Protozoan Grazing, Bacterial Activity, and Mineralization in Two-Stage Continuous Cultures

In two-stage continuous cultures, at bacterial concentrations, biovolumes, and growth rates similar to values found in Lake Vechten, ingestion rates of heterotrophic nanoflagellates (HNAN) increased from 2.3 bacteria HNAN⁻¹ · h⁻¹ at a growth rate of 0.15 day⁻¹ to 9.2 bacteria · HNAN⁻¹ · h⁻¹ at a growth rate of 0.65 day⁻¹. On a yeast extract medium with a C/N/P ratio of 100:15:1.2 (Redfield ratio), a mixed bacterial population showed a yield of 18% (C/C) and a specific carbon content of 211 fg of C · μm⁻³. The HNAN carbon content and yield were estimated at 127 fg of C · μm⁻³ and 47% (C/C). Although P was not growth limiting, HNAN accelerated the mineralization of PO₄-P from dissolved organic matter by 600%. The major mechanism of P remineralization appeared to be direct consumption of bacteria by HNAN. N mineralization was performed mainly (70%) by bacteria but was increased 30% by HNAN. HNAN did not enhance the decomposition of the relatively mineral-rich dissolved organic matter. An accelerated decomposition of organic carbon by protozoa may be restricted to mineral-poor substrates and may be explained mainly by protozoan nutrient regeneration. Growth and grazing in the cultures were compared with methods for in situ estimates. Thymidine incorporation by actively growing bacteria yielded an empirical conversion factor of 1.1 × 10¹⁸ bacteria per mol of thymidine incorporated into DNA. However, nongrowing bacteria also showed considerable incorporation. Protozoan grazing was found to be accurately measured by uptake of fluorescently labeled bacteria, whereas artificial fluorescent microspheres were not ingested, and selective prokaryotic inhibitors blocked not only bacterial growth but also protozoan grazing.     

The Effect of Grazing by a Ciliated Protozoan on Phosphorus Limitation of Heterotrophic Bacteria in Batch Culture1

ABSTRACT. The yield of the bacterium Enterobacter aerogenes and the ciliate Colpidium colpoda was dependent on initial phosphorus concentrations in batch cultures containing 125 or 250 mg/liter glutamate and 50–1000 μg/liter phosphorus. For both, yield per unit phosphorus declined at higher phosphorus concentrations. A marked decline in growth rate in bacterial cultures was coincident with the depletion of dissolved phosphorus and the development of rapid orthophosphate turnover times. Colpidium introduced to these cultures consumed about 16,000 bacteria/h/ciliate while multiplying exponentially and relieved phosphorus limitation, as indicated by a longer turnover-time for phosphate. The longer turnover-time was due to the reduction of bacterial numbers; in cultures with ciliates, bacteria appear to be more active in taking up phosphate, and much of the total phosphorus accumulates in ciliates. Ciliates released both inorganic and organic phosphorus, but the organic phosphorus did not accumulate to excess in the cultures to an extent that would indicate that it is less used by bacteria. Although ciliates release enough phosphorus to account for ca. 20% of the bacterial uptake, ciliates appear to behave as phosphorus sinks as much as phosphorus recyclers in these closed systems.     

Flagellate Predation on a Bacterial Model Community: Interplay of Size-Selective Grazing, Specific Bacterial Cell Size, and Bacterial Community Composition

The influence of grazing by the bacterivorous nanoflagellate Ochromonas sp. strain DS on the taxonomic and morphological structures of a complex bacterial community was studied in one-stage chemostat experiments. A bacterial community, consisting of at least 30 different strains, was fed with a complex carbon source under conditions of low growth rate (0.5 day⁻¹ when nongrazed) and low substrate concentration (9 mg liter⁻¹). Before and after the introduction of the predator, the bacterial community composition was studied by in situ techniques (immunofluorescence microscopy and fluorescent in situ hybridization), as well as by cultivation on agar media. The cell sizes of nonspecifically stained and immunofluorescently labeled bacteria were measured by image analysis. Grazing by the flagellate caused a bidirectional change in the morphological structure of the community. Medium-size bacterial cells, which dominated the nongrazed community, were largely replaced by smaller cells, as well as by cells contained in large multicellular flocs. Cell morphological changes were combined with community taxonomic changes. After introduction of the flagellate, the dominating strains with medium-size cells were largely replaced by single-celled strains with smaller cells on the one hand and, on the other hand, by Pseudomonas sp. strain MWH1, which formed the large, floc-like forms. We assume that size-selective grazing was the major force controlling both the morphological and the taxonomic structures of the model community.     

土壤原生动物群落及其生态功能

土壤原生动物是土壤微生物区系的重要组成部分。在土壤生态系统中 ,由于微生物与微动物的生命活动及其相互作用 ,从而形成了土壤的物质循环和能量转化。土壤原生动物既参与了微生物所介导的物质转化和能量循环 ,又参与了动物对微生物的捕食作用。由于原生动物具有丰富的种类和多样性以及巨大的生物量 ,所以土壤原生动物的群落及其生态功能 ,已引起了人们的广泛关注 ,并且研究理论与方法日益深入。但我国在这方面的研究报道较少 ,本文拟从群落与生态功能方面的进展做一概述。1　土壤原生动物的群落特征土壤与淡水原生动物最早是由Ａｎｔｏｎ…     

Impacts of Multiwalled Carbon Nanotubes on Nutrient Removal from Wastewater and Bacterial Community Structure in Activated Sludge

Background

The increasing use of multiwalled carbon nanotubes (MWCNTs) will inevitably lead to the exposure of wastewater treatment facilities. However, knowledge of the impacts of MWCNTs on wastewater nutrient removal and bacterial community structure in the activated sludge process is sparse.

Aims

To investigate the effects of MWCNTs on wastewater nutrient removal, and bacterial community structure in activated sludge.

Methods

Three triplicate sequencing batch reactors (SBR) were exposed to wastewater which contained 0, 1, and 20 mg/L MWCNTs. MiSeq sequencing was used to investigate the bacterial community structures in activated sludge samples which were exposed to different concentrations of MWCNTs.

Results

Exposure to 1 and 20 mg/L MWCNTs had no acute (1 day) impact on nutrient removal from wastewater. After long-term (180 days) exposure to 1 mg/L MWCNTs, the average total nitrogen (TN) removal efficiency was not significantly affected. TN removal efficiency decreased from 84.0% to 71.9% after long-term effects of 20 mg/L MWCNTs. After long-term exposure to 1 and 20 mg/L MWCNTs, the total phosphorus removal efficiencies decreased from 96.8% to 52.3% and from 98.2% to 34.0% respectively. Further study revealed that long-term exposure to 20 mg/L MWCNTs inhibited activities of ammonia monooxygenase and nitrite oxidoreductase. Long-term exposure to 1 and 20 mg/L MWCNTs both inhibited activities of exopolyphosphatase and polyphosphate kinase. MiSeq sequencing data indicated that 20 mg/L MWCNTs significantly decreased the diversity of bacterial community in activated sludge. Long-term exposure to 1 and 20 mg/L MWCNTs differentially decreased the abundance of nitrifying bacteria, especially ammonia-oxidizing bacteria. The abundance of PAOs was decreased after long-term exposure to 20 mg/L MWCNTs. The abundance of glycogen accumulating organisms (GAOs) was increased after long-term exposure to 1 mg/L MWCNTs.

Conclusion

MWCNTs have adverse effects on biological wastewater nutrient removal, and altered the diversity and structure of bacterial community in activated sludge.     

Bacterial Community Structure and Function along a Heavy Metal Gradient

The response of the planktonic, sediment, and epilithic bacterial communities to increasing concentrations of heavy metals was determined in a polluted river. None of the communities demonstrated a pollution-related effect on bacterial numbers (viable and total), heterotrophic activity, resistance to Pb or Cu, or species diversity as determined by either the Shannon-Wiener diversity index or rarefaction. The lack of correlation between concentrations of heavy metals and resistance in the sediment bacterial community was investigated and found to be due at least in part to the high pH of the river water and the resultant reduction in heavy metal toxicity. The three different communities demonstrated characteristic profiles based on the relative abundances of bacterial strains grouped according to functional similarities.     

Characterization of Bacterial Community Structure on a Weathered Pegmatitic Granite

This study exploited the contrasting major element chemistry of a pegmatitic granite to investigate mineralogical influences on bacterial community structure. Intact crystals of variably weathered muscovite, plagioclase, K-feldspar, and quartz were extracted, together with whole-rock granite. Environmental scanning electron microscopy revealed a diversity of bacterial structures, with rods and cocci clearly visible on surfaces of all mineral types. Bacterial automated ribosomal intergenic spacer analysis was used to generate a ribotype profile for each mineral. A randomization test revealed that community fingerprints differed between different mineral types, whereas canonical correspondence analysis (CCA) showed that mineral chemistry affected individual bacterial ribotypes. CCA also revealed that Al, Si, and Ca had a significant impact on bacterial community structure within the system, which contrasts with the finding within fungal communities that although Al and Si also had a significant impact, K rather than Ca was important. The bacterial populations associated with different minerals were different. Members of each of these populations were found almost exclusively on a single mineral type, as was previously reported for fungal populations. These results show that bacterial community structure was driven by the chemical composition of minerals, indicating selective pressure by individual chemical elements on bacterial populations in situ.     

Functional and Structural Adaptations of Bacterial Communities Growing on Particulate Substrates under Stringent Nutrient Limitation

Biomass recycle reactors (BRRs) were used as a model system to study the functional and structural adaptations of mixed bacterial communities in response to the imposition of increasingly severe nutrient limitation. BRRs were fed synthetic media containing either spinach homogenate or autoclaved yeast cells to simulate the complex mixtures of particulate carbon sources that are often present in nature. In the BRRs fed spinach homogenate, the biomass (measured as particulate protein) exhibited a physiological response similar to previous studies as detected by 40–80% reductions in respiratory potential and by relatively stable catabolic ectoenzyme activities. Concomitant adaptations in bacterial community structure were detected by PCR-DGGE and RT-PCR-DGGE of 16S rDNA and 16S rRNA fragments, respectively. The microbial community structure was dynamic even after the biomass had reached a quasi-steady state with respect to physiological measurements. In the BRRs fed yeast cells, respiratory potentials increased 2- to 5-fold during the initial portion of the BRR run and a-glucosidase and b-glucosidase activities increased 2- to 4-fold. Substantial bacterial community shifts were also detected in both the rDNA and rRNA profiles, indicating that this community was also structurally dynamic. These experiments suggest that phylogenetically different bacteria sustained the functional activities in these ecosystems in response to increasingly stringent nutrient limitation.     

冬季上海市城区河道中原生动物群落的结构特征

于2007年11月至2008年1月,对上海市城区经过初步修复的四条河道(午潮港、横港、朝阳河和曹杨环浜)中原生动物的群落结构和多样性进行了调查.共鉴定出原生动物88种,其中鞭毛虫31种,肉足虫13种,纤毛虫44种.除曹杨环浜无优势种外,其他三条河道的种类均以耐污种类为优势种,如波豆虫 Bodo sp.、滴虫 Monas sp.、隐藻 Cryptomonas sp.等;四条河道均呈现纤毛虫和鞭毛虫种类较为丰富,肉足虫相对较少的现象.四条河道中原生动物多样性指数的平均值变动在1.14～2.87之间;密度变动在900.35～2837.89 ind/ml间.分析发现,前期生态治理较为成功的曹杨环浜具有多样性指数高、密度大、无明显优势种等特征,而其他三条河道中原生动物种类相对较单一,且分布不均匀,主要优势种为一些耐污种类.提示经过人工合理的修复,可以有效改善受污染河道的状况.因此对已经初步修复河道的生态系统进行评估,探索和制定出有针对性的修复方案,并对其加以合理的维护,对建立健康、稳态的河道生态系统是十分必要的.     

Bacterial Community Structure and Location in Stilton Cheese

The microbial diversity occurring in Stilton cheese was evaluated by 16S ribosomal DNA analysis with PCR-denaturing gradient gel electrophoresis. DNA templates for PCR experiments were directly extracted from the cheese as well as bulk cells harvested from a variety of viable-count media. The variable V3 and V4-V5 regions of the 16S genes were analyzed. Closest relatives of Lactococcus lactis, Enterococcus faecalis, Lactobacillus plantarum, Lactobacillus curvatus, Leuconostoc mesenteroides, Staphylococcus equorum, and Staphylococcus sp. were identified by sequencing of the DGGE fragments. Fluorescently labeled oligonucleotide probes were developed to detect Lactococcus lactis, Lactobacillus plantarum, and Leuconostoc mesenteroides in fluorescence in situ hybridization (FISH) experiments, and their specificity for the species occurring in the community of Stilton cheese was checked in FISH experiments carried out with reference cultures. The combined use of these probes and the bacterial probe Eub338 in FISH experiments on Stilton cheese sections allowed the assessment of the spatial distribution of the different microbial species in the dairy matrix. Microbial colonies of bacteria showed a differential location in the different parts of the cheese examined: the core, the veins, and the crust. Lactococci were found in the internal part of the veins as mixed colonies and as single colonies within the core. Lactobacillus plantarum was detected only underneath the surface, while Leuconostoc microcolonies were homogeneously distributed in all parts observed. The combined molecular approach is shown to be useful to simultaneously describe the structure and location of the bacterial flora in cheese. The differential distribution of species found suggests specific ecological reasons for the establishment of sites of actual microbial growth in the cheese, with implications of significance in understanding the ecology of food systems and with the aim of achieving optimization of the fermentation technologies as well as preservation of traditional products.     

Benthic Bacterial Production and Protozoan Predation in a Silty Freshwater Environment

The interrelation of heterotrophic bacteria with bacterivorous protists has been widely studied in pelagic environments, but data on benthic habitats, especially in freshwater systems, are still scarce. We present a seasonal study focusing on bacterivory by heterotrophic nanoflagellates (HNF) and ciliates in the silty sediment of a temperate macrophyte-dominated oxbow lake. From January 2001 to February 2002 we monitored the standing stock of bacteria and protozoa, bacterial secondary production (BSP, ³H-thymidine, and ¹⁴C-leucine incorporation), and grazing rates of HNF and ciliates on bacteria (FLB uptake) in the oxic sediment of the investigated system. BSP ranged from 470 to 4050 µg C L^–1 wet sediment h^–1. The bacterial compartment turned out to be highly dynamic, indicated by population doubling times (0.6–10.0 d), which were comparable to those in the water column of the investigated system. Yet, the control mechanisms acting upon the bacterial population led to a relative constancy of bacterial standing stock during a year. Ingestion rates of protozoan grazers were 0–20.0 bacteria HNF^–1 h^–1 and 0–97.6 bacteria ciliate^–1 h^–1. HNF and ciliates together cropped 0–14 (mean 4)% of BSP, indicating that they did not significantly contribute to benthic bacterial mortality during any period of the year. The low impact of protozoan grazing was due to the low numbers of HNF and ciliates in relation to bacteria (1.8–3.5 × 10⁴ bacteria HNF^–1, 0.9–3.1 × 10⁶ bacteria ciliate^–1). Thus, grazing by HNF and ciliates could be ruled out as a parameter regulating bacterial standing stock or production in the sediment of the investigated system, but the factors responsible for the limitation of benthic protistan densities and the fate of benthic BSP remained unclear.     

Bacterial Community Structure Associated with a Dimethylsulfoniopropionate-Producing North Atlantic Algal Bloom

The bacteria associated with oceanic algal blooms are acknowledged to play important roles in carbon, nitrogen, and sulfur cycling, yet little information is available on their identities or phylogenetic affiliations. Three culture-independent methods were used to characterize bacteria from a dimethylsulfoniopropionate (DMSP)-producing algal bloom in the North Atlantic. Group-specific 16S rRNA-targeted oligonucleotides, 16S ribosomal DNA (rDNA) clone libraries, and terminal restriction fragment length polymorphism analysis all indicated that the marine Roseobacter lineage was numerically important in the heterotrophic bacterial community, averaging >20% of the 16S rDNA sampled. Two other groups of heterotrophic bacteria, the SAR86 and SAR11 clades, were also shown by the three 16S rRNA-based methods to be abundant in the bloom community. In surface waters, the Roseobacter, SAR86, and SAR11 lineages together accounted for over 50% of the bacterial rDNA and showed little spatial variability in abundance despite variations in the dominant algal species. Depth profiles indicated that Roseobacter phylotype abundance decreased with depth and was positively correlated with chlorophyll a, DMSP, and total organic sulfur (dimethyl sulfide plus DMSP plus dimethyl sulfoxide) concentrations. Based on these data and previous physiological studies of cultured Roseobacter strains, we hypothesize that this lineage plays a role in cycling organic sulfur compounds produced within the bloom. Three other abundant bacterial phylotypes (representing a cyanobacterium and two members of the α Proteobacteria) were primarily associated with chlorophyll-rich surface waters of the bloom (0 to 50 m), while two others (representing Cytophagales and δ Proteobacteria) were primarily found in deeper waters (200 to 500 m).     

Changes in Bacterial Community Composition and Dynamics and Viral Mortality Rates Associated with Enhanced Flagellate Grazing in a Mesoeutrophic Reservoir

Bacterioplankton from a meso-eutrophic dam reservoir was size fractionated to reduce (<0.8-μm treatment) or enhance (<5-μm treatment) protistan grazing and then incubated in situ for 96 h in dialysis bags. Time course samples were taken from the bags and the reservoir to estimate bacterial abundance, mean cell volume, production, protistan grazing, viral abundance, and frequency of visibly infected cells. Shifts in bacterial community composition (BCC) were examined by denaturing gradient gel electrophoresis (DGGE), cloning and sequencing of 16S rDNA genes from the different treatments, and fluorescence in situ hybridization (FISH) with previously employed and newly designed oligonucleotide probes. Changes in bacterioplankton characteristics were clearly linked to changes in mortality rates. In the reservoir, where bacterial production about equaled protist grazing and viral mortality, community characteristics were nearly invariant. In the “grazer-free” (0.8-μm-filtered) treatment, subject only to a relatively low mortality rate (~17% day⁻¹) from viral lysis, bacteria increased markedly in concentration. While the mean bacterial cell volume was invariant, DGGE indicated a shift in BCC and FISH revealed an increase in the proportion of one lineage within the beta proteobacteria. In the grazing-enhanced treatment (5-μm filtrate), grazing mortality was ~200% and viral lysis resulted in mortality of 30% of daily production. Cell concentrations declined, and grazing-resistant flocs and filaments eventually dominated the biomass, together accounting for >80% of the total bacteria by the end of the experiment. Once again, BCC changed strongly and a significant fraction of the large filaments was detected using a FISH probe targeted to members of the Flectobacillus lineage. Shifts of BCC were also reflected in DGGE patterns and in the increases in the relative importance of both beta proteobacteria and members of the Cytophaga-Flavobacterium cluster, which consistently formed different parts of the bacterial flocs. Viral concentrations and frequencies of infected cells were highly significantly correlated with grazing rates, suggesting that protistan grazing may stimulate viral activity.     

Impact of Protists on the Activity and Structure of the Bacterial Community in a Rice Field Soil

Flooded rice fields have become a model system for the study of soil microbial ecology. In Italian rice fields, in particular, aspects from biogeochemistry to molecular ecology have been studied, but the impact of protistan grazing on the structure and function of the prokaryotic community has not been examined yet. We compared an untreated control soil with a γ-radiation-sterilized soil that had been reinoculated with a natural bacterial assemblage. In order to verify that the observed effects were due to protistan grazing and did not result from sterilization, we set up a third set of microcosms containing sterilized soil that had been reinoculated with natural assemblage bacteria plus protists. The spatial and temporal changes in the protistan and prokaryotic communities were examined by denaturing gradient gel electrophoresis (DGGE) and terminal restriction fragment length polymorphism (T-RFLP) analysis, respectively, both based on the small-subunit gene. Sequences retrieved from DGGE bands were preferentially affiliated with Cercozoa and other bacteriovorous flagellates. Without protists, the level of total DNA increased with incubation time, indicating that the level of the microbial biomass was elevated. Betaproteobacteria were preferentially preyed upon, while low-G+C-content gram-positive bacteria became more dominant under grazing pressure. The bacterial diversity detectable by T-RFLP analysis was greater in the presence of protists. The level of extractable NH₄⁺ was lower and the level of extractable SO₄²⁻ was higher without protists, indicating that nitrogen mineralization and SO₄²⁻ reduction were stimulated by protists. Most of these effects were more obvious in the partially oxic surface layer (0 to 3 mm), but they could also be detected in the anoxic subsurface layer (10 to 13 mm). Our observations fit well into the overall framework developed for protistan grazing, but with some modifications pertinent to the wetland situation: O₂ was a major control, and O₂ availability may have limited directly and indirectly the development of protists. Although detectable in the lower anoxic layer, grazing effects were much more obvious in the partially oxic surface layer.     

Soil Bacterial and Fungal Community Structure Across a Range of Unimproved and Semi-Improved Upland Grasslands

Changes in soil microbial community structure due to improvement are often attributed to concurrent shifts in floristic community composition. The bacterial and fungal communities of unimproved and semi-improved (as determined by floristic classification) grassland soils were studied at five upland sites on similar geological substrata using both broad-scale (microbial activity and fungal biomass) and molecular [terminal restriction fragment length polymorphism (TRFLP), automated ribosomal intergenic spacer analysis (ARISA)] approaches. It was hypothesized that microbial community structure would be similar in soils from the same grassland type, and that grassland vegetation classifications could thus be used as predictors of microbial community structure. Microbial community measurements varied widely according to both site and grassland type, and trends in the effect of grassland improvement differed between sites. These results were consistent with those from similar studies, and indicated that floristic community composition was not a stable predictor of microbial community structure across sites. This may indicate a lack of correlation between grassland plant composition and soil microbial community structure, or that differences in soil chemistry between sites had larger impacts on soil microbial populations than plant-related effects.