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Background: Picophytoplankton are abundant and can contribute greatly to primary production in eutrophic lakes. Mychonastes species are among the common eukaryotic picophytoplankton in eutrophic lakes. We used third-generation sequencing technology to sequence the whole genome of Mychonastes homosphaera isolated from Lake Chaohu, a eutrophic freshwater lake in China., Result: The 24.23 Mbp nuclear genome of M.homosphaera, harboring 6649 protein-coding genes, is more compact than the genomes of the closely related Sphaeropleales species. This genome streamlining may be caused by a reduction in gene family number, intergenic size and introns. The genome sequence of M.homosphaera reveals the strategies adopted by this organism for environmental adaptation in the eutrophic lake. Analysis of cultures and the protein complement highlight the metabolic flexibility of M.homosphaera, the genome of which encodes genes involved in light harvesting, carbohydrate metabolism, and nitrogen and microelement metabolism, many of which form functional gene clusters. Reconstruction of the bioenergetic metabolic pathways of M.homosphaera, such as the lipid, starch and isoprenoid pathways, reveals characteristics that make this species suitable for biofuel production., Conclusion: The analysis of the whole genome of M. homosphaera provides insights into the genome streamlining, the high lipid yield, the environmental adaptation and phytoplankton evolution.

Thermal effluents from nuclear power plants greatly change the environmental and ecological conditions of the receiving marine water body, but knowledge about their impact on microbial ecology is limited. Here we used high-throughput sequencing of the 16S rRNA gene to examine marine bacterioplankton metacommunity assembly across thermal gradients in two representative seasons (i.e., winter and summer) in a subtropical bay located on the northern coast of the South China Sea. We found high heterogeneity in bacterioplankton community compositions (BCCs) across thermal gradients and between seasons. The spatially structured temperature gradient created by thermal effluents was the key determinant of BCCs, but its influence differed by season. Using a metacommunity approach, we found that in the thermal discharge area, i.e., where water is frequently exchanged with surrounding seawater and thermal effluent water, the BCC spatial patterns were shaped by species sorting rather than by mass effects from surrounding seawater or by dilution of thermal effluent water by surrounding seawater. However, this effect of species sorting was weaker in summer than in winter seawater. In both seasons, the bacterioplankton community structure was predominately determined by niche sharing; however, the relative importance of niche segregation was enhanced in summer seawater. Our findings suggest that for the seasonal differences in metacommunity processes, the BCCs of subtropical summer seawater were more sensitive to temperature and were more difficult to predict than those of winter seawater in the face of different intensities of thermal impacts. IMPORTANCE Understanding the mechanisms of bacterial community assembly across environmental gradients is one of the major goals of marine microbial ecology. Thermal effluents from two nuclear power plants have been present in the subtropical Daya Bay for more than 20 years and have generated a comparatively stable and long thermal gradient (a temperature increase from 0 to 10°C). The environmental patches across thermal gradients are heterogeneous and very strongly interconnected on a microbial scale; thus, this is a useful model for the study of the metacommunity processes (i.e., patch dynamics, species sorting, mass effects, and neutral processes) that underlie marine bacterioplankton assembly. The significance of our research is to reveal how environmental conditions and dispersal-related processes interact to influence bacterioplankton metacommunity processes and their seasonal differences across thermal gradients. Our results may advance the understanding of marine microbial ecology under future conditions of global warming., (Copyright © 2019 American Society for Microbiology.)

Association network approaches have recently been proposed as a means for exploring the associations between bacterial communities. In the present study, high-throughput sequencing was employed to investigate the seasonal variations in the composition of bacterioplankton communities in six eutrophic urban lakes of Nanjing City, China. Over 150,000 16S rRNA sequences were derived from 52 water samples, and correlation-based network analyses were conducted. Our results demonstrated that the architecture of the co-occurrence networks varied in different seasons. Cyanobacteria played various roles in the ecological networks during different seasons. Co-occurrence patterns revealed that members of Cyanobacteria shared a very similar niche and they had weak positive correlations with other phyla in summer. To explore the effect of environmental factors on species-species co-occurrence networks and to determine the most influential environmental factors, the original positive network was simplified by module partitioning and by calculating module eigengenes. Module eigengene analysis indicated that temperature only affected some Cyanobacteria; the rest were mainly affected by nitrogen associated factors throughout the year. Cyanobacteria were dominant in summer which may result from strong co-occurrence patterns and suitable living conditions. Overall, this study has improved our understanding of the roles of Cyanobacteria and other bacterioplankton in ecological networks., (Copyright © 2016 Elsevier B.V. All rights reserved.)

Epibiotic bacteria on surfaces of submerged macrophytes play important roles in the ecological processes of shallow lakes. However, their community ecology and dynamics are far from understood in comparison with those of bacterioplankton. Here, we conducted a comparative study of the species diversity and composition of epibiotic bacterial and the surrounding bacterioplankton communities of a common submerged macrophyte, Potamogeton crispus, in 12 lakes at a regional scale in China. We found that in different freshwater lakes, epibiotic bacteria possessed higher taxonomic richness than bacterioplankton did. There existed a marked divergence in the community structure between epibiotic bacteria and bacterioplankton. Alphaproteobacteria was the most dominant group for epibiotic bacteria, whereas Actinobacteria dominated bacterioplankton. Although variations in both bacterioplankton and epibiotic bacterial community compositions in different lakes were better explained by environmental than spatial factors, both environment and space had more intensified effects on epibiotic bacteria. This implied more complex and diverse 'microhabitats' for epibiotic bacteria on surfaces of submerged macrophytes, which may lead to higher variations of epibiotic bacteria than bacterioplankton. Our study suggested that epibiotic bacteria exhibited higher diversity and distinct community composition than the surrounding bacterioplankton. More attention should be focused on the productive and diverse microbial habitats on submerged macrophytes., (© 2014 Federation of European Microbiological Societies. Published by John Wiley & Sons Ltd. All rights reserved.)

Lake eutrophication associated with algal bloom has become a major environmental challenge in China. Filter feeding organisms, e.g., silver carp, bighead carp, and zebra mussel, have been widely used to manipulate water environment through their top-down effects. The bivalve Anodonta woodiana is widely distributed across China, and has been used for bio-manipulation of some water bodies. In situ experiments were performed in a bay of Lake Dianchi and its surrounding ponds to study the filtering capacity and the filter feeding rate of Anodonta woodiana in these aguatic habitats, and to determine the controlling factors. The results showed that there was a relationship between filtration rate and total suspended substances measured in laboratory during August and September 2001 when the water temperature was 20 +/- 2 degrees C, which was expressed as y = 4 380.41 e(- 0.0184x) (R2 = 0.621, P < 0.05) based on at least squares analyses. The filtration rate was strongly related to the body weight by measuring in laboratory over 24 hours during August 2001 when the water temperature was 20 +/- 2 C. At least squares analyses gave the equation y = 2 904.16 + 12 076.24e(-0.0034x) (R2 = 0.9825, P = < 0.05). A slight variation of filtration rate was found over 24 hours, which could be explained by the bivalves' adaptation to the experimental circumstances rather than the daily change of its filtration feeding. In general, the filtration capacity of natural Anodonta woodiana population in the water bodies was very limited, as a result of its small population size. No significant selective feeding on algae was found by contrasting the relative abundance of algae in the habitats and the guts of Anodonta woodiana. The feeding selectivity on algae was neither correlated with the size of algae, nor with the initial abundance of algae in water column.

Microcystis blooms have a marked effect on microbial taxonomical diversity in eutrophic lakes, but their influence on the composition of microbial functional genes is still unclear. In this study, the free-living microbial functional genes (FMFG) composition was investigated in the period before Microcystis blooms (March) and during Microcystis blooms (July) using a comprehensive functional gene array (GeoChip 5.0). The composition and richness of FMFG in the water column was significantly different between these two periods. The FMFG in March was enriched in the functional categories of nitrogen, sulfur, and phosphorus cycling, whereas the FMFG in July was enriched in carbon cycling, organic remediation, and metal homeostasis. Molecular ecological network analysis further demonstrated fewer functional gene interactions and reduced complexity in July than in March. Module hubs of the March network were mediated by functional genes associated with carbon, nitrogen, sulfur, and phosphorus, whereas those in July by a metal homeostasis functional gene. We also observed stronger deterministic processes in the FMFG assembly in July than in March. Collectively, this study demonstrated that Microcystis blooms induced significant changes in FMFG composition and metabolic potential, and abundance—information, which can support the understanding and management of biogeochemical cycling in eutrophic lake ecosystems. [ABSTRACT FROM AUTHOR]

Simple Summary: The effects of the presence of predators (fish and shrimp) on the assemblage composition and diversity of phytoplankton were accurately characterized using outdoor mesocosms containing natural phytoplankton and zooplankton communities coupled with high-throughput sequencing. The results showed that the alpha diversity of phytoplankton and the relative abundance of Chlorophyceae increased with the addition of the fish Pelteobagrus fulvidraco, while the former decreased and the latter increased with the addition of the shrimp Exopalaemon modestus. The alpha diversity of phytoplankton and the relative abundance of Chlorophycea increased with the addition of fish and shrimp together, but these changes were less than the sum of the individual impacts of these two predators. Intraguild predation (IGP) can have a significant impact on phytoplankton biomass, but its effects on their diversity and assemblage composition are not well understood. In this study, we constructed an IGP model based on the common three-trophic food chain of "fish (or shrimp)–large branchiopods (Daphnia)–phytoplankton", and investigated the effects of IGP on phytoplankton assemblage composition and diversity in outdoor mesocosms using environmental DNA high-throughput sequencing. Our results indicated that the alpha diversities (number of amplicon sequence variants and Faith's phylogenetic diversity) of phytoplankton and the relative abundance of Chlorophyceae increased with the addition of Pelteobagrus fulvidraco, while similar trends were found in alpha diversities but with a decrease in the relative abundance of Chlorophyceae in the Exopalaemon modestus treatment. When both predators were added to the community, the strength of collective cascading effects on phytoplankton alpha diversities and assemblage composition were weaker than the sum of the individual predator effects. Network analysis further showed that this IGP effect also decreased the strength of collective cascading effects in reducing the complexity and stability of the phytoplankton assemblages. These findings contribute to a better understanding of the mechanisms underlying the impacts of IGP on lake biodiversity, and provide further knowledge relevant to lake management and conservation. [ABSTRACT FROM AUTHOR]

Aquaculture has significant impacts on freshwater lakes, but plankton communities, as key components of the microbial food web, are rarely considered when assessing the impacts of aquaculture. Revealing the dynamics of plankton communities, including bacterioplankton, phytoplankton and zooplankton, under anthropological disturbances is critical for predicting the freshwater ecosystem functioning in response to future environmental changes. In the present study, we examined the impacts of aquaculture on water quality, plankton diversity and the co-occurrence patterns within plankton metacommunities in a shallow freshwater lake. The study zones are influenced by the 20-year historical intensive aquaculture, but now they are undergoing either ecological aquaculture or ecological restoration. Our results showed that ecological aquaculture was more efficient in nitrogen removal than ecological restoration. Moreover, lower bacterioplankton diversity but higher phytoplankton and zooplankton diversity were found in the ecological aquaculture and ecological restoration zones compared to the control zone. The lower network connectivity of the plankton metacommunities in the ecological aquaculture and ecological restoration zones indicated the decreasing complexity of potential microbial food web, suggesting a possible lower resistance of the plankton metacommunities to future disturbance. Furthermore, plankton communities of different trophic levels were driven under distinct mechanisms. The bacterioplankton community was primarily affected by abiotic factors, whereas the phytoplankton and zooplankton communities were explained more by trophic interactions. These results revealed the impacts of aquaculture on the plankton communities and their potential interactions, thereby providing fundamental information for better understanding the impacts of aquaculture on freshwater ecosystem functioning. [Display omitted] • A comprehensive inquiry into plankton communities revealed impacts of aquaculture. • Aquaculture declined bacterial richness, but increased those of phyto-/zooplankton. • Aquaculture lowered the network connectivity of plankton metacommunities. • Trophic interactions enhanced the model explanation for the plankton communities. [ABSTRACT FROM AUTHOR]

A regime shift between a macrophyte-dominated clear state and a phytoplankton-dominated turbid state can have considerable impact on ecosystem structure and function of shallow lakes. However, very little is known about the response of the methanogenic archaeal community in the sediment during this regime shift. We investigated the methanogenic archaeal community at two sites in the large, shallow, eutrophic Taihu Lake over the course of one year. One site is located in Meiliang Bay and is dominated by Microcystis blooms, and the other site is located in East Taihu Bay and is dominated by aquatic macrophytes. Terminal restriction fragment length polymorphism (T-RFLP) and phylogenetic analyses of archaeal 16S rRNA genes were used to analyze the methanogenic community. Higher ratio of methanogens in Archaea was observed in East Taihu Bay than in Meiliang Bay. The methanogenic archaeal community was dominated by the Methanobacteriales and the LDS cluster in macrophytes-dominated East Taihu Bay, while it was dominated by the Methanosarcinaceae, Methanobacteriales, and the LDS cluster in Microcystis-dominated Meiliang Bay. Clustering analysis of all of the samples revealed differences in the composition of the methanogenic archaeal communities between the two sites that were independent of seasonal variations. Further statistical analysis indicated that the chlorophyll a (Chla) concentration had a profound impact on the composition of the methanogenic archaeal community in Meiliang Bay, whereas it was primarily influenced by total organic carbon (TOC) levels in East Taihu Bay. Overall, this investigation demonstrates that intra-habitat differences in the composition of methanogenic archaeal communities are likely driven by changes in the available organic materials. [ABSTRACT FROM PUBLISHER]

Abstract: Metal (Cd, Pb, Cr, Ni, Mn, Cu, and Zn) concentrations in different fish species sampled from two distinct (phytoplankton- and macrophyte-dominated) lake zones of a large, shallow freshwater lake, Taihu Lake, were investigated. Concentrations of most metals in muscle of the small-sized fish (Protosalanx hyalocranius, Pseudorasbora parva, and Rhodeus ocellatus) were always significantly higher than those of the large-sized (Carassius auratus, Cyprinus carpio, and Aristichthys nobilis) and carnivorous fish (Pelteobagrus fulvidraco, Cultrichthys erythropterus, and Erythroculter ilishaeformis). Metal accumulation in the small-sized fish from the phytoplankton-dominated lake zone was always greater than those from the macrophyte-dominated lake zone in summer. However, no significant differences were observed between the two lake zones for most metals in the small-sized fish collected in winter. Metal accumulation in gills, liver, and intestine of the large-sized fish from the phytoplankton-dominated lake zone was generally greater than those from the macrophyte-dominated lake zone in summer. The presence of distinct ecological regions in the lake might affect the metal distribution in the small-sized or large-sized fish. For the carnivorous fish, however, metal concentrations in fish tissues from the two different lake zones were not significantly different, suggesting that metal accumulation in carnivorous fish might be less influenced by the ecological status of the lake. [Copyright &y& Elsevier]

Within-lake horizontal heterogeneity of bacterioplankton community composition (BCC) was investigated in the large and shallow subtropical Taihu Lake (2338 km2, maximum depth < 3 m). Samples were collected at 17 sites along a trophic gradient ranging from mesotrophic to hypertrophic areas in August and September 2004. These sites cover two alternative stable states of shallow lakes, which are basically characterized by the dominance or the lack of submerged macrophytes. In the case of Taihu Lake, the macrophyte-dominated state is characterized by clear water and immobilized sediment, and the state largely lacking macrophytes is characterized by the dominance of phytoplankton, frequent wind-driven re-suspension of sediments, and a high turbidity. Three different methods, i.e. denaturing gradient gel electrophoresis (DGGE), reverse line blot hybridization (RLB) with probes targeting 17 freshwater bacterial groups, and 16S rRNA gene cloning and sequencing, were used for analysis of BCC. The BCC varied strongly between the two alternative ecological states, but less pronounced between phytoplankton-dominated sites even spanning chlorophyll a gradients from 16.5 (mesotrophic) to 229.8 μg l−1 (hypertrophic). The 16S rRNA gene library representing the turbid water state contained many sequences closely related to sequences previously obtained from soil or freshwater sediment samples. Furthermore, sequences representing two new lineages of freshwater Actinobacteria were obtained from the investigated samples. Comparative statistical analyses of BCC along the investigated ecological gradients revealed that the dominance of submersed macrophytes was the most influential factor on BCC, responsible for a major part of the observed within-habitat heterogeneity of BCC in Taihu Lake. [ABSTRACT FROM AUTHOR]

Planktonic microbial community structure and classical food web were investigated in the large shallow eutrophic Lake Taihu (2338 km2, mean depth 1.9 m) located in subtropical Southeast China. The water column of the lake was sampled biweekly at two sites located 22 km apart over a period of twelve month. Site 1 is under the regime of heavy eutrophication while Site 2 is governed by wind-driven sediment resuspension. Within-lake comparison indicates that phosphorus enrichment resulted in increased abundance of microbial components. However, the coupling between total phosphorus and abundance of microbial components was different between the two sites. Much stronger coupling was observed at Site 1 than at Site 2. The weak coupling at Site 2 was mainly caused by strong sediment resuspension, which limited growth of phytoplankton and, consequently, growth of bacterioplankton and other microbial components. High percentages of attached bacteria, which were strongly correlated with the biomass of phytoplankton, especially Microcystis spp., were found at Site 1 during summer and early autumn, but no such correlation was observed at Site 2. This potentially leads to differences in carbon flow through microbial food web at different locations. Overall, significant heterogeneity of microbial food web structure between the two sites was observed. Site-specific differences in nutrient enrichment (i.e. nitrogen and phosphorus) and sediment resuspension were identified as driving forces of the observed intra-habitat differences in food web structure. [ABSTRACT FROM AUTHOR]

One of the key questions in microbial ecology is if seasonal patterns of bacterial community composition (BCC) observed in one year repeat in the following years. We have investigated if the recorded annual dynamics of a species-like Polynucleobacter (subcluster PnecB) population allowed the prediction of the population dynamics in another year. The abundance of PnecB bacteria in the pelagic of temperate Lake Mondsee was investigated by fluorescence in situ hybridization (FISH) over three consecutive years. The PnecB bacteria formed a persistent population, and were present in the entire water body of the lake. Two of the three investigated years differed strongly in summer temperatures and precipitation, which resulted in markedly different growth conditions. But despite of these different environmental conditions, the PnecB population demonstrated remarkably similar seasonal dynamics in the three investigated years. Water temperature was the best predictor of the population dynamics during the first half of the annual cycles. Statistical analysis also indicated influences of phytoplankton and metazooplankton successions on the PnecB population dynamics. Furthermore, 65 lakes and ponds were investigated for the presence of PnecB bacteria. They were detected in the majority (78%) of circum-neutral and alkaline freshwater habitats, but not in any investigated acidic or saline habitat. [ABSTRACT FROM AUTHOR]

Heavy metal distribution in aquatic ecosystems can be influenced by a variety of factors. In this study, the spatial distribution and seasonal variation of heavy metals (Cd, Ni, Cu, Zn, Cr, and Pb) in lake water and sediments of different lake zones of a large, shallow, eutrophic freshwater lake, Taihu Lake, were investigated. Metal concentrations in the river water, bloom assemblages, and macrophyte materials were also determined. The results demonstrated that metal distribution in Taihu Lake showed distinct patterns in different seasons. Metal concentrations in rivers around Taihu Lake showed some peaks that may contribute to the elevated metal concentrations in lake water and sediments. However, the metal concentrations in the river water did not fluctuate significantly with months (March, July, and December). The dissolved metal concentrations in the phytoplankton-dominated zone of the lake were significantly higher than those in the macrophyte-dominated lake zone in summer, which could be attributed to the different dominated primary producers in the two lake zones. Statistical analysis results demonstrated that the dissolved metal concentrations were positively correlated with water turbidity for all metals in July. However, the positive correlations disappeared for most metals of March and December samples. The results of this study could provide useful information for further understanding of the transportation and fates of heavy metals in different freshwater lake ecosystems. [ABSTRACT FROM AUTHOR]