云南热泉中氨氧化古菌的accA基因与amoA基因丰度与环境因子NO2－和NO3－的相关性

【目的】氨氧化古菌(ammonia-oxidizing archaea,AOA)可能通过近期刚发现的3-羟基丙酸盐/4-羟基丁酸盐途径(3-hydroxypropionate/4-hydroxybutyrate cycle,HP/HB)来固定CO2,在海洋和土壤环境下进行化能自养型生长。云南热泉系统已被证明具有丰富的AOA多样性。本论文旨在调查云南不同热泉中,这种CO2固定途径的关健酶——乙酰辅酶A羧化酶基因acc A和古菌氨单加氧酶基因amo A,及原核微生物16S rRNA基因的丰度变化,以及它们与环境因子的相关性。【方法】选择20处代表性热泉沉积物样品,通过荧光定量PCR技术,获得各目的基因丰度;利用R软件包对各样点地化参数进行主成分分析(Principal Component Analysis,PCA),并通过Mantel test检验各目的基因和地化参数间的相关性。【结果】细菌和古菌16S rRNA基因的丰度范围分别在6.6×107至4.19×1011和1.27×106至1.51×1011拷贝/g沉积物;古菌acc A和amo A基因的丰度范围为8.89×103至6.49×105和7.64×103至4.36×105拷贝/g沉积物,Mantel test结果显示acc A和amo A基因丰度间具有极显著的相关性(R=0.98,P0.001),两者又分别都与热泉内的NO2-和NO3-浓度存在显著相关,与p H值等其它环境因子没有明显统计学意义上的相关性。【结论】云南地区热泉间的细菌和古菌丰度,以及两者比例关系都存在较大差异;相关性的统计结果进一步证明了热泉环境下的氨氧化古菌是通过HP/HB途径进行CO2固定;本次研究并未发现氨氧化古菌的丰度与环境p H存在明显统计学意义上的相关性,这与常温土壤环境的相关研究结果存在不同。     

云南地区热泉中氨氧化菌丰度对环境条件的响应

【目的】研究热泉中的氨氧化菌对于理解全球氮循环作用至关重要,而人们对于热泉中环境条件对氨氧化菌丰度分布的影响还知之甚少。本研究旨在研究云南热泉中氨氧化菌的丰度以及热泉环境因子(例如:温度、氨浓度及pH等)对氨氧化菌丰度的影响。【方法】在所选取的热泉中,采集沉积物、菌席或泉华样品。使用RNA逆转录、定量聚合酶链式反应及荧光原位杂交等技术对样品中各微生物种群进行定量分析。【结果】所选取的热泉沉积物、菌席或泉华中微生物总量大约为108-109细胞/g。其中,氨氧化古菌(AOA)占样品中微生物总量的0.02-1.32%,而氨氧化细菌数量低于检测下限。地球化学参数和AOA相对丰度的相关性统计分析显示,氨氧化古菌相对丰度值与NH3、NO2-、NO3-浓度和温度等具有统计学意义上的相关性,而其与Fe2+和及盐度无统计学意义上的相关性。【结论】在所调查的热泉中,氨氧化微生物种群主要由AOA组成,AOA在热泉中的氨氧化生物地球化学过程中起着重要作用。热泉中多个环境因子一起控制着AOA丰度在不同热泉中的分布特征,而某些环境因子,如盐度-和Fe2+浓度,可能不是控制AOA分布特征的关键因素。     

Microbial Silicification in Sinters from Two Terrestrial Hot Springs in the Uzon Caldera,Kamchatka, Russia

Silicification of microbial communities is the most pervasive form of mineralization in two terrestrial hot springs in the Uzon Caldera. X-ray diffraction and electron microscopy reveal a diverse sinter mineral assemblage dominated by opal-A with accessory sulfur, sulfides, alunite group minerals, oxides, and oxyhydroxides. Aluminum laminations (reported for the first time) noted in one deposit may slow opal-A transformational rates enabling mineralized microbial remnants to exist longer in the rock record. Although preservation of microbial forms decreases over time, the collective mineral assemblage and patterning suggests that they are the most persistent lines of evidence of life in the geologic record.     

Community Composition and Abundance of Ammonia-Oxidizing Archaea in Sediments from the Changjiang Estuary and its Adjacent Area in the East China Sea

Community composition and abundance of ammonia-oxidizing archaea (AOA) were investigated using ammonia monooxygenase α subunit (amoA) in sediments from the Changjiang estuary and its adjacent area in the East China Sea (ECS). Real-time quantitative polymerase chain reaction (qPCR), clone libraries and sequencing were performed to characterize the AOA community. Clone libraries analysis showed that the majority of amoA sequences fell within the Nitrosopumilus cluster. Correlation analysis showed that AOA diversity was closely related to the nitrite concentration, which was consistent with the canonical correspondence analysis (CCA) where a significant association between nitrite and AOA community composition was observed. The qPCR results were found to be significantly correlated with the environmental parameters. In the gravity cores, a significant positive correlation was found between ammonium concentrations and amoA gene copy numbers from different sediment depths at station S31. At station S33, however, ammonium concentration had a negative correlation and nitrite concentration had a positive correlation with amoA gene copy numbers. In the surface sediments, chlorophyll a concentration had a negative correlation and nitrate concentration had a positive correlation with amoA gene copy numbers. Compared amoA gene copy numbers from AOA with those from ammonia-oxidizing β-proteobacteria (β-AOB) in the same studied areas, the amoA gene copy ratio of β-AOB to AOA was negatively correlated with the phosphate concentration and dissolved oxygen concentration, but was not significantly correlated with either ammonium concentrations or salinity. Our data provided valuable information to achieve a better understanding of the potential role of ammonia oxidizers at the interface between terrestrial and marine environments.     

Effect of iron on phytoplankton production in the Sargasso Sea

Addition of chelated iron at concentrations of 0.5, 1.0, 10 and 100μg Fe·l^?1 to Sargasso Sea phytoplankton assemblages did not affect the rate of photosynthesis during 4-h incubation experiments. In experiments with 72-h incubations, however, iron enhanced carbon assimilation. The enhancement was independent of iron concentration.     

Hydrogen sulfide concentrations in indoor air of thermal springs

This study aimed to assess hydrogen sulfide (H₂S) concentrations in the pool indoor air of hot springs and its link to some physicochemical properties of the springs in Ardabil province. Twenty-two hot springs from different regions were selected and monitored for H₂S concentrations using a portable gas meter. Respective mean concentrations of H₂S in hot springs indoor air were 9.11 ± 11. Ghotour Souei hot springs had the highest concentration of H₂S with a mean concentration of 29.4 ± 7.7 and 25.2 ± 8.16 ppm at the source and general pool areas, respectively. Oxidation-reduction potential and pH of the water were the most important factor influencing H₂S concentrations in the hot springs. H₂S concentrations in indoor air of Ardabil hot springs were noticeably higher than OEL-TWA and OEL-STEL, and therefore may pose important risks for human health on both short-and long-term exposures.     

Nitrification in terrestrial hot springs of Iceland and Kamchatka

Archaea have been detected recently as a major and often dominant component of the microbial communities performing ammonia oxidation in terrestrial and marine environments. In a molecular survey of archaeal ammonia monooxygenase (AMO) genes in terrestrial hot springs of Iceland and Kamchatka, the amoA gene encoding the alpha-subunit of AMO was detected in a total of 14 hot springs out of the 22 investigated. Most of these amoA-positive hot springs had temperatures between 82 and 97 degrees C and pH range between 2.5 and 7. In phylogenetic analyses, these amoA genes formed three independent lineages within the known sequence clusters of marine or soil origin. Furthermore, in situ gross nitrification rates in Icelandic hot springs were estimated by the pool dilution technique directly on site. At temperatures above 80 degrees C, between 56 and 159 mumol NO(3)(-) L(-1) mud per day was produced. Furthermore, addition of ammonium to the hot spring samples before incubation yielded a more than twofold higher potential nitrification rate, indicating that the process was limited by ammonia supply. Our data provide evidence for an active role of archaea in nitrification of hot springs in a wide range of pH values and at a high temperature.     

Improving the yield from fermentative hydrogen production

Efforts to increase H₂ yields from fermentative H₂ production include heat treatment of the inoculum, dissolved gas removal, and varying the organic loading rate. Although heat treatment kills methanogens and selects for spore-forming bacteria, the available evidence indicates H₂ yields are not maximized compared to bromoethanesulfonate, iodopropane, or perchloric acid pre-treatments and spore-forming acetogens are not killed. Operational controls (low pH, short solids retention time) can replace heat treatment. Gas sparging increases H₂ yields compared to un-sparged reactors, but no relationship exists between the sparging rate and H₂ yield. Lower sparging rates may improve the H₂ yield with less energy input and product dilution. The reasons why sparging improves H₂ yields are unknown, but recent measurements of dissolved H₂ concentrations during sparging suggest the assumption of decreased inhibition of the H₂-producing enzymes is unlikely. Significant disagreement exists over the effect of organic loading rate (OLR); some studies show relatively higher OLRs improve H₂ yield while others show the opposite. Discovering the reasons for higher H₂ yields during dissolved gas removal and changes in OLR will help improve H₂ yields.     

Activity of bacteria in water of hot springs from Southern and Central Kamchatskaya geothermal provinces, Kamchatka Peninsula, Russia

The hot-spring waters of numerous hot springs at the Kamchatka Peninsula, Russia differ in their chemical characteristics and elemental composition. Total bacterial abundance (TBA) as well as enzymatically active and respiring bacteria was enumerated in water samples collected from the Nalychevskie, Oksinskie, Apapelskie, and Dachnye hot springs. 5-Carboxyfluorescein diacetate activity was detected in all water samples and comprised 29-65% of the TBA as determined by 4',6-diamidino-2-phenylindol staining. The respiratory activity of iron-oxidizing bacteria was assayed by 5-cyano-2,3-ditolyltetrazolium chloride reduction. Respiring cells accounted for 9-14% of the TBA, indicating a positive correlation with the number of iron-oxidizing bacteria from the hot-spring biomats. Enumeration of heterotrophic bacteria revealed a high-density bacterial population only in the water of the Apapelskie hot spring, which has a temperature of 36 degrees C. Therefore, it appears that heterotrophic and iron-oxidizing bacteria inhabiting the hot-spring waters are essential for the geochemical processes occurring in hydrothermal systems.     

Eggs of pelagic fish from the Sargasso Sea with special reference to Anguilliformes

Pelagic fish eggs from IKMT hauls, taken during the 1979 Sargasso Sea Expedition, were sorted and classified according to structural aspects. 13 types were distinguished, one of them classified as exocoetid, two of them as anguilliform. One of the anguilliform egg types could be determined as belonging toDerichthys serpentinus.     

Roles of microorganisms other than Clostridium and Enterobacter in anaerobic fermentative biohydrogen production systems--a review

Anaerobic fermentative biohydrogen production, the conversion of organic substances especially from organic wastes to hydrogen gas, has become a viable and promising means of producing sustainable energy. Successful biological hydrogen production depends on the overall performance (results of interactions) of bacterial communities, i.e., mixed cultures in reactors. Mixed cultures might provide useful combinations of metabolic pathways for the processing of complex waste material ingredients, thereby supporting the more efficient decomposition and hydrogenation of biomass than pure bacteria species would. Therefore, understanding the relationships between variations in microbial composition and hydrogen production efficiency is the first step in constructing more efficient hydrogen-producing consortia, especially when complex and non-sterilized organic wastes are used as feeding substrates. In this review, we describe recent discoveries on bacterial community composition obtained from dark fermentation biohydrogen production systems, with emphasis on the possible roles of microorganisms that co-exist with common hydrogen producers.     

Comparison of electrophoretic and meristic characters of 0-group eel larvae from the Sargasso Sea

Marked differences between continental samples of American and European eels have been detected electrophoretically in allele frequencies at the MDH-2 locus. Starch gel electrophoresis carried out on board F. R. V. Anton Dohrn during the eel expedition to the Sargasso Sea in 1979 revealed a similar clear-cut genetic difference in a sample of 0-groupAnguilla leptocephali, thus confirming the classical theory of Schmidt (1932). The MDH-2 genotypes provide an additional diagnostic character for the distinction between youngA. anguilla andA. rostrata leptocephali. Species identification by biochemical genetic characters did not correspond with that by meristic characters (myomere numbers) in ca. 13 % of the specimens studied; this discrepancy mainly concerns leptocephali of theA. anguilla genotype. The results obtained are critically discussed.     

Diversity and spatial distribution of amoA-encoding archaea in the deep-sea sediments of the tropical West Pacific Continental Margin

Aims:  The ecological characteristics of the deep-sea amoA -encoding archaea (AEA) are largely unsolved. Our aim was to study the diversity, structure and distribution of the AEA community in the sediments of the tropical West Pacific Continental Margin, to develop a general view of the AEA biogeography in the deep-sea extreme environment.
Methods and Results:  Archaeal amoA clone libraries were constructed. Diverse and novel amoA sequences were identified, with the Bohol Sea, Bashi Strait and Sibuyan Sea harbouring the highest and the Bicol Shelf the lowest AEA diversity. Phylogenetic and statistical analyses illustrate a heterogeneous distribution of the AEA community, probably caused by the differential distribution of the terrestrial or estuarine AEA in the various sampling sites.
Conclusions:  The deep-sea sedimentary environments potentially harbour diverse and novel AEA in the tropical West Pacific Continental Margin. The stations in the Philippine inland seas (including station 3043) may represent AEA assemblages with various terrestrial influences and the stations connected directly to the open Philippine Sea may represent marine environment-dominant AEA assemblages.
Significance and Impact of Study:  Our study indicates the potential importance of geological and climatic events in the transport of terrestrial micro-organisms to the deep-sea sedimentary environments, almost totally neglected previously.     

Morphology and taxonomic significance of the otoliths of some bathypelagic Anguilloidei and Saccopharyngoidei from the Sargasso Sea

The sagittal otoliths of seven anguilliform species belonging to the families Nemichthyidae, Serrivomeridae and Eurypharyngidae are described and illustrated, and a key for their identification is provided. Although the leptocephali of the various fish species treated here have similar otoliths, some species develop specific otolith characteristics during the adult stage. The shape as well as the ratio of fish length to otolith length ratio in adults may serve as a taxonomic aid. Since the sagittae of these fishes can be used for specific identification, the digested remains of prey in the stomachs and guts of predators can be identified.     

Genome sequence of Oceanicaulis sp. strain HTCC2633, isolated from the Western Sargasso Sea

The genus Oceanicaulis represents dimorphic rods that were originally isolated from a marine dinoflagellate. Here, we announce the genome sequence of Oceanicaulis sp. strain HTCC2633, isolated by dilution-to-extinction culturing from the Sargasso Sea. The genome information of strain HTCC2633 indicates a chemoorganotrophic way of life of this strain.     

Phytoplankton distribution patterns in the northwestern Sargasso Sea revealed by small subunit rRNA genes from plastids

Phytoplankton species vary in their physiological properties, and are expected to respond differently to seasonal changes in water column conditions. To assess these varying distribution patterns, we used 412 samples collected monthly over 12 years (1991–2004) at the Bermuda Atlantic Time-Series Study site, located in the northwestern Sargasso Sea. We measured plastid 16S ribosomal RNA gene abundances with a terminal restriction fragment length polymorphism approach and identified distribution patterns for members of the Prymnesiophyceae, Pelagophyceae, Chrysophyceae, Cryptophyceae, Bacillariophyceae and Prasinophyceae. The analysis revealed dynamic bloom patterns by these phytoplankton taxa that begin early in the year, when the mixed layer is deep. Previously, unreported open-ocean prasinophyte blooms dominated the plastid gene signal during convective mixing events. Quantitative PCR confirmed the blooms and transitions of Bathycoccus, Micromonas and Ostreococcus populations. In contrast, taxa belonging to the pelagophytes and chrysophytes, as well as cryptophytes, reached annual peaks during mixed layer shoaling, while Bacillariophyceae (diatoms) were observed only episodically in the 12-year record. Prymnesiophytes dominated the integrated plastid gene signal. They were abundant throughout the water column before mixing events, but persisted in the deep chlorophyll maximum during stratified conditions. Various models have been used to describe mechanisms that drive vernal phytoplankton blooms in temperate seas. The range of taxon-specific bloom patterns observed here indicates that different ‘spring bloom'' models can aptly describe the behavior of different phytoplankton taxa at a single geographical location. These findings provide insight into the subdivision of niche space by phytoplankton and may lead to improved predictions of phytoplankton responses to changes in ocean conditions.     

Distribution Patterns of Strongylocentrotus Sea Urchins along the Coast of Eastern Kamchatka

The distribution patterns of three sea urchin species of the genus Strongylocentrotus in relation to depth, type of substrate, surf action, and to some hydrological parameters were studied along the coast of eastern Kamchatka and in adjacent waters in 1984–1996. The sea urchin Strongylocentrotus polyacanthus dominated the open coast on rocky subintertidal sites with increased surf action and standard oceanic salinity. S. droebachiensis prevailed in shoals with lower salinity, higher water temperature and lower turbulence (enclosed and semienclosed bays). S. pallidus dominated at depths corresponding to the position of the cold intermediate layer deeper than 30–50 m with normal oceanic salinity and lower temperature.     

Nucleation of calcite on the sheaths of cyanobacteria using a simple diffusion cell

A method allowing observation of calcium carbonate nucleation on the sheaths of cyanobacteria and other microorganisms is described. Nucleation of calcite was obtained on the sheaths of Lyngbya aestuarii and Scy‐tonema myochrous cultures but not on Entophysalis major and Pseudanabaena minuta. Differences in the rate of nucleation were also noted in media of differing salinity.     

Hydrogen and polyhydroxybutyrate producing abilities of microbes from diverse habitats by dark fermentative process

Thirty five bacterial isolates from diverse environmental sources such as contaminated food, nitrogen rich soil, activated sludges from pesticide and oil refineries effluent treatment plants were found to belong to Bacillus, Bordetella, Enterobacter, Proteus, and Pseudomonas sp. on the basis of 16S rRNA gene sequence analysis. Under dark fermentative conditions, maximum hydrogen (H₂) yields (mol/mol of glucose added) were recorded to be 0.68 with Enterobacter aerogenes EGU16 followed by 0.63 with Bacillus cereus EGU43 and Bacillus thuringiensis EGU45. H₂ constituted 63–69% of the total biogas evolved. Out of these 35 microbes, 18 isolates had the ability to produce polyhydroxybutyrate (PHB), which varied up to 500 mg/l of medium, equivalent to a yield of 66.6%. The highest PHB yield was recorded with B. cereus strain EGU3. Nine strains had high hydrolytic activities (zone of hydrolysis): lipase (34–38 mm) – Bacillus sphaericus strains EGU385, EGU399 and EGU542; protease (56–62 mm) – Bacillus sp. strains EGU444, EGU447 and EGU445; amylase (23 mm) – B. thuringiensis EGU378, marine bacterium strain EGU409 and Pseudomonas sp. strain EGU448. These strains with high hydrolytic activities had relatively low H₂ producing abilities in the range of 0.26–0.42 mol/mol of glucose added and only B. thuringiensis strain EGU378 had the ability to produce PHB. This is the first report among the non-photosynthetic microbes, where the same organism(s) – B. cereus strain EGU43 and B. thuringiensis strain EGU45, have been shown to produce H₂ – 0.63 mol/mol of glucose added and PHB – 420–435 mg/l medium.