Bacterivory of metazooplankton, ciliates and flagellates in a newly flooded reservoir

Bacterial consumption by metazoan zooplankton and phagotrophic protists was measured in situ during the period of thermal stratification in the epilimnion (1 m) and metalimnion (7 m) of a newly flooded reservoir (Sep reservoir, France). The mean bacterial consumption was 2.53 x 10⁶ bacterial l^-1 h^-1 at 1m and 0.97 x 10⁶ bacteria l^-1 h^-1 at 7m. The main consumers over the whole study period were the cladocerans Daphnia longispina and Ceriodaphnia quadrangula, accounting on average for 72% of the potential total predation of bacteria at 1 m and 56% at m, especially during the months of May-June and August. Heterotrophic nanoflagellates (HNF), which accounted for 12% estimated total predation of bacteria at 1 m and 13% at 7m, only exerted a limited predation, mainly by a Monas-type cell. Ciliates, dominated in terms of abundance by Pelagohalteria viridis, accounted for 4% of total predation in the epilimnion (0.00-0.42 x 10⁶ bacteria l^-1 h^-1). In a newly flooded reservoir, metazoan zooplankton appear to be the main consumers of bacteria. Predation of ciliates and HNF by zooplanktonic crustaceans could account for the low contribution of components of the microbial loop to bacterial consumption.      

Succession of microbial communities and changes of incremental oil in a post-polymer flooded reservoir with nutrient stimulation

Applied Microbiology and Biotechnology - Further exploitation of the residual oil underground in post-polymer flooded reservoirs is attractive and challengeable. In this study, indigenous microbial...     

Summer fluctuations of microbial planktonic communities in a eutrophic lake--Cierva Point, Antarctica

A eutrophic lake at Cierva Point, Antarctic Peninsula was surveyedduring the summers of 1997 and 1998. Phytoplankton size fractions(micro-, nano- and picoplankton) were analysed, as well as theabundance of bacterioplankton and planktonic ciliates. No permanentvertical stratification was found owing to the shallowness ofthe lake. Both nutrient concentrations and chlorophyll a valuesindicated highly eutrophic conditions, which are a consequenceof a natural enrichment by seabirds. Significant differencesin temperature between the 1997 and 1998 seasons strongly influencedmost of the biological features. The phytoplankton communityshowed a high algal species-richness, with important contributionsof epilithic, cryobiontic and soil algae. The dominant algalgroup was Chlorophyta, mainly represented by Chlamydomonas aff.celerrima, followed by Chl. aff. braunii. Some replacement ofphytoplanktonic species took place in summer and was more evidentin 1998. Picophytoplankton reached high densities, similar tothose reported from other Antarctic lakes. Bacterioplanktonabundances were typical of eutrophic and hypereutrophic lakes.There was a positive correlation between bacterial and totalphytoplankton abundance. Ciliates reached some very high peaks,with higher figures than those reported for other Antarcticsystems with similar trophic status.     

Population genomics in natural microbial communities

Little is known about the evolutionary processes that structure and maintain microbial diversity because, until recently, it was difficult to explore individual-level patterns of variation at the microbial scale. Now, community-genomic sequence data enable such variation to be assessed across large segments of microbial genomes. Here, we discuss how population-genomic analysis of these data can be used to determine how selection and genetic exchange shape the evolution of new microbial lineages. We show that once independent lineages have been identified, such analyses enable the identification of genome changes that drive niche differentiation and promote the coexistence of closely related lineages within the same environment. We suggest that understanding the evolutionary ecology of natural microbial populations through population-genomic analyses will enhance our understanding of genome evolution across all domains of life.     

Bacteriocidal effects of brevetoxin on natural microbial communities

The sensitivity of bacteria to the marine neurotoxins, brevetoxins, produced by the dinoflagellate Karenia brevis and raphidophytes Chattonella spp. remains an open question. We investigated the bacteriocidal effects of brevetoxin (PbTx-2) on the abundance and community composition of natural microbial communities by adding it to microbes from three coastal marine locations that have varying degrees of historical brevetoxin exposure: (1) Great Bay, New Jersey, (2) Rehoboth Bay, Delaware and (3) Sarasota Bay, Florida. The populations with limited or no documented exposure were more susceptible to the effects of PbTx-2 than the Gulf of Mexico populations which are frequently exposed to brevetoxins. The community with no prior documented exposure to brevetoxins showed significant (p = 0.03) changes in bacterial abundance occurring with additions greater than 2.5 μg PbTx-2 L⁻¹. Brevetoxin concentrations during K. brevis blooms range from ∼2.5 to nearly 100 μg L⁻¹ with typical concentrations of ∼10–30 μg L⁻¹. In contrast to the unexposed populations, there was no significant decrease in bacterial cell number for the microbial community that was frequently exposed to brevetoxins, which implies variable sensitivity in natural communities. The diversity in the bacterial communities that were sensitive to PbTx-2 declined upon exposure. This suggests that the PbTx-2 was selecting for or against specific species. Mortality was much higher in the 200 μg PbTx-2 L⁻¹ treatment after 48 h and >37% of the species disappeared in the bacterial communities with no documented exposure. These results suggest that toxic red tides may play a role in structuring bacterial communities.     

Coexistence of mixotrophs, autotrophs, and heterotrophs in planktonic microbial communities

We examine what circumstances allow the coexistence of microorganisms following different nutritional strategies, using a mathematical model. This model incorporates four nutritional types commonly found in planktonic ecosystems: (1) heterotrophic bacteria that consume dissolved organic matter and are prey to some of the other organisms; (2) heterotrophic zooflagellates that depend entirely on bacterial prey; (3) phototrophic algae that depend only on light and inorganic nutrients, and (4) mixotrophs that photosynthesize, take up inorganic nutrients, and consume bacterial prey. Mixotrophs are characterized by a parameter representing proportional mixing of phototrophic and heterotrophic nutritional strategies. Varying this parameter, a range of mixotrophic strategies was examined in hypothetical habitats differing in supplies of light, dissolved organic carbon, and dissolved inorganic phosphorous. Mixotrophs expressing a wide range of mixotrophic strategies persisted in model habitats with low phosphorus supply, but only those with a strategy that is mostly autotrophic persisted with high nutrient supply, and then only when light supply was also high. Organisms representing all four nutritional strategies were predicted to coexist in habitats with high phosphorus and light supplies. Coexistence involves predation by zooflagellates and mixotrophs balancing the high competitive ability of bacteria for phosphorus, the partitioning of partially overlapping resources between all populations, and possibly nonequlibrium dynamics. In most habitats, the strategy predicted to maximize the abundance of mixotrophs is to be mostly photosynthetic and supplement nutritional needs by consuming bacteria.     

Impact of fumigants on soil microbial communities.

Agricultural soils are typically fumigated to provide effective control of nematodes, soilborne pathogens, and weeds in preparation for planting of high-value cash crops. The ability of soil microbial communities to recover after treatment with fumigants was examined using culture-dependent (Biolog) and culture-independent (phospholipid fatty acid [PLFA] analysis and denaturing gradient gel electrophoresis [DGGE] of 16S ribosomal DNA [rDNA] fragments amplified directly from soil DNA) approaches. Changes in soil microbial community structure were examined in a microcosm experiment following the application of methyl bromide (MeBr), methyl isothiocyanate, 1,3-dichloropropene (1,3-D), and chloropicrin. Variations among Biolog fingerprints showed that the effect of MeBr on heterotrophic microbial activities was most severe in the first week and that thereafter the effects of MeBr and the other fumigants were expressed at much lower levels. The results of PLFA analysis demonstrated a community shift in all treatments to a community dominated by gram-positive bacterial biomass. Different 16S rDNA profiles from fumigated soils were quantified by analyzing the DGGE band patterns. The Shannon-Weaver index of diversity, H, was calculated for each fumigated soil sample. High diversity indices were maintained between the control soil and the fumigant-treated soils, except for MeBr (H decreased from 1.14 to 0.13). After 12 weeks of incubation, H increased to 0.73 in the MeBr-treated samples. Sequence analysis of clones generated from unique bands showed the presence of taxonomically unique clones that had emerged from the MeBr-treated samples and were dominated by clones closely related to Bacillus spp. and Heliothrix oregonensis. Variations in the data were much higher in the Biolog assay than in the PLFA and DGGE assays, suggesting a high sensitivity of PLFA analysis and DGGE in monitoring the effects of fumigants on soil community composition and structure. Our results indicate that MeBr has the greatest impact on soil microbial communities and that 1,3-D has the least impact.     

The microbial loop in the planktonic communities in lakes with various trophic status

The structure of planktic trophic chains was studied in eight lakes of European Russia and five lakes in Central Asia. The lakes differed in the level of productivity, morphometric parameters, and the type of agitation and mineralization. It is found that the microbial loop of picophototrophic organisms, bacteria, heterotrophic flagellates, infusoria, and viruses constitutes 12.3-64.7% of the total plankton biomass. Positive correlation between the biomass of microbial community and the primary production of phytoplankton is observed, whereas no relation is revealed between the share of microorganisms in the plankton biomass and the trophic status of the water body. The presence of a great number of cladocerans decreased the role of the microbial loop in the structural organization of the planktic community. Heterotrophic flagellates consuming 3-81% of daily bacterial production were the principal cause of bacteria elimination only in some of the studied water bodies.     

Social interaction in synthetic and natural microbial communities

Social interaction among cells is essential for multicellular complexity. But how do molecular networks within individual cells confer the ability to interact? And how do those same networks evolve from the evolutionary conflict between individual‐ and population‐level interests? Recent studies have dissected social interaction at the molecular level by analyzing both synthetic and natural microbial populations. These studies shed new light on the role of population structure for the evolution of cooperative interactions and revealed novel molecular mechanisms that stabilize cooperation among cells. New understanding of populations is changing our view of microbial processes, such as pathogenesis and antibiotic resistance, and suggests new ways to fight infection by exploiting social interaction. The study of social interaction is also challenging established paradigms in cancer evolution and immune system dynamics. Finding similar patterns in such diverse systems suggests that the same ‘social interaction motifs’ may be general to many cell populations.     

Changes in coral microbial communities in response to a natural pH gradient

Surface seawater pH is currently 0.1 units lower than pre-industrial values and is projected to decrease by up to 0.4 units by the end of the century. This acidification has the potential to cause significant perturbations to the physiology of ocean organisms, particularly those such as corals that build their skeletons/shells from calcium carbonate. Reduced ocean pH could also have an impact on the coral microbial community, and thus may affect coral physiology and health. Most of the studies to date have examined the impact of ocean acidification on corals and/or associated microbiota under controlled laboratory conditions. Here we report the first study that examines the changes in coral microbial communities in response to a natural pH gradient (mean pH_T 7.3–8.1) caused by volcanic CO₂ vents off Ischia, Gulf of Naples, Italy. Two Mediterranean coral species, Balanophyllia europaea and Cladocora caespitosa, were examined. The microbial community diversity and the physiological parameters of the endosymbiotic dinoflagellates (Symbiodinium spp.) were monitored. We found that pH did not have a significant impact on the composition of associated microbial communities in both coral species. In contrast to some earlier studies, we found that corals present at the lower pH sites exhibited only minor physiological changes and no microbial pathogens were detected. Together, these results provide new insights into the impact of ocean acidification on the coral holobiont.     

Spatial distribution of viruses associated with planktonic and attached microbial communities in hydrothermal environments

Viruses play important roles in marine surface ecosystems, but little is known about viral ecology and virus-mediated processes in deep-sea hydrothermal microbial communities. In this study, we examined virus-like particle (VLP) abundances in planktonic and attached microbial communities, which occur in physical and chemical gradients in both deep and shallow submarine hydrothermal environments (mixing waters between hydrothermal fluids and ambient seawater and dense microbial communities attached to chimney surface areas or macrofaunal bodies and colonies). We found that viruses were widely distributed in a variety of hydrothermal microbial habitats, with the exception of the interior parts of hydrothermal chimney structures. The VLP abundance and VLP-to-prokaryote ratio (VPR) in the planktonic habitats increased as the ratio of hydrothermal fluid to mixing water increased. On the other hand, the VLP abundance in attached microbial communities was significantly and positively correlated with the whole prokaryotic abundance; however, the VPRs were always much lower than those for the surrounding hydrothermal waters. This is the first report to show VLP abundance in the attached microbial communities of submarine hydrothermal environments, which presented VPR values significantly lower than those in planktonic microbial communities reported before. These results suggested that viral lifestyles (e.g., lysogenic prevalence) and virus interactions with prokaryotes are significantly different among the planktonic and attached microbial communities that are developing in the submarine hydrothermal environments.     

Characterisation of culture-independent and -dependent microbial communities in a high-temperature offshore chalk petroleum reservoir

Recent studies have indicated that oil reservoirs harbour diverse microbial communities. Culture-dependent and culture-independent methods were used to evaluate the microbial diversity in produced water samples of the Ekofisk oil field, a high temperature, and fractured chalk reservoir in the North Sea. DGGE analyses of 16S rRNA gene fragments were used to assess the microbial diversity of both archaeal and bacterial communities in produced water samples and enrichment cultures from 4 different wells (B-08, X-08, X-18 and X-25). Low diversity communities were found when 16S rDNA libraries of bacterial and archaeal assemblages were generated from total community DNA obtained from produced water samples and enrichment cultures. Sequence analysis of the clones indicated close matches to microbes associated with high-temperature oil reservoirs or other similar environments. Sequences were found to be similar to members of the genera Thermotoga, Caminicella, Thermoanaerobacter, Archaeoglobus, Thermococcus, and Methanobulbus. Enrichment cultures obtained from the produced water samples were dominated by sheathed rods. Sequence analyses of the cultures indicated predominance of the genera Petrotoga, Arcobacter, Archaeoglobus and Thermococcus. The communities of both produced water and enrichment cultures appeared to be dominated by thermophilic fermenters capable of reducing sulphur compounds. These results suggest that the biochemical processes in the Ekofisk chalk reservoir are similar to those observed in high-temperature sandstone reservoirs.     

模拟油藏条件下内源微生物群落空间分布规律

【背景】油藏内源微生物群落是开展内源微生物驱油技术的物质基础,由于油藏多孔介质取样技术难度大、成本高,实施内源微生物驱油后从注入端到产出端多孔介质中的内源微生物空间分布规律尚不明确。【目的】通过室内长岩心连续驱替实验模拟油藏内源微生物驱油过程,分析实施后不同空间位点油砂上吸附的内源微生物群落结构,揭示从注入端到产出端内源微生物群落的空间分布规律。【方法】借助高通量测序技术及荧光定量PCR技术解析不同空间位点油砂原位微生物群落信息。【结果】注入端到产出端不同空间位点生态环境的差异及菌属间的相互作用造成油藏内源微生物群落空间分布差异,存在明显的好氧、厌氧空间演替变化规律。岩心前端主要存在一些好氧类的产生物表面活性剂类微生物如假单胞菌属,岩心中部主要存在兼性和厌氧类的微生物如地芽孢杆菌、厌氧杆菌属,岩心末端主要分布严格厌氧类细菌和产甲烷古菌,厌氧类微生物代谢产生的H2、CO2和乙酸分子可以为产甲烷古菌提供代谢底物。【结论】通过室内物模油砂研究,首次明确了内源微生物群落在多孔介质中从注入端到产出端的空间分布规律,证实油藏内源微生物的好氧、厌氧空间接替分布规律,深化了对油藏内源微生物的认识。     

Acidophilic microbial communities associated with a natural, biodegraded hydrocarbon seepage

Characterization of microbial communities present in a surface petroleum seep in which hydrocarbons have been biodegraded for thousands of years in order to improve the understanding on natural petroleum biodegradation. DNA was extracted from a natural, surface petroleum seep and subjected to culture independent analysis (rRNA gene-based denaturing gradient gel electrophoresis and phylogenetic analysis of clone libraries). Molecular analysis suggested dominance by acidophilic bacteria, especially Alphaproteobacteria (mainly bacteria related to Acidiphilium and Acidocella). Archaea were not detected, but fungi were present. pH of the samples was around 3.5. Acidophilic microbial communities are associated with an acidic petroleum seep. Microbial community structure analysis gives information on the environmental conditions under which petroleum biodegradation occurs. This knowledge could be applied to define conditions for specific cultivation or activity measurements. The activity of acidophilic micro-organisms deserves more attention with respect to their involvement in natural petroleum degradation. This knowledge will contribute to the design of oil bioremediation strategies for polluted acidic settings.     

Testing the functional significance of microbial composition in natural communities

Ecologists have long studied the relationship between biotic composition and ecosystem functioning in larger organisms; however, only recently has this relationship been investigated widely in microorganisms. Recent studies are reviewed within a framework of three experimental approaches that are often used to study larger organisms: environmental treatment, common garden, and reciprocal transplant experiments. Although the composition of microorganisms cannot be easily manipulated in the field, applying these approaches to intact microbial communities can begin to tease apart the effects of microbial composition from environmental parameters on ecosystem functioning. The challenges in applying these approaches to microorganisms are highlighted and it is discussed how the experimental approach and duration affects a study's interpretation. In general, long-term environmental treatment experiments identify correlative relationships between microbial composition and ecosystem functioning, whereas short-term common garden experiments demonstrate that microbial composition influences ecosystem functioning. Finally, reciprocal transplants simultaneously test for interactive effects of the environment and composition on functioning. The studies reviewed provide evidence that, at least in some cases, microbial composition influences ecosystem functioning. It is concluded that whole-community experiments offer a way to test whether information about microbial composition will help predict ecosystem responses to global change.     

The impact of Cenozoic cooling on assemblage diversity in planktonic foraminifera

The Cenozoic planktonic foraminifera (PF) (calcareous zooplankton) have arguably the most detailed fossil record of any group. The quality of this record allows models of environmental controls on macroecology, developed for Recent assemblages, to be tested on intervals with profoundly different climatic conditions. These analyses shed light on the role of long-term global cooling in establishing the modern latitudinal diversity gradient (LDG)—one of the most powerful generalizations in biogeography and macroecology. Here, we test the transferability of environment-diversity models developed for modern PF assemblages to the Eocene epoch (approx. 56–34 Ma), a time of pronounced global warmth. Environmental variables from global climate models are combined with Recent environment–diversity models to predict Eocene richness gradients, which are then compared with observed patterns. The results indicate the modern LDG—lower richness towards the poles—developed through the Eocene. Three possible causes are suggested for the mismatch between statistical model predictions and data in the Early Eocene: the environmental estimates are inaccurate, the statistical model misses a relevant variable, or the intercorrelations among facets of diversity—e.g. richness, evenness, functional diversity—have changed over geological time. By the Late Eocene, environment–diversity relationships were much more similar to those found today.     

Short-term response of nutrients,carbon and planktonic microbial communities to floodplain wetland inundation

Environmental flows were released to the Macquarie Marshes (~210,000 ha) in north-west NSW of Australia between October and December 2005, inundating an estimated 24,600 ha of floodplain area. According to the flood pulse concept, the marsh floodplains would have stored large amounts of nutrients and carbon during dry antecedent conditions, which would be released into the overlaying flood water. Field studies were conducted in mid-December 2005 at two sites, one on open floodplain woodland with a sparse canopy of River Red Gum and ground cover dominated by saltbushes and the other on open floodplain with black roly-poly. At each site, nutrients, dissolved organic carbon (DOC), planktonic bacteria and phytoplankton were monitored daily for a 6-day period from the overlaying water of a floodplain inundated by the environmental water release. Those in mesocosms deployed in situ, containing marsh floodplain sediments that had been inundated artificially, were also monitored. The mesocosm results from both the sites showed that release of nitrogen was rapid, attaining mean concentrations of total nitrogen of 3.7–14.8 mg l⁻¹, followed by more gradual increases in total phosphorus (mean concentrations 0.6–0.8 mg l⁻¹) and DOC (26.1–50.2 mg l⁻¹) within the 6-day experiment; planktonic microbial communities developed concomitantly with the increasing concentrations of nutrients and DOC, attaining mean densities of (6.0–6.9) × 10⁶ cells ml⁻¹ of planktonic bacteria and (80.7–81.4) × 10³ cells ml⁻¹ of phytoplankton; and for each site the overall measured condition of the mesocosm tended to approach that of the Marshes, over the course of the 6-day experiment. The present study (both observational and experimental) demonstrates that the floodplain sediments in the Marshes, which have been exposed to dry antecedent conditions, release nutrients and carbon to the overlaying flood water following inundation. These resources are thought to have been stored during the dry antecedent phase in accord with the flood pulse concept. Based on the mesocosm experiment, the released nutrients and carbon are in turn most likely to be used by microbial components, such as bacteria and algae, which develop within days of inundation of the floodplain sediments. Thus, environmental flow release provides potential for floodplains to attain a series of ecological responses including initial release of inorganic nutrients and dissolved organic matter and increase in planktonic bacteria and phytoplankton.     

Man's impact on a newly formed reservoir

A newly formed reservoir in the southwestern part of the United States was analyzed for man's impact on the eutrophication of the impoundment. The analysis of the ¹⁴C net productivity (mg ¹²C/m² per day) indicated that the area studied was naturally eutrophic. Significant differences in net production were observed among the sites, as the area where man's recreational activities are highly concentrated had a significantly higher production rate than the other sites investigated. Mean monthly estimate of production for all the sites, and monthly and yearly estimates for the area studied are also included.