Seasonal modulation of bacterioplankton community at a temperate eutrophic shallow lake

At the present time, there is still a lack of information about environmental parameters modulating variations on bacterial diversity in temperate lakes, particularly from Portugal. Fermentelos Lake (Central Portugal) is a shallow water body that sustains an important wetland area. The strong nutrient inputs from agriculture and industrial runoffs have led to its current eutrophic status. The present work aimed to understand which factors modulate the seasonal bacterioplankton diversity at this lake using 16S rRNA PCR-denaturing gradient gel electrophoresis (DGGE) and multivariate analysis. Environmental data demonstrated eutrophic features throughout all samples with nitrate concentrations reaching 12.0 mg N (NO₃ ⁻) l⁻¹ in March 2006, while the highest conductivity (609 μS cm⁻¹), soluble reactive phosphorus (0.37 mg l⁻¹), total suspended solids (87.2 mg l⁻¹) and chlorophyll a (286.6 μg l⁻¹) levels were recorded in August 2007. Over the past two decades there was a general increase in nitrate, pH and conductivity levels at this lake, suggesting the eutrophication process is still in progress. Multivariate analysis showed that summer versus winter DGGE patterns could be established for bacterial assemblages and were mainly defined by water temperature and chlorophyll a. Actinobacteria were dominant throughout the study period although a general preference for higher temperature, pH, total suspended solids, conductivity, soluble reactive phosphorus (SRP) and chlorophyll a levels was observed. The highest concentrations of nitrogen sources were related to Bacteroidetes and phototrophic eukaryote (cryptophycean) dominance. The expansion of Betaproteobacteria, Alphaproteobacteria and Cyanobacteria phylotypes was generally associated to high temperature, pH, conductivity and SRP values.     

Phylogenetic comparisons of a coastal bacterioplankton community with its counterparts in open ocean and freshwater systems

In order to extend previous comparisons between coastal marine bacterioplankton communities and their open ocean and freshwater counterparts, here we summarize and provide new data on a clone library of 105 SSU rRNA genes recovered from seawater collected over the western continental shelf of the USA in the Pacific Ocean. Comparisons to previously published data revealed that this coastal bacterioplankton clone library was dominated by SSU rRNA gene phylotypes originally described from surface waters of the open ocean, but also revealed unique SSU rRNA gene lineages of beta Proteobacteria related to those found in clone libraries from freshwater habitats. beta Proteobacteria lineages common to coastal and freshwater samples included members of a clade of obligately methylotrophic bacteria, SSU rRNA genes affiliated with Xylophilus ampelinus, and a clade related to the genus Duganella. In addition, SSU rRNA genes were recovered from such previously recognized marine bacterioplankton SSU rRNA gene clone clusters as the SAR86, SAR11, and SAR116 clusters within the class Proteobacteria, the Roseobacter clade of the alpha subclass of the Proteobacteria, the marine group A/SAR406 cluster, and the marine Actinobacteria clade. Overall, these results support and extend previous observations concerning the global distribution of several marine planktonic prokaryote SSU rRNA gene phylotypes, but also show that coastal bacterioplankton communities contain SSU rRNA gene lineages (and presumably bacterioplankton) shown previously to be prevalent in freshwater habitats.     

Respiration in eutrophic lakes: the contribution of bacterioplankton and bacterial growth yield

The contribution of bacterioplankton to total plankton respirationwas measured in two eutrophic Danish lakes and in experimentalenclosures treated with planktivorous fish and nutrients. Bacterialrespiration was calculated from measured oxygen uptake ratesin particles passing a 1.0-µm pore size filter, the rateswere then corrected for the size distribution of glucose uptake.During summer the respiration of the planktonic bacteria contributed{small tilde}50% of the community respiration in the two lakes.Prolific phytoplankton growth induced by biomanipulation andnutrient addition created situations where the contributionof the bacteria decreased to 20%. High bacterial contributionsto community respiration were found when the phytoplankton biomassdecreased. Simultaneous measurements of bacterial respirationand production (by means of [³H]thymidine incorporation) allowedan estimation of bacterial growth yield, which ranged from 9to 66%. In the two lakes the growth yield was constant witha mean of 29 ± 5% (±SD, RQ = 1). The variabilityof the growth yield was larger in the enclosures. The wide range(9–66%) was mainly caused by changes in bacterial netproduction without concomitant changes in respiration. The discussionincludes an evaluation of the oxygen uptake method in size fractionatedsamples and the availability of labile organic substrates asa factor controlling bacterial growth yield. Present address: Institute of Biology and Chemistry, Universityof Roskilde, P. Box 260, DK-4000 Roskilde, Denmark     

Activity profiles of bacterioplankton in a eutrophic river

1. The significance of microbial diversity in processing dissolved organic matter (DOM) is largely unknown. We investigated the range of functional diversity in the bacterioplankton from a eutrophic river by profiling extracellular enzyme activities (EEA) and substrate-induced respiration (SIR) patterns.
2. The EEA profiles consisted of assays for 21 hydrolases, measured using fluorogenic substrates arrayed on 96-well microplates. Commercially available BiOLOG^® GN and ECO plates, which contained 120 different substrates, were used for the SIR profiles.
3. The EEA data were more dynamic than the SIR. Five enzymes, leucine aminopeptidase, alkaline phosphatase, alanine aminopeptidase, arginine aminopeptidase and β-glucosidase, showed consistently high activity; ten others were ubiquitous at lower activity levels; the remainder were detected intermittently. The SIR data showed less temporal variability. With one exception (citrate), the 20 substrates that generated the largest responses were all saccharides or their derivatives.
4. The EEA and SIR data did not generally correlate. Both methods were effective for ordinating bacterioplankton although, unlike the SIR, the EEA ordination followed a clear temporal trajectory.
5. Because the SIR profiles are based on a culture response, whilst the EEA profiles measure activity of the extant community, the latter appear to be more directly linked to the mechanics of DOM processing.     

乌梁素海浮游细菌群落结构及其对富营养化因子的响应

【目的】揭示乌梁素海浮游细菌的群落结构及其对富营养化环境因子的响应,认识乌梁素海浮游细菌多样性,以丰富微生物与富营养化关系的理论。【方法】提取水体浮游细菌总DNA,利用细菌通用引物对63F/1387R进行PCR扩增,构建小口、沙尖北和红圪卜3个湖区16S rRNA基因克隆文库;以典型对应分析(CCA)方法解析浮游细菌群落结构对环境因子的响应。【结果】各湖区中富营养化程度最重的红圪卜位点细菌多样性、丰富度及均匀度最高,而富营养化程度最轻的小口位点细菌多样性、丰富度及均匀度最低。Proteobacteria、Bacteroidetes和Actinobacteria为水体中优势类群。α-、γ-、δ-Proteobacteria,Actinobacteria及Bacteroidetes等菌群丰度随着水体的富营养化程度改变而有显著的变化。各湖区皆存在许多可能具有污染物降解及驱动生源要素循环能力的细菌类群。CCA分析表明TN、NH4+、NO3-和COD等水体指标对浮游细菌群落结构组成的影响较大。此外,乌梁素海水体内未知细菌类群很多;且不同于一般淡水生态系统,乌梁素海中存在9.6%的轻度嗜盐碱性细菌。【结论】乌梁素海水体中浮游细菌多样性较高,细菌群落结构复杂、其类群组成与富营养化因子紧密相关。     

Resilience of a zooplankton community subjected to marine intrusion in a tropical coastal lagoon

One of the main disturbances on Imboassica Lagoon is the occasional artificial opening of its sand bar. Following two such events, two environmental gradients were observed. One was directly related to entry of marine water (salinity gradient); and the other to a decrease in dilution of the nutrient load, because of water level reduction (trophic status gradient). Two stations were sampled. At Station 1, located near the sand bar, salinity increase caused a decrease in the total zooplankton density and a shift in community composition due to a loss of relatively small individuals (i.e. rotifers) and the subsequent entrance of larger ones (i.e. copepods). High diversity was related to salinity increases. At Station 2, located near the mouth of a sewage canal, the total zooplankton abundance and dominance were related to the salinity increase, while the highest richness and the lowest dominance were obtained at a high trophic state. The zooplankton community showed high persistence and resilience, which together with other ecological features in the system, returned to the pre-disturbance state 2 months after the sand bar was closed. Canonical correspondence analysis was a useful tool to assess system resilience.     

Seasonal dynamics of bacterioplankton community structure in a eutrophic lake as determined by 5S rRNA analysis.

Community structure of bacterioplankton was studied during the major growth season for phytoplankton (April to October) in the epilimnion of a temperate eutrophic lake (Lake Plusssee, northern Germany) by using comparative 5S rRNA analysis. Estimates of the relative abundances of single taxonomic groups were made on the basis of the amounts of single 5S rRNA bands obtained after high-resolution electrophoresis of RNA directly from the bacterioplankton. Full-sequence analysis of single environmental 5S rRNAs enabled the identification of single taxonomic groups of bacteria. Comparison of partial 5S rRNA sequences allowed the detection of changes of single taxa over time. Overall, the whole bacterioplankton community showed two to eight abundant (>4% of the total 5S rRNA) taxa. A distinctive seasonal succession was observed in the taxonomic structure of this pelagic community. A rather-stable community structure, with seven to eight different taxonomic units, was observed beginning in April during the spring phytoplankton bloom. A strong reduction in this diversity occurred at the beginning of the clear-water phase (early May), when only two to four abundant taxa were observed, with one taxon dominating (up to 72% of the total 5S rRNA). The community structure during summer stagnation (June and July) was characterized by frequent changes of different dominating taxa. During late summer, a dinoflagellate bloom (Ceratium hirudinella) occurred, with Comamonas acidovorans (beta-subclass of the class Proteobacteria) becoming the dominant bacterial species (average abundance of 43% of the total 5S rRNA). Finally, the seasonal dynamics of the community structure of bacterioplankton were compared with the abundances of other major groups of the aquatic food web, such as phyto- and zooplankton, revealing that strong grazing pressure by zooplankton can reduce microbial diversity substantially in pelagic environments.     

Seasonal differences in bacterial community composition following nutrient additions in a eutrophic lake

We examined the effects of nutrient amendments on epilimnetic freshwater bacteria during three distinct periods in the eutrophic Lake Mendota's seasonal cycle (spring overturn, summer stratification and autumn overturn). Microcosm treatments enriched solely with phosphorus containing compounds did not result in a large bacterial community composition (BCC) change or community activity response (assessed via alkaline phosphatase activity, APA) relative to the controls during any season. Treatments enriched with carbon‐ and nitrogen‐containing compounds resulted in a dramatic BCC change and a large APA increase in the autumn and spring seasons, but only treatments receiving carbon, nitrogen and phosphorus (CNP) exhibited similar responses in the summer season. Despite the fact that the amendments created similar CNP concentration conditions across seasons, the BCC following amendment greatly varied among seasons. 16S rRNA gene sequence analysis indicated that many common freshwater bacterial lineages from the Alpha‐ and Betaproteobacteria class and Bacteroidetes phylum were favoured following nutrient (CNP) addition, but individual taxa were generally not favoured across all seasons. Targeted quantitative PCR analysis revealed that the abundance of the Actinobacteria acIB1 cluster decreased in all microcosms during all three seasons, while the Flavobacterium aquatile (spring) and ME‐B0 (summer) clusters of Bacteroidetes increased following CNP addition. These results suggest a particular bacterial group is not universally favoured by increased nutrient loads to a lake; therefore, efforts to predict which bacteria are involved in nutrient cycling during these periods must take into account the seasonality of freshwater bacterial communities.     

Uptake of amino acids by uncultivated bacterioplankton of a eutrophic water reservoir

Water bacterioplankton species (clones) feeding on lysine and glycine were revealed in experimental microecosystems using nonsterile cultivation. The structure of the community was analyzed by separation of amplified fragments of the bacterial 16S rRNA gene of by denaturing gradient gel electrophoresis. The dominant species (clones) of the bacterioplankton were identified by molecular cloning and determining the nucleotide sequence of part of the 16S gene of ribosomal RNA. It was found that glycine, one of the prevalent amino acids of a eutrophic reservoir, and lysine, whose content in natural water is lower, are nutrient substrates for various subdominant bacterioplankton species (clones). Thus, free-living bacterial species are highly specialized for the uptake of individual amino acids.     

Concentrations of nitrogen in sandy sediments of a eutrophic estuarine lagoon

Concentrations of sediment organic nitrogen, dissolved inorganic nitrogen (ammonium, nitrite and nitrate), and dissolved organic nitrogen (DON) in sediments were measured at two sites in a eutrophic estuarine lagoon. One is a shallow aerobic site where macrobenthos are abundant and the other is a deep anaerobic site devoid of macrobenthos. Four species of macrobenthos (Bivalvia: Corbicula japonica, Annelida: Notomastus sp., Neanthes japonica and Oligochaeta sp.) were found in 8 sandy sediment cores collected at a shallow site in three succcessive summers. DON (170–1500 μg atom N l-1) was the major constituent of dissolved nitrogen with 10 times greater concentration than ammonium (55–180 μg atom N l-1) and 1000 times greater than nitrate (0.14–5.9 μg atom N l-1) and nitrite (0.21–1.4 μg atom N l-1). The ammonium content in anaerobic muddy sediments at the deep site (210–350 μg atom N l-1) was higher than in aerobic sandy sediments, whereas DON was higher in aerobic sediments than anaerobic sediments (90–240 μg atom N l-1). In aerobic sediments, depth profiles of DIN were nearly constant whereas DON was mostly highest at the surface. On the other hand, the increase of DON and ammonium was observed where macrobenthos was found. The occurrence of macrobenthos and high content of DON and ammonium content in the layers of sediment may suggest the influence of macrobenthos in the partitioning of nitrogen species through their motion and excretion. This revised version was published online in July 2006 with corrections to the Cover Date.     

Structuring of bacterioplankton diversity in a large tropical bay

Structuring of bacterioplanktonic populations and factors that determine the structuring of specific niche partitions have been demonstrated only for a limited number of colder water environments. In order to better understand the physical chemical and biological parameters that may influence bacterioplankton diversity and abundance, we examined their productivity, abundance and diversity in the second largest Brazilian tropical bay (Guanabara Bay, GB), as well as seawater physical chemical and biological parameters of GB. The inner bay location with higher nutrient input favored higher microbial (including vibrio) growth. Metagenomic analysis revealed a predominance of Gammaproteobacteria in this location, while GB locations with lower nutrient concentration favored Alphaproteobacteria and Flavobacteria. According to the subsystems (SEED) functional analysis, GB has a distinctive metabolic signature, comprising a higher number of sequences in the metabolism of phosphorus and aromatic compounds and a lower number of sequences in the photosynthesis subsystem. The apparent phosphorus limitation appears to influence the GB metagenomic signature of the three locations. Phosphorus is also one of the main factors determining changes in the abundance of planktonic vibrios, suggesting that nutrient limitation can be observed at community (metagenomic) and population levels (total prokaryote and vibrio counts).     

大水面放养水葫芦对富营养化湖泊水体可培养细菌群落结构的影响

【目的】了解大水面放养水葫芦对富营养化湖泊水体可培养细菌群落结构和多样性的影响。【方法】采用稀释平板法,分别对云南滇池紫根水葫芦放养区(ZW)、野生型普通水葫芦放养区(PW)、未放养水葫芦对照区(CK)水体中细菌进行分离,并对其16S r RNA序列进行分析。【结果】分别从ZW、PW、CK 3种水体分离得到54、49、40株菌落形态差异的细菌,Shannon-Wiener多样性指数分别为3.17、3.07、2.73,细菌数量分别为1.35×107、8.35×106、2.70×106 CFU/L。16S r RNA序列分析表明,ZW、PW、CK 3种水体可培养细菌主要包括变形菌门α亚群(Alphaproteobacteria,35.1%、32.4%和40%)、放线菌门(Actinobacteria,18.9%、32.4%和20%)、变形菌门β亚群(Betaproteobacteria,13.5%、5.9%和16.0%)、变形菌门γ亚群(Gammaproteobacteria,13.5%、14.6%和12.0%)、拟杆菌门(Bacteroidetes,13.5%、8.8%和8.0%)和厚壁菌门(Firmicutes,2.7%、5.9%和4.0%)。在属的水平上,3种水体仅有鞘氨醇盒菌属(Sphingopyxis)、红细菌属(Rhodobacter)、黄色杆菌属(Xanthobacter)、新鞘脂菌属(Novosphingobium)、鞘氨醇单胞菌属(Sphingomonas)、假单胞菌属(Pseudomonas)、微杆菌属(Microbacterium)、链霉菌属(Steptomyces)、黄杆菌属(Flavobacterium)、芽孢杆菌属(Bacillus)等10个属的细菌为共有菌属。【结论】大水面放养水葫芦提高了富营养化湖泊水体中可培养细菌的多样性,改变了细菌的群落结构。     

Evaluation of a eutrophic coastal lagoon ecosystem from the study of bottom sediments

Morphological reconstruction and biogeochemical characterisation of the lagoon of Comacchio (Italy) were carried out in order to provide recommendations for the recovery, conservation and sustainable management of the Fattibello-Spavola coastal lagoon ecosystem. Samples were taken in two seasons: July 1997 and November 1998. The irregular morphology of the Fattibello lagoon affects depositional processes and seawater exchange (tidal currents). Several depressions retain part of the dense water of the saline wedge; these stagnant waters became sinks for fine terrigenous and organic matter. The basin is already extensively supplied with N and P compounds from land. The inflow is demonstrated by the large quantity of organic C, N and organic and inorganic P compounds in the superficial sediment. The ratios between the various forms of macronutrients indicate that the organic matter is primarily of autochthonous origin, with relatively low C/N ratios (8.4±0.6 and 8.1±0.6 in July and November, respectively). Shallow areas were almost always oxygenated by tidal currents and thus rich in organisms, with a predominance of molluscs and Ficopomatus enigmaticus. However, the trophic equilibrium of the ecosystem was affected by the accumulation of organic matter in the depressions, favoured by the increased hydrodynamics during the autumn. These accumulations generate high oxygen consumption and release considerable quantities of nutrients into the water column, with the risk of serious dystrophy throughout the basin during the summer. Local dredging and an improvement of the circulation have been suggested and carried out to contain these processes. Reclamation measures in the longer term were proposed.     

Characterisation of the culturable heterotrophic bacterial community in a small eutrophic lake (Priest Pot)

The community composition and structure of planktonic heterotrophic bacteria (903 isolates) sampled from a small eutrophic lake in northern England (Priest Pot) was studied with respect to season (four samples) and depth (to 3.1 m). Bacteria (887) were isolated on tryptic soy broth agar and identified to 48 genera using fatty acid methyl ester analysis. The two most abundant genera isolated were Aeromonas and Pseudomonas which, respectively, dominated the middle to bottom depths in August and all depths in February. The structure of the sampled community was described using: species richness, Simpson's index and the Shannon-Wiener index. All three indices detected a number of significant differences with depth demonstrating stratification. The greatest stratification of the bacterial community was observed in August when bacterial counts correlated strongly and negatively with diversity. Using structural measures was found to be preferable to the use of species frequencies in the analysis of perturbation and succession in community structure. Insensitivity to one or more of eight antibiotics was observed in 71% (61/86) of the isolates tested particularly in Gram-negative genera. Bacteriocinogeny and lysogeny was observed in 36% (32/90) of isolates. Using sensitive indicator strains, two of 10 producing strains produced virus, while the others produced bacteriocins.     

Changes in bacterioplankton community structure and activity with depth in a eutrophic lake as revealed by 5S rRNA analysis

The community structure of bacterioplankton was studied at different depths (0 to 25 m) of a temperate eutrophic lake (Lake Plusssee in northern Germany) by using comparative 5S rRNA analysis. The relative amounts of taxonomic groups were estimated from 5S rRNA bands separated by high-resolution electrophoresis. Comparison of partial 5S rRNA sequences enabled detection of changes in single taxa over space and during seasons. Overall, the bacterioplankton community was dominated by 3 to 14 abundant (>4% of the total 5S rRNA) taxa. In general, the number of 5S rRNA bands (i.e., the number of bacterial taxa) decreased with depth. In the fall, when thermal stratification and chemical stratification were much more pronounced than they were in the spring, the correlation between the depth layers and the community structure was more pronounced. Therefore, in the fall each layer had its own community structure; i.e., there were different community structures in the epilimnion, the metalimnion, and the hypolimnion. Only three 5S rRNA bands were detected in the hypolimnion during the fall, and one band accounted for about 70% of the total 5S rRNA. The sequences of individual 5S rRNA bands from the spring and fall were different for all size classes analyzed except two bands, one of which was identified as Comamonas acidivorans. In the overall analysis of the depth profiles, the diversity in the epilimnion contrasted with the reduced diversity of the bacterioplankton communities in the hypolimnion, and large differences occurred in the composition of the epilimnion at different seasons except for generalists like C. acidivorans.     

Influence of suspended particulate matter on nutrient biogeochemistry of a tropical shallow lagoon,Chilika, India

The behaviour of suspended particulate matter (SPM), salinity profile, dissolved nutrients, total (T.Chl-a) and size fractionated chlorophyll-a (F.Chl-a) were studied seasonally at Chilika Lagoon, east coast of India, during 2008–2009. The study showed large spatio-temporal variations among these parameters. The concentration of dissolved inorganic nitrogen and inorganic phosphate were found to be maximum during the monsoon, followed by post- and pre-monsoon, although the mean N:P ratios, which indicate the relative availability of N with respect to P, were 9.13 ± 3.09, 16.57 ± 11.53 and 5.47 ± 3.13, respectively. It was evident from the results that during pre-monsoon and postmonsoon, the lagoon exhibits nitrogen limitation. Mean T.Chl-a biomass in the lagoon showed distinct seasonality with maximum values during the pre-monsoon (23.12 ± 9.75 mg m^?3) followed by monsoon and post-monsoon. Irrespective of seasons, maximum T.Chl-a was found in the northern part of the lagoon. SPM concentrations during the monsoon were relatively higher in the freshwater dominated zones compared to seawater dominated areas, indicating its riverine sources. The correlation between SPM and various dissolved nutrients (p < 0.05) suggests its influence on the physico-chemical conditions at varying levels. It is summarized that seasonal variation of SPM and nutrients contributed by rivers, wind induced re-suspension events and in situ  regeneration processes play a crucial role in the lagoon biogeochemical cycle.     

The phytoplankton community of a eutrophic reservoir

The dynamics of the phytoplankton community of a eutrophic reservoir are described for a two year period. Fifty-eight species were recorded, 25 of them common. Bacillariophyta dominated during the winter and early spring and Chlorophyta during late spring, to be replaced by a bloom of Cyanophyta. The mean and peak biomass of phytoplankton was 8.6 mg 1^–1 and 40.8 mg 1^–1 in 1981, and 8.3 mg 1^–1 and 37.6 mg 1^–1 in 1982. Temperature accounted for 67.3% and pH for 8% of the variation in total phytoplankton biomass over the two year period, using a multiple regression technique.Both horizontal and vertical patchiness, measured as an index of mean crowding, were recorded in the reservoir. Horizontal aggregations were associated with spring blooms of Chlorophyta and summer blooms of Cyanophyta, while vertical aggregations were most marked during the summer bloom of Cyanophyta. Concentrations of phytoplankton were influenced by wind, the prevailing southwesterly wind accumulating algae in the northeasterly arm of the reservoir during much of the year.     

Influence of macrophyte decomposition on growth rate and community structure of okefenokee swamp bacterioplankton

Dissolved substances released during decomposition of the white water lily (Nymphaea odorata) can alter the growth rate of Okefenokee Swamp bacterioplankton. In microcosm experiments dissolved compounds released from senescent Nymphaea leaves caused a transient reduction in the abundance and activity of water column bacterioplankton, followed by a period of intense bacterial growth. Rates of [H]thymidine incorporation and turnover of dissolved d-glucose were depressed by over 85%, 3 h after the addition of Nymphaea leachates to microcosms containing Okefenokee Swamp water. Bacterial activity subsequently recovered; after 20 h [H]thymidine incorporation in leachate-treated microcosms was 10-fold greater than that in control microcosms. The recovery of activity was due to a shift in the composition of the bacterial population toward resistance to the inhibitory compounds present in Nymphaea leachates. Inhibitory compounds released during the decomposition of aquatic macrophytes thus act as selective agents which alter the community structure of the bacterial population with respect to leachate resistance. Soluble compounds derived from macrophyte decomposition influence the rate of bacterial secondary production and the availability of microbial biomass to microconsumers.