Stratified Communities of Active Archaea in Shallow Sediments of the Pearl River Estuary, Southern China

Marine subsurface sediments represent a novel archaeal biosphere with unknown physiology. To get to know the composition and ecological roles of the archaeal communities within the sediments of the Pearl River Estuary, Southern China, the diversity and vertical distribution of active archaea in a sediment core were characterized by 16S rRNA phylogenetic analysis of clone libraries derived from RNA. In this study, the archaeal diversity above, within, and beneath the sulfate-methane transition zone (SMTZ) in the Pearl River Estuary sediment core was described. The majority of the clones obtained from the metabolically active fraction of the archaeal community were most closely related to miscellaneous crenarchaeotal group and terrestrial miscellaneous euryarchaeotal group. Notably, although the Pearl River Estuary sediment belong to high methane and high organic carbon environment, sequences affiliated with methanotrophic and methanogenic archaea were detected as minor group in 16S rRNA clone libraries. No obvious evidence suggested that these unknown archaeal phylotypes related directly to anaerobic oxidation of methane in SMTZ. This is the first phylogenetic analysis of the metabolically active fraction of the archaeal community in the coastal sediment environments.     

Diversity and spatio-temporal distribution of ammonia-oxidizing Archaea and Bacteria in sediments of the Westerschelde estuary

The diversity and spatio-temporal distribution of ammonia-oxidizing Archaea (AOA) and Bacteria (AOB) were investigated along a salinity gradient in sediments of the Westerschelde estuary. Sediment samples were collected from three sites with different salinities, and at six time points over the year. Denaturing gradient gel electrophoresis of PCR-amplified 16S rRNA and amoA gene fragments was used to identify the AOA and AOB present. Members of the AOA were mainly belonging to the Crenarchaeota Group 1, which were found at all sites, while members of the genus Nitrosomonas, which were abundant at the brackish sites, and of the genus Nitrosospira, which were present in early spring at the marine sites, were found to be the dominant AOB. Statistical analysis indicated that salinity and temperature were the main factors controlling the diversity and distribution of both AOA and AOB. Variability in net primary production rates was also correlated with species composition of both groups, but changes in the nitrite concentration only to the distribution of the AOA.     

Diversity and distribution of ammonia-oxidizing Archaea in the seasonally frozen soils in Northeastern China

The genetic diversity and distribution of ammonia-oxidizing Archaea (AOA) in nine seasonally frozen soils sampled around the city of Harbin, China, is analyzed based on archaeal amoA gene. Soil samples are divided into four groups by its properties: fertilized/unfertilized mesic (well-balanced supply of moisture) soils and fertilized/unfertilized hydric (abundant of moisture) soils. Clone libraries based on AOA amoA gene polymerase chain reaction products are constructed, and the phylogenetic analysis at 5 % cutoff level shows that AOA members mainly belong to the soil/sediment lineage which includes four clusters, and very few archaeal amoA gene sequences fall into the marine lineage. The four groups of soils have different archaeal amoA gene assemblage, and the available nitrogen and organic carbon are significantly correlated with diversity indexes. The result shows that long-term artificial amendment such as fertilization and agriculture cultivation has an important impact on AOA community shift in terrestrial environment. Moisture may drive the shape of different AOA communities by changing the aerobic environment into anaerobic. Soil composition is another noticeable factor effect AOA community, which can help the shape of a special AOA community with only two species.     

Diversity and abundance of ammonia-oxidizing prokaryotes in sediments from the coastal Pearl River estuary to the South China Sea

In the present study the diversity and abundance of nitrifying microbes including ammonia-oxidizing archaea (AOA) and betaproteobacteria (beta-AOB) were investigated, along with the physicochemical parameters potentially affecting them, in a transect of surface sediments from the coastal margin adjacent to the Pearl River estuary to the slope in the deep South China Sea. Nitrifying microbial diversity was determined by detecting the amoA (ammonia monooxygenase subunit A) gene. An obvious community structure shift for both AOA and beta-AOB from the coastal marginal areas to the slope in the deep-sea was detected, while the OTU numbers of AOA amoA were more stable than those of the beta-AOB. The OTUs of beta-AOB increased with the distance from the coastal margin areas to the slope in the deep-sea. Beta-AOB showed lower diversity with dominant strains in a polluted area but higher diversity without dominant strains in a clean area. Moreover, the diversity of beta-AOB was correlated with pH values, while no noticeable relationships were established between AOA and physicochemical parameters. Beta-AOB was more sensitive to transect environmental variability and might be a potential indicator for environmental changes. Additionally, the surface sediments surveyed in the South China Sea harboured diverse and distinct AOA and beta-AOB phylotypes different from other environments, suggesting the endemicity of some nitrifying prokaryotes in the South China Sea.     

Diversity in Chemotaxis Mechanisms among the Bacteria and Archaea

The study of chemotaxis describes the cellular processes that control the movement of organisms toward favorable environments. In bacteria and archaea, motility is controlled by a two-component system involving a histidine kinase that senses the environment and a response regulator, a very common type of signal transduction in prokaryotes. Most insights into the processes involved have come from studies of Escherichia coli over the last three decades. However, in the last 10 years, with the sequencing of many prokaryotic genomes, it has become clear that E. coli represents a streamlined example of bacterial chemotaxis. While general features of excitation remain conserved among bacteria and archaea, specific features, such as adaptational processes and hydrolysis of the intracellular signal CheY-P, are quite diverse. The Bacillus subtilis chemotaxis system is considerably more complex and appears to be similar to the one that existed when the bacteria and archaea separated during evolution, so that understanding this mechanism should provide insight into the variety of mechanisms used today by the broad sweep of chemotactic bacteria and archaea. However, processes even beyond those used in E. coli and B. subtilis have been discovered in other organisms. This review emphasizes those used by B. subtilis and these other organisms but also gives an account of the mechanism in E. coli.     

珠江口表层沉积物石油类含量、分布及变化趋势

采用紫外分光光度法测定了2006、2009、2010和2011年夏季珠江口表层沉积物中的石油类含量,并与历史数据进行了比较。结果表明:5年中夏季珠江口表层沉积物的石油类平均含量分别为127.2μg/g、318.0μg/g、134.1μg/g、和118.5μg/g;珠江口内站位的石油类含量明显高于口外站位;相同站位的石油类含量年际间波动较大;本世纪的石油类含量明显高于二十世纪八九十年代。以《海洋沉积物质量》第一类标准来评价,4年珠江口表层沉积物石油类含量的站位超标率分别为0、25%、10%和5%。影响珠江口海域沉积物中石油类含量的主要因素有陆源排污输入、溢油和水动力条件等。     

珠江广州河段轮虫的时空分布研究

2004年4月-2007年3月,对珠江广州河段轮虫群落结构的时空变化进行了三年的调查研究。调查期间,共发现轮虫56种。优势种为裂痕龟纹轮虫(Anuraeopsis fissa),微型多突轮虫(Proalides subtilis),西式三肢轮虫(Filinia novaezealandiae),角突臂尾轮虫(Brachionus angularis),尾突臂尾轮虫(Brachionus caudatus),暗小异尾轮虫(Trichocerca pusilla),蛭态目(Bdelloidea sp.)和萼花臂尾轮虫(Brachionus calyciflorus)。调查发现,珠江径流量对轮虫密度有重要影响。在丰水期,两个采样站点(分别为中大码头和黄埔码头)的轮虫密度变化不大,而在枯水期,位于下游的黄埔码头的轮虫密度显著低于上游的中大码头。轮虫的密度高峰出现在秋季(9月底至12月初)。中大码头轮虫的最高峰出现在2004年12月初,为5975ind./L;黄埔码头的轮虫高峰出现在2004年4月中旬,为5877ind.·L^-1。轮虫密度变化范围为4~5975 ind.·L^-1。中大码头轮虫密度的平均值为1627±233 ind.·L^-1;而黄埔码头的平均值为1051±147 ind.·L^-1。     

珠江口伶仃洋海域底层游泳动物的季节变化

珠江口伶仃洋海域是渔业资源的重要栖息地,近年来由于人类活动的加剧导致生态环境质量下降。为进一步了解栖息环境恶化对渔业资源的影响,于2009年8月至2010年4月采用底拖网在珠江口伶仃洋海域进行了游泳动物4个季节的调查。共鉴定游泳动物92种,其中鱼类54种,甲壳类32种和头足类6种。游泳动物种数夏季最高,为52种,春季最低,仅35种,春、夏季和冬、春季种类季节更替显著。优势种组成较为稳定,以日本蟳(Charybdis japonica)、黑斑口虾蛄(Oratosquilla kempi)和棘头梅童鱼(Collichthys lucidus)为主要优势种,其中日本蟳为全年优势种,平均尾数密度占总密度的8.07%～26.22%。游泳动物资源密度和尾数密度季节变化趋势一致,均为夏季最高,秋季和春季次之,冬季最低。珠江口伶仃洋海域温度和盐度有明显的季节变化,夏季和秋季温度较高,盐度较低,冬季和春季温度较低,而盐度较高。温度是伶仃洋海域游泳动物种类和数量季节变化的主要因子。与历史资料比较,珠江口主要经济鱼、虾类出现小型化趋势。     

Stratification of Archaeal communities in shallow sediments of the Pearl River Estuary,Southern China

Microorganisms are known to play fundamental roles in the biogeochemical cycling of carbon in the coastal environments. To get to know the composition and ecological roles of the archaeal communities within the sediments of the Pearl River Estuary, Southern China, the diversity and vertical distribution of archaea in a sediment core was reported based on the 16S rRNA and mcrA genes for the first time. Quantitative PCR analysis revealed that archaea were present at 10⁶–10⁷ 16S rRNA gene copies/g (wet weight) in the sediment core, and the proportion of mcrA versus 16S rRNA gene copies varied from 11 to 45%. 16S rRNA gene libraries were constructed and analyzed for the top layer (0–6 cm), middle layer (18–24 cm), sulfate-methane transition zone (SMTZ, 32–42 cm), and bottom layer (44–50 cm) sediments. The results indicated that Miscellaneous Crenarchaeotal Group (MCG) was the main component in the sediments. The MCG archaea could be further divided into six subgroups: MCG-A, B, C, D, E, and F. On the other hand, mcrA sequences from methanogens related to the order Methanomicrobiales and ANME-2 methanotrophs were detected in all sediment layers. Taken together, our data revealed a largely unknown archaeal community in which MCG dominated within the Pearl River estuarine sediments, while methanogens and methane-oxidizing archaea putatively involving in methane metabolism, were also found in the community. This is the first important step towards elucidating the biogeochemical roles of these archaea in the Pearl River Estuary.     

Diversity and abundance of ammonia-oxidizing archaea and bacteria in polluted mangrove sediment

Ammonia oxidation by microorganisms is a critical process in the nitrogen cycle. Recent research results show that ammonia-oxidizing archaea (AOA) are both abundant and diverse in a range of ecosystems. In this study, we examined the abundance and diversity of AOA and ammonia-oxidizing beta-proteobacteria (AOB) in estuarine sediments in Hong Kong for two seasons using the ammonia monooxygenase A subunit gene (amoA) as molecular biomarker. Relationships between diversity and abundance of AOA and AOB and physicochemical parameters were also explored. AOB were more diverse but less abundant than AOA. A few phylogenetically distinct amoA gene clusters were evident for both AOA and AOB from the mangrove sediment. Pearson moment correlation analysis and canonical correspondence analysis (CCA) were used to explore physicochemical parameters potentially important to AOA and AOB. Metal concentrations were proposed to contribute potentially to the distributions of AOA while total phosphorus (TP) was correlated to the distributions of AOB. Quantitative PCR estimates indicated that AOA were more abundant than AOB in all samples, but the ratio of AOA/AOB (from 1.8 to 6.3) was smaller than most other studies by one to two orders. The abundance of AOA or AOB was correlated with pH and temperature while the AOA/AOB ratio was with the concentrations of ammonium. Several physicochemical factors, rather than any single one, affect the distribution patterns suggesting that a combination of factors is involved in shaping the dynamics of AOA and AOB in the mangrove ecosystem.     

Distribution and Risk Assessment of Heavy Metals in Sediments of the Pearl River Estuary,Southern China

Sediment cores collected at six freshwater discharge outlets of the Pearl River Estuary were analyzed for metal (Al, Fe, Cr, Pb, and Cd) concentration and risk assessment. The contents of Cr, Pb, Fe, and Al in these samples were measured by Inductively Coupled Plasma Optical Emission Spectrometry (ICP-OES), and Cd was measured by Inductively Coupled Plasma Mass Spectrometry (ICP-MS). The result showed that the concentration ranged (in mg/kg dry weight) as follows: Al, 7,880–97,700; Fe, 30,100–51,900; Cd, 0.23–1.09; Cr, 48.7–109; Pb, 22.3–70.2; respectively. The sediments of different particle size were measured and the result showed that the pelitic fraction (< 0.05 mm) was more enriched in heavy metals. Cd and Pb showed a similar spatial distribution in the sediment, which reflected similar anthropogenic origins. In addition, the temporal distribution of Cr, Pb, and Cd showed a light increase from the 1970s to the 2000s. Furthermore, the enrichment factor (EF) and the geo-accumulation index (I_geo) were used to comprehensively evaluate the pollution degree of heavy metals. The findings will be useful in proposing measures for strategic environmental control in estuaries.     

Phylogenetic Diversity of Archaea and Bacteria in a Deep Subsurface Paleosol

Abstract A low-biomass paleosol 188 m below the ground surface at the Department of Energy's Hanford Site in south-central Washington State was recovered and maintained at the in situ temperature (17°C) as an intact core or homogenized sediment for 0, 1, 3, 10, and 21 weeks post-sampling. Bacterial and archaeal 16S rRNA genes were amplified by PCR and cloned. Of 746 bacterial and 190 archaeal clones that were categorized by restriction fragment length polymorphism (RFLP), 242 bacterial and 16 archaeal clones were partially sequenced and compared against the small subunit ribosomal RNA database (RDP) and GenBank. Six bacterial and 16 archaeal clones sequences, with little similarity to those in public databases, were sequenced in their entirety, and subjected to more detained phylogenetic analysis. The most frequently occurring clones types were related to Pseudomonas, Bacillus, Micrococcus, Clavibacter, Nocardioides, Burkholderia, Comamonas, and Erythromicrobium. Clone sequences whose RDP similarity value was ≥0.6 consistently grouped with their nearest RDP neighbor during phylogenetic analysis. Six truly novel eubacterial sequences were identified; they consistently cluster with or near the Chloroflexaceae and sequences recovered from the Sargasso Sea. Sixteen unique archaeal RFLP groups were identified from 190 randomly-sampled clones. The novel archaeal rDNA clones formed a coherent clade along the major Crenarchaea branch containing all previously described mesophilic crenarchae clones, but remained firmly associated with 16S rDNA clones previously obtained from a thermal Fe/S spring in Yellowstone National Park. The wealth of group-specific genetic information identified during this study will now allow us to address specific hypotheses related to in situ stimulation of these deep subsurface microorganisms and changes in microbial community composition resulting from subsurface contamination or remediation processes at the Hanford Site. Revised: 21 October 1997; Accepted: 20 November 1997     

Emergy evaluations of three aquaculture systems on wetlands surrounding the Pearl River Estuary,China

Emergy and economic analysis, accompanied by sensitivity analysis, were used to evaluate the ecological economic characteristics of three fish aquaculture systems on wetlands surrounding the Pearl River Estuary in China. The sustainability of these systems was compared to two aquaculture systems and two wetland systems, to provide reference conditions for the best use of limited wetland areas. We found that the three systems studied had similar emergy characteristics, despite their very different economic characteristics. Counter intuitively, the high economic input and output mode did not have higher environmental impact or lower sustainability compared with low economic input and output mode. Apparently, the sustainability of an intensive aquaculture system is determined mainly by how many natural renewable resources are exploited. The large differences in economic benefit and environmental impacts between the mangrove reserve and the aquaculture systems demonstrated the important role of nature reserves on preserving the sustainability of an estuary. Transformity (TR) and Emergy Yield Ratio (EYR) are both indicators of system efficiency, but from different points of view, and they produced opposite results in assessing the efficiency of the same system in this study. The ratio of EYR to TR might be used in addition to the EYR and transformity as a discreet perspective on overall system production efficiency.     

Genomic adaptation to eutrophication of ammonia-oxidizing archaea in the Pearl River estuary

Ammonia-oxidizing archaea (AOA) are ubiquitous in natural ecosystems, and they are responsible for a significant fraction of ammonia oxidation globally. Since the first AOA isolate was established a decade ago, molecular surveys of their environmental distribution [based primarily on amplicon sequencing of the amoA, which codes for the alpha subunit of ammonia monooxygenase (AMO)], show that their habitats are believed to range from marine to terrestrial environments. However, the mechanisms of adaptation underpinning to their habitat expansion remain poorly understood. Here, we report that AOA accounts for almost all of the ammonia oxidizers in the shelf water adjacent to the Pearl River estuary (PRE), with the Nitrosopumilus maritimus SCM1-like (SCM1-like) being the main amoA genotype. Using a metagenomic approach, seven high-quality AOA genomes were reconstructed from the PRE. Phylogenetic analysis indicated that four of these genomes with high completeness were closely affiliated with the Nitrosomatrinus catalina strain SPOT01, which was originally isolated off the coast of California. Genomic comparison revealed that the PRE AOA genomes encoded genes functioning in amino acid synthesis, xenobiotic biodegradation metabolism and transportation of inorganic phosphate and heavy metals. This illustrates the different adaptations of AOA in one of the largest estuaries in China, which is strongly influenced by anthropogenic input. Overall, this study provides additional genomic information about estuarine AOA and highlights the importance of their contribution to nitrification in eutrophic coastal environments.     

Ecosystem Health Assessment in the Pearl River Estuary of China by Considering Ecosystem Coordination

Marine ecosystem is a complex nonlinear system. However, ecosystem health assessment conventionally builds on a linear superposition of changes in ecosystem components and probably fails to evaluate nonlinear interactions among various components. To better reflect the intrinsic interactions and their impacts on ecosystem health, an ecosystem coordination index, defined as the matching level of ecosystem structure/services, is proposed and incorporated into the ecosystem health index for a systematic diagnosis in the Pearl River Estuary, China. The analysis results show that the ecosystem health index over the last three decades decreased from 0.91 to 0.50, indicating deteriorating from healthy to unhealthy status. The health index is 3–16% lower than that calculated using the common method without considering ecosystem coordination. Ecosystem health degradation in the Pearl River Estuary manifested as significant decreases in structure/services and somewhat mismatching among them. Overall, the introduction of coordination in ecosystem health assessment could improve the understanding of the mechanism of marine ecosystem change and facilitate effective restoration of ecosystem health.     

Diversity of Bacteria and Archaea associated with a carbonate-rich metalliferous sediment sample from the Rainbow vent field on the Mid-Atlantic Ridge

Two sediment cores were collected in an inactive area of the deep-sea hydrothermal vent field Rainbow (36 degrees N on the Mid-Atlantic Ridge). Metals and carbonates were abundant throughout the cores; calcite (CaCO3) was found throughout the cores while dolomite [CaMg(CO3)2] and siderite (FeCO3) were only found in deeper layers. Using polymerase chain reaction (PCR)-amplified 16S rRNA gene sequence analysis, we examined the bacterial and archaeal diversity in a sediment layer that contained the three carbonates. The retrieved bacterial and archaeal sequences were new and less than 4% of the sequences exhibited 94% or more identity with that of cultured organisms. The analysis of the composition of the bacterial library revealed a high diversity of sequences. Half of the bacterial clones was affiliated to the gamma-Proteobacteria. Most of them had environmental sequences retrieved from deep-sea sediments as closest relatives, some of which being distantly related to free-living and symbiotic sulfur-oxidizers. Other sequences clustered in the alpha-, delta- and epsilon-Proteobacteria, the 'Bacteroidetes', the 'Planctomycetes', the 'Nitrospirae', the 'Actinobacteria', the 'Chlorobi ' and the 'Verrumicrobia'. Based on clonal abundance and sequence comparisons, phylotype groups putatively involved in the oxydation of sulfur compounds appeared to dominate in the studied sample. The majority of the archaeal sequences clustered in an euryarchaeotic lineage recently identified in the walls of black smokers suggesting a possible thermophilic way of life of these uncultured microorganisms. Oxygen isotopic composition of siderite and dolomite indicated that they were formed at 67 degrees C and 94 degrees C respectively. Together with chemical and microbiological data, this suggested that hydrothermal fluids may have circulated through this sediment.     

Life history of the Indo‐Pacific humpback dolphin in the Pearl River Estuary,southern China

We studied life history characteristics of the Hong Kong/Pearl River Estuary population of Indo‐Pacific humpback dolphins (Sousa chinensis), based on data from 120 specimens stranded between 1995 and 2009, 40 individuals biopsied at sea, and a long‐term (14+ yr) photo‐identification study. Ages were determined for 112 specimens by thin‐sectioning teeth and counting growth layer groups. Estimated length at birth was 101 cm. Longevity was at least 38 yr, and there was little difference in growth patterns of males and females. Growth was described by a Bayesian two‐phase Gompertz model; asymptotic length was reached at 249 cm. The tooth pulp cavity filled at an average of 18.5 yr of age. Physical maturity was reached at between 14 and 17 yr of age, apparently a few years after attainment of sexual maturity. Maximum lengths and weights of about 268 cm and 240 kg were attained. Females appear to lose all their spots by 30 yr, although males may retain some spotting throughout life. Calving occurred throughout the year, with a broad peak from March to June. Of 60 females monitored at sea for >14 yr of the study, none were documented to have more than three calves, suggestive of low reproductive output or low calf survival.     

珠江口超微型浮游植物时空分布及其与环境因子的关系

对珠江口及近海区域进行了夏季和冬季超微型浮游植物(0.2-3μm)调查,分析了其时空分布及其与环境因子的关系.夏季,珠江口浮游植物密度与磷酸盐成显著正相关,且N/P远远高于30,表明浮游植物受到P限制.夏季超微型藻数量比冬季高一个数量级,其丰度与盐度成显著正相关而和营养盐(溶解性无机氮(DIN),PO4-P,SiO4-Si)显著负相关,表明珠江口超微型藻受到径流的负面影响,表现出其数量在虎门附近海域低,随着咸淡水混合程度的加剧逐渐增大的分布特征;超微型浮游植物叶绿素a在总叶绿素a中的比例也表现为河口上游低,到万山群岛附近海域达到最大,推测近海高光照、低营养盐更适宜超微型藻的生长,同时也说明超微型浮游植物适应贫营养环境的生态特点.     

珠江口水体浮游细菌种群多样性空间分布特征

为认识珠江口水体浮游细菌的多样性分布规律,运用聚合酶链式反应-变性梯度凝胶电泳(PCR-DGGE)和多维尺度分析(MDS)的方法,研究了春季珠江口十个站位表底水层浮游细菌种群16SrRNA基因多样性特征。研究结果表明,珠江口浮游细菌种群具有丰富的基因多样性;不同站位细菌群落结构和优势种群变化显著:大多数站位表底层细菌群落结构比较相似,河口外站位(A12,A14和C5),表底层细菌群落结构差异性较大:多样性分析表明A14,B6和C5站位底层细菌多样性大于表层。遗传发育分析表明,序列归属于变形细菌(Proteobacteria),酸杆菌(Acidobacteria),蓝细菌(Cyanobacteria),厚壁细菌(Firmicutes)和放线菌(Actinobacteria)。变形细菌(Proteobacteria)种类最多,从河口内淡水区到河口外海水区都有大量分布,是珠江口水域占优势的菌群;同时也检测到种类丰富的放线菌(Actinobacteria)的存在,也是珠江口水域的优势菌群。