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 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。     

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.     

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.     

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     

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.     

Diversity and Abundance of Ammonia-Oxidizing Archaea and Bacteria in Diverse Chinese Paddy Soils

Ammonia-oxidizing archaea (AOA) and bacteria (AOB) in three types of paddy soils of China before and after rice plantation were investigated by using an integrated approach including geochemistry, 454 pyrosequencing, and quantitative polymerase chain reaction (PCR). The abundances of AOA amoA gene were 1～2 orders of magnitude higher than AOB amoA gene. The types of paddy soils had important impacts on the diversities of both AOA and AOB via clay mineralogy (smectite or illite-rich) and bioavailability of ammonium. The Nitrososphaera subcluster 5 and Nitrosopumilis cluster of AOA, and Nitrosomonas subcluster 5 and Nitrosospira subcluster 3 of AOB were well adapted to soils with high ammonium concentrations. AOA and AOB community structures were different before and after rice plantation, likely due to changes of pH and ammonium fertilization. The Nitrosospira subclusters 2 and 9 were well adapted to acidic paddy soils. However, the sensitivity of AOA and AOB community structures to these factors may be complicated by other geochemical conditions. The results of this study collectively demonstrated that multiple environmental factors, such as clay mineralogy, ammonium content and total organic carbon as well as soil pH, shaped AOA and AOB community structure and abundance.     

Quantitative analyses of ammonia-oxidizing Archaea and bacteria in the sediments of four nitrogen-rich wetlands in China

With the rapid development of ammonia-synthesizing industry, the ammonia-nitrogen pollution in wetlands acting as the sink of point and diffuse pollution has been increased dramatically. Most of ammonia-nitrogen is oxidized at least once by ammonia-oxidizing prokaryotes to complete the nitrogen cycle. Current research findings have expanded the known ammonia-oxidizing prokaryotes from the domain Bacteria to Archaea. However, in the complex wetlands environment, it remains unclear whether ammonia oxidation is exclusively or predominantly linked to Archaea or Bacteria as implied by specific high abundance. In this research, the abundance and composition of Archaea and Bacteria in sediments of four kinds of wetlands with different nitrogen concentration were investigated by using quantitative real-time polymerase chain reaction, cloning, and sequencing approaches based on amoA genes. The results indicated that AOA distributed widely in wetland sediments, and the phylogenetic tree revealed that archaeal amoA functional gene sequences from wetlands sediments cluster as two major evolutionary branches: soil/sediment and sediment/water. The bacteria functionally dominated microbial ammonia oxidation in different wetlands sediments on the basis of molecule analysis, potential nitrification rate, and soil chemistry. Moreover, the factors influencing AOA and AOB abundances with environmental indicator were also analyzed, and the results addressed the copy numbers of archaeal and bacterial amoA functional gene having the higher correlation with pH and ammonia concentration. The pH had relatively great negative impact on the abundance of AOA and AOB, while ammonia concentration showed positive impact on AOB abundance only. These findings could be fundamental to improve understanding of the importance of AOB and AOA in nitrogen and other nutrients cycle in wetland ecosystems.     

Metagenomic and Small-Subunit rRNA Analyses Reveal the Genetic Diversity of Bacteria, Archaea, Fungi, and Viruses in Soil

Recent studies have highlighted the surprising richness of soil bacterial communities; however, bacteria are not the only microorganisms found in soil. To our knowledge, no study has compared the diversities of the four major microbial taxa, i.e., bacteria, archaea, fungi, and viruses, from an individual soil sample. We used metagenomic and small-subunit RNA-based sequence analysis techniques to compare the estimated richness and evenness of these groups in prairie, desert, and rainforest soils. By grouping sequences at the 97% sequence similarity level (an operational taxonomic unit [OTU]), we found that the archaeal and fungal communities were consistently less even than the bacterial communities. Although total richness levels are difficult to estimate with a high degree of certainty, the estimated number of unique archaeal or fungal OTUs appears to rival or exceed the number of unique bacterial OTUs in each of the collected soils. In this first study to comprehensively survey viral communities using a metagenomic approach, we found that soil viruses are taxonomically diverse and distinct from the communities of viruses found in other environments that have been surveyed using a similar approach. Within each of the four microbial groups, we observed minimal taxonomic overlap between sites, suggesting that soil archaea, bacteria, fungi, and viruses are globally as well as locally diverse.     

Emergy and economic evaluations of four fruit production systems on reclaimed wetlands surrounding the Pearl River Estuary,China

Emergy and economic methods were used to evaluate and compare a traditional tropical fruit cultivation system, for bananas, and three newly introduced fruit cultivation systems, for papaya, guava and wampee, on reclaimed wetlands of the Pearl River Estuary, China. The goal of this study was to apply ecological engineering principles to fruit production system designs to maximize total emergy benefits and sustainability. The evaluations considered input structure, production efficiency, environmental impacts, economic viability and sustainability. The market effects on emergy exchange were assessed both for purchasing the inputs to production and for selling the fruit. These market effects were also considered in the evaluation of sustainability by using the Emergy Index for Sustainable Development (EISD), which was evaluated with and without taking the change in natural capital (i.e., soil organic matter) into consideration. The results showed that all three of the newly introduced systems are much more sustainable than the traditional banana production system. The guava production system had the highest value of the Emergy Sustainability Index (ESI = 0.40). The high price of wampee gave it the highest economic yield/cost ratio (4.87) and EISD (0.73). Emergy and economic evaluations are complementary methods, with emergy analysis shedding more light on environmental support and impacts of the production systems not considered in the market value, and economic analysis focusing on the effects of markets on fruit production. The Emergy Exchange Ratio (EER) was proposed as a bridge between emergy and economic evaluations for specific systems and/or processes.     

Low Temperature Decreases the Phylogenetic Diversity of Ammonia-Oxidizing Archaea and Bacteria in Aquarium Biofiltration Systems

The phylogenetic diversity and species richness of ammonia-oxidizing archaea (AOA) and bacteria (AOB) were examined with aquarium biofiltration systems. Species richness, deduced from rarefaction analysis, and diversity indices indicated that the phylogenetic diversity and species richness of AOA are greater than those of AOB; the diversity of AOA and of AOB is minimized in cold-water aquaria. This finding implies that temperature is a key factor influencing the population structure and diversity of AOA and AOB in aquarium biofiltration systems.     

Salinity-dominated change in community structure and ecological function of Archaea from the lower Pearl River to coastal South China Sea

Archaea have multiple roles in global biogeochemical cycles. However, we still have limited knowledge about how environmental factors affect the diversity and function of different archaeal lineages. The goal of this study was to examine the change in the abundance and community structure of Archaea in the sediments collected from the lower Pearl River (mainly North River tributary), its estuary, and coastal South China Sea (SCS) in order to evaluate how archaeal ecological function might change along the salinity gradient. Pyrosequencing of the 16S rDNA gene of Archaea was performed on sediment samples from Feilaixia Dam on the North River tributary to Wanshan islands, which have a salinity range of 0.1 to 31.2?‰. Consistent with the salt tolerance of cultivated representatives, methanogens in the genera Methanoregula, Methanosaeta, and Methanosarcina and Nitrososphaera within Thaumarchaeota of the ammonia-oxidizing Archaea (AOA) were abundant in freshwater sediments of the North River tributary, whereas the marine-associated genera Methanococcoides and Nitrosopumilus were the most abundant methanogens and AOA, respectively, in the estuary and coastal SCS. However, the percentages of total methanogens decreased and Thaumarchaeota increased with salinity, respectively. The phylum Crenarchaeota was largely represented by class-level lineages with no cultivated representatives, which collectively were more abundant in the estuary and coastal SCS in comparison to freshwater sites. This study indicates that salinity is the dominating factor affecting archaeal community structure and ecological function from the North River tributary of the Pearl River, its estuary, and coastal SCS, which is consistent with salinity control on microbial diversity in other regions of the world.     

珠江口伶仃洋海域小型底栖生物丰度和生物量

分别于2006年7-8月(夏)、2007年4月(春)和10月(秋)对珠江口伶仃洋附近海域小型底栖生物丰度和生物量进行调查.3个航次共鉴定小型底栖生物类群15类,包括线虫、桡足类、多毛类、介形类、动吻动物、端足类、颚咽动物、涟虫、纽虫、腹足类、双壳类、星虫、螠虫、原足类和其他未鉴定种类;春、夏、秋3个航次小型底栖生物丰度分别为(272.1+281.9)、(165.1±147.1)和(246.4±369.3) ind·10 cm-2,线虫为主要优势类群,分别占小型底栖生物总丰度的86.8％、83.5％和93.4％.小型底栖生物丰度垂直分布不均匀,分布于沉积物0～2 cm、2～5 cm、5～10 cm的数量比例分别为54.1％、35.2％和10.8％,线虫分布于沉积物0～5 cm数量比例为87.4％;春、夏、秋3个航次小型底栖生物生物量分别为(374.6±346.9)、(274.1±352.2)和(270.8±396.0) μg·10 cm-2,多毛类平均生物量最高,分别占小型底栖生物总生物量的30.1％、46.7％和46.0％,其次为线虫(25.2％、20.1％和34.0％)和介形类(20.6％、15.3％和14.8％).伶仃洋小型底栖生物丰度平面分布呈现从北向南升高、东部高于西部的趋势.伶仃洋小型底栖生物丰度、生物量分布与水深呈显著正相关.