Ribosomal tag pyrosequencing of DNA and RNA from benthic coral reef microbiota: community spatial structure, rare members and nitrogen-cycling guilds

Ribosomal tag libraries based on DNA and RNA in coral reef sediment from Hawaii show the microbial community to be dominated by the bacterial phyla Proteobacteria, Firmicutes and Actinobacteria, the archaeal order Nitrosopumilales and the uncultivated divisions Marine Group III (Euryarchaeota) and Marine Benthic Group C (Crenarchaeota). Operational taxonomic units (OTUs) number in the high thousands, and richness varies with site, presence or absence of porewater sulfide (sediment depth), and nucleotide pool. Rank abundance curves of DNA-based libraries, but not RNA-based libraries, possess a tail of low abundance taxa, supporting the existence of an inactive 'rare' biosphere. While bacterial libraries from two oxic samples differ markedly, those from two anoxic (sulfidic) samples are similar. The four dominant bacterial OTUs are members of genera that include pathogens, but are found in marine environments, and include facultative anaerobes, i.e. dissimilatory nitrate reducers and denitrifiers. This may explain their abundance in both oxic and anoxic samples. A numerous archaeon is closely related to the lithoautotrophic ammonia oxidizer Nitrosopumilus maritimus. Known bacterial ammonia oxidizers are essentially absent, but bacterial nitrite oxidizers are abundant. Although other studies of this reef found evidence for anaerobic ammonia oxidizers, primer bias rendered that clade invisible to this study.     

Altitude ammonia-oxidizing bacteria and archaea in soils of Mount Everest

To determine the abundance and distribution of bacterial and archaeal ammonia oxidizers in alpine and permafrost soils, 12 soils at altitudes of 4000–6550 m above sea level (m a.s.l.) were collected from the northern slope of the Mount Everest (Tibetan Plateau), where the permanent snow line is at 5800–6000 m a.s.l. Communities were characterized by real-time PCR and clone sequencing by targeting on amo A genes, which putatively encode ammonia monooxygenase subunit A. Archaeal amo A abundance was greater than bacterial amo A abundance in lower altitude soils (≤5400 m a.s.l.), but this situation was reversed in higher altitude soils (≥5700 m a.s.l.). Both archaeal and bacterial amo A abundance decreased abruptly in higher altitude soils. Communities shifted from a Nitrosospira amo A cluster 3a-dominated ammonia-oxidizing bacteria community in lower altitude soils to communities dominated by a newly designated Nitrosospira ME and cluster 2-related groups and Nitrosomonas cluster 6 in higher altitude soils. All archaeal amo A sequences fell within soil and sediment clusters, and the proportions of the major archaeal amo A clusters changed between the lower altitude and the higher altitude soils. These findings imply that the shift in the relative abundance and community structure of archaeal and bacterial ammonia oxidizers may result from selection of organisms adapted to altitude-dependent environmental factors in elevated soils.     

Nitrospira-dominated biofilm within a thermal artesian spring: a case for nitrification-driven primary production in a geothermal setting

Water chemistry, energetic modeling, and molecular analyses were combined to investigate the microbial ecology of a biofilm growing in a thermal artesian spring within Hot Springs National Park, AR. This unique fresh water spring has a low dissolved chemical load and is isolated from both light and direct terrestrial carbon input - resulting in an oligotrophic ecosystem limited for fixed carbon and electron donors. Evaluation of energy yields of lithotrophic reactions putatively linked to autotrophy identified the aerobic oxidation of methane, hydrogen, sulfide, ammonia, and nitrite as the most exergonic. Small subunit (SSU) rRNA gene libraries from biofilm revealed a low-diversity microbial assemblage populated by bacteria and archaea at a gene copy ratio of 45:1. Members of the bacterial family 'Nitrospiraceae', known for their autotrophic nitrite oxidation, dominated the bacterial SSU rRNA gene library (approximately 45%). Members of the Thaumarchaeota ThAOA/HWCGIII (>96%) and Thaumarchaeota Group I.1b (2.5%), which both contain confirmed autotrophic ammonia oxidizers, dominated the archaeal SSU rRNA library. Archaea appear to dominate among the ammonia oxidizers, as only ammonia monooxygenase subunit A (amoA) genes belonging to members of the Thaumarchaeota were detected. The geochemical, phylogenetic, and genetic data support a model that describes a novel thermophilic biofilm built largely by an autotrophic nitrifying microbial assemblage. This is also the first observation of 'Nitrospiraceae' as the dominant organisms within a geothermal environment.     

Ammonium supply rate influences archaeal and bacterial ammonia oxidizers in a wetland soil vertical profile

Oxidation of ammonia, the first step in nitrification, is carried out in soil by bacterial and archaeal ammonia oxidizers and recent studies suggest possible selection for the latter in low-ammonium environments. In this study, we investigated the selection of ammonia-oxidizing archaea and bacteria in wetland soil vertical profiles at two sites differing in terms of the ammonium supply rate, but not significantly in terms of the groundwater level. One site received ammonium through decomposition of organic matter, while the second, polluted site received a greater supply, through constant leakage of an underground septic tank. Soil nitrification potential was significantly greater at the polluted site. Quantification of amoA genes demonstrated greater abundance of bacterial than archaeal amoA genes throughout the soil profile at the polluted site, whereas bacterial amoA genes at the unpolluted site were below the detection limit. At both sites, archaeal, but not the bacterial community structure was clearly stratified with depth, with regard to the soil redox potential imposed by groundwater level. However, depth-related changes in the archaeal community structure may also be associated with physiological functions other than ammonia oxidation.     

Growth of ammonia-oxidizing archaea in soil microcosms is inhibited by acetylene

Autotrophic ammonia-oxidizing bacteria were considered to be responsible for the majority of ammonia oxidation in soil until the recent discovery of the autotrophic ammonia-oxidizing archaea. To assess the relative contributions of bacterial and archaeal ammonia oxidizers to soil ammonia oxidation, their growth was analysed during active nitrification in soil microcosms incubated for 30 days at 30 °C, and the effect of an inhibitor of ammonia oxidation (acetylene) on their growth and soil nitrification kinetics was determined. Denaturing gradient gel electrophoresis (DGGE) analysis of bacterial ammonia oxidizer 16S rRNA genes did not detect any change in their community composition during incubation, and quantitative PCR (qPCR) analysis of bacterial amoA genes indicated a small decrease in abundance in control and acetylene-containing microcosms. DGGE fingerprints of archaeal amoA and 16S rRNA genes demonstrated changes in the relative abundance of specific crenarchaeal phylotypes during active nitrification. Growth was also indicated by increases in crenarchaeal amoA gene copy number, determined by qPCR. In microcosms containing acetylene, nitrification and growth of the crenarchaeal phylotypes were suppressed, suggesting that these crenarchaea are ammonia oxidizers. Growth of only archaeal but not bacterial ammonia oxidizers occurred in microcosms with active nitrification, indicating that ammonia oxidation was mostly due to archaea in the conditions of the present study.     

Factors Driving Potential Ammonia Oxidation in Canadian Arctic Ecosystems: Does Spatial Scale Matter?

Ammonia oxidation is a major process in nitrogen cycling, and it plays a key role in nitrogen limited soil ecosystems such as those in the arctic. Although mm-scale spatial dependency of ammonia oxidizers has been investigated, little is known about the field-scale spatial dependency of aerobic ammonia oxidation processes and ammonia-oxidizing archaeal and bacterial communities, particularly in arctic soils. The purpose of this study was to explore the drivers of ammonia oxidation at the field scale in cryosols (soils with permafrost within 1 m of the surface). We measured aerobic ammonia oxidation potential (both autotrophic and heterotrophic) and functional gene abundance (bacterial amoA and archaeal amoA) in 279 soil samples collected from three arctic ecosystems. The variability associated with quantifying genes was substantially less than the spatial variability observed in these soils, suggesting that molecular methods can be used reliably evaluate spatial dependency in arctic ecosystems. Ammonia-oxidizing archaeal and bacterial communities and aerobic ammonia oxidation were spatially autocorrelated. Gene abundances were spatially structured within 4 m, whereas biochemical processes were structured within 40 m. Ammonia oxidation was driven at small scales (<1m) by moisture and total organic carbon, whereas gene abundance and other edaphic factors drove ammonia oxidation at medium (1 to 10 m) and large (10 to 100 m) scales. In these arctic soils heterotrophs contributed between 29 and 47% of total ammonia oxidation potential. The spatial scale for aerobic ammonia oxidation genes differed from potential ammonia oxidation, suggesting that in arctic ecosystems edaphic, rather than genetic, factors are an important control on ammonia oxidation.     

亚高山/高山森林土壤有机层氨氧化细菌和氨氧化古菌丰度特征

为了解季节性冻融作用对川西亚高山/高山地区土壤氨氧化微生物群落的影响,采用qPCR技术,以氨单加氧酶基因的α亚基(amoA)为标记,在生长阶段、冻结阶段、融化阶段中的9个关键时期调查了该地区不同森林群落：岷江冷杉(Abies faxoniana)原始林(PF)、岷江冷杉(A. faxoniana)和红桦(Betula albosinensis)混交林(MF)、岷江冷杉次生林(SF)土壤有机层的氨氧化细菌(ammonia-oxidizing bacteria, AOB)和氨氧化古菌(ammonia-oxidizing archaea, AOA)丰度的特征。结果表明,三个森林群落土壤有机层中都具有相当数量的氨氧化细菌和古菌,均表现出从生长阶段至冻结阶段显著降低,在冻结阶段最低,但冻结阶段后显著增加,在融化阶段为全年最高的趋势。土壤氨氧化微生物类群结构(AOA/AOB)受负积温影响明显。冻结后期三个森林群落土壤负积温最大时,AOA数量明显高于AOB,但其他关键时期土壤氨氧化微生物类群结构与群落类型密切相关。高海拔的PF群落土壤有机层表现为AOA>AOB(冻结初期除外),低海拔的SF群落中表现为AOB>AOA(冻结后期除外),而MF群落则仅在融冻期和生长季节末期表现为AOB>AOA。这些结果为认识亚高山/高山森林及其相似区域的生态过程提供了一定的科学依据。     

Changes in Diversity and Functional Gene Abundances of Microbial Communities Involved in Nitrogen Fixation, Nitrification, and Denitrification in a Tidal Wetland versus Paddy Soils Cultivated for Different Time Periods

In many areas of China, tidal wetlands have been converted into agricultural land for rice cultivation. However, the consequences of land use changes for soil microbial communities are poorly understood. Therefore, we investigated bacterial and archaeal communities involved in inorganic nitrogen turnover (nitrogen fixation, nitrification, and denitrification) based on abundances and relative species richness of the corresponding functional genes along a soil chronosequence ranging between 50 and 2,000 years of paddy soil management compared to findings for a tidal wetland. Changes in abundance and diversity of the functional groups could be observed, reflecting the different chemical and physical properties of the soils, which changed in terms of soil development. The tidal wetland was characterized by a low microbial biomass and relatively high abundances of ammonia-oxidizing microbes. Conversion of the tidal wetlands into paddy soils was followed by a significant increase in microbial biomass. Fifty years of paddy management resulted in a higher abundance of nitrogen-fixing microbes than was found in the tidal wetland, whereas dominant genes of nitrification and denitrification in the paddy soils showed no differences. With ongoing rice cultivation, copy numbers of archaeal ammonia oxidizers did not change, while that of their bacterial counterparts declined. The nirK gene, coding for nitrite reductase, increased with rice cultivation time and dominated its functionally redundant counterpart, nirS, at all sites under investigation. Relative species richness showed significant differences between all soils with the exception of the archaeal ammonia oxidizers in the paddy soils cultivated for 100 and 300 years. In general, changes in diversity patterns were more pronounced than those in functional gene abundances.     

Thermostability and photostability of photosystem II of the resurrection plant Haberlea rhodopensis studied by chlorophyll fluorescence

The stability of PSII in leaves of the resurrection plant Haberlea rhodopensis to high temperature and high light intensities was studied by means of chlorophyll fluorescence measurements. The photochemical efficiency of PSII in well-hydrated Haberlea leaves was not significantly influenced by temperatures up to 40 degrees C. Fo reached a maximum at 50 degrees C, which is connected with blocking of electron transport in reaction center II. The intrinsic efficiency of PSII photochemistry, monitored as Fv/Fm was less vulnerable to heat stress than the quantum yield of PSII electron transport under illumination (phiPSII). The reduction of phiPSII values was mainly due to a decrease in the proportion of open PSII centers (qP). Haberlea rhodopensis was very sensitive to photoinhibition. The light intensity of 120 micromol m(-2) s(-1) sharply decreased the quantum yield of PSII photochemistry and it was almost fully inhibited at 350 micromol m(-2) s(-1). As could be expected decreased photochemical efficiency of PSII was accompanied by increased proportion of thermal energy dissipation, which is considered as a protective effect regulating the light energy distribution in PSII. When differentiating between the three components of qN it was evident that the energy-dependent quenching, qE, was prevailing over photoinhibitory quenching, qI, and the quenching related to state 1-state 2 transitions, qT, at all light intensities at 25 degrees C. However, the qE values declined with increasing temperature and light intensities. The qI was higher than qE at 40 degrees C and it was the major part of qN at 45 degrees C, indicating a progressing photoinhibition of the photosynthetic apparatus.     

Microbial population structure in a stratified,acidic pit lake in the Iberian Pyrite Belt

Abstract

We examined the geochemistry and bacterial and archaeal community structure in the acidic (pH < 2.4) pit lake at Peña de Hierro, near the headwaters of the Río Tinto. The lake has strong vertical gradients in light, O₂, pH, conductivity, and dissolved ions. Bacterial and archaeal communities between 0 and 32?m displayed low species richness and evenness. Relatives of iron cycling taxa accounted for 60-90% of the operational taxonomic units (OTUs) throughout the water column. Relatives of heterotrophic, facultative Fe(III)-reducing species made up more than a third of the bacterial and archaeal community in the photic zone. Taxa related to Fe(II) oxidizers Ferrithrix thermotolerans and Acidithix ferrooxidans were also abundant in the photic zone. Below the photic zone, relatives of the lithoautotrophic Fe(II) oxidizers Leptospirillum ferrooxidans and Ferrovum myxofaciens bloomed at different depths within or just below the oxycline. Thermoplasmatales predominated in the deep, microoxic zone of the lake. The microbial population structure of the lake appears to be influenced by the production of oxygen and organic matter by phototrophs in a narrow zone at the lake surface and by strong geochemical gradients present in the water column that create distinct niches for separate Fe(II) oxidizers.     

Free nitrous acid selectively inhibits and eliminates nitrite oxidizers from nitrifying sequencing batch reactor

In a complete nitrification sequencing batch reactor (CNSBR), where ammonium containing wastewater (200–1,000 mg N/L) is completely oxidized to nitrate up to 2.4 kg NH₄ ⁺–N/m³ d, both ammonia oxidizers and nitrite oxidizers were enriched in the sludge granules. Quantitative fluorescence in situ hybridization analyses of the sludge granules of the CNSBR showed that ammonia oxidizers and nitrite oxidizers occupied 31 and 4.2% of total bacteria, respectively. Most of the nitrite oxidizers were Nitrobacter species (95% of the nitrite oxidizers) and the remainder was Nitrospira species. The population of nitrite oxidizers was significantly higher than that of partial nitrification SBR (PNSBR) where most of the ammonium was oxidized to nitrite. The PNSBR had 37% (ammonia oxidizers) and 0.4% (nitrite oxidizers) of total bacteria. Comparative study with CNSBR and PNSBR revealed that free nitrous acid, rather than free ammonia, played a critical inhibition role to wash out nitrite oxidizers from the reactor. The concentrations of free ammonia and nitrite as well as free nitrous acid in the CNSBR selected Nitrobacter as the dominant nitrite oxidizers rather than Nitrospira.     

The occurrence of chemolitho-autotrophic nitrifiers in water-saturated grassland soils

Relatively high most probable number (MPN) counts of chemolithotrophic nitrite oxidizers were present in water-saturated soils compared with MPNs and activity of ammonia oxidizers. These high numbers of nitrite oxidizers were confirmed by fluorescent antibody counts and potential activity measurements. Application of different nitrite concentrations in the MPN procedure discriminated within the community of nitrite oxidizers and revealed a large number of nitrite-sensitive nitrite oxidizers and a subcommunity of nitrite-insensitive nitrite oxidizers. The size of this subcommunity was small but corresponded with the low numbers of ammonium oxidizers. Numbers of nitrite-sensitive nitrite oxidizers outnumbered the ammonia oxidizing bacteria by 2–4 orders of magnitude in these soils. The possibility is discussed that the fraction of the nitrite-insensitive cells was active as aerobic nitrite oxidizers, whereas the nitrite-sensitive cells represented an inactive group of nitrite oxidizers growing as heterotrophs or as anaerobes reducing nitrite. In this situation, both MPN enumerations at a low nitrite concentration and activity measurements could give false information about the size of the in situ nitrite-oxidizing community.     

Dim nocturnal illumination alters coupling of circadian pacemakers in Siberian hamsters,<Emphasis Type="Italic"> Phodopus sungorus</Emphasis>

The circadian pacemaker of mammals comprises multiple oscillators that may adopt different phase relationships to determine properties of the coupled system. The effect of nocturnal illumination comparable to dim moonlight was assessed in male Siberian hamsters exposed to two re-entrainment paradigms believed to require changes in the phase relationship of underlying component oscillators. In experiment 1, hamsters were exposed to a 24-h light-dark-light-dark cycle previously shown to split circadian rhythms into two components such that activity is divided between the two daily dark periods. Hamsters exposed to dim illumination (<0.020 lx) during each scotophase were more likely to exhibit split rhythms compared to hamsters exposed to completely dark scotophases. In experiment 2, hamsters were transferred to winter photoperiods (10 h light, 14 h dark) from two different longer daylengths (14 h or 18 h light daily) in the presence or absence of dim nighttime lighting. Dim nocturnal illumination markedly accelerated adoption of the winter phenotype as reflected in the expansion of activity duration, gonadal regression and weight loss. The two experiments demonstrate substantial efficacy of light intensities generally viewed as below the threshold of circadian systems. Light may act on oscillator coupling through rod-dependent mechanisms.Abbreviations activity duration - DD constant dark or dim - E evening oscillator - ETV estimated testis volume - LDLD light-dark-light-dark cycle - LED light emitting diode - M morning oscillator - SCN suprachiasmatic nuclei - free-running period     

Light/dark cycles in the growth of the red microalga porphyridium sp

The effect of light/dark cycles on the growth of the red microalga Porphyridium sp. was studied in a tubular loop bioreactor with light/dark cycles of different frequencies and in two 35-L reactors: a bubble column reactor and an air-lift reactor. Photon flux densities were in the range of 50 to 300 μE m-2 s-1, and flow rates were 1 to 10 L min-1. Under conditions of low illumination and high flow rates, similar results were obtained for the bubble column and air-lift reactors. However, higher productivities-in terms of biomass and polysaccharide-were recorded in the air-lift reactor under high light intensity and low gas flow rates. The interactions of both photosynthesis and photoinhibition with the fluid dynamics in the bioreactors was taken as the main element that allowed us to interpret the differences in performance of the bubble column and the air-lift reactor. It is suggested that the cyclic distribution of dark periods in the air-lift reactor facilitates better recovery from the photoinhibition damage suffered by the cells. Copyright 1998 John Wiley & Sons, Inc.     

低温光抑制恢复过程中黄瓜叶片PSⅡ活性及其电子传递对PSⅠ的影响

以“津春4号”黄瓜为试材,通过测定黄瓜叶片叶绿素荧光快速诱导动力学曲线和对820 nm光的吸收曲线,结合叶绿素荧光淬灭分析,研究低温光胁迫(4℃,200 μmol·m-2·s-1)6 h后,黄瓜叶片在常温(25℃)不同光强(0、15、200μmol·m-2·s-1)下PS Ⅰ和PS Ⅱ活性的恢复,以及恢复过程中PS Ⅰ与PS Ⅱ的相互作用.结果表明:低温光胁迫6h后,PS Ⅰ和PS Ⅱ发生不同程度的光抑制.在常温恢复阶段,PS Ⅱ活性快速恢复且对光强不敏感;PS Ⅰ活性在弱光下(15 μmol·m-2·s-1)快速恢复,在较强光(200 μmol·m-2·s-1)下恢复较慢.在低温光抑制恢复过程中,常温下PS Ⅱ活性恢复较快可能导致PS Ⅱ向PS Ⅰ的线性电子传递过快,进而抑制PS Ⅰ的活性恢复.因此,在进行黄瓜抗冷性育种时,不应该仅追求较高的PS Ⅱ抗性和较快的PS Ⅱ恢复速度,还应该注意两个光系统活性的协调.在生产中,应当在低温逆境发生及其之后较长一段时间内采取措施降低叶表面光照强度,以利于对植株光合机构的保护和光合活性的恢复.     

BIOLUMINESCENCE AND CHLOROPLAST MOVEMENT IN THE DINOFLAGELLATE PYROCYSTIS LUNULA1

The lunate cysts of Pyrocystis lunula have a bioluminescent emission spectrum with a peak intensity of 477.5 ± 1 mμ. The light originates from the protoplasm in the center of the cysts. Six to eight hr after the cysts were placed in the dark, they produced 300 to 800 times more luminescence than controls maintained under constant, illumination. Plastids contract distally when the cysts are placed in the dark. If kept in the dark, the plastids contract distally and expand with a circadian rhythm persisting several days. At intensities of 2200 μm cm-’or less, the plastids are expanded. The plastids are contracted into the central area of the cysts at light intensities of 4000 μw cm-² and above. The Gymnodinium stage of the life cycle is not bioluminescent.