Large sulfur bacteria and the formation of phosphorite

Phosphorite deposits in marine sediments are a long-term sink for an essential nutrient, phosphorus. Here we show that apatite abundance in sediments on the Namibian shelf correlates with the abundance and activity of the giant sulfur bacterium Thiomargarita namibiensis, which suggests that sulfur bacteria drive phosphogenesis. Sediments populated by Thiomargarita showed sharp peaks of pore water phosphate (/=50 grams of phosphorus per kilogram). Laboratory experiments revealed that under anoxic conditions, Thiomargarita released enough phosphate to account for the precipitation of hydroxyapatite observed in the environment.     

Subtidal gastropods consume sulfur-oxidizing bacteria: evidence from coastal hydrothermal vents

The black abalone (Haliotis cracherodii), a commercially important shallow-water gastropod common off White Point, Southern California, is found frequently at subtidal hydrothermal vents within mats of filamentous sulfur-oxidizing bacteria. Foraging vent abalones actively consume the bacteria and confine their nightly feeding forays to bacterial mats surrounding the vents. The growth of abalones consuming the sulfur bacteria exceeds that of control individuals consuming microalgae and is comparable to reported growth rates of abalones consuming macroalgae. Thus, off White Point, the black abalone may derive a portion of its nutrition from the subsidy of geothermal energy.     

Interstitial nitrate profiles and oxidation of sedimentary organic matter in the eastern equatorial atlantic

Pore-water nitrate concentrations in six pelagic eastern equatorial Atlantic cores increase from bottom water values (22 micromolar) to 40 micromolar at a depth of about 5 centimeters, then decrease to undetectable levels at depths as shallow as 40 centimeters. These nitrate concentrations and concentration gradients reflect zones of oxygen reduction, nitrate reduction, and sulfate reduction in the sediments. The estimated benthic flux of nitrate to the ocean from our data is much less than the total globalflux of nitrate to deep waters, even though these equatorial sediments underlie a productive upwelling zone. The estimated denitrification rate in our study area suggests that pelagic sediments may be important sites of marine denitrification.     

Nitrous oxide production in nearshore marine sediments

Coastal marine sediments are shown to be a net source of nitrous oxide. The rates of nitrous oxide flux from sediments in Narragansett Bay, Rhode Island, ranged from 20 to more than 900 nanomoles per square meter per hour. Sediments from a eutrophic area had higher rates of net nitrous oxide production than sediments from relatively unpolluted sites. The benthic, nitrous oxide source exceeds the nitrous oxide source to the bay from sewage treatment plant effluent.     

Growth rates of phosphate nodules from the continental margin off peru

Modern sea-floor phosphorite nodules sampled from off the coast of Peru are shown to grow at rates of millimeters per thousand years in spite of the fact that the measured accumulation rates of the underlying sediment are two to four orders of magnitude faster. Phosphate nodules grow downward into soft sediment, and the rates of phosphorus accumulation into nodules are approximately equal to the upward diffusive flux of dissolved phosphate inferred from pore water profiles. These results demonstrate that phosphorus in nodules originates from regeneration in sediments rather than as a result of direct precipitation from bottom waters.     

Aldrin: removal from lake water by flocculent bacteria

Floc-forming bacteria isolated from Lake Erie adsorb and concentrate aldrin from colloidal dispersion so that the settling of the bacterial flocs removes aldrin from the water phase. Contemporary sediments forming in Lake Erie contain aldrin and could adsorb more. The sediments consist of a conglomerate floc of bacteria, diatoms, and inorganic and detrital particles. Flocculent bacteria also adsorb microparticulates, and this adsorption capacity represents a mechanism for sediment formation and for the removal of suspended particles including aldrin from the water column.     

Dimethyl sulfide in the surface ocean and the marine atmosphere: a global view

Dimethyl sulfide (DMS) has been identified as the major volatile sulfur compound in 628 samples of surface seawater representing most of the major oceanic ecozones. In at least three respects, its vertical distribution, its local patchiness, and its distribution in oceanic ecozones, the concentration of DMS in the sea exhibits a pattern similar to that of primary production. The global weightedaverage concentration of DMS in surface seawater is 102 nanograms of sulfur (DMS) per liter, corresponding to a global sea-to-air flux of 39 x 10(12) grams of sulfur per year. When the biogenic sulfur contributions from the land surface are added, the biogenic sulfur gas flux is approximately equal to the anthropogenic flux of sulfur dioxide. The DMS concentration in air over the equatorial Pacific varies diurnally between 120 and 200 nanograms of sulfur (DMS) per cubic meter, in agreement with the predictions of photochemical models. The estimated source flux of DMS from the oceans to the marine atmosphere is in agreement with independently obtained estimates of the removal fluxes of DMS and its oxidation products from the atmosphere.     

Interaction of beggiatoa and rice plant: detoxification of hydrogen sulfide in the rice rhizosphere

Beggiatoa was obtained from six habitats, including four water-saturated soils from rice fields. The isolate of Beggiatoa from Bernard clay, when reinoculated into soil treatments from pure culture, significantly reduced hydrogen sulfide levels in soils and increased oxygen release from rice plants. Rice plants significantly increased Beggiatoa survival in flooded soils. Some hydrogen sulfide was necessary for survival of the Bernard clay isolate; high concentrations of hydrogen sulfide killed the Bernard clay isolate but were tolerated by a Crowley silt loam isolate from Eagle Lake, Texas. The results suggest that Beggiatoa may be an element of wetlands plant ecosystems.     

Methane production from acetate and associated methane fluxes from anoxic coastal sediments

The apparent microbial conversion of acetate to methane ranges seasonally from 0.7 to 88 micromoles per liter of whole wet sediment per hour in the top 5 centimeters of methane-producing sediments underlying sulfate-reducing sediments in Cape Lookout Bight, North Carolina. The associated methane flux across the sediment-water interface into overlying waters exhibits the same seasonal pattern. Significant methane production from acetate is observed only in sulfate-depleted sediments.     

Manganese flux from continental margin sediments in a transect through the oxygen minimum

The flux of manganese from continental margin sediments to the ocean was measured with a free-vehicle, benthic flux chamber in a transect across the continental shelf and upper slope of the California margin. The highest fluxes were observed on the shallow continental shelf. Manganese flux decreased linearly with bottom water oxygen concentration, and the lowest fluxes occurred in the oxygen minimum zone (at a depth of 600 to 1000 meters). Although the flux of manganese from continental shelf sediments can account for the elevated concentrations observed in shallow, coastal waters, the flux from sediments that intersect the oxygen minimum cannot produce the subsurface concentration maximum of dissolved manganese that is observed in the Pacific Ocean.     

船舶压载水与沉积物细菌多样性比较分析

利用Illumina HiS eq 2500高通量测序平台对船舶压载水及沉积物微生物进行测序,共获得67 255条有效序列,736个OTU,通过生物信息分析,研究了压载舱中沉积物和压载水细菌群落结构及其多样性。结果显示:船舶压载舱沉积物中可培细菌总数较压载水中可培细菌总数高3个数量级。压载水中优势类群是变形菌(Proteobacteria 70.20%)、拟杆菌(Bacteroidetes 13.38%)、放线菌(Actinobacteria 10.33%)和Marinimicrobia_SAR406_clade 2.81%。压载舱中沉积物的优势类群为变形菌(Proteobacteria 95.45%)、厚壁菌(Firmicutes 2.23%)。     

Ancient ice islands in salt lakes of the central andes

Massive blocks of freshwater ice and frozen sediments protrude from shallow, saline lakes in the Andes of southwestern Bolivia and northeastern Chile. These ice islands range up to 1.5 kilometers long, stand up to 7 meters above the water surface, and may extend out tens of meters and more beneath the unfrozen lake sediments. The upper surfaces of the islands are covered with dry white sediments, mostly aragonite or calcite. The ice blocks may have formed by freezing of the fresh pore water of lake sediments during the "little ice age." The largest blocks are melting rapidly because of possibly recent increases in geothermal heat flux through the lake bottom and undercutting by warm saline lake water during the summer.     

Impact of humans on the flux of terrestrial sediment to the global coastal ocean

Here we provide global estimates of the seasonal flux of sediment, on a river-by-river basis, under modern and prehuman conditions. Humans have simultaneously increased the sediment transport by global rivers through soil erosion (by 2.3 +/- 0.6 billion metric tons per year), yet reduced the flux of sediment reaching the world's coasts (by 1.4 +/- 0.3 billion metric tons per year) because of retention within reservoirs. Over 100 billion metric tons of sediment and 1 to 3 billion metric tons of carbon are now sequestered in reservoirs constructed largely within the past 50 years. African and Asian rivers carry a greatly reduced sediment load; Indonesian rivers deliver much more sediment to coastal areas.     

珠江三角洲冲积平原土壤镉高含量区形成原因

通过现场采样及室内分析方法,研究了珠江三角洲冲积平原土壤Cd高含量区形成的原因。调查发现,在西江和北江冲积平原存在Cd的高含量分布区。Cd高含量区仅分布于第四纪海陆交互相,从地表至深部含量变化不大,为珠江三角洲形成过程中,富含Cd的西江和北江冲积物质在珠江三角洲沉积而成。Cd高含量区空间分布特征明显,控制因素显著,属于由地质作用引起。这一结论与多数研究者认为是人为因素引起的具有根本差别。     

Bacterial taxa that limit sulfur flux from the ocean

Flux of dimethylsulfide (DMS) from ocean surface waters is the predominant natural source of sulfur to the atmosphere and influences climate by aerosol formation. Marine bacterioplankton regulate sulfur flux by converting the precursor dimethylsulfoniopropionate (DMSP) either to DMS or to sulfur compounds that are not climatically active. Through the discovery of a glycine cleavage T-family protein with DMSP methyltransferase activity, marine bacterioplankton in the Roseobacter and SAR11 taxa were identified as primary mediators of DMSP demethylation to methylmercaptopropionate. One-third of surface ocean bacteria harbor a DMSP demethylase homolog and thereby route a substantial fraction of global marine primary production away from DMS formation and into the marine microbial food web.     

High deleterious genomic mutation rate in stationary phase of Escherichia coli

In natural habitats, bacteria spend most of their time in some form of growth arrest. Little is known about deleterious mutations in such stages, and consequently there is limited understanding of what evolutionary events occur. In a deleterious mutation accumulation experiment in prolonged stationary phase of Escherichia coli, about 0.03 slightly deleterious mutations were observed per genome per day. This is over an order of magnitude higher than extrapolations from fast-growing cells, but in line with inferences from observations in adaptive stationary phase mutation experiments. These findings may affect understanding of bacterial evolution and the emergence of bacterial pathogenicity.     

磁性铁锆改性沸石覆盖对河道底泥磷释放的控制效果

通过批量吸附实验考察磁性铁锆改性沸石对水中磷酸盐的去除性能,再通过底泥培养实验考察磁性铁锆改性沸石覆盖对河道底泥磷释放的控制效果。结果表明:磁性铁锆改性沸石对水中磷酸盐的吸附能力良好。无论是在自然状态下,还是在缺氧控制状态下,河道底泥均向上覆水体中释放出一定数量的溶解性活性磷(SRP),而磁性铁锆改性沸石覆盖可以有效控制河道底泥中磷的释放,使得上覆水体中SRP浓度处于非常低的水平(0. 007～0. 031 mg/L)。当覆盖层受到破坏并使覆盖材料与表层底泥混合之后,磁性铁锆改性沸石仍然可以极大地降低上覆水体中SRP浓度,并且使底泥中潜在可移动态磷向较为稳定和非常稳定的磷形态转变,以及促使底泥中生物可利用性磷向非生物可利用性磷转变,使得底泥中磷发生释放的风险降低。以上结果初步表明,磁性铁锆改性沸石是一种非常有希望用于控制河道底泥中磷释放的覆盖材料。     

黑麦草（Lolium perenne）根际细菌多样性对Ni污染沉积物修复效果的响应

应用黑麦草(Lolium perenne)对某滨海城市南排污河的重金属污染沉积物——底泥进行植物修复,并结合变性梯度凝胶电泳(DGGE)分析了黑麦草根际土壤的重金属Ni含量和细菌多样性的关系。结果表明,黑麦草对Ni的修复效果较好,种植黑麦草后根际土壤Ni浓度降低了11.8%。根际土壤中Ni有效态含量与根际土壤pH值的变化呈较好的正相关关系,相关系数为0.9688。对根际土壤细菌多样性进行分析,重金属Ni含量变化能够影响土壤细菌的多样性,根际土壤细菌多样性随黑麦草的生长而不断演变,且与根际土壤中Ni浓度变化有密切联系。对DGGE电泳后回收的部分片段进行测序并建立了进化树,结果表明,测序片段与非培养方法得到的菌种的同源性较高,且其均在土壤或河道底泥的相关研究中被发现。不同时期细菌群体组成和Shan non指数随着修复时间而变化,并与细菌总数有正相关关系。     

西藏达则错盐湖沉积背景与有机沉积结构

以西藏拟溞(Daphniopsis tibetana Sars)为优势浮游动物物种的低盐度盐湖是西藏湖泊的一个重要类型,以达则错为代表,分析了其沉积背景及沉积物组成。结果如下:(1)湖泊敞水区无机沉积以内生化学沉积为主,可代表深水盐湖无机沉积物的自然沉积过程。(2)达则错盐湖浮游植物以蓝藻、硅藻、裸藻、绿藻为主,总生物量11.35 mg/L;浮游动物生物量为4.92 mg/L,其中西藏拟溞占 82.30%;浮游植物残体受盐梯度影响在盐梯度层之上聚集,而浮游动物残体及粪粒(Fecal pellets)因外表有碳酸盐附着可穿过盐梯度层沉积湖底,生物残体与浮游动物代谢产物构成了沉积有机物的物质基础。(3)表层沉积物平均含水量为66.70%,粒径0.004-0.02 mm范围内的颗粒物含量最大,占20.42%,其次为<0.004 mm的粘土,占4.53%。(4)表层沉积物总有机碳(TOC)平均含量为27.99 mg/g(干重),其中颗粒有机碳(POC)约为18.11 mg/g,占TOC的64.70%;在POC中,西藏拟溞粪粒贡献最大,约占POC的60.48%,占TOC的39.06%,占沉积物总量的1.12%,其次为西藏拟溞残体,占POC的38.85%。分析结果表明盐湖因其独特的水化学和生物学特征具有较强的沉积能力,以化学沉积为主的无机沉积及以西藏拟溞粪粒和残肢碎屑为主的有机沉积构成了该类型盐湖颗粒物沉降及沉积的主要过程。     

上海港到港船舶压载水沉积物细菌群落多样性

为了解船舶压载水沉积物中微生物多样性,利用Illumina Mi Seq 2500高通量测序平台对上海港到港船舶压载水沉积物中细菌基因样本进行测序,并进行生物信息分析。从11份压载水沉积物样品中共检测到420 069条有效序列,微生物群落分析结果显示共有38门、98纲、226目、393科、704属细菌,优势类群为变形菌门(Proteobacteria 72.98%)、放线菌门(Actinobacteria 9.11%)、拟杆菌门(Bacteroidetes 8.71%)、绿弯菌门(Chloroflexi 4.06%)、芽单胞菌门(Gemmatimonadetes 1.47%)、酸杆菌门(Acidobacteria 1.18%)和其他(2.50%)。本次研究在压载水沉积物中检测到了分枝杆菌属(Mycobacterium)、游动球菌属(Planococcus)、假单胞菌属(Paenibacillus)、类芽孢杆菌属(Streptomyces)和链霉菌属(Inquilinus)的致病菌或条件致病菌。结果显示压载水沉积物中微生物多样性丰富,要充分重视我国到港船舶压载水沉积物中微生物以及致病菌的研究,为阐明外来致病菌通过压载水途径入侵的机制和防控奠定基础。