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 degrees 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.     

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.     

Descriptions of Eumonhystera borealis n. sp., Sphaerolaimus occidentalis n. sp., and a Redescription of S. gracilis de Man 1876 (Nemata) from Bothnian Bay,Baltic Sea

The free-living nematodes Eumonhystera borealis n. sp., Sphaerolaimus occidentalis n. sp., and S. gracilis de Man 1876 from Bothnian Bay in the northern Baltic Sea are described and illustrated. Eumonhystera borealis n. sp. differs from other species by its small body size (314-393 μm), narrow body (a = 37-49), and large anterior amphids. In Sphaerolaimus occidentalis n. sp. the amphids are posterior to the buccal cavity, and it differs from other similar species by having two sclerotized rings in the posterior part of the buccal cavity. An intersex is reported for S. gracilis. Sphaerolaimus gracilis is cannibalistic or a predator of other species, with a preference for E. borealis n. sp. Sphaerolaimus occidentalis n. sp. coexists with S. gracilis at depths of 80 m but not at 12 m.     

Evaluation of the Spatial Pattern of Steinernema riobravis in Corn Plots

The vertical and horizontal spatial patterns of a naturally occurring population of the entomopathogenic nematode Steinernema riobravis (Rhabditida: Steinernematidae) were investigated in corn field soil by laboratory and field bioassays. This nematode appears to be endemic to the Lower Rio Grande Valley of Texas, where it was found parasitizing prepupae and pupae of both corn earworm, Helicoverpa zea, and fall armyworm, Spodoptera frugiperda (Lepidoptera: Noctuidae). Corn earworm prepupa was the bioassay host used to detect S. riobravis from soil in previously harvested corn plots. Steinernema riobravis occurred at soil depths of 5-30 cm. The maximum nematode density was in the upper 20 cm of soil, and the lowest density occurred at soil depth of 25-30 cm. The field and laboratory bioassays performed on the top 20 era of soil resulted in S. riobravis-infected corn earworm of 49 and 34%, respectively, whereas at 25-30 cm soil depths 11 and 4.5% of the H. zea were infected, respectively. The horizontal spatial pattern of this nematode was patchy or aggregated. Our study provides new information on the spatial pattern of S. riobravis in its natural habitat and indicates the need to augment its natural biocontrol efficacy.     

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.     

New data about deep-water solitary ahermatypic scleractinians of the shelf of Vietnam

This paper reports data on deep-water solitary ahermatypic corals that were collected on the shelf of Vietnam. Among these, 28 species belonging to 16 genera and eight families were identified; 9 species are first records for the South China Sea, and 2 species (Deltocyathus radiatus sp. n. and Flabellum septodentatus sp. n.) are described as new to science. Dendrophyllia sp. (33 indiv. in sample) and Truncatoflabellum crassum (28 indiv. in sample) formed massive aggregations. The taxonomically richest genera were Flabellum, Truncatoflabellum, and Caryophyllia. Coral density and species diversity were highest at depths of 90–230 and 285–390 m, respectively. Deep-water corals of Vietnam are integral with the coral fauna of the Indo-Polynesian Province. The data we obtained contribute to the knowledge of the composition and chorology of the worldwide fauna of solitary corals.     

Photosynthesis and respiration of a deep-water periphyton community (Macclesfield Bank,South China Sea)

The production parameters of the deep-water periphyton were investigated on the Macclesfield Bank (South China Sea) at depths down to 240 m. At 70–90 m depths the substrate is composed of the remains of dead corals and fragments of porous calcareous material overgrown with red coralline and articulated thalline algae Halimeda sp. At 220–240 m depths the substrate consists of rhodolites, which are individual unattached nodules encrusted mainly with red calcareous coralline algae Lithophyllum sp., Porolithon sp. and red lamellar alga Hypoglossum sp. At all depths the substrate is pierced with green filiform algae Ostreobium sp. and covered with benthic diatom algae. The zooperiphyton in the studied area is comprised of bryozoans, sponges, foraminifers and drilling mollusks. Respiration (R) and the gross (Pg) and net (Pn) primary production of the deepwater periphyton community were determined using the oxygen technique (polarographic electrode) at values of photosynthetically active radiation (PAR) close to natural levels. At 70–90 m depths the Pg of the photoperiphyton was 23.3 mg O₂/(m² h), and the Pn of the community had negative values due to respiration of phytoand mainly zooperiphyton and bacteria. At 220–240 m depths, where less than 0.001% of the surface PAR penetrates, the Pg of the phytoperiphyton decreased to 9.6 mg O₂/(m² h), and the R of the community was 25.9 mg O₂/(m² h). A high efficiency of light energy utilization by the phytoperiphyton was found. The apparent quantum yield (Fa) for algae collected at 70–90 m depths was close to the maximum level of 0.097. The values of Fn that we obtained for 220–240 m depths and calculated from identical data [27], were much higher than theoretical values, which cannot be explained based on modern views on the mechanisms of photosynthesis. Possible sources of errors are discussed. It is proposed that we observed additional evolution of oxygen as the result of H₂O₂ degradation.     

Photoadaptation and Protection against Active Forms of Oxygen in the Symbiotic Procaryote Prochloron sp. and Its Ascidian Host

Superoxide dismutase, ascorbate peroxidase, and catalase activities were studied in the symbiotic photosynthetic procaryote Prochloron sp. and its ascidian host Lissoclinum patella. The protein-specific activities of these antioxidant enzymes in the Prochloron sp. and L. patella collected at different depths from the Great Barrier Reef, Australia, were directly proportional to irradiance, whereas the pigment concentrations in the Prochloron sp. were inversely proportional to irradiance. The presence of a cyanide-sensitive superoxide dismutase, presumably a Cu-Zn metalloprotein, in the Prochloron sp. extends the possible phylogenetic distribution of this protein. The concentration of UV-absorbing mycosporine-like amino acids is inversely proportional to irradiance in both the host and symbiont, suggesting that these compounds may not provide sufficient protection against UV radiation in high-irradiance environments. The significant differences in the specific activities of these antioxidant enzymes, cellular photosynthetic pigment concentrations, and UV-absorbing compounds from high- and low-irradiance habitats constitute an adaptive response to different photic environments. These photoadaptive responses are essential to prevent inhibition of photosynthesis by high fluxes of visible and UV radiation.     

Distribution of Recent ostracod species in the Lake Qinghai area in northwestern China and its ecological significance

In order to interpret the climate-change data using the ecological characteristics of the ostracods from the drill cores in Lake Qinghai, the distribution of Recent ostracods was studied in Lake Qinghai area. A total of 34 species belonging to the Ostracoda class of Crustacea were collected from different bodies of water in the Lake Qinghai area, and the ecological information for Recent ostracod species was studied. Among these 34 species, Cypris pubera, Eucypris dulcifons, Ilyocypris sp. 1, Ilyocypris sp. 2, Fabaeformiscandona caudata, Fabaeformiscandona hyalina, Herpetocypris reptans, Prionocypris gansenensis, Potamocypris villosa, Potamocypris smaragdina, Paralimnocythere compressa and Subulacypris sp. were first reported by us in the Lake Qinghai area. Some of the species identified exhibited cosmopolitan distributions, at least in the Holarctic region, but P. gansenensis and Ilyocypris echinata appeared to be restricted to the cold regions in northwestern China.The ecological significance of the primary ostracod species in the Lake Qinghai area was described according to the observations made during our time in the field and according to data from a number of reports. Our results indicate that the species diversity and abundance of ostracods may be related to water salinity in the Lake Qinghai area. The ecological information for ostracods can be used to distinguish different water environments and types based on the characteristics of one species or of an assemblage of several species.     

A Survey of Escherichia coli and Salmonella in the Hyporheic Zone of a Subtropical Stream: Their Bacteriological,Physicochemical and Environmental Relationships

The Hyporheic Zone is among the most important interstitial freshwater habitats, but the relationship between biotic and abiotic factors in this zone remains under-explored. Enterobacteria were expected to be present, but no specific studies had ever confirmed this prediction. The aim of this study was, therefore, to evaluate the total coliforms, Escherichia coli and Salmonella spp. in hyporheic water and to determine the relationship of the physical, chemical and environmental factors at different depths in a rainforest stream. To this end, thirty-six water samples were collected at three depths in sites located in the first, second and third orders in diverse substrates. The total coliforms, Escherichia coli and Salmonella sp. were evaluated in terms of their CFU/ml. In the interstitial samples, coliforms were detected in 100% of the samples. The total coliform counts had higher values at intermediate depths, while E. coli and Salmonella spp. instead had higher values at intermediate and large depths, often reaching or exceeding the values of the surface samples. Our results revealed that Salmonella spp. and the coliforms have different microhabitat preferences. Salmonella spp. and coliform species prefer deposition areas, such as lateral sides of pools, curves and bars, but they have a tendency to distribute into different depths, likely due to temperature differences. Salmonella spp. prefer compact substrata, with fewer fluids passing through and with upwelling areas with lower oxygen inflow. The coliform species showed the opposite preference. Our results suggest that bacterial variation is related to environmental factors and physical-chemical parameters within the HZ and may play a key role in the microbial diversity and distribution in these ecosystems.     

Species composition and distribution of Zoarcidae in the northern part of the Sea of Japan from the data of trawl surveys

Species composition, ratio, distribution, and size composition of Zoarcidae on the shelf and the upper part of the continental slope of the northern part of Japan at depths of 5 to 700 m were analyzed on the basis of four trawl surveys. In the studied area, nine species of Zoarcidae were found: Bilabria sp., Bothrocara hollandi, Davidijordania lacertina, Lycodes japonicus, L. nakamurae, L. cf. yamatoi, L. tanakae, L. toyamensis, and L. cf. ushakovi. Data on catches, density of distribution at different depths, and size composition are listed for each species. Four species: B. hollandi, L. tanakae, L. nakamurae, and L. cf. yamatoi have the greatest biomass and numbers among zoarcids in the northern part of the Sea of Japan. It was shown that zoarcids from the northern part of the Sea of Japan, similar to most demersal fish, perform seasonal migrations from the depths of 200 to 500 m, which they inhabit in the summer period, to depths larger than 400 m in the winter. It was found that the most common species of Zoarcidae (B. hollandi, L. tanakae, L. nakamurae, L. cf. yamatoi, and L. toyamensis) dwell mainly in waters of the intermediate water mass and the upper part of the Sea of Japan water mass. These species are abundant at depths larger than 200 m, which permits assigning them to a mesobenthal ecological group. All of the studied species of Zoarcidae from the given region are stenothermal—the temperature range of their habitation is below 2°C, as a rule, from 0.3 to 2.5°C.     

Vertical Distribution of Plant-parasitic Nematodes in Sandy Soil under Soybean

Vertical distribution of five plant-parasitic nematodes was examined in two north Florida soybean fields in 1987 and 1988. Soil samples were collected from 0-15 cm, 15-30 cm, and 30-45 cm deep at each site. Soil at the three depths consisted of approximately 96% sand. More than 50% of Belonolaimus longicaudatus population densities occurred in the upper 15-cm soil layer at planting, but the species became more evenly distributed through the other depths as the season progressed. Criconemella sphaerocephala was evenly distributed among the three depths in one field but was low (< 20% of the total density) in the upper 15 cm at a second site. Maximum population densities of Pratylenchus brachyurus were observed at 15-30 cm on most sampling dates. Vertical distributions of Meloidogyne incognita and Paratrichodorus minor were erratic and showed seasonal variation. A diagnostic sample from the upper 0-15 cm of these soybean fields revealed only a minority of the populations of most of the phytoparasitic species present.     

Microbial Communities from Methane Hydrate-Bearing Deep Marine Sediments in a Forearc Basin

Microbial communities in cores obtained from methane hydrate-bearing deep marine sediments (down to more than 300 m below the seafloor) in the forearc basin of the Nankai Trough near Japan were characterized with cultivation-dependent and -independent techniques. Acridine orange direct count data indicated that cell numbers generally decreased with sediment depth. Lipid biomarker analyses indicated the presence of viable biomass at concentrations greater than previously reported for terrestrial subsurface environments at similar depths. Archaeal lipids were more abundant than bacterial lipids. Methane was produced from both acetate and hydrogen in enrichments inoculated with sediment from all depths evaluated, at both 10 and 35°C. Characterization of 16S rRNA genes amplified from the sediments indicated that archaeal clones could be discretely grouped within the Euryarchaeota and Crenarchaeota domains. The bacterial clones exhibited greater overall diversity than the archaeal clones, with sequences related to the Bacteroidetes, Planctomycetes, Actinobacteria, Proteobacteria, and green nonsulfur groups. The majority of the bacterial clones were either members of a novel lineage or most closely related to uncultured clones. The results of these analyses suggest that the microbial community in this environment is distinct from those in previously characterized methane hydrate-bearing sediments.     

Soil respiration in Pinus tabulaeformis forest during dormant period at Huoditang forest zone in the Qinling Mountains, China

Soil CO₂ efflux in forest ecosystems during dormant season is one of the key components of the forest ecosystem carbon balance. Little work has been done to quantify soil CO₂ efflux in most forests in China in special time because of difficulty in taking measurements. Soil respiration in a natural secondary Pinus tabulaeformis forest at Huoditang in the Qinling Mountains was measured from October to December in 2006 by means of open-path dynamic chamber technique. Relationships of soil respiration rate (R_s) with mean soil temperature (MST) and mean volumetric soil moisture content (MVSC) in different depths (0-5 cm and 5-10 cm) were examined in the current study. We found that (1) At the same observation site (upper-part, middle-part or under-part), there were tremendous temporal and spatial variations in R_s with variation coefficients of 48.38%, 82.51% and 81.88% in October, November and December, respectively; (2) There was a significant exponent relationship between diurnal mean soil respiration rate (F_c) and diurnal mean soil temperature (DMST) when DMST > 8.5°C for both soil depths (0-5 cm and 5-10 cm) examined. The temperature sensitivity of soil respiration, known as the Q₁₀ value, was 1.297 and 1.323 in soil depths of 0-5 cm and 5-10 cm, respectively; (3) Relationship between R_s and MVSC was complex in soil depths of 0-5 cm and 5-10 cm; (4) Soil CO₂ efflux from October to December in 2006 in the experimental area was (977.37 ± 88.43) to (997.19 ± 80.73) gCm⁻² (p = 0.005).     

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。     

Optimization of Spongiochloris sp. biomass production in the abattoir digestate

In the present study, the abattoir digestate was used as a culture medium for Spongiochloris sp. growth with added mineral components under optimized conditions in batch culture. Firstly, an Hadamard matrix was used to investigate the impact of certain influencing factors on the Spongiochloris sp. growth. Then, a fractional factorial design 2^7-4 was successfully employed to optimize the concentration of different added components to abattoir digestate for increased Spongiochloris sp. biomass production. The major influencing factors were NaHCO₃ and FeSO₄ at a level of 2000 mg/L and 5 mg/L, respectively. A high biomass production of 5.29 × 10⁶ cell/mL and an important content of chlorophyll a of 65.32 mg/L were obtained after 42 days of culture of Spongiochloris sp. on the defined abattoir medium at static conditions.     

A new species of <Emphasis Type="Italic">Hamaticolax</Emphasis> Ho &amp; Lin, 2006 (Copepoda: Bomolochidae) from deep water macrourids in the Mediterranean

Hamaticolax resupinus n. sp. is described from specimens collected from the gill cavities of Coelorinchus mediterraneus Iwamoto & Ungaro and Coryphaenoides mediterraneus (Giglioli) (Gadiformes: Macrouridae) caught in the Western Mediterranean Sea at depths between 1,236 and 1,626 m. Hamaticolax resupinus n. sp. closely resembles H. maleus Oldewage, 1994, but differs from the latter by its smaller body size and in having a genital double-somite in the female that is markedly wider than the free abdominal somites and has strongly convex lateral margins. The new species is only the second bomolochid found on a macrourid host and is the first from depths in excess of 1,200 m. Hamaticolax resupinus n. sp. also represents the first parasitic copepod recorded from Coe. mediterraneus and only the third one from Cor. mediterraneus worldwide.