Particle-attached and free-living bacterial communities in a contrasting marine environment: Victoria Harbor, Hong Kong

Diversity of particle-attached and free-living marine bacteria in Victoria Harbor, Hong Kong, and its adjacent coastal and estuarial environments was investigated using DNA fingerprinting and clone library analysis. Denaturing gradient gel electrophoresis (DGGE) analysis of 16S rRNA genes showed that bacterial communities in three stations of Victoria Harbor were similar, but differed from those in adjacent coastal and estuarine stations. Particle-attached and free-living bacterial community composition differed in the Victoria Harbor area. DNA sequencing of 28 bands from DGGE gel showed Alphaproteobacteria was the most abundant group, followed by the Bacteroidetes, and other Proteobacteria. Bacterial species richness (number of DGGE bands) differed among stations and populations (particle-attached and free-living; bottom and surface). BIOENV analysis indicated that the concentrations of suspended solids were the major contributing parameter for the spatial variation of total bacterial community structure. Samples from representative stations were selected for clone library (548 clones) construction and their phylogenetic distributions were similar to those of sequences from DGGE. Approximately 80% of clones were affiliated to Proteobacteria, Bacteroidetes and Cyanobacteria. The possible influences of dynamic pollution and hydrological conditions in the Victoria Harbor area on the particle-attached and free-living bacterial community structures were discussed.

Vertical distribution of bacterial and archaeal communities along discrete layers of a deep-sea cold sediment sample at the East Pacific Rise (similar to 13 degrees N)

The community structure and vertical distribution of prokaryotes in a deep-sea (ca. 3,191 m) cold sediment sample (ca. 43 cm long) collected at the East Pacific Rise (EPR) similar to 13 degrees N were studied with 16SrDNA-based molecular analyses. Total community DNA was extracted from each of four discrete layers EPRDS-1, -2, -3 and -4 (from top to bottom) and 16S rDNA were amplified by PCR. Cluster analysis of DGGE profiles revealed that the bacterial communities shifted sharply between EPRDS-1 and EPRDS-2 in similarity coefficient at merely 49%. Twenty-three sequences retrieved from DGGE bands fell into 11 groups based on BLAST and bootstrap analysis. The dominant groups in the bacterial communities were Chloroflexi, Gamma proteobacteria, Actinobacterium and unidentified bacteria, with their corresponding percentages varying along discrete layers. Pairwise Fst (F-statistics) values between the archaeal clone libraries indicated that the archaeal communities changed distinctly between EPRDS-2 and EPRDS-3. Sequences from the archaeal libraries were divided to eight groups. Crenarchaea Marine Group I (MGI) was prevalent in EPRDS-1 at 83%, while Uncultured Crenarchaea group II B (UCII B) abounded in EPRDS-4 at 61%. Our results revealed that the vertically stratified distribution of prokaryotic communities might be in response to the geochemical settings and suggested that the sampling area was influenced by hydrothermalism. The copresence of members related to hydrothermalism and cold deep-sea environments in the microbial community indicated that the area might be a transitional region from hydrothermal vents to cold deep-sea sediments.

Diversity and spatial distribution of sediment ammonia-oxidizing crenarchaeota in response to estuarine and environmental gradients in the Changjiang Estuary and East China Sea

Ammonia-oxidizing archaea (AOA) have recently been found to be potentially important in nitrogen cycling in a variety of environments, such as terrestrial soils, wastewater treatment reactors, marine waters and sediments, and especially in estuaries, where high input of anthropogenic nitrogen is often experienced. The sedimentary AOA diversity, community structure and spatial distribution in the Changjiang Estuary and the adjacent East China Sea were studied. Multivariate statistical analysis indicated that the archaeal amoA genotype communities could be clustered according to sampling transects, and the station located in an estuarine mixing zone harboured a distinct AOA community. The distribution of AOA communities correlated significantly with the gradients of surface-water salinity and sediment sorting coefficient. The spatial distribution of putative soil-related AOA in certain sampling stations indicated a strong impact of the Changjiang freshwater discharge on the marine benthic microbial ecosystem. Besides freshwater, nutrients, organic matter and suspended particles, the Changjiang Diluted Water might also contribute to the transport of terrestrial archaea into the seawater and sediments along its flow path.

Benthic foraminifera and bottom water evolution in the middle-southern Okinawa Trough during the last 18 ka

A piston sediment core E017 from the middle-southern Okinawa Trough was investigated. A preliminary study of the deep-water evolution since 18 cal. ka BP was performed based on the quantitative census data of benthic foraminiferal fauna, together with planktonic foraminiferal oxygen and carbon isotope, AMS(14)C dating, and the previous results achieved in the southern Okinawa Trough. The result shows that the benthic fauna was dominated by Bulimina aculeata (d'Orbigny), Uvigerina peregrina (Cushman), Hispid Uvigerina and Uvigerina dirupta (Todd) during the glaciation-deglaciation before 9.2 cal. ka BP, while Epistominella exigua (Brady), Pullenia bulloides (d'Orbigny), Cibicidoides hyalina (Hofker), Sphaeroidina bulloides (d'Orbigny) and Globocassidulina subglobosa (Brady) predominated the fauna in the post-glacial period after 9.2 cal. ka BP. The benthic foraminifera accumulation rate (BFAR), paleoproductivity estimates and benthic foraminiferal assemblage conformably indicate that surface water paleoproductivity and organic matter flux during the glaciation-deglaciation were higher than those of the post-glacial period in the middle-southern Okinawa Trough, and gradually enhanced from the southern to the central Okinawa Trough during the glaciation-deglaciation, which could be caused by the discrepancy of the terrigenous nutrients supply. High abundances of E exigua, an indicator of pulsed organic matter input, after 9.2 cal. ka. BP may indicate that the intensity of seasonally riverine pulsed flux during the post-glacial period was stronger than that of the glaciation-deglaciation period, and the seasonal influx in the central trough might be stronger than in the south. The temporal distributions of the typical species indicating bottom water oxygen content and ventilation condition show that the ventilation of the bottom water during the post-glacial period is more active than the glaciation-deglaciation, which reflects that the evolution of the intermediate and deep waters of the northwestern Pacific during the last glaciation has no evident influence on the deep-water of the middle-southern Okinawa Trough. Additionally, the variations in agglutinated benthic foraminiferal abundance and other carbonate dissolution proxies indicate that carbonate dissolution gradually increased since the last 18 ka in the Okinawa Trough and rapidly enhanced at 9.2 cal. ka BP. The modern shallow carbonate lysocline could form at 3 cal. ka BP.

Benthic foraminiferal distribution in surface sediments along continental slope of the southern Okinawa Trough: dependance on water masses and food supply

Benthic foraminiferal analysis of 29 samples in surface sediments from the southern Okinawa Trough is carried out. The results indicate that benthic foraminiferal abundance decreases rapidly with increasing water depth. Percentage frequencies of agglutinated foraminifera further confirm the modem shallow carbonate lysocline in the southern Okinawa Trough. From continental shelf edge to the bottom of Okinawa Trough, benthic foraminiferal fauna in the surface sediments can be divided into 5 assemblages: (1) Continental shelf break assemblage, dominated by Cibicides pseudoungerianus, corresponds to subsurface water mass of the Kuroshio Current; (2) upper continental slope assemblage, dominated by Cassidulina carinata, Globocassidulina subglobosa, corresponds to intermediate water mass of the Kuroshio Current; (3) intermediate continental slope assemblage, dominated by Uvigerina hispida, corresponds to the Okinawa Trough deep water mass above the carbonate lysocline; (4), lower continental slope - trough bottom assemblage, dominated by Pullenia bulloides, Epistominella exigua and Cibicidoides hyalinus, corresponds to deep water mass of the Okinawa Trough; and (5) trough bottom agglutinated assemblage, dominated by Rhabdammina spp., Bathysiphon flavidus, corresponds to I strongly dissolved environment of the trough bottom. The benthic foraminiferal fauna in the southern Okinawa Trough are controlled jointly by water masses and food supply. Water temperature, oxygen concentration and carbonate dissolution of the water masses are important controlling factors especially for the continental shelf break and trough bottom assemblages. The food supply also plays an important role in these benthic foraminiferal assemblages along the western slope. of the Okinawa Trough. Both the abundance and the 5 assemblages of benthic foraminifera correspond well to the organic matter supply along the continental slope and a lateral transport of TSM (total suspended matter) and POC (particulate organic carbon) from the shelf break to the deep water is also an important food supply for benthic fauna in this region.

胶州湾和东太平洋海隆(~13°N)沉积物微生物多样性研究

海洋是一个巨大的生态系统，多样的微生物是构成海洋生态系统的基本元素。海洋微生物的群落结构及演变深刻的反映着海洋生态系统的变迁。本文采用分子生物学技术，研究了近海沉积物生态系统——胶州湾沉积物中细菌的多样性、群落结构的时空演替规律以及远洋深海沉积物生态系统——东太平洋海隆北纬13o附近深海沉积物中细菌和古细菌群落结构沿沉积物断层的分布情况，结果表明在两处沉积物中，微生物群落的结构都与环境因子有显著的相关性，是反映海洋沉积物环境特征的重要（分子）标志物，并且可能在这些环境中参与生物地球化学循环等重要过程。 1.从胶州湾不同区域的8个代表性站点采集4个季度的沉积物样品。提取总基因组DNA，利用16S rDNA作为分子标记，采用克隆文库对胶州湾沉积物中细菌群落的组成、空间分布和季节演替规律进行了研究。结果显示沉积物中的细菌具有高度多样性，来自于13个细菌门，同时还有28%的未鉴定克隆，表明胶州湾沉积物中蕴藏着巨大的微生物资源。其中已鉴定的优势种群是α-、β-、γ-、δ-变形细菌、绿弯菌、厚壁菌、蓝细菌和放线菌。同时还包括酸杆菌、拟杆菌、浮霉菌、疣微菌、芽单胞菌、绿菌、梭杆菌、异常球菌-栖热菌等类群的存在。将各克隆库的组成与温度、总碳、总氮等环境因子结合分析，结果显示细菌群落结构更替的主要驱动力是季节变化所带来的温度等环境因子的演变。对数据库中与本研究所获得序列具有最近亲缘关系序列的来源环境进行分析表明，胶州湾中细菌群落受航运活动、水产养殖、重金属污染等人类活动的明显影响，同时这些活动表现出显著的空间特异性，比如C4和D6等站点明显受到航运活动的影响，而A3和Y1等站点则容易受到沿岸径流所带来的淡水和油污染的影响。 2.分别利用PCR-DGGE和克隆文库技术对东太平洋海隆北纬13o附近深海柱状沉积物样品中细菌和古菌群体进行研究，结果显示这些微生物群落沿四个分别代表不同沉积年代断层明显的成层分布，与环境因子结合分析表明这种成层分布与氧化还原性质等地球化学特征的成层分布相吻合，提示我们该生态系统中的微生物受到环境因子的巨大作用，同时也表明这些微生物可能参与该生态系统中硫、金属元素代谢等过程。通过系统发育分析，四个断层中的微生物群落中呈现出很多与热液活动相关的个体（其中34.7%的细菌序列和31%的古菌序列与来源于各种热液环境的序列具有最近的亲缘关系）。但总体群落结构分析表明该区域可能属于热液活动影响区域的边缘，处于从热液活动环境到普通的低温沉积物环境的过渡区域。 3.将在胶州湾和东太平洋海隆北纬13o附近海洋沉积物生态系统中都存在的优势细菌类群（α-、β-、γ-、δ-变形细菌和放线菌、绿弯菌、厚壁菌、酸杆菌、浮霉菌）进行系统发育分析和背景比较分析，结果显示两处沉积物中的细菌优势种群虽然在大类群上很多是相同的，但是可能由于两处沉积物中不同物理化学等环境因子的选择作用（如胶州湾的近海特征和人为活动，东太平洋深海特点和热液活动），而导致优势种群在系统发育关系上距离比较远。这表明独特的微生物群落结构，特别是优势种群的群落结构信息是描述特定环境生态系统的重要方面。本研究表明在全球环境变迁中,自然环境因子和人类活动都在深刻改变着微生物群落的结构和功能。本文阐述了在环境变迁特定时期两处沉积物生态系统中的微生物群落结构及时空差异，为研究大范围生态系统的演变提供了依据，同时也为在两处沉积物环境中进行微生物参与的生物地球化学研究奠定了基础。

Influence of filtering and biodeposition by the cultured scallop Chlamys farreri on benthic-pelagic coupling in a eutrophic bay in China

In coastal ecosystems, suspension-cultured bivalve filter feeders may exert a strong impact on phytoplankton and other suspended particulate matter and induce strong pelagic-benthic coupling via intense filtering and biodeposition. We designed an in situ method to determine spatial variations in the filtering-biodeposition process by intensively suspension-cultured scallops Chlamys farreri in summer in a eutrophic bay (Sishili Bay, China), using cylindrical biodeposition traps directly suspended from longlines under ambient environmental conditions. Results showed that bivalve filtering-biodeposition could substantially enhance the deposition of total suspended material and the flux of C, N and P to the benthos, indicating that the suspended filter feeders could strongly enhance pelagic-benthic coupling and exert basin-scale impacts in the Sishili Bay ecosystem. The biodeposition rates of 1-yr-old scallops varied markedly among culture sites (33.8 to 133.0 mg dry material ind.(-1) d(-1)), and were positively correlated with seston concentrations. Mean C, N and P biodeposition rates were 4.00, 0.51, 0.11 mg ind.-1 d-1, respectively. The biodeposition rates of 2-yr-old scallops were almost double these values. Sedimentation rates at scallop culture sites averaged 2.46 times that at the reference site. Theoretically, the total water column of the bay could be filtered by the cultured scallops in 12 d, with daily seston removal amounting to 64%. This study indicated that filtering-biodeposition by suspension-cultured scallops could exert long-lasting top-down control on phytoplankton biomass and other suspended material in the Sishili Bay ecosystem. In coastal waters subject to anthropogenic N and P inputs, suspended bivalve aquaculture could be advantageous, not only economically, but also ecologically, by functioning as a biofilter and potentially mitigating eutrophication pressures. Compared with distribution-restricted wild bivalves, suspension-cultured bivalves in deeper coastal bays may be more efficient in processing seston on a basin scale.

Methane emissions by alpine plant communities in the Qinghai-Tibet Plateau

For the first time to our knowledge, we report here methane emissions by plant communities in alpine ecosystems in the Qinghai-Tibet Plateau. This has been achieved through long-term field observations from June 2003 to July 2006 using a closed chamber technique. Strong methane emission at the rate of 26.2 +/- 1.2 and 7.8 +/- 1.1 mu g CH4 m(-2) h(-1) was observed for a grass community in a Kobresia humilis meadow and a Potentilla fruticosa meadow, respectively. A shrub community in the Potentilla meadow consumed atmospheric methane at the rate of 5.8 +/- 1.3 mu g CH4 m(-2) h(-1) on a regional basis; plants from alpine meadows contribute at least 0.13 Tg CH4 yr(-1) in the Tibetan Plateau. This finding has important implications with regard to the regional methane budget and species-level difference should be considered when assessing methane emissions by plants.

Distribution and species diversity of plant communities along transect on the Northeastern Tibetan plateau

The distribution and species diversity of plant communities along a 600 km transect through the northeastern Tibetan Plateau (32 degrees 42'-35 degrees 07' N, 101 degrees 02'-97 degrees 38' E) with altitudes from 3255 to 4460 m are described. The transect started from the Youyi Bridge of Banma through Dari, Maqin and Maduo to Zaling Lake. The data from 47 plots along the transect are summarized and analyzed. The mean annual temperature, the mean annual rainfall and the length of growing season decreases from 2.6 to -4.5 degrees C, from 767.2 to 240.1 mm, from 210 to 140 days, respectively, along the transect from the southeastern Banma to northwestern Zaling Lake. The number of vascular plant species recorded in 47 plots is 242 including 2 tree, 34 shrub, 206 herb species. Main vegetation types on the transect from southeast to northwest are: Sabina convallium forest, Picea likiangensis forest, Pyracantha fortuneana + Spiraea alpina shrub, Hippophae neurocarpu shrub, Sibiraea angustata + Polygonum viviparum shrub, Stellera chamaejasme herb meadow, Potentilla fruticosa + Salix obscura + Carex sp. Shrub, Kobresia capillifolia meadow, P. froticosa + Kobresia humilis shrub, Caragana jubata + S. obscura shrub, Kobresia tibetica meadow, Kobresia pygmaea meadow, K. pygmaea + Stipa purpurea steppe meadow, Stipa purpurea steppe. Plant richness and diversity index all showed a decreasing trend with increasing of elevation along transect from southeast to northwest. Detailed information on altitudinal ranges and distribution of the alpine vegetation, vascular flora and environments over the alpine zone at northeastern Tibetan Plateau provides baseline records relevant to future assessment of probable effects of global climate changes.

Evaluation of the Specialist Libraries/Communities of Practice. Report for National Library for Health

Cooper, J., Spink, S., Thomas, R. & Urquhart, C. (2005). Evaluation of the Specialist Libraries/Communities of Practice. Report for National Library for Health. Aberystwyth: Department of Information Studies, University of Wales Aberystwyth. Sponsorship: National Library for Health (NLH)

Moving Communities of Practice forward: the challenge for the National electronic Library for Health and its Virtual Branch Libraries

Yeoman, A., Urquhart, C. & Sharp, S. (2003). Moving Communities of Practice forward: the challenge for the National electronic Library for Health and its Virtual Branch Libraries. Health Informatics Journal, 9(4), 241-252. Previously appeared as a conference paper for the iSHIMR2003 conference (Proceedings of the Eighth International Symposium on Health Information Management Research, June 1-3, 2003, Boras, Sweden) Sponsorship: NHS Information Authority/National electronic Library for Health

Developing communities of practice in the NeLH (National electronic Library for Health)

Urquhart, C., Yeoman, A., Sharp, S. (2003). Developing communities of practice in the NeLH (National electronic Library for Health). In Proceedings of the UKAIS (UK Academy for Information Systems) annual conference, University of Warwick, April 2003. Sponsorship: NHS Information Authority/National electronic Library for Health

Doing Good in American Communities: Congregations and Service Organizations Working Together

A Research Report from the "Organizing Religious Work Project," Hartford Institute for Religion Research Hartford Seminary