Molecular detection of potentially toxic cyanobacteria and their associated bacteria in lake water column and sediment

We investigated the molecular diversity of cyanobacteria and bacteria during a water bloom in a lake with a long history of toxic cyanobacterial blooms (Lake Kastoria, Greece). We also tested the hypothesis whether bloom-forming cyanobacteria are preserved in the lake’s sediment 2 years after the bloom. The dominant cyanobacteria during the bloom included the potentially toxin-producing Microcystis aeruginosa and several other Chroococcales forms closely related to the genus Microcystis. This suggests that the use of cyanobacterial-specific primers seems to be very informative in describing the cyanobacteria during the water blooms. The bacterial community showed high diversity, consisting mostly of singleton and doubleton phylotypes. The majority of the phylotypes were typical lake bacteria including some potential pathogens and toxin metabolising bacteria, suggesting that the dominant toxic cyanobacteria did not have any significant effect on the bacterial community structure. In the sediment, 2 years after the water bloom, no bloom-forming cyanobacteria were retrieved, suggesting that they cannot be preserved in the sediment. Similar to the water column, sediment bacterial diversity was also high, consisting mostly of yet-uncultured bacteria that are related to environments where organic matter degradation takes place.     

Massive Regime Shifts and High Activity of Heterotrophic Bacteria in an Ice-Covered Lake

In winter 2009/10, a sudden under-ice bloom of heterotrophic bacteria occurred in the seasonally ice-covered, temperate, deep, oligotrophic Lake Stechlin (Germany). Extraordinarily high bacterial abundance and biomass were fueled by the breakdown of a massive bloom of Aphanizomenon flos-aquae after ice formation. A reduction in light resulting from snow coverage exerted a pronounced physiological stress on the cyanobacteria. Consequently, these were rapidly colonized, leading to a sudden proliferation of attached and subsequently of free-living heterotrophic bacteria. Total bacterial protein production reached 201 µg C L⁻¹ d⁻¹, ca. five times higher than spring-peak values that year. Fluorescence in situ hybridization and denaturing gradient gel electrophoresis at high temporal resolution showed pronounced changes in bacterial community structure coinciding with changes in the physiology of the cyanobacteria. Pyrosequencing of 16S rRNA genes revealed that during breakdown of the cyanobacterial population, the diversity of attached and free-living bacterial communities were reduced to a few dominant families. Some of these were not detectable during the early stages of the cyanobacterial bloom indicating that only specific, well adapted bacterial communities can colonize senescent cyanobacteria. Our study suggests that in winter, unlike commonly postulated, carbon rather than temperature is the limiting factor for bacterial growth. Frequent phytoplankton blooms in ice-covered systems highlight the need for year-round studies of aquatic ecosystems including the winter season to correctly understand element and energy cycling through aquatic food webs, particularly the microbial loop. On a global scale, such knowledge is required to determine climate change induced alterations in carbon budgets in polar and temperate aquatic systems.     

Analysis of bacterial communities in a municipal duck pond during a phytoplankton bloom and isolation of Anatilimnocola aggregata gen. nov., sp. nov., Lacipirellula limnantheis sp. nov. and Urbifossiella limnaea gen. nov., sp. nov. belonging to the phylum Planctomycetes

Waterbodies such as lakes and ponds are fragile environments affected by human influences. Suitable conditions can result in massive growth of phototrophs, commonly referred to as phytoplankton blooms. Such events benefit heterotrophic bacteria able to use compounds secreted by phototrophs or their biomass as major nutrient source. One example of such bacteria are Planctomycetes, which are abundant on the surfaces of marine macroscopic phototrophs; however, less data are available on their ecological roles in limnic environments. In this study, we followed a cultivation-independent deep sequencing approach to study the bacterial community composition during a cyanobacterial bloom event in a municipal duck pond. In addition to cyanobacteria, which caused the bloom event, members of the phylum Planctomycetes were significantly enriched in the cyanobacteria-attached fraction compared to the free-living fraction. Separate datasets based on isolated DNA and RNA point towards considerable differences in the abundance and activity of planctomycetal families, indicating different activity peaks of these families during the cyanobacterial bloom. Motivated by the finding that the sampling location harbours untapped bacterial diversity, we included a complementary cultivation-dependent approach and isolated and characterized three novel limnic strains belonging to the phylum Planctomycetes.     

湖泊蓝藻水华发生机理研究进展

蓝藻水华是富营养化湖泊常见的生态灾害,通过产生毒素、死亡分解时使水体缺氧和破坏正常的食物网威胁到饮用水安全、公众健康和景观,会造成严重的经济损失和社会问题,揭示其发生机理是进行防治的基础。综述了蓝藻水华发生机理的主要假说和证据,主要分为环境因子(营养盐、氮磷比、温度、微量元素、浮游动物牧食、水文和气象条件等)和生理生态特性(伪空泡、胶质鞘、CO2浓缩机制、适应低光强、贮藏营养物质、防晒、产毒素和固氮等)两个方面;评述了主要新理论,展望了今后的研究。到目前为止的研究表明寻找一两个关键因子并不能阐明蓝藻水华的发生机理。现存的理论或假说尽管已经在蓝藻水华的防治实践中产生重要作用,但仍然未能清楚地阐释其发生的客观规律。认为蓝藻水华是在各种环境因子(外因)的耦合驱动下,水华蓝藻由于其独特的生理生态特性(内因),产生巨大的生物量而在浮游植物群落中占绝对优势,在合适的水文气象条件下集聚于水表而形成。因此水华机理的研究应同时关注水华蓝藻的生理生态学规律和蓝藻水华发生的各种环境条件。不同环境因子协同影响水华蓝藻的不同生理生态特性的表达,从而影响水华的发生过程,将可能是以后研究的重点。蓝藻水华机理的研究在微观方面正趋向于应用分子生物学手段分析蓝藻生理过程,宏观方面则将广泛应用遥感遥测技术观测全湖蓝藻的变化规律。今后加强对水华蓝藻生理生态特性的基因表达与调控和环境多因子耦合作用于蓝藻水华过程的研究将有重要意义。蓝藻水华的机理研究包括现象、过程和原因3个层次的问题,通过大量的现象和过程的研究,不断揭示其发生过程中水华蓝藻的群落演替、种群发展、细胞活性和分子机理等变化规律,才能找到其发生的真正原因,为其防治提供理论依据和更好的治理措施。在蓝藻水华防治方面,控制营养盐和生态修复可能将是今后很长时间内最根本最有效和最具操作性的方法。     

The effect of environmental parameters and cyanobacterial blooms on phytoplankton dynamics of a Portuguese temperate Lake

The increasing occurrence of cyanobacterial blooms in freshwaters is of great concern due to the ability of many cyanobacteria to produce cyanotoxins. In the present work, the eutrophied Vela Lake (Central Portugal), used for recreational purposes and as a water source for agriculture, was monitored every fortnight between 2000 and 2001. Phytoplankton diversity and densities were measured and correlated to environmental parameters. A seasonal phytoplanktonic succession was observed and it was mainly correlated with conductivity, temperature, total suspended solids and nutrients availability (particularly phosphorus). Diatoms were dominant during winter months (inferior temperatures and higher nutrients availability) followed by green algae in early spring and then cyanobacteria from late spring until early autumn (less nutrient availability and higher temperatures). A massive cyanobacterial bloom of Aphanizomenon flos-aquae occurred early in May 2001 and was preceded by the lowest nitrogen levels measured in the water during all the study period. At the time of this bloom senescence, dissolved oxygen was severely depleted and a massive death of ichthyofauna was recorded. A Microcystis aeruginosa bloom was also detected in July 2001 and it occurred following a rapid decrease in abundance of green algae and diatoms. By considering not only the environmental parameters but also the occurrence of cyanobacterial blooms as explanatory variables in a canonical correspondence analysis, the variance explained for the phytoplanktonic assemblage during the study period was increased in about 7% achieving a total of 61.0%, indicating a correlation that may be due to the known competitive advantage and/or allelopathy of the bloom-forming cyanobacteria towards microalgae.     

Seasonal shifts in community composition and proteome expression in a sulphur-cycling cyanobacterial mat

Seasonal changes in light and physicochemical conditions have strong impacts on cyanobacteria, but how they affect community structure, metabolism, and biogeochemistry of cyanobacterial mats remains unclear. Light may be particularly influential for cyanobacterial mats exposed to sulphide by altering the balance of oxygenic photosynthesis and sulphide-driven anoxygenic photosynthesis. We studied temporal shifts in irradiance, water chemistry, and community structure and function of microbial mats in the Middle Island Sinkhole (MIS), where anoxic and sulphate-rich groundwater provides habitat for cyanobacteria that conduct both oxygenic and anoxygenic photosynthesis. Seasonal changes in light and groundwater chemistry were accompanied by shifts in bacterial community composition, with a succession of dominant cyanobacteria from Phormidium to Planktothrix, and an increase in diatoms, sulphur-oxidizing bacteria, and sulphate-reducing bacteria from summer to autumn. Differential abundance of cyanobacterial light-harvesting proteins likely reflects a physiological response of cyanobacteria to light level. Beggiatoa sulphur oxidation proteins were more abundant in autumn. Correlated abundances of taxa through time suggest interactions between sulphur oxidizers and sulphate reducers, sulphate reducers and heterotrophs, and cyanobacteria and heterotrophs. These results support the conclusion that seasonal change, including light availability, has a strong influence on community composition and biogeochemical cycling of sulphur and O₂ in cyanobacterial mats.     

Analysis of the Attached Microbial Community on Mucilaginous Cyanobacterial Aggregates in the Eutrophic Lake Taihu Reveals the Importance of Planctomycetes

The phylogenetic diversity of the microbial community assemblage of the carpet-like mucilaginous cyanobacterial blooms in the eutrophic Lake Taihu was investigated. 16S ribosomal DNA clone libraries produced from the DNA of cyanobacterial assemblages that had been washed to remove unattached bacteria contained only cyanobacteria. However, a further treatment which included grinding the freeze-dried material to physically detach cells followed by the removal of larger cells by filtration allowed us to detect a large variety of bacteria within the cyanobacterial bloom community. Interestingly, the dominant members of the microbial community were Planctomycetes followed by Cytophaga–Flavobacterium–Bacteroides (CFB), Betaproteobacteria, and Gammaproteobacteria. The analysis of the 16S ribosomal DNA clone libraries made from enrichment culture revealed much higher phylogenetic diversity of bacteria. Dominant bacterial groups in the enrichment system were identified as members of the Alphaproteobacteria, Betaproteobacteria, Gammaproteobacteria, and Deltaproteobacteria subdivisions, CFB group, and Planctomycetes. In addition, the clone libraries constructed from Planctomycetes-specific 16S ribosomal RNA primers also verified that the enrichment allowed a diversity of Planctomycetes to proliferate, although the community composition was altered after enrichment.     

Diversity and dynamics of microcystin—Producing cyanobacteria in China's third largest lake, Lake Taihu

Microcystins (MC), the most prevalent group of harmful cyanobacterial hepatotoxins, are primarily produced by strains of cyanobacteria in Microcystis, Anabaena and Planktothrix. Lake Taihu, which is the third largest freshwater lake in China, is a hypertrophic shallow lake in eastern China that has experienced lake-wide cyanobacterial blooms annually during the last few decades. In this study, PCR-DGGE was used to evaluate the diversity of potential MC-producing cyanobacteria and real-time PCR was used to analyze the dynamics of this population based on the presence of the mcy gene in samples collected during a year long study. The results revealed that all MC-producing genotypes detected belonged to the genus Microcystis. In addition, the MC-producing genotype communities were more diverse during the bloom season than the non-bloom season, and the diversity in the late bloom period was lower than the diversity in the early bloom period. Furthermore, the abundance of MC-producing genotypes increased dramatically during the bloom development period, reaching its peak in late summer (September). The results also suggested that the highest mcy gene concentration lagged behind the highest MC concentration, and the potential MC-producing cyanobacterial community shift lagged behind the development of blooms.     

Lysogeny and lytic viral production during a bloom of the cyanobacterium Synechococcus spp

Lytic viral production and lysogeny were investigated in cyanobacteria and heterotrophic bacteria during a bloom of Synechococcus spp. in a pristine fjord in British Columbia, Canada. Triplicate seawater samples were incubated with and without mitomycin C and the abundances of heterotrophic bacteria, cyanobacteria, total viruses and infectious cyanophage were followed over 24 h. Addition of mitomycin C led to increases in total viral abundance as well as the abundance of cyanophages infecting Synechococcus strain DC2. Given typical estimates of burst size, these increases were consistent with 80% of the heterotrophic bacteria and 0.6% of Synechococcus cells being inducible by the addition of mitomycin C. This is the highest percentage of lysogens reported for a natural microbial community and demonstrates induction in a marine Synechococcus population. It is likely that the cyanophage production following the addition of mitomycin C was much higher than that titered against a single strain of Synechococcus; hence this estimate is a minimum. In untreated seawater samples, lytic viral production was estimated to remove ca. 27% of the gross heterotrophic bacterial production, and a minimum of 1.0% of the gross cyanobacterial production. Our results demonstrate very high levels of lysogeny in the heterotrophic bacterial community, outside of an oligotrophic environment, and the presence of inducible lysogens in Synechococcus spp. during a naturally occurring bloom. These data emphasize the need for further examination of the factors influencing lytic and lysogenic viral infection in natural microbial communities.     

Role of Predatory Bacteria in the Termination of a Cyanobacterial Bloom

Changes in cyanobacterial abundance and in the occurrence of bacteria of bacteria capable of lysing cyanobacteria were monitored over a period of 6 months (May to October 1998) in eutrophic Brome Lake (Quebec, Canada), in which dense cyanobacterial blooms recur regularly. By screening lake water, we isolated two strains of lytic bacteria, from the family Cytophagaceae. When tested on 12 cyanobacteria and 6 heterotrophic bacteria, strain 1 lysed only Anabaena flos-aquae and strain 2 lysed only Synechococcus cedorum, Synechococcus leopoliensis, Synechococcus elongatus, and Anacystic nidulans: both liquid and agar-grown cultures of these cyanobacteria were lysed. The number of plaque forming units of bacteria increased dramatically during the decline of the bloom. The results are consistent with an important role for these host-specific lytic bacteria in control and elimination of cyanobacterial blooms in this lake.     

Four years of experimental climate change modifies the microbial drivers of N2O fluxes in an upland grassland ecosystem

Emissions of the trace gas nitrous oxide (N₂O) play an important role for the greenhouse effect and stratospheric ozone depletion, but the impacts of climate change on N₂O fluxes and the underlying microbial drivers remain unclear. The aim of this study was to determine the effects of sustained climate change on field N₂O fluxes and associated microbial enzymatic activities, microbial population abundance and community diversity in an extensively managed, upland grassland. We recorded N₂O fluxes, nitrification and denitrification, microbial population size involved in these processes and community structure of nitrite reducers (nirK) in a grassland exposed for 4 years to elevated atmospheric CO₂ (+200 ppm), elevated temperature (+3.5 °C) and reduction of summer precipitations (?20%) as part of a long‐term, multifactor climate change experiment. Our results showed that both warming and simultaneous application of warming, summer drought and elevated CO₂ had a positive effect on N₂O fluxes, nitrification, N₂O release by denitrification and the population size of N₂O reducers and NH₄ oxidizers. In situ N₂O fluxes showed a stronger correlation with microbial population size under warmed conditions compared with the control site. Specific lineages of nirK denitrifier communities responded significantly to temperature. In addition, nirK community composition showed significant changes in response to drought. Path analysis explained more than 85% of in situ N₂O fluxes variance by soil temperature, denitrification activity and specific denitrifying lineages. Overall, our study underlines that climate‐induced changes in grassland N₂O emissions reflect climate‐induced changes in microbial community structure, which in turn modify microbial processes.     

Phylogenetically Diverse Denitrifying and Ammonia-Oxidizing Bacteria in Corals Alcyonium gracillimum and Tubastraea coccinea

To date, the association of coral–bacteria and the ecological roles of bacterial symbionts in corals remain largely unknown. In particular, little is known about the community components of bacterial symbionts of corals involved in the process of denitrification and ammonia oxidation. In this study, the nitrite reductase (nirS and nirK) and ammonia monooxygenase subunit A (amoA) genes were used as functional markers. Diverse bacteria with the potential to be active as denitrifiers and ammonia-oxidizing bacteria (AOB) were found in two East China Sea corals: stony coral Alcyonium gracillimum and soft coral Tubastraea coccinea. The 16S rRNA gene library analysis demonstrated different communities of bacterial symbionts in these two corals of the same location. Nitrite reductase nirK gene was found only in T. coccinea, while both nirK and nirS genes were detected in A. gracillimum, which might be the result of the presence of different bacterial symbionts in these two corals. AOB rather than ammonia-oxidizing archaea were detected in both corals, suggesting that AOB might play an important role in the ammonia oxidation process of the corals. This study indicates that the coral bacterial symbionts with the potential for nitrite reduction and ammonia oxidation might have multiple ecological roles in the coral holobiont, which promotes our understanding of bacteria-mediated nitrogen cycling in corals. To our knowledge, this study is the first assessment of the community structure and phylogenetic diversity of denitrifying bacteria and AOB in corals based on nirK, nirS, and amoA gene library analysis.     

Successional patterns of key genes and processes involved in the microbial nitrogen cycle in a salt marsh chronosequence

Here, we investigated the patterns of microbial nitrogen cycling communities along a chronosequence of soil development in a salt marsh. The focus was on the abundance and structure of genes involved in N fixation (nifH), bacterial and archaeal ammonium oxidation (amoA; AOB and AOA), and the abundances of genes involved in denitrification (nirS, nirK, nosZ). Potential nitrification and denitrification activities were also measured, and increases in nitrification were found in soils towards the end of succession, whereas denitrification became maximal in soils at the intermediate stages. The nifH, nirK and nirS gene markers revealed increases in the sizes of the respective functional groups towards the intermediate stage (35 years), remaining either constant (for nifH) or slightly declining towards the latest stage of succession (for nirK and nirS). Moreover, whereas the AOB abundance peaked in soils at the intermediate stage, that of AOA increased linearly along the chronosequence. The abundance of nosZ was roughly constant, with no significant regression. The drivers of changes in abundance and structure were identified using path analysis; whereas the ammonia oxidizers (AOA and AOB) showed patterns that followed mainly N availability, those of the nitrogen fixers followed plant diversity and soil structure. The patterns of denitrifiers were group-dependent, following the patterns of plant diversity (nirK and nirS) and belowground shifts (nosZ). The variation observed for the microbial groups associated with the same function highlights their differential contribution at different stages of soil development, revealing an interplay of changes in terms of niche complementarity and adaptation to the local environment.     

Increased risk of cyanobacterial blooms in northern high‐latitude lakes through climate warming and phosphorus enrichment

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氮磷营养盐添加对二甲基巯基丙酸内盐合成与降解细菌及其功能基因的影响

【目的】二甲基巯基丙酸内盐(dimethylsulfoniopropionate,DMSP)是海洋中主要的有机硫化物之一,是海洋细菌硫的主要来源,海洋细菌将其分解成"冷室气体"二甲基硫(dimethylsulfide,DMS),对调节全球气候变化和驱动地球硫循环有重要作用。本研究通过中国东海水体的现场围隔实验模拟海水富营养化对DMSP、DMS产量以及DMSP合成基因(dsyB和mmtN)和降解基因(dddP和dmdA)及相关功能细菌的影响。【方法】通过流式细胞仪计数92个围隔海水样品中微微型浮游生物的数量,采用Illumina MiSeq测序技术对海水样品中细菌的16S rRNA基因进行高通量测序,利用荧光定量PCR技术定量测定16S rRNA基因、DMSP合成及降解基因的丰度。【结果】研究发现,同时添加硝酸盐(6.00μmol/L)和磷酸盐(0.375μmol/L)能促进叶绿素a、DMSP、DMS的浓度上升。对于DMSP合成基因,只加磷酸盐能促进dsyB及Phaeobacter等相应物种的富集,虽然同时添加硝酸盐和磷酸盐使dsyB富集,但相对只加磷酸盐却不利于dsyB积累;同时添加硝酸盐和磷酸盐也抑制Alteromonas的生长,进而抑制了mmtN的富集。对于DMSP降解基因,同时加入硝酸盐和磷酸盐促进了dddP及Thalassococcus、Thalassobius、Loktanella和Shimia等物种的富集,却抑制了SAR11、Sulfitobacter等的富集,从而导致dmdA无法被富集。【结论】氮限制能更好地促进DMSP合成基因的表达,从而迫使细菌增加DMSP的合成以应对氮营养条件不足的生存环境,并进而提高DMSP脱甲基化的比例为细菌提供更多能量;而在硝酸盐和磷酸盐充足情况下,细菌相对减少DMSP的合成且更倾向于裂解DMSP产生DMS来降低硫同化的比例。本研究结果强调了海水富营养化对细菌合成与降解DMSP过程的影响。     

Abundance and diversity of eukaryotic rather than bacterial community relate closely to the trophic level of urban lakes

Scientific understanding of biotic effects on the water trophic level is lacking for urban lakes during algal bloom development stage. Based on the Illumina MiSeq sequencing, quantitative polymerase chain reaction (PCR), and multiple statistical analyses, we estimated distribution patterns and ecological roles of planktonic bacteria and eukaryotes in urban lakes during algal bloom development stage (i.e., April, May, and June). Cyanobacteria and Chlorophyta mainly dominated algal blooms. Bacteria exhibited significantly higher absolute abundance and community diversity than eukaryotes, whereas abundance and diversity of eukaryotic rather than bacterial community relate closely to the water trophic level. Multinutrient cycling (MNC) index was significantly correlated with eukaryotic diversity rather than bacterial diversity. Stronger species replacement, broader environmental breadth, and stronger phylogenetic signal were found for eukaryotic community than for bacterial community. In contrast, bacterial community displayed stronger community stability and environmental constraint than eukaryotic community. Stochastic and differentiating processes contributed more to community assemblies of bacteria and eukaryotes. Our results emphasized that a strong linkage between planktonic diversity and MNC ensured a close relationship between planktonic diversity and the water trophic level of urban lakes. Our findings could be useful to guide the formulation and implementation of environmental lake protection measures.     

不同恢复阶段热带森林土壤nirS型反硝化微生物群落结构及多样性特征

探明热带森林土壤反硝化微生物群落结构及多样性，对于理解反硝化引起的N₂O排放及缓解全球变暖具有重要意义。本研究以西双版纳3个不同恢复阶段热带森林类型[即白背桐（Mallotus paniculatus，MP）、崖豆藤（Millttia leptobotrya，ML）群落、群落及高檐蒲桃（Syzygium oblatum，SO）群落]为研究对象，揭示土壤nirS型反硝化微生物群落组成及多样性的干湿季变化，分析热带森林恢复过程中土壤理化环境变化对nirS型反硝化细菌群落的影响。结果表明，变形菌门（Proteobacteria）和酸杆菌门（Acidobacteria）相对丰度表现为恢复前期高于恢复后期，而脱氯单胞菌属（Dechloromonas）、嗜盐单胞菌属（Halomonas）和罗思河小杆菌属（Rhodanobacter）表现为恢复后期高于恢复前期；绿弯菌门（Chloroflexi）和放线菌门（Actinobacteria）均随恢复年限增加而增加，而贪铜菌属（Cupriavidus）和假单胞菌属（Pseudomonas）的相对丰度表现为随恢复年限增加而降低。9月份各样地新检测出的属数量表现为：SO （19种） > MP （13种） > ML （7种）。土壤nirS型反硝化微生物群落的Shannon多样性指数表现为：高檐蒲桃群落 > 崖豆藤群落 > 白背桐群落，且9月（湿季） > 3月（干季）。相关分析表明，热带森林恢复引起土壤N库（全氮、NH₄⁺、NO₃^-）、C有效性（微生物量碳、易氧化碳）及微气候（土壤含水率与温度）的改变，能够显著影响nirS型反硝化细菌群落的结构及多样性。主成分分析结果表明，土壤硝态氮、微生物量碳、全氮及易氧化碳是调控不同恢复阶段热带森林土壤nirS型反硝化细菌群落结构及多样性变化的主控因子，其次为土壤水分、温度、水解氮、pH、铵态氮、有机碳、容重及C/N。     

Host-Specificity and Dynamics in Bacterial Communities Associated with Bloom-Forming Freshwater Phytoplankton

Many freshwater phytoplankton species have the potential to form transient nuisance blooms that affect water quality and other aquatic biota. Heterotrophic bacteria can influence such blooms via nutrient regeneration but also via antagonism and other biotic interactions. We studied the composition of bacterial communities associated with three bloom-forming freshwater phytoplankton species, the diatom Aulacoseira granulata and the cyanobacteria Microcystis aeruginosa and Cylindrospermopsis raciborskii. Experimental cultures incubated with and without lake bacteria were sampled in three different growth phases and bacterial community composition was assessed by 454-Pyrosequencing of 16S rRNA gene amplicons. Betaproteobacteria were dominant in all cultures inoculated with lake bacteria, but decreased during the experiment. In contrast, Alphaproteobacteria, which made up the second most abundant class of bacteria, increased overall during the course of the experiment. Other bacterial classes responded in contrasting ways to the experimental incubations causing significantly different bacterial communities to develop in response to host phytoplankton species, growth phase and between attached and free-living fractions. Differences in bacterial community composition between cyanobacteria and diatom cultures were greater than between the two cyanobacteria. Despite the significance, major differences between phytoplankton cultures were in the proportion of the OTUs rather than in the absence or presence of specific taxa. Different phytoplankton species favoring different bacterial communities may have important consequences for the fate of organic matter in systems where these bloom forming species occur. The dynamics and development of transient blooms may also be affected as bacterial communities seem to influence phytoplankton species growth in contrasting ways.     

Rhizosphere microbial community and its response to plant species and soil history

The plant rhizosphere is a dynamic environment in which many parameters may influence the population structure, diversity and activity of the microbial community. Two important factors determining the structure of microbial community present in the vicinity of plant roots are plant species and soil type. In the present study we assessed the structure of microbial communities in response to four plant species (i.e. maize (Zea mays L.), oat (Avena sativa L.), barley (Hordeum vulgare L.) and commercial grass mix) planted in soil with different land use history (i.e. arable land under crop rotation, maize monoculture and permanent grassland). Both factors, plant species and land use history, showed clear effects on microbial community and diversity as determined by PCR-DGGE fingerprinting with universal and group-specific bacterial primers. Moreover, we explored the rhizosphere effect of these plant species on the abundance of bacterial antagonists of the potato pathogen Rhizoctonia solani AG3. The data showed that the abundance and taxonomic composition of antagonists differed clearly between the different plants. The highest percentages of antagonists were found in maize and grass rhizosphere. When antagonistic Pseudomonas populations were compared, the highest, abundance and diversity of antagonists were detected in barley and oat rhizospheres, as compared to maize and grass rhizosphere. The results obtained in our study demonstrate clearly that plant species and soil type are two important factors affecting the structure of total bacterial, Pseudomonas and Bacillus community.