assimilating 3-chloro-1,2-propanediol was isolated from soil by enrichment culture. The strain was identified as Alcaligenes sp. by taxonomic studies. The crude extracts of the cells had dehalogenating activities and converted various halohydrins to the corresponding epoxides. 3-Chloro-1,2-propanediol was degraded stereospecifically by the strain, liberating chloride ion. The residual isomer was found to be the (S)-form (99.4% enantiomeric excess). (S)-3-Chloro-1,2-propanediol was obtained from the racemate by use of this strain in 38% yield, and (S)-glycidol (99.4% enantiomeric excess) was subsequently synthesized from the obtained (S)-3-chloro-1,2-propanediol by alkaline treatment.     

The brackishwater hyporheic zone: invertebrate community structure across a novel ecotone

This study describes a hyporheic zone that exists beneath a river-dominated estuary in North Wales, and which spans the freshwater/saltwater boundary. A series of 72 cores was taken from the Aber Estuary, in September, at depths from 10–60 cm below the bed surface. Site 1 was above the extreme high water mark and therefore was never inundated by salt water. Site 5 was the furthest downstream and was inundated twice daily by incoming tides. Substrates contained more gravel at the upstream sites and closer to the bed surface, with more sand and silt at downstream sites and at depth. Salinity of interstitial water increased both with distance away from Site 1 and with increasing depth into the zone, reaching a maximum of 15‰ at 60 cm at Site 5, as measured at low tide. Longitudinal and vertical zonations of the invertebrate taxa were evident, and densities were greater in the top 40 cm than below. Nematodes were especially abundant from 10–60 cm, and genera differed along the estuary. Oligochaetes were well represented at most sites, with the less saline sites yielding Naididae, Enchytraeidae, Aeolosomatidae and Tubificidae; Site 5 was dominated by Tubifex costatus. Chironomid larvae were most abundant to 40 cm at Sites 1 and 2 (primarily Brillia modesta, Corynoneura sp., Tanytarsus sp., and unidentified Tanypodinae), but they were also found at Site 3 (to 60 cm), and at 10 cm at Site 5 (Orthocladius sp.). Nymphs of mayflies and caddisfly larvae were found primarily at Site 1, but small stonefly nymphs and elmid beetle larvae were taken at Site 2 depths where the interstitial water was brackish. The most saline sediments were populated by the triclad Uteriporus vulgaris, the polychaete Nereis sp., and snails (Hydrobia sp.). Site, salinity, pH, and sand and silt contents appeared to influence species distribution most; together, these explained 37.8% of the variance (CANOCO). There was an overall negative relationship between silt content of the sediments and total invertebrate density. The hyporheic zone of the Aber Estuary is thus not only influenced by surface water and, presumably, estuarine groundwater exchanges, but is further complicated, biologically, by having a salinity gradient running through it. The term `brackishwater hyporheic zone' (BHZ) is proposed to describe this and similar systems.     

The topsoil as the major store of the propagules of vesicular-arbuscular mycorrhizal fungi in southeast Australian sandstone soils

The formation of vesicular-arbuscular mycorrhizae (VAM) in intact soil profiles from two sites in southeastern Australia were measured at two depths using a bioassay grown in intact soil cores. Intact soil cores were taken from (1) topsoil (0–15 cm) and (2) subsoil (15–30 cm) four times during 1990. Seeds of Acacialinifolia (Vent.) Willd. (Mimosaceae) were sown into the cores and plants harvested 8 and 12 weeks after sowing. For 1990, at both sites and in all seasons, VAM most readily developed in the roots of seedlings of A. linifolia grown in topsoil. Limited VAM occurred in roots grown in subsoil cores. Most colonisation of roots by VAM occurred from cores collected during spring and summer. Spore numbers were quantified for each site and depth by wet-sieving 100-g samples of air-dried soil and counting turgid spores containing oil droplets. Three types of spores were found in the soils. Few spores were extracted from all soils sampled, and for the most abundant of the spore types at least twice as many spores occurred in the topsoil than in the subsoil for all seasons examined. As most of the propagules that initiate VAM infection were observed in the topsoil, disturbances which involve the removal and storage of the top 15 cm will adversely affected these fungi.     

Ecophysiological properties of photosynthesizing bacteria from the Black Sea chemocline zone

In May 1998, during the fifty-first voyage on board the research vessel Professor Vodyanitskii, a comparative study was conducted of the species diversity of green and purple sulfur bacteria in the water column of the chemocline zone at deep-sea stations and on the bottom surface of the Black Sea shallow regions. At three deep-sea stations, the accumulation of photosynthesizing bacteria in the chemocline zone at a depth of 85-115 m was revealed on the basis of the distribution of potential values of carbon dioxide light fixation. The location of the site of potential carbon dioxide light fixation suggests that the photosynthesis may be determined by the activity of the brown Chlorobium sp., revealed earlier at these depths. Enrichment cultures of brown sulfur bacteria were obtained from samples taken at the deep-sea stations. By morphology, these bacteria, assigned to Chlorobium sp., appear as nonmotile straight or slightly curved rods 0.3-0.5 x 0.7-1.2 microm in size; sometimes, they form short chains. Ultrathin sections show photosynthesizing antenna-like structures, chlorosomes, typical of Chlorobiaceae. The cultures depended on the presence of NaCl (20 g/l) for growth, which corresponds to the mineralization of Black Sea water. The bacteria could grow photoautotrophically, utilizing sulfide, but the Black Sea strains grew much more slowly than the known species of brown sulfur bacteria isolated from saline or freshwater meromictic lakes. The best growth of the strains studied in this work occurred in media containing ethanol (0.5 g) or sodium acetate (1 g/l) and low amounts of sulfide (0.4 mM), which is consistent with the conditions of syntrophic growth with sulfidogens. The data obtained allow us to conclude that the cultures of brown sulfur bacteria are especially adapted to developing at large depths under conditions of electron donor deficiency owing to syntrophic development with sulfate reducers. The species composition of the photosynthetic bacteria developing in the bottom sediments of shallow stations differed substantially from that observed at deep-sea stations. Pure cultures of the green Chlorobium sp. BS 1C and BS 2C (chlorobactin as the carotenoid), purple sulfur bacteria Chromatium sp. BS 1Ch (containing spirilloxanthine series pigments), and Thiocapsa marina BS 2Tc (containing the carotenoid okenone) were obtained from samples of sediments at shallow-water stations. Brown sulfur bacteria were absent in the sediment samples obtained from the Black Sea shallow-water stations 1 and 2.     

Vertical Profile of PAHs and Dredging Depth of River Sediments

Sediment dredging is an effective engineering measure to reduce the negative effects of PAHs pollution on water environment. The dredging depth is a key parameter in environmental dredging engineering. A guidance of environmental dredging depth needed to reduce the toxicity risk was developed which was specifically designed for the removal of river sediments contaminated by PAHs based on the mean effect range median quotients (mean-ERM-q). The dredging depths for removing river sediments were calculated based on the vertical profile of PAHs content and the quality guidelines of sediment. Pinghu water system was carried out to determine the dredging depths of sediments from nine rivers by the proposed method. Each sediment core was collected from different river. The results showed the profiles of PAHs in sediment cores were irregular and diverse due to river dredging events and human activities in different periods. The risk assessment of PAHs toxicity showed one of nine cores with moderate-high probability, 4 of nine cores with low-moderate probability and the others with low toxicity risk. The achievement can offer a reference to the dredging engineering in other similar river systems.     

Sponges Collected by the Swedish Deep Sea Expedition

The paper deals with sponges collected in the Atlantic by the Swedish Deep Sea Expedition. The collection contains six species of the genera Malaco-saccus, Chonelasma, heptonema, Asbestopluma , and Chondrocladia , which are well known from the deep-sea. Three new species are described, viz. Asbestopluma quadriserialis sp.n., Chondrocladia al-batrossi sp.n., and C. burtoni sp.n. A survey of the knowledge of the Atlantic deep-sea sponge fauna shows that 118 species are at present known from depths of more than 2 000 m. About 35% of the species were found four or more times, whereas about 47% are known only from the type locality. 63 species were taken more than once, and 50 species are known also from depths of less than 2 000 m.     

Four new species of Hydromedusae (Cnidaria, Hydrozoa) from the coast of south-western Africa

Four previously unknown species of hydromedusae are described from plankton samples collected during oceanographic cruises undertaken along the south-western coast of Africa. The Anthomedusa Bythotiara capensis sp.n., known from a single specimen, was found in shallow waters of the Cape region (South Africa). The Leptomedusa Margalefia intermedia gen. et sp.n. collected in Namibian waters, possesses desmoneme cnidocysts. This category of cnidocysts is previously unreported in the Leptomedusae, but is common in Anthomedusae and in the limnomedusan family Proboscidactylidae. Margalefia seems to occupy a position intermediate between the families Tirannidae and Laodiceidae. Two species of Limnomedusae, Aglauropsis edwardsii sp.n. and Proboscidactyla menoni sp.n. were frequent at several stations in Namibian waters between depths of 50 m and the surface.     

Leaching of Escherichia coli O157:H7 in diverse soils under various agricultural management practices

Application of animal manures to soil as crop fertilizers is an important means for recycling the nitrogen and phosphorus which the manures contain. Animal manures also contain bacteria, including many types of pathogens. Manure pathogen levels depend on the source animal, the animal's state of health, and how the manure was stored or treated before use. Rainfall may result in pathogen spread into soil by runoff from stored or unincorporated manure or by leaching through the soil profile. Steady rainfall consisting of 16.5 mm h(-1) was applied to 100-mm disturbed soil cores that were treated with manure and inoculated with Escherichia coli O157:H7 strain B6914. The level of B6914 in leachate was near the inoculum level each hour for 8 h, as was the level of B6914 at several soil depths after 24 h, indicating that there was a high rate of growth. Bacterial movement through three different types of soil was then compared by using disturbed (tilled) and intact (no-till) soil cores and less intense rainfall consisting of 25.4 mm on 4 consecutive days and then four more times over a 17-day period. Total B6914 levels exceeded the inoculum levels for all treatments except intact clay loam cores. B6914 levels in daily leachate samples decreased sharply with time, although the levels were more constant when intact sandy loam cores were used. The presence of manure often increased total B6914 leachate and soil levels in intact cores but had the opposite effect on disturbed soil cores. Ammonia and nitrate levels correlated with B6914 and total coliform levels in leachate. We concluded that tillage practice, soil type, and method of pathogen delivery affect but do not prevent vertical E. coli O157:H7 and coliform transport in soil and that soluble nitrogen may enhance transport.