Changes in activity and community structure of methane-oxidizing bacteria over the growth period of rice

The activity and community structure of methanotrophs in compartmented microcosms were investigated over the growth period of rice plants. In situ methane oxidation was important only during the vegetative growth phase of the plants and later became negligible. The in situ activity was not directly correlated with methanotrophic cell counts, which increased even after the decrease in in situ activity, possibly due to the presence of both vegetative cells and resting stages. By dividing the microcosms into two soil and two root compartments it was possible to locate methanotrophic growth and activity, which was greatest in the rhizoplane of the rice plants. Molecular analysis by denaturing gradient gel electrophoresis and fluorescent in situ hybridization (FISH) with family-specific probes revealed the presence of both families of methanotrophs in soil and root compartments over the whole season. Changes in community structure were detected only for members of the Methylococcaceae and could be associated only with changes in the genus Methylobacter and not with changes in the dominance of different genera in the family Methylococcaceae. For the family Methylocystaceae stable communities in all compartments for the whole season were observed. FISH analysis revealed evidence of in situ dominance of the Methylocystaceae in all compartments. The numbers of Methylococcaceae cells were relatively high only in the rhizoplane, demonstrating the importance of rice roots for growth and maintenance of methanotrophic diversity in the soil.     

Hydrogenase activity in nitrogen-fixing methane-oxidizing bacteria

Hydrogenase activity in cells of the nitrogen-fixing methane-oxidizing bacterium strain 41 of the Methylosinus type increased markedly when growth was dependent upon the fixation of gaseous nitrogen. A direct relationship may exist between hydrogenase and nitrogenase in this bacterium. Acetylene reduction was supported by the presence of hydrogen gas.     

稻田土壤亚硝酸盐型甲烷厌氧氧化菌群落结构的时空特征

稻田是温室气体甲烷的重要排放源之一,对全球气候变化具有重要影响.由隶属于NC10门的Candidatus Methylomirabilis oxyfera(M.oxyfera)-like细菌介导的亚硝酸盐型甲烷厌氧氧化是控制稻田甲烷排放的新途径.目前,有关此类微生物群落在稻田土壤中的时空分布特征及其环境影响因素尚不明确...     

Winter phytoplankton community structure in three shallow temperate lakes during ice cover

The general model of seasonal phytoplankton succession in temperate lakes suggests that winter phytoplankton growth is minimal under ice-cover. However, some studies have found diverse phytoplankton communities during winter. The primary objectives of this study were to determine the species composition and the changes in the winter phytoplankton community structure under the ice. For 2 consecutive winters, phytoplankton samples were collected under ice-cover at 4 sites on 3 lakes in Arrowwood National Wildlife Refuge (ANWR), near Pingree, North Dakota. Ninety taxa were identified and enumerated. Densities of several of these taxa frequently exceeded 10⁶ cells l^–1. The winter phytoplankton communities in these lakes were dominated by flagellates, principally cryptomonads, a synurophyte (Synura uvella), small chrysophytes (Chrysococcus spp., Kephyrion spp.) and a dinoflagellate (Peridinium aciculiferum), as well as non-flagellate microchlorophytes (Monoraphidium spp., Ankistrodesmus spp., and Pseudodictyosphaerium sp.), a cyanobacterium (Gloeocapsa aeruginosa) and centric diatoms (Stephanodiscus minutulus, S. parvus and Cyclotella meneghiniana).     

Substantial differences in littoral fish community structure and dynamics in subtropical and temperate shallow lakes

1. Fish play a key role in the functioning of temperate shallow lakes by affecting nutrient exchange among habitats as well as lake trophic structure and dynamics. These processes are, in turn, strongly influenced by the abundance of submerged macrophytes, because piscivorous fish are often abundant at high macrophyte density. Whether this applies to warmer climates as well is virtually unknown. 2. To compare fish community structure and dynamics in plant beds between subtropical and temperate shallow lakes we conducted experiments with artificial submerged and free‐floating plant beds in a set of 10 shallow lakes in Uruguay (30°–35°S) and Denmark (55°–57°N), paired along a gradient of limnological characteristics. 3. The differences between regions were more pronounced than differences attributable to trophic state. The subtropical littoral fish communities were characterised by higher species richness, higher densities, higher biomass, higher trophic diversity (with predominance of omnivores and lack of true piscivores) and smaller body size than in the comparable temperate lakes. On average, fish densities were 93 ind. m⁻² (±10 SE) in the subtropical and 10 ind. m⁻² (±2 SE) in the temperate lakes. We found a twofold higher total fish biomass per unit of total phosphorus in the subtropical than in the temperate lakes, and as fish size is smaller in the former, the implication is that more energy reaches the littoral zone fish community of the warmer lakes. 4. Plant architecture affected the spatial distribution of fish within each climate zone. Thus, in the temperate zone fish exhibited higher densities among the artificial free‐floating plants while subtropical fish were denser in the artificial submerged plant beds. These patterns appeared in most lakes, regardless of water turbidity or trophic state. 5. The subtropical littoral fish communities resembled the fish communities typically occurring in temperate eutrophic and hypertrophic lakes. Our results add to the growing evidence that climate warming may lead to more complex and omnivory‐dominated food webs and higher density and dominance of smaller‐sized fish. This type of community structure may lead to a weakening of the trophic cascading effects commonly observed in temperate shallow lakes and a higher risk of eutrophication.     

The relationship between zooplankton community structure and lake characteristics in temperate lakes (Northern Wisconsin, USA)

Zooplankton community structure can be affected by within-lakeand by watershed ecological factors, including water chemistry(related to landscape position), lake morphology and human activityin the watershed. We hypothesized that all three groups of driverswould be correlated with zooplankton species richness and speciescomposition for lakes in northern Wisconsin. Data collectedfrom 52 lakes allowed us to explore the relationship of zooplanktoncommunity structure with ecological drivers. We found that crustaceanzooplankton species richness was not significantly correlatedwith independent environmental variables derived from PCA ordination,nor with measures of community structure based on NMS ordination.However, species composition was correlated with environmentalgradients. Larger zooplankton species (Daphnia pulicaria, Epischuralacustris, Skistodiaptomus oregonensis, Mesocyclops americanus)occurred in large and deep lakes low in the landscape gradient,whereas the smaller species Ceriodaphnia dubia, Daphnia retrocurvaand Leptodiaptomus minutus tended to occur high in the landscape.This shift in species composition was correlated with increasedconductivity, primary productivity and the hypolimnetic refugescharacteristic of larger deeper lakes lower in the landscape.Riparian housing development and littoral zone habitat (measuredas building density and by abundance of logs in littoral zones)were not correlated with zooplankton community structure. Inthese relatively low-impact lakes, natural drivers are stillthe most significant determinants of zooplankton community structure.     

Viruses in subarctic lakes and their impact on benthic and pelagic bacteria

Virus–bacterium interactions were investigated in the pelagic and benthic habitats in a set of lakes along an altitudinal gradient in the subarctic northern Sweden. Viral and bacterial abundances showed a significant variation between the lakes, with the highest benthic microbial abundances recorded in a high-altitude lake [993 m above sea level (a.s.l.)], whereas the highest pelagic microbial abundances were found in a low-altitude lake (270 m a.s.l.). In the pelagic habitat, there was also a distinct difference in microbial abundances between the summer–autumn and the winter sampling occasion. A positive relationship was noted between viruses and bacteria in both the pelagic and the benthic habitats. Visibly virus-infected bacterial cells were uncommon in the pelagic habitat and undetectable in the benthos. Both lytic and lysogenic pelagic viral production rates were undetectable or low; thus, a possible explanation for the relative high viral abundances found in the water column could be an allochthonous input of viruses or release of sediment-derived viruses. Overall, our results provide novel information about the relevance of viruses in the subarctic region and indicate that viruses play only a minor role in the nutrient and carbon cycling in the microbial communities of subarctic lakes.     

Facilitative interactions among the pelagic community of temperate migratory terns,tunas and dolphins

We studied habitat and behavioral interactions among the marine community of top pelagic predators over the Atlantic continental shelf, observed from shipboard surveys off the northeastern United States. We hypothesized that foraging seabirds, specifically common terns Sterna hirundo and roseate terns S. dougallii, associate positively with the distribution and abundance of large, easily‐detected subsurface marine predators, as a result of facilitative interactions. Few rigorous tests examine the effect of interspecific interactions on seabird distributions, though many papers note the importance of environmental influences. Fewer, still, assess facilitation, defined as positive interactions among multiple taxa (birds, fish, mammals), where individuals use foraging neighbors for improved prey detection or enhanced prey availability. Our use of spatiotemporal‐structured Bayesian hierarchical models allowed us to test for fine‐scale associations of common and roseate terns with aggregations of tunas and cetaceans, and with standard oceanographic parameters. High tern abundance was linked to relatively high tuna densities and low dolphin densities, as well as high sea surface temperatures, shallow water, and proximity to shore. The fact that terns foraged when in the presence of tunas or relatively dense dolphin pods supports our hypothesis that the mechanism behind this spatial association involves positive interspecific interactions (attraction), a phenomenon that has been described but rarely quantified. This study reveals that community structure depends on static and dynamic covariates alike, ranging from bathymetry to the movement of other guild members. To improve the efficacy of predictive modeling, ecosystem approaches to applied conservation management should integrate not only habitat, but also behavior and community factors into analyses, especially in the case of marine spatial planning.     

The rapid switch-off of nitrogenase activity in obligate methane-oxidizing bacteria

Nitrogenase activity in the obligate methaneoxidizing bacterium Methylococcus capsulatus (Bath) was added ammonia. This observation was extended to include other ammonia. This observation was extended to include other representative N₂-fixing species of methanotrophs. The ammonia switch-off of nitrogenase in M. capsulatus (Bath) was reversed on washing cells to remove excess ammonia, in the presence of chloramphenicol, suggesting that a form of covalent modification of nitrogenase may occur. Replacing the oxidizable substrate methanol with formaldehyde, formate, ethanol or hydrogen had no effect on nitrogenase switch-off. A number of potential nitrogen sources or intermediates of nitrogen metabolism such as glutamine, asparagine, glutamate and alanine when tested, did not effect switch-off. However, the rapid inhibition of nitrogenase activity of M. capsulatus (Bath) could be achieved by adding the uncoupler carbonylcyanide m-chlorophenylhydrazone or nitrite. The glutamine synthetase inhibitor methionine sulphoximine blocked the switch-off effect of ammonia, indicating that the metabolism of ammonia may be essential for switch-off to occur. Inhibitors of glutamate synthase did not alleviate the ammonia switch-off response. Methionine sulphoximine did not alleviate the rapid inhibition of nitrogenase by carbonylcyanide m-chlorophenylhydrazone indicating that the shortterm regulation of nitrogenase by uncouplers and ammonia proceed via different mechanisms.Abbreviations MSX methionine-DL-sulphoximine - DON 6-diazo-5-oxo-L-norleucine - GS glutamine synthetase - GOGAT glutamine 2-oxoglutarate aminotransferase (glutamate synthase) - CCCP carbonylcyanide m-chlorophenyl hydrazone     

Active bacteria (CTC+) in temperate lakes: temporal and cross-system variations

The temporal variation in the abundance and proportion of highlyrespiration-active bacteria in the eutrophic lakes Esrum andFrederiksborg Slotssø was determined with the redox dye5-cyano-2,3-ditolyl tetrazolium chloride (CTC). In addition,a comparative late summer study was undertaken across a gradientof nutrient enrichment in Danish lakes. The purpose was to investigatethe importance of substrate (chlorophyll) and temperature forthe control of CTC-active cells (CTC+). The abundance of CTC+cells was much lower and more variable than the total numberof cells counted after 4',6-diamidino-2-phenylindole (DAPI)staining. The proportion of CTC+ cells in Lake Esrum and FrederiksborgSlotssø was normally <5%, and between 2.5 and 20%in 14 other lakes. The abundance as well as the proportion ofCTC+ cells increased with chlorophyll in Lake Esrum and FrederiksborgSlotssø, and chlorophyll explained 43% of the variabilityin CTC+ abundance. In the comparative study, the abundance ofCTC+ cells increased along the chlorophyll gradient, which explained49% of the variability. The results showed that the abundanceand, to a lesser degree, the proportion of CTC+ bacteria werecontrolled by substrate supply. One consequence of the low abundanceof active bacteria is that in situ growth rates scaled to CTC+cells are 3- to 7-fold higher than those scaled to DAPI counts.It is suggested that studies on factors controlling bacterioplanktonactivity at the single-cell level should be investigated scaledto active cells.     

Habitat structure determines resource use by zooplankton in temperate lakes

While the importance of terrestrial linkages to aquatic ecosystems is well appreciated, the degree of terrestrial support of aquatic consumers remains debated. Estimates of terrestrial contributions to lake zooplankton have omitted a key food source, phytoplankton produced below the mixed layer. We used carbon and nitrogen stable isotope data from 25 Pacific Northwest lakes to assess the relative importance of particulate organic matter (POM) from the mixed layer, below the mixed layer and terrestrial detritus to zooplankton. Zooplankton and deep POM were depleted in 13C relative to mixed layer POM in lakes that can support deep primary production. A Bayesian stable isotope mixing model estimated that terrestrial detritus contributed <5% to zooplankton production, and confirms the role of lake optical and thermal properties; deep POM accounted for up to 80% of zooplankton production in the clearest lakes. These results suggest terrestrial support of lake zooplankton production is trivial.     

Effects of habitat complexity on community structure and predator avoidance behaviour of littoral zooplankton in temperate versus subtropical shallow lakes

1. Structural complexity may stabilise predator–prey interactions and affect the outcome of trophic cascades by providing prey refuges. In deep lakes, vulnerable zooplankton move vertically to avoid fish predation. In contrast, submerged plants often provide a diel refuge against fish predation for large‐bodied zooplankton in shallow temperate lakes, with consequences for the whole ecosystem. 2. To test the extent to which macrophytes serve as refuges for zooplankton in temperate and subtropical lakes, we introduced artificial plant beds into the littoral area of five pairs of shallow lakes in Uruguay (30°–35°S) and Denmark (55°–57°N). We used plants of different architecture (submerged and free‐floating) along a gradient of turbidity over which the lakes were paired. 3. We found remarkable differences in the structure (taxon‐richness at the genus level, composition and density) of the zooplankton communities in the littoral area between climate zones. Richer communities of larger‐bodied taxa (frequently including Daphnia spp.) occurred in the temperate lakes, whereas small‐bodied taxa characterised the subtropical lakes. More genera and a higher density of benthic/plant‐associated cladocerans also occurred in the temperate lakes. The density of all crustaceans, except calanoid copepods, was significantly higher in the temperate lakes (c. 5.5‐fold higher). 4. Fish and shrimps (genus Palaemonetes) seemed to exert a stronger predation pressure on zooplankton in the plant beds in the subtropical lakes, while the pelagic invertebrate Chaoborus sp. was slightly more abundant than in the temperate lakes. In contrast, plant‐associated predatory macroinvertebrates were eight times more abundant in the temperate than in the subtropical lakes. 5. The artificial submerged plants hosted significantly more cladocerans than the free‐floating plants, which were particularly avoided in the subtropical lakes. Patterns indicating diel horizontal migration were frequently observed for both overall zooplankton density and individual taxa in the temperate, but not the subtropical, lakes. In contrast, patterns of diel vertical migration prevailed for both the overall zooplankton and for most individual taxa in the subtropics, irrespective of water turbidity. 6. Higher fish predation probably shapes the general structure and dynamics of cladoceran communities in the subtropical lakes. Our results support the hypothesis that horizontal migration is less prevalent in the subtropics than in temperate lakes, and that no predator‐avoidance behaviour effectively counteracts predation pressure in the subtropics. Positive effects of aquatic plants on water transparency, via their acting as a refuge for zooplankton, may be generally weak or rare in warm lakes.     

Abundance and diversity of aerobic anoxygenic phototrophic bacteria in saline lakes on the Tibetan plateau

Aerobic anoxygenic phototrophic (AAP) bacteria are heterotrophic prokaryotes that are capable of utilizing light as an energy source but are not capable of producing molecular oxygen. Recently, multiple studies have found that AAP bacteria are widely distributed in oceans and estuaries and may play an important role in carbon cycling. However, AAP bacteria in inland lake ecosystems have not been investigated in depth. In this study, the abundance and diversity of the pufL-M genes, encoding photosynthetic reaction centers of AAP bacteria, were determined in the oxic water column and anoxic sediments of saline lakes (Qinghai, Erhai, and Gahai Lakes) on the Tibetan Plateau, China. Our results indicated that AAP bacteria were abundant in inland lakes, with the proportion of AAP bacteria (in total bacteria) comparable to those in the oceans, but with a lower diversity. Salinity and pH were found to be potential factors controlling the AAP bacterial diversity and community composition. Our data have implications for a better understanding of the potential role of AAP bacteria in carbon cycling in inland lake ecosystems.     

Microbial community structure in moraine lakes and glacial meltwaters, Mount Everest

The bacterial diversity and abundance in two moraine lakes and two glacial meltwaters (5140, 5152, 5800 and 6350 m above sea level, respectively) in the remote Mount Everest region were examined through 16S rRNA gene clone library and flow cytometry approaches. In total, 247 clones were screened by RFLP and 60 16S rRNA gene sequences were obtained, belonging to the following groups: Proteobacteria (8% alpha subdivision, 21% beta subdivision, and 1% gamma subdivision), Cytophaga-Flavobacteria-Bacteroides (CFB) (54%), Actinobacteria (4%), Planctomycetes (2%), Verrucomicrobia (2%), Fibrobacteres (1%) and Eukaryotic chroloplast (3%), respectively. The high dominance of CFB distinguished the Mount Everest waters from other mountain lakes. The highest bacterial abundance and diversity occurred in the open moraine lake at 5152 m, and the lowest in the glacial meltwater at 6350 m. Low temperature at high altitude is considered to be critical for component dominancy. At the same altitude, nutrient availability plays a role in regulating population structure. Our results also show that the bacteria in Mount Everest may be derived from different sources.     

Plant community structure determines primary productivity in shallow,eutrophic lakes

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Diversity, activity, and abundance of sulfate-reducing bacteria in saline and hypersaline soda lakes

Soda lakes are naturally occurring highly alkaline and saline environments. Although the sulfur cycle is one of the most active element cycles in these lakes, little is known about the sulfate-reducing bacteria (SRB). In this study we investigated the diversity, activity, and abundance of SRB in sediment samples and enrichment cultures from a range of (hyper)saline soda lakes of the Kulunda Steppe in southeastern Siberia in Russia. For this purpose, a polyphasic approach was used, including denaturing gradient gel electrophoresis of dsr gene fragments, sulfate reduction rate measurements, serial dilutions, and quantitative real-time PCR (qPCR). Comparative sequence analysis revealed the presence of several novel clusters of SRB, mostly affiliated with members of the order Desulfovibrionales and family Desulfobacteraceae. We detected sulfate reducers and observed substantial sulfate reducing rates (between 12 and 423 micromol/dm(3) day(-1)) for most lakes, even at a salinity of 475 g/liter. Enrichments were obtained at salt saturating conditions (4 M Na(+)), using H(2) or volatile fatty acids as electron donors, and an extremely halophilic SRB, strain ASO3-1, was isolated. Furthermore, a high dsr gene copy number of 10(8) cells per ml was detected in a hypersaline lake by qPCR. Our results indicate the presence of diverse and active SRB communities in these extreme ecosystems.     

云贵高原典型湖滨湿地好氧甲烷氧化细菌群落结构和数量的时空动态

湖泊生态系统排放的甲烷（CH₄）大部分来自湖滨湿地,好氧甲烷氧化细菌（methane-oxidizing bacteria,MOB）在减轻CH₄从湖泊系统向大气的排放中起着至关重要的作用。湖滨湿地好氧MOB群落分布及其影响因素尚不清楚。采用qPCR、末端限制性片段长度多态性（T-RFLP）等方法,分四季对贵州草海湖滨湿地宽敞水域至落干区沉积物中好氧MOB群落组成和数量进行了研究。草海湖滨湿地沉积中甲烷氧化单加氧酶功能基因（pomA）丰度较高,在1.78×10⁷-2.73×10⁸拷贝数/g干沉积物之间,好氧MOB由I型（Methylococcus and Methylobacter）和II型（Methylosinus）组成,I型主要分布在宽敞水域（长期淹水区）,而干湿过渡区和偶尔积水区主要为II型,呈现出明显的空间变化,推测湖滨湿地长期淹水区甲烷的氧化由I型主导,而相对干旱的区域II型主导,而这种差异可能是导致湖滨湿地甲烷排放高度异质性的一个重要因素。研究结果对揭示湖滨湿地甲烷排放时空异质性的微生物生态机制奠定了基础。     

Soil microbial diversity, community structure and denitrification in a temperate riparian zone

Nitrate (NO ₃ ^– ) removal in riparian zones bordering agricultural areas occurs via plant uptake, microbial immobilisation and bacterial denitrification. Denitrification is a desirable mechanism for removal because the bacterial conversion of NO ₃ ^– to N gases permanently removes NO ₃ ^– from the watershed. A field and laboratory study was conducted in riparian soils adjacent to Carroll Creek, Ontario, Canada, to assess the spatial distribution of denitrification relative to microbial community structure and microbial functional diversity. Soil samples were collected in March, June, and August 1997 at varying soil depths and distances from the stream. Denitrification measurements made using the acetylene block technique on intact soil cores were highly variable and did not show any trends with riparian zone location. Microbial community composition and functional diversity were determined using sole carbon source utilization (SCSU) on Biolog® GN microplates. Substrate richness, evenness and diversity (Shannon index) were greatest within the riparian zone and may also have been influenced by a rhizosphere effect. A threshold relationship between denitrification and measures of microbial community structure implied minimum levels of richness, evenness and diversity were required for denitrification.