Composition of freshwater bacterial communities associated with cyanobacterial blooms in four Swedish lakes

Vertical and horizontal assemblage patterns of bacterial communities in a eutrophic river receiving domestic wastewater in southeast China

Bacterial communities in rivers receiving untreated domestic wastewater may show specific spatial assemblage patterns due to a wide range of physicochemical conditions created by periodic algal bloom. However, there are significant gaps in understanding environmental forces that drive changes in microbial assemblages in polluted rivers. In this study, we applied high-throughput sequencing of 16S rRNA gene amplicons to perform comprehensive spatio-temporal profiling of bacterial community structure in a local river segment receiving domestic wastewater discharge in southeast China. Multivariate statistics were then used to analyse links between bacterial community structure and environmental factors. Non-metric multidimensional scaling (NMDS) plots showed that the bacterial community structure was different between upstream and downstream sections of the river. While the upstream water contained a high proportion of bacteria degrading xenobiotic aromatic compounds, the downstream water experiencing stronger algal bloom had a more diverse bacterial community which included the genus Aeromonas comprising 14 species, most of which are human pathogens. Least discriminant analysis (LDA) effect size revealed that the surface water was mainly inhabited by aerobic microorganisms capable of degrading aromatic compounds, and also contained bacterial genera including pathogenic species. In contrast, in the bottom water we found, along with aromatic compound-degrading species, anaerobic denitrifiers and Fe³⁺-reducing and fermentative bacteria. Variance partitioning canonical correspondence analysis (VPA) showed that nutrient ratios had a stronger contribution to bacterial dissimilarities than other major physicochemical factors (temperature, pH, dissolved oxygen, total organic carbon, and chlorophyll a). These results show that microbial communities in rivers continuously receiving domestic wastewater have specific longitudinal and vertical assemblage patterns and may contain pathogenic species presenting a high threat to public health. These factors should be taken into consideration while developing pollution management strategies.

Ubiquity and quantitative significance of bacterioplankton lineages inhabiting the oxygenated hypolimnion of deep freshwater lakes

The oxygenated hypolimnion accounts for a volumetrically significant part of the global freshwater systems. Previous studies have proposed the presence of hypolimnion-specific bacterioplankton lineages that are distinct from those inhabiting the epilimnion. To date, however, no consensus exists regarding their ubiquity and abundance, which is necessary to evaluate their ecological importance. The present study investigated the bacterioplankton community in the oxygenated hypolimnia of 10 deep freshwater lakes. Despite the broad geochemical characteristics of the lakes, 16S rRNA gene sequencing demonstrated that the communities in the oxygenated hypolimnia were distinct from those in the epilimnia and identified several predominant lineages inhabiting multiple lakes. Catalyzed reporter deposition fluorescence in situ hybridization revealed that abundant hypolimnion-specific lineages, CL500-11 (Chloroflexi), CL500-3, CL500-37, CL500-15 (Planctomycetes) and Marine Group I (Thaumarchaeota), together accounted for 1.5-32.9% of all bacterioplankton in the hypolimnion of the lakes. Furthermore, an analysis of single-nucleotide variation in the partial 16S rRNA gene sequence (oligotyping) suggested the presence of different sub-populations between lakes and water layers among the lineages occurring in the entire water layer (for example, acI-B1 and acI-A7). Collectively, these results provide the first comprehensive overview of the bacterioplankton community in the oxygenated hypolimnion of deep freshwater lakes.

Temporal patterns of phyto- and bacterioplankton and their relationships with environmental factors in Lake Taihu, China

Phytoplankton and bacterioplankton are integral components of aquatic food webs and play essential roles in the structure and function of freshwater ecosystems. However, little is known about how phyto- and bacterioplankton may respond synchronously to changing environmental conditions. Thus, we analyzed simultaneously the composition and structure of phyto- and bacterioplankton on a monthly basis over 12 months in cyanobacteria-dominated areas of Lake Taihu and compared their responses to changes in environmental factors. Metric multi-dimensional scaling (mMDS) revealed that the temporal variations of phyto- and bacterioplankton were significant. Time lag analysis (TLA) indicated that the temporal pattern of phytoplankton tended to exhibit convergent dynamics while bacterioplankton showed highly stable or stochastic variation. A significant directional change was found for bacterioplankton at the genus level and the slopes (rate of change) and regression R² (low stochasticity or stability) were greater if Cyanobacteria were included, suggesting a higher level of instability in the bacterial community at lower taxonomy level. Consequently, phytoplankton responded more rapidly to the change in environmental conditions than bacterioplankton when analyzed at the phylum level, while bacterioplankton were more sensitive at the finer taxonomic resolution in Lake Taihu. Redundancy analysis (RDA) results showed that environmental variables collectively explained 51.0% variance of phytoplankton and 46.7% variance of bacterioplankton, suggesting that environmental conditions have a significant influence on the temporal variations of phyto- and bacterioplankton. Furthermore, variance partitioning indicated that the bacterial community structure was largely explained by water temperature and nitrogen, suggesting that these factors were the primary drivers shaping bacterioplankton.

Ecophysiology of Freshwater Verrucomicrobia Inferred from Metagenome-Assembled Genomes

Microbes are critical in carbon and nutrient cycling in freshwater ecosystems. Members of the Verrucomicrobia are ubiquitous in such systems, and yet their roles and ecophysiology are not well understood. In this study, we recovered 19 Verrucomicrobia draft genomes by sequencing 184 time-series metagenomes from a eutrophic lake and a humic bog that differ in carbon source and nutrient availabilities. These genomes span four of the seven previously defined Verrucomicrobia subdivisions and greatly expand knowledge of the genomic diversity of freshwater Verrucomicrobia. Genome analysis revealed their potential role as (poly)saccharide degraders in freshwater, uncovered interesting genomic features for this lifestyle, and suggested their adaptation to nutrient availabilities in their environments. Verrucomicrobia populations differ significantly between the two lakes in glycoside hydrolase gene abundance and functional profiles, reflecting the autochthonous and terrestrially derived allochthonous carbon sources of the two ecosystems, respectively. Interestingly, a number of genomes recovered from the bog contained gene clusters that potentially encode a novel porin-multiheme cytochrome c complex and might be involved in extracellular electron transfer in the anoxic humus-rich environment. Notably, most epilimnion genomes have large numbers of so-called "Planctomycete-specific" cytochrome c-encoding genes, which exhibited distribution patterns nearly opposite to those seen with glycoside hydrolase genes, probably associated with the different levels of environmental oxygen availability and carbohydrate complexity between lakes/layers. Overall, the recovered genomes represent a major step toward understanding the role, ecophysiology, and distribution of Verrucomicrobia in freshwater. IMPORTANCE Freshwater Verrucomicrobia spp. are cosmopolitan in lakes and rivers, and yet their roles and ecophysiology are not well understood, as cultured freshwater Verrucomicrobia spp. are restricted to one subdivision of this phylum. Here, we greatly expanded the known genomic diversity of this freshwater lineage by recovering 19 Verrucomicrobia draft genomes from 184 metagenomes collected from a eutrophic lake and a humic bog across multiple years. Most of these genomes represent the first freshwater representatives of several Verrucomicrobia subdivisions. Genomic analysis revealed Verrucomicrobia to be potential (poly)saccharide degraders and suggested their adaptation to carbon sources of different origins in the two contrasting ecosystems. We identified putative extracellular electron transfer genes and so-called "Planctomycete-specific" cytochrome c-encoding genes and identified their distinct distribution patterns between the lakes/layers. Overall, our analysis greatly advances the understanding of the function, ecophysiology, and distribution of freshwater Verrucomicrobia, while highlighting their potential role in freshwater carbon cycling.

Characterising and predicting cyanobacterial blooms in an 8-year amplicon sequencing time course

Cyanobacterial blooms occur in lakes worldwide, producing toxins that pose a serious public health threat. Eutrophication caused by human activities and warmer temperatures both contribute to blooms, but it is still difficult to predict precisely when and where blooms will occur. One reason that prediction is so difficult is that blooms can be caused by different species or genera of cyanobacteria, which may interact with other bacteria and respond to a variety of environmental cues. Here we used a deep 16S amplicon sequencing approach to profile the bacterial community in eutrophic Lake Champlain over time, to characterise the composition and repeatability of cyanobacterial blooms, and to determine the potential for blooms to be predicted based on time course sequence data. Our analysis, based on 135 samples between 2006 and 2013, spans multiple bloom events. We found that bloom events significantly alter the bacterial community without reducing overall diversity, suggesting that a distinct microbial community-including non-cyanobacteria-prospers during the bloom. We also observed that the community changes cyclically over the course of a year, with a repeatable pattern from year to year. This suggests that, in principle, bloom events are predictable. We used probabilistic assemblages of OTUs to characterise the bloom-associated community, and to classify samples into bloom or non-bloom categories, achieving up to 92% classification accuracy (86% after excluding cyanobacterial sequences). Finally, using symbolic regression, we were able to predict the start date of a bloom with 78-92% accuracy (depending on the data used for model training), and found that sequence data was a better predictor than environmental variables.

Virus found in a boreal lake links ssDNA and dsDNA viruses

Viruses have impacted the biosphere in numerous ways since the dawn of life. However, the evolution, genetic, structural, and taxonomic diversity of viruses remain poorly understood, in part because sparse sampling of the virosphere has concentrated mostly on exploring the abundance and diversity of dsDNA viruses. Furthermore, viral genomes are highly diverse, and using only the current sequence-based methods for classifying viruses and studying their phylogeny is complicated. Here we describe a virus, FLiP (Flavobacterium-infecting, lipid-containing phage), with a circular ssDNA genome and an internal lipid membrane enclosed in the icosahedral capsid. The 9,174-nt-long genome showed limited sequence similarity to other known viruses. The genetic data imply that this virus might use replication mechanisms similar to those found in other ssDNA replicons. However, the structure of the viral major capsid protein, elucidated at near-atomic resolution using cryo-electron microscopy, is strikingly similar to that observed in dsDNA viruses of the PRD1-adenovirus lineage, characterized by a major capsid protein bearing two β-barrels. The strong similarity between FLiP and another member of the structural lineage, bacteriophage PM2, extends to the capsid organization (pseudo T = 21 dextro) despite the difference in the genetic material packaged and the lack of significant sequence similarity.

Complete Genome Sequence of an Aquaculture-Associated Phage, FL-1, Infecting Flavobacterium spp

FL-1, a myophage of Flavobacterium, was found to have a 53-kb genome with 87 putative coding sequences.

Emerging microbiota during cold storage and temperature abuse of ready-to-eat salad​

Introduction: Ready-to-eat (RTE) leafy vegetables have a natural leaf microbiota that changes during different processing and handling steps from farm to fork. The objectives of this study were (i) to compare the microbiota of RTE baby spinach and mixed-ingredient salad before and after seven days of storage at 8°C or 15°C; (ii) to explore associations between bacterial communities and the foodborne pathogens Listeria monocytogenes, pathogenic Yersinia enterocolitica, and pathogen model organism Escherichia coli O157:H7 gfp+ when experimentally inoculated into the salads before storage; and (iii) to investigate if bacterial pathogens may be detected in the 16S rRNA amplicon dataset. Material and methods: The microbiota was studied by means of Illumina 16S rRNA amplicon sequencing. Subsets of samples were inoculated with low numbers (50-100 CFU g-1) of E. coli O157:H7 gfp+, pathogenic Y. enterocolitica or L. monocytogenes before storage. Results and discussion: The composition of bacterial communities changed during storage of RTE baby spinach and mixed-ingredient salad, with Pseudomonadales as the most abundant order across all samples. Although pathogens were present at high viable counts in some samples, they were only detected in the community-wide dataset in samples where they represented approximately 10% of total viable counts. Positive correlations were identified between viable counts of inoculated strains and the abundance of Lactobacillales, Enterobacteriales, and Bacillales, pointing to positive interactions or similar environmental driver variables that may make it feasible to use such bacterial lineages as indicators of microbial health hazards in leafy vegetables. The data from this study contribute to a better understanding of the bacteria present in RTE salads and may help when developing new types of biocontrol agents.​.

Variation of microbial communities and functional genes during the biofilm formation in raw water distribution systems and associated effects on the transformation of nitrogen pollutants

This study aimed to investigate the variation of microbial communities and functional genes during the biofilm formation in raw water distribution systems without prechlorination and associated effects on the transformation of nitrogen pollutants by using a designed model pipe system. The results showed the transformation of nitrogen pollutants was obvious during the biofilm formation. The richness and diversity of the microbial communities changed significantly. The higher abundance of Nitrospirae in biofilm samples significantly contributed to biological nitrification. In particular, the stable content of Bacteroidetes in the biofilm and soluble microbial products released by the biomass might have enhanced the increase in dissolved organic nitrogen. In addition, the variation tendency of nitrogen functional gene abundances and their strong effects on NH₄⁺-N, NO₂^--N, and NO₃^--N transformation were clearly observed. These findings provide new insights into the evolution of microbial communities and functional genes during the initial operation period of real-world raw water distribution pipes and highlight management and possible safety issues in the subsequent water treatment process.

Nutrient Stoichiometry Shapes Microbial Community Structure in an Evaporitic Shallow Pond

Nutrient availability and ratios can play an important role in shaping microbial communities of freshwater ecosystems. The Cuatro Ciénegas Basin (CCB) in Mexico is a desert oasis where, perhaps paradoxically, high microbial diversity coincides with extreme oligotrophy. To better understand the effects of nutrients on microbial communities in CCB, a mesocosm experiment was implemented in a stoichiometrically imbalanced pond, Lagunita, which has an average TN:TP ratio of 122 (atomic). The experiment had four treatments, each with five spatial replicates – unamended controls and three fertilization treatments with different nitrogen:phosphorus (N:P) regimes (P only, N:P = 16 and N:P = 75 by atoms). In the water column, quantitative PCR of the 16S rRNA gene indicated that P enrichment alone favored proliferation of bacterial taxa with high rRNA gene copy number, consistent with a previously hypothesized but untested connection between rRNA gene copy number and P requirement. Bacterial and microbial eukaryotic community structure was investigated by pyrosequencing of 16S and 18S rRNA genes from the planktonic and surficial sediment samples. Nutrient enrichment shifted the composition of the planktonic community in a treatment-specific manner and promoted the growth of previously rare bacterial taxa at the expense of the more abundant, potentially endemic, taxa. The eukaryotic community was highly enriched with phototrophic populations in the fertilized treatment. The sediment microbial community exhibited high beta diversity among replicates within treatments, which obscured any changes due to fertilization. Overall, these results showed that nutrient stoichiometry can be an important factor in shaping microbial community structure.

Spatiotemporal analysis of microbial community dynamics during seasonal stratification events in a freshwater lake (Grand Lake, OK, USA)

Many freshwater lakes undergo seasonal stratification, where the formation of phototrophic blooms in the epilimnion and subsequent sedimentation induces hypoxia/anoxia in the thermocline and hypolimnion. This autochthonously produced biomass represents a major seasonal organic input that impacts the entire ecosystem. While the limnological aspects of this process are fairly well documented, relatively little is known regarding the microbial community response to such events, especially in the deeper anoxic layers of the water column. Here, we conducted a spatiotemporal survey of the particle-associated and free-living microbial communities in a warm monomictic freshwater reservoir (Grand Lake O’ the Cherokees) in northeastern Oklahoma, USA. Pre-stratification samples (March) harbored a homogeneous community throughout the oxygenated water column dominated by typical oligotrophic aquatic lineages (acl clade within Actinobacteria, and Flavobacterium within the Bacteroidetes). The onset of phototrophic blooming in June induced the progression of this baseline community into two distinct trajectories. Within the oxic epilimnion, samples were characterized by the propagation of phototrophic (Prochlorococcus), and heterotrophic (Planctomycetes, Verrucomicrobia, and Beta-Proteobacteria) lineages. Within the oxygen-deficient thermocline and hypolimnion, the sedimentation of surface biomass induced the development of a highly diverse community, with the enrichment of Chloroflexi, “Latescibacteria”, Armatimonadetes, and Delta-Proteobacteria in the particle-associated fraction, and Gemmatimonadetes and “Omnitrophica” in the free-living fraction. Our work documents the development of multiple spatially and temporally distinct niches during lake stratification, and supports the enrichment of multiple yet-uncultured and poorly characterized lineages in the lake’s deeper oxygen-deficient layers, an ecologically relevant microbial niche that is often overlooked in lakes diversity surveys.

Competition and niche separation of pelagic bacteria in freshwater habitats

Freshwater bacterioplankton assemblages are composed of sympatric populations that can be delineated, for example, by ribosomal RNA gene relatedness and that differ in key ecophysiological properties. They may be free-living or attached, specialized for particular concentrations or subsets of substrates, or invest a variable amount of their resources in defence traits against protistan predators and viruses. Some may be motile and tactic whereas others are not, with far-reaching implications for their respective life styles and niche partitioning. The co-occurrence of competitors with overlapping growth requirements has profound consequences for the stability of community functions; it can to some extent be explained by habitat factors such as the microscale complexity and spatiotemporal variability of the lacustrine environments. On the other hand, the composition and diversity of freshwater microbial assemblages also reflects non-equilibrium states, dispersal and the stochasticity of community assembly processes. This review synoptically discusses the competition and niche separation of heterotrophic bacterial populations (defined at various levels of phylogenetic resolution) in the pelagic zone of inland surface waters from a variety of angles, focusing on habitat heterogeneity and the resulting biogeographic distribution patterns, the ecophysiological adaptations to the substrate field and the interactions of prokaryotes with predators and viruses.

Analysis of biofilm bacterial communities under different shear stresses using size-fractionated sediment

Microorganisms are ubiquitous in aqueous environments and are crucial for biogeochemical processes, but their community structures and functions remain poorly understood. In this paper, a rotating reactor was designed to study the effects of substrata and flow conditions on sediment bacterial communities using 16S rRNA gene sequencing, assaying three groups of size-fractionated sediments and three different levels of applied shear stress. Proteobacteria, Firmicutes, and Bacteroidetes were the dominant phyla of the microbial communities, with more anaerobic bacteria and opportunistic pathogens being detected under static water conditions, while more aerobic bacteria were detected under dynamic water flow conditions. Most of the top 10 genera were present in all the samples; however, there were significant differences in the species abundance. Paludibacter and Comamonadaceae_unclassified were the most abundant genera under static and dynamic conditions, respectively. Under static water conditions, the medium-grained sediment had the highest microbial diversity, followed by the fine and coarse sediments. Under dynamic water flow conditions, a higher flow velocity corresponded to a greater microbial diversity. Overall, there was no significant difference in the community richness or diversity between the static and dynamic water flow conditions. This study is beneficial for further understanding the heterogeneities of microbial communities in natural aquatic ecosystems.

Variation of bacterial communities in water and sediments during the decomposition of Microcystis biomass

The bacterial community composition in water and sediment samples during the decomposition of Microcystis biomass were analyzed using the 454 pyrosequencing technique. We found dramatic shifts in the bacterial community composition of water and sediments after the addition of Microcystis biomass. Among all the detected phyla, only Firmicutes was found to be dominant in both water and sediment samples. The genus Clostridium sensu stricto was the absolutely dominant group in Firmicutes and showed drastic variations with incubation time during the decomposition process. Peak values in relative abundance of Clostridium sensu stricto appeared in the first few days for water and sediment samples. Environmental factors such as pH, dissolved oxygen (DO), and dissolved organic carbon (DOC) in water samples showed drastic variations during the decomposing process, which might be the prominent forces driving the variation of bacterial communities. The abundant genus, Clostridium sensu stricto, were thought to be well adapted to higher DOC and turbidity and lower pH and DO conditions. Compared with the sediment samples, the decomposition of Microcystis biomass had greater influence on the bacterial community composition in water and Clostridium sensu stricto might play important roles in the process of Microcystis biomass decomposition.

Characterization of N-Acyl Homoserine Lactones in Vibrio tasmaniensis LGP32 by a Biosensor-Based UHPLC-HRMS/MS Method

Since the discovery of quorum sensing (QS) in the 1970s, many studies have demonstrated that Vibrio species coordinate activities such as biofilm formation, virulence, pathogenesis, and bioluminescence, through a large group of molecules called N-acyl homoserine lactones (AHLs). However, despite the extensive knowledge on the involved molecules and the biological processes controlled by QS in a few selected Vibrio strains, less is known about the overall diversity of AHLs produced by a broader range of environmental strains. To investigate the prevalence of QS capability of Vibrio environmental strains we analyzed 87 Vibrio spp. strains from the Banyuls Bacterial Culture Collection (WDCM911) for their ability to produce AHLs. This screening was based on three biosensors, which cover a large spectrum of AHLs, and revealed that only 9% of the screened isolates produced AHLs in the defined experimental conditions. Among these AHL-producing strains, Vibrio tasmaniensis LGP32 is a well-known pathogen of bivalves. We further analyzed the diversity of AHLs produced by this strain using a sensitive bioguided UHPLC-HRMS/MS approach (Ultra-High-Performance Liquid Chromatography followed by High-Resolution tandem Mass Spectrometry) and we identified C10-HSL, OH-C12-HSL, oxo-C12-HSL and C14:1-HSL as QS molecules. This is the first report that documents the production of AHL by Vibrio tasmaniensis LGP32.

Relationship of Microbiota and Cyanobacterial Secondary Metabolites in Planktothricoides-Dominated Bloom

The identification of phytoplankton species and microbial biodiversity is necessary to assess water ecosystem health and the quality of water resources. We investigated the short-term (2 days) vertical and diel variations in bacterial community structure and microbially derived secondary metabolites during a cyanobacterial bloom that emerged in a highly urbanized tropical reservoir. The waterbody was largely dominated by the cyanobacteria Planktothricoides spp., together with the Synechococcus, Pseudanabaena, Prochlorothrix, and Limnothrix. Spatial differences (i.e., water depth) rather than temporal differences (i.e., day versus night) better-explained the short-term variability in water quality parameters and bacterial community composition. Difference in bacterial structure suggested a resource-driven distribution pattern for the community. We found that the freshwater bacterial community associated with cyanobacterial blooms is largely conserved at the phylum level, with Proteobacteria (β-proteobateria), Bacteroidetes, and Actinobacteria as the main taxa despite the cyanobacterial species present and geographical (Asia, Europe, Australia, and North America) or climatic distinctions. Through multivariate statistical analyses of the bacterial community, environmental parameters, and secondary metabolite concentrations, we observed positive relationships between the occurrences of cyanobacterial groups and off-flavor compounds (2-methyisoborneol and β-ionone), suggesting a cyanobacterial origin. This study demonstrates the potential of 16S rRNA gene amplicon sequencing as a supporting tool in algal bloom monitoring or water-resource management.

Diversity and community structure of cyanobacteria and other microbes in recycling irrigation reservoirs

Recycling irrigation reservoirs (RIRs) are emerging aquatic environments of global significance to crop production, water conservation and environmental sustainability. This study characterized the diversity and population structure of cyanobacteria and other detected microbes in water samples from eight RIRs and one adjacent runoff-free stream at three ornamental crop nurseries in eastern (VA1 and VA3) and central (VA2) Virginia after cloning and sequencing the 16S rRNA gene targeting cyanobacteria and chloroplast of eukaryotic phytoplankton. VA1 and VA2 utilize a multi-reservoir recycling irrigation system with runoff channeled to a sedimentation reservoir which then overflows into transition and retention reservoirs where water was pumped for irrigation. VA3 has a single sedimentation reservoir which was also used for irrigation. A total of 208 operational taxonomic units (OTU) were identified from clone libraries of the water samples. Among them, 53 OTUs (358 clones) were cyanobacteria comprising at least 12 genera dominated by Synechococcus species; 59 OTUs (387 clones) were eukaryotic phytoplankton including green algae and diatoms; and 96 were other bacteria (111 clones). Overall, cyanobacteria were dominant in sedimentation reservoirs, while eukaryotic phytoplankton and other bacteria were dominant in transition/retention reservoirs and the stream, respectively. These results are direct evidence demonstrating the negative impact of nutrient-rich horticultural runoff, if not contained, on natural water resources. They also help in understanding the dynamics of water quality in RIRs and have practical implications. Although both single- and multi-reservoir recycling irrigation systems reduce the environmental footprint of horticultural production, the former is expected to have more cyanobacterial blooming, and consequently water quality issues, than the latter. Thus, a multi-reservoir recycling irrigation system should be preferred where feasible.

Characterization of bacterial community associated with phytoplankton bloom in a eutrophic lake in South Norway using 16S rRNA gene amplicon sequence analysis

Interactions between different phytoplankton taxa and heterotrophic bacterial communities within aquatic environments can differentially support growth of various heterotrophic bacterial species. In this study, phytoplankton diversity was studied using traditional microscopic techniques and the bacterial communities associated with phytoplankton bloom were studied using High Throughput Sequencing (HTS) analysis of 16S rRNA gene amplicons from the V1-V3 and V3-V4 hypervariable regions. Samples were collected from Lake Akersvannet, a eutrophic lake in South Norway, during the growth season from June to August 2013. Microscopic examination revealed that the phytoplankton community was mostly represented by Cyanobacteria and the dinoflagellate Ceratium hirundinella. The HTS results revealed that Proteobacteria (Alpha, Beta, and Gamma), Bacteriodetes, Cyanobacteria, Actinobacteria and Verrucomicrobia dominated the bacterial community, with varying relative abundances throughout the sampling season. Species level identification of Cyanobacteria showed a mixed population of Aphanizomenon flos-aquae, Microcystis aeruginosa and Woronichinia naegeliana. A significant proportion of the microbial community was composed of unclassified taxa which might represent locally adapted freshwater bacterial groups. Comparison of cyanobacterial species composition from HTS and microscopy revealed quantitative discrepancies, indicating a need for cross validation of results. To our knowledge, this is the first study that uses HTS methods for studying the bacterial community associated with phytoplankton blooms in a Norwegian lake. The study demonstrates the value of considering results from multiple methods when studying bacterial communities.

Seasonal Variation in Abundance and Diversity of Bacterial Methanotrophs in Five Temperate Lakes

Lakes are significant sources of methane (CH₄) to the atmosphere. Within these systems, methanotrophs consume CH₄ and act as a potential biofilter mitigating the emission of this potent greenhouse gas. However, it is still not well understood how spatial and temporal variation in environmental parameters influence the abundance, diversity, and community structure of methanotrophs in lakes. To address this gap in knowledge, we collected water samples from three depths (surface, middle, and bottom) representing oxic to suboxic or anoxic zones of five different Swedish lakes in winter (ice-covered) and summer. Methanotroph abundance was determined by quantitative real time polymerase chain reaction and a comparison to environmental variables showed that temperature, season as well as depth, phosphate concentration, dissolved oxygen, and CH₄ explained the observed variation in methanotroph abundance. Due to minimal differences in methane concentrations (0.19 and 0.29 μM for summer and winter, respectively), only a weak and even negative correlation was observed between CH₄ and methanotrophs, which was possibly due to usage of CH₄. Methanotrophs were present at concentrations ranging from 10⁵ to 10⁶ copies/l throughout the oxic (surface) and suboxic/anoxic (bottom) water mass of the lakes, but always contributed less than 1.3% to the total microbial community. Relative methanotroph abundance was significantly higher in winter than in summer and consistently increased with depth in the lakes. Phylogenetic analysis of pmoA genes in two clone libraries from two of the ice-covered lakes (Ekoln and Ramsen) separated the methanotrophs into five distinct clusters of Methylobacter sp. (Type I). Terminal restriction fragment length polymorphism analysis of the pmoA gene further revealed significant differences in methanotrophic communities between lakes as well as between winter and summer while there were no significant differences between water layers. The study provides new insights into diversity, abundance, community composition and spatial as well as temporal distribution of freshwater methanotrophs in low-methane dimictic lakes.

A Global eDNA Comparison of Freshwater Bacterioplankton Assemblages Focusing on Large-River Floodplain Lakes of Brazil

With its network of lotic and lentic habitats that shift during changes in seasonal connection, the tropical and subtropical large-river systems represent possibly the most dynamic of all aquatic environments. Pelagic water samples were collected from Brazilian floodplain lakes (total n = 58) in four flood-pulsed systems (Amazon [n = 21], Araguaia [n = 14], Paraná [n = 15], and Pantanal [n = 8]) in 2011-2012 and sequenced via 454 for bacterial environmental DNA using 16S amplicons; additional abiotic field and laboratory measurements were collected for the assayed lakes. We report here a global comparison of the bacterioplankton makeup of freshwater systems, focusing on a comparison of Brazilian lakes with similar freshwater systems across the globe. The results indicate a surprising similarity at higher taxonomic levels of the bacterioplankton in Brazilian freshwater with global sites. However, substantial novel diversity at the family level was also observed for the Brazilian freshwater systems. Brazilian freshwater bacterioplankton richness was relatively average globally. Ordination results indicate that Brazilian bacterioplankton composition is unique from other areas of the globe. Using Brazil-only ordinations, floodplain system differentiation most strongly correlated with dissolved oxygen, pH, and phosphate. Our data on Brazilian freshwater systems in combination with analysis of a collection of freshwater environmental samples from across the globe offers the first regional picture of bacterioplankton diversity in these important freshwater systems.

Microbial Activity Response to Solar Radiation across Contrasting Environmental Conditions in Salar de Huasco, Northern Chilean Altiplano

In high altitude environments, extreme levels of solar radiation and important differences of ionic concentrations over narrow spatial scales may modulate microbial activity. In Salar de Huasco, a high-altitude wetland in the Andean mountains, the high diversity of microbial communities has been characterized and associated with strong environmental variability. Communities that differed in light history and environmental conditions, such as nutrient concentrations and salinity from different spatial locations, were assessed for bacterial secondary production (BSP, ³H-leucine incorporation) response from short-term exposures to solar radiation. We sampled during austral spring seven stations categorized as: (a) source stations, with recently emerged groundwater (no-previous solar exposure); (b) stream running water stations; (c) stations connected to source waters but far downstream from source points; and (d) isolated ponds disconnected from ground sources or streams with a longer isolation and solar exposure history. Very high values of 0.25 μE m^-2 s^-1, 72 W m^-2 and 12 W m^-2 were measured for PAR, UVA, and UVB incident solar radiation, respectively. The environmental factors measured formed two groups of stations reflected by principal component analyses (near to groundwater sources and isolated systems) where isolated ponds had the highest BSP and microbial abundance (35 microalgae taxa, picoeukaryotes, nanoflagellates, and bacteria) plus higher salinities and PO₄^3- concentrations. BSP short-term response (4 h) to solar radiation was measured by ³H-leucine incorporation under four different solar conditions: full sun, no UVB, PAR, and dark. Microbial communities established in waters with the longest surface exposure (e.g., isolated ponds) had the lowest BSP response to solar radiation treatments, and thus were likely best adapted to solar radiation exposure contrary to ground source waters. These results support our light history (solar exposure) hypothesis where the more isolated the community is from ground water sources, the better adapted it is to solar radiation. We suggest that factors other than solar radiation (e.g., salinity, PO₄^3-, NO₃^-) are also important in determining microbial productivity in heterogeneous environments such as the Salar de Huasco.

The Microbiota of Recreational Freshwaters and the Implications for Environmental and Public Health

The microbial communities in recreational freshwaters play important roles in both environmental and public health perspectives. In this study, the bacterial community structure and its associations with freshwater environments were investigated by analyzing the summertime microbiomes of three beach waters in Ohio (East Fork, Delaware, and Madison lakes) together with environmental and microbial water quality parameters. From the swimming season of 2009, 21 water samples were collected from the three freshwater beaches. From the samples, 110,000 quality-checked bacterial 16S rRNA gene sequences were obtained and analyzed, resulting in an observation of 4500 bacterial operational taxonomic units (OTUs). The most abundant bacteria were Mycobacterium and Arthrobacter of the Actinobacteria (33.2%), Exiguobacterium and Paenisporosarcina of the Firmicutes (23.4%), Planktothrix and Synechococcus of the Cyanobacteria (20.8%), and Methylocystis and Polynucleobacter of the Proteobacteria (16.3%). Considerable spatial and temporal variations were observed in the bacterial community of Actinobacteria, Cyanobacteria, and Firmicutes, where the bacterial community structure was greatly influenced by hydrological and weather conditions. The most influential factors were (1) water inflow for Bacteroidia and Clostridia, (2) turbidity for Gammaproteobacteria, (3) precipitation for Bacilli, and (4) temperature and pH for Cyanobacteria. One noticeable microbial interaction in the bacterial community was a significant negative relationship between Cyanobacteria and Bacilli (P < 0.05). Concerning beach water quality, the level of the genetic markers for cyanobacterial toxin (mcyA) was linked to the abundance of Cyanobacteria. In addition, unique distributions of the genera Enterococcus, Staphylococcus, Streptococcus, Bacteroides, Clostridium, Finegoldia, Burkholderia, and Klebsiella, together with a high density of fecal indicator Escherichia coli, were markedly observed in the sample from Madison Lake on July 13, suggesting a distinctly different source of bacterial loading into the lake, possibly fecal contamination. In conclusion, deep sequencing-based microbial community analysis can provide detailed profiles of bacterial communities and information on potential public health risks at freshwater beaches.

Bacterial Communities Associated with Four Cyanobacterial Genera Display Structural and Functional Differences: Evidence from an Experimental Approach

To overcome the limitations associated with studying the interactions between bacterial communities (BCs) and cyanobacteria in natural environments, we compared the structural and functional diversities of the BCs associated with 15 non-axenic cyanobacterial strains in culture and two natural BCs sampled during cyanobacterial blooms. No significant differences in richness and diversity were found between the natural and cultivated BCs, although some of the cyanobacterial strains had been isolated 11 years earlier. Moreover, these BCs shared some similar characteristics, such as a very low abundance of Actinobacteria, but they display significant differences at the operational taxonomic unit (OTU) level. Overall, our findings suggest that BCs associated with cyanobacteria in culture are good models to better understand the interactions between heterotrophic bacteria and cyanobacteria. Additionally, BCs associated with heterocystous cyanobacterial strains cultivated in Z8X culture medium without nitrate (Aphanizomenon–Dolichospermum) demonstrated significant differences compared to BCs associated with non-heterocystous strains cultivated in Z8 culture medium (Planktothrix–Microcystis) in terms of their composition and their ability to utilize different carbon sources, suggesting the potential influence of cyanobacterial metabolism and/or culture media on associated BCs. Finally, half of the dominant OTUs in these BCs were specifically associated with cyanobacteria or other phytoplankton, whereas the remaining OTUs were generally associated with ecosystems containing high organic matter content, such as sludge or intestines.

Vertical partitioning of freshwater bacterioplankton community in a deep mesotrophic lake with a fully oxygenated hypolimnion (Lake Biwa, Japan)

In freshwater microbial ecology, extensive studies are attempting to characterize the vast majority of uncultivated bacterioplankton taxa. However, these studies mainly focus on the epilimnion and little is known regarding the bacterioplankton inhabiting the hypolimnion of deep holomictic lakes, despite its biogeochemical importance. In this study, we investigated the bacterioplankton community composition in a deep freshwater lake with a fully oxygenated hypolimnion (Lake Biwa, Japan) using high-throughput 16S rRNA gene amplicon sequencing. Sampling at a pelagic site over 15 months throughout the water column revealed that the community composition in the hypolimnion was significantly different from that in the epilimnion. The bacterial community in the hypolimnion was composed of groups dominating in the whole water layer (e.g., bacI-A1 and acI-B1) and groups that were hypolimnion habitat specialists. Among the hypolimnion specialists, members of Chloroflexi and Planctomycetes were highly represented (e.g., CL500-11, CL500-15 and CL500-37), followed by members of Acidobacteria, Chlorobi and nitrifiers (e.g., Ca. Nitrosoarchaeum, Nitrosospira and Nitrospira). This study identified the number of previously understudied taxa dominating the deep aerobic freshwater habitat, suggesting that the biogeochemical cycling there is driven by the microbial community that are different from that in the epilimnion.

Characterization of the cyanobacteria and associated bacterial community from an ephemeral wetland in New Zealand

New Zealand ephemeral wetlands are ecologically important, containing up to 12% of threatened native plant species and frequently exhibiting conspicuous cyanobacterial growth. In such environments, cyanobacteria and associated heterotrophs can influence primary production and nutrient cycling. Wetland communities, including bacteria, can be altered by increased nitrate and phosphate due to agricultural practices. We have characterized cyanobacteria from the Wairepo Kettleholes Conservation Area and their associated bacteria. Use of 16S rRNA amplicon sequencing identified several operational taxonomic units (OTUs) representing filamentous heterocystous and non-heterocystous cyanobacterial taxa. One Nostoc OTU that formed macroscopic colonies dominated the cyanobacterial community. A diverse bacterial community was associated with the Nostoc colonies, including a core microbiome of 39 OTUs. Identity of the core microbiome associated with macroscopic Nostoc colonies was not changed by the addition of nutrients. One OTU was highly represented in all Nostoc colonies (27.6%-42.6% of reads) and phylogenetic analyses identified this OTU as belonging to the genus Sphingomonas. Scanning electron microscopy showed the absence of heterotrophic bacteria within the Nostoc colony but revealed a diverse community associated with the colonies on the external surface.

A novel uncultured heterotrophic bacterial associate of the cyanobacterium Moorea producens JHB

BACKGROUND

Filamentous tropical marine cyanobacteria such as Moorea producens strain JHB possess a rich community of heterotrophic bacteria on their polysaccharide sheaths; however, these bacterial communities have not yet been adequately studied or characterized.

RESULTS AND DISCUSSION

Through efforts to sequence the genome of this cyanobacterial strain, the 5.99 MB genome of an unknown bacterium emerged from the metagenomic information, named here as Mor1. Analysis of its genome revealed that the bacterium is heterotrophic and belongs to the phylum Acidobacteria, subgroup 22; however, it is only 85 % identical to the nearest cultured representative. Comparative genomics further revealed that Mor1 has a large number of genes involved in transcriptional regulation, is completely devoid of transposases, is not able to synthesize the full complement of proteogenic amino acids and appears to lack genes for nitrate uptake. Mor1 was found to be present in lab cultures of M. producens collected from various locations, but not other cyanobacterial species. Diverse efforts failed to culture the bacterium separately from filaments of M. producens JHB. Additionally, a co-culturing experiment between M. producens JHB possessing Mor1 and cultures of other genera of cyanobacteria indicated that the bacterium was not transferable.

CONCLUSION

The data presented support a specific relationship between this novel uncultured bacterium and M. producens, however, verification of this proposed relationship cannot be done until the "uncultured" bacterium can be cultured.

Evaluating methods for purifying cyanobacterial cultures by qPCR and high-throughput Illumina sequencing

Cyanobacteria are commonly found in association with other microorganisms, which constitutes a great challenge during the isolation of cyanobacterial strains. Although several methods have been published for obtaining axenic cyanobacterial cultures, their efficiency is usually evaluated by observing the growth of non-cyanobacteria in culture media. In order to verify whether uncultured bacteria should be a concern during cyanobacterial isolation, this work aimed to detect by molecular methods sequences from cyanobacteria and other bacteria present before and after a technique for obtaining axenic cultures from plating and exposure of Fischerella sp. CENA161 akinetes to the Extran detergent and sodium hypochlorite. Solutions containing 0.5, 1, and 2% sodium hypochlorite were able to remove contaminant bacterial CFUs from the culture. However, qPCR pointed that the quantity of sequences amplified with universal bacteria primers was higher than the number of cyanobacteria-specific sequences before and after treatments. The presence of uncultured bacteria in post-hypochlorite cultures was confirmed by high-throughput Illumina sequencing. These results suggest that culturing may overlook the presence of uncultured bacteria associated to cyanobacterial strains and is not sufficient for monitoring the success of cyanobacterial isolation by itself. Molecular methods such as qPCR could be employed as an additional measure for evaluating axenity in cyanobacterial strains.

Temporal Patterns in Bacterioplankton Community Composition in Three Reservoirs of Similar Trophic Status in Shenzhen, China

The bacterioplankton community composition's (BCC) spatial and temporal variation patterns in three reservoirs (Shiyan, Xikeng, and LuoTian Reservoir) of similar trophic status in Bao'an District, Shenzhen (China), were investigated using PCR amplification of the 16S rDNA gene and the denaturing gradient gel electrophoresis (DGGE) techniques. Water samples were collected monthly in each reservoir during 12 consecutive months. Distinct differences were detected in band number, pattern, and density of DGGE at different sampling sites and time points. Analysis of the DGGE fingerprints showed that changes in the bacterial community structure mainly varied with seasons, and the patterns of change indicated that seasonal forces might have a more significant impact on the BCC than eutrophic status in the reservoirs, despite the similar Shannon-Weiner index among the three reservoirs. The sequences obtained from excised bands were affiliated with Cyanobacteria, Firmicutes, Bacteriodetes, Acidobacteria, Actinobacteria, Planctomycetes, and Proteobacteria.

Pyrosequencing analysis of bacterial communities in Lake Bosten, a large brackish inland lake in the arid northwest of China

The bacteria inhabiting brackish lake environments are poorly known, and there are few studies on the microbial diversity of these environments. Lake Bosten, a large brackish inland lake, is the largest lake in Xinjiang Province in northwestern China. Because sediments record past limnic changes, the analysis of sedimentary bacteria in Lake Bosten may help elucidate bacterial responses to environmental change. We employed 454 pyrosequencing to investigate the diversity and bacterial community composition in Lake Bosten. A total of 48 230 high-quality sequence reads with 16 314 operational taxonomic units were successfully obtained from the 4 selected samples, and they were numerically dominated by members of the Deltaproteobacteria (17.1%), Chloroflexi (16.1%), Betaproteobacteria (12.6%), Bacteroidetes (6.6%), and Firmicutes (5.7%) groups, accounting for more than 58.1% of the bacterial sequences. The sediment bacterial communities and diversity were consistently different along the 2 geographic environmental gradients: (i) freshwater–brackish water gradient and (ii) oligotrophic–mesotrophic habitat gradient. Deltaproteobacteria, Chloroflexi, and Betaproteobacteria were amplified throughout all of the sampling sites. More Bacteroidetes and Firmicutes were found near the Kaidu River estuary (site 14). Our investigation showed that Proteobacteria did not display any systematic change along the salinity gradient, and numerous 16S rRNA sequences could not be identified at the genus level. Our data will provide a better understanding of the diversity and distribution of bacteria in arid region brackish lakes.

Sediment amino acids as indicators of anthropogenic activities and potential environmental risk in Erhai Lake, Southwest China

Total hydrolysable amino acids (THAAs) constitute the most important fraction of labile nitrogen. Anthropogenic activities directly influence various biogeochemical cycles and then accelerate lake ecosystem deterioration. This is the first study that has established the relationship between sediment THAAs and anthropogenic activities using dated sediment cores, and evaluated the possibility of THAAs release at the sediment interface based on changes in environmental conditions in Erhai Lake. The results showed that historical distribution and fractions of THAAs could be divided into three stages: a stable period before the 1970s, a clear increasing period from the 1970s to 1990s, and a gradually steady period that started after the 1990s. The chemical fraction, aromatic and sulfur amino acids (AAs) accounted for only ≤3% of THAAs. Basic AAs accounted for 5-17% of THAAs, and remained at a relatively stable level. However, acidic and neutral AAs, which accounted for 19-44% and 35-69% of THAAs, respectively, were the predominant factors causing THAAs to increase due to rapid agricultural intensification and intensification of contemporary sedimentation of phytoplankton or macrophytes since the 1970s. These trends were closely related to both anthropogenic activities and natural processes, which implied that sediment THAAs could act as an effective indicator that reflects anthropogenic activities and aquatic environmental characteristics. The current contributions of sediment THAAs on TN and TOC were <5% and 1.5%, respectively. However, the dramatic increase in THAAs in the sediment cores indicated that there was a huge potential source of labile nitrogen for the overlying water under certain environmental conditions. Correlation analysis suggested that the release of THAAs was negatively correlated with pH, whereas positively correlated with bacterial number and degree of OM mineralization, which particularly depend on the stability of HFOM. Therefore, the risk of sediment THAAs release might increase when the sediment environment continuously changes.

The interaction between cyanobacteria and zooplankton in a more eutrophic world

As blooms of cyanobacteria expand and intensify in freshwater systems globally, there is increasing interest in their ecological effects. In addition to being public health hazards, cyanobacteria have long been considered a poor quality food for key zooplankton grazers that link phytoplankton to higher trophic levels. While past laboratory studies have found negative effects of nutritional constraints and defensive traits (i.e., toxicity and colonial or filamentous morphology) on the fitness of large generalist grazers (i.e., Daphnia), cyanobacterial blooms often co-exist with high biomass of small-bodied zooplankton in nature. Indeed, recent studies highlight the remarkable diversity and flexibility in zooplankton responses to cyanobacterial prey. Reviewed here are results from a wide range of laboratory and field experiments examining the interaction of cyanobacteria and a diverse zooplankton taxa including cladocerans, copepods, and heterotrophic protists from temperate to tropical freshwater systems. This synthesis shows that longer exposure to cyanobacteria can shift zooplankton communities toward better-adapted species, select for more tolerant genotypes within a species, and induce traits within the lifetime of individual zooplankton. In turn, the function of bloom-dominated plankton ecosystems, the coupling between primary producers and grazers, the stability of blooms, and the potential to use top down biomanipulation for controlling cyanobacteria depend largely on the species, abundance, and traits of interacting cyanobacteria and zooplankton. Understanding the drivers and consequences of zooplankton traits, such as physiological detoxification and selective vs. generalist grazing behavior, are therefore of major importance for future studies. Ultimately, co-evolutionary dynamics between cyanobacteria and their grazers may emerge as a critical regulator of blooms.

Eichhornia azurea decomposition and the bacterial dynamic: an experimental research

Organic decomposition is a complex interaction between chemical, physical and biological processes, where the variety of aquatic vascular plants is essential for the trophic dynamics of freshwater ecosystems. The goal of this study was to determine the aquatic macrophyte Eichhornia azurea (Sw.) Kunth decomposition rate, the time relation with the limnological parameters, and whether this relationship is a result of decomposition processes. To that end, we collected water and leaves of E. azurea in Surf Leopoldo, PR. The experiment consisted of two treatments: 25 containers with 450 mL of water and 0.8 g of biomass dry weight were used with or without the addition of macrophytes. Samples were collected in triplicate at times 0, 3 h, 6 h, 12 h, 24 h, 72 h, 120 h, 168 h and 240 h. When the container was removed, the plant material was dried in an oven. After 48 h, the material was measured to obtain the final dry weight. Analyses of pH, conductivity, dissolved oxygen, total phosphorus N-ammonia (NH₄), soluble reactive phosphorus (PO₄) and dissolved organic carbon were performed, and the decomposition rate was calculated. The results showed significant temporal variation of limnological parameters in the study. Additionally, dissolved oxygen, conductivity, dissolved organic carbon and total phosphorus were correlated with the dry weight of the biomass, suggesting that E. azurea decomposition significantly interferes with the dynamics of these variables.

Microcystin-degrading bacteria affect mcyD expression and microcystin synthesis in Microcystis spp

Cyanobacterial blooms occur increasingly often and cause ecological, economic and human health problems worldwide. Microcystins (MCs) are the dominant toxins produced by cyanobacteria and are implicated in epidemic disease and environmental problems. Extensive research has been reported on the various regulating factors, e.g., light, temperature, nutrients such as nitrogen and phosphorus, pH, iron, xenobiotics, and predators, that influence microcystin (MC) synthesis, but little is known about the effects of cyanobacteria-associated bacteria on MC synthesis. A considerable number of studies have focused on interactions between Microcystis species and their associated bacteria. In this study, we evaluated the effects of MC-degrading bacteria (MCDB) on MC synthesis gene mcyD expression and MC synthesis in axenic strain PCC7806, non-axenic strain FACHB905, and colony strain FACHB1325 of Microcystis by quantitative real-time polymerase chain reaction (RT-PCR) assay and enzyme-linked immunosorbent assay (ELISA). We demonstrate for the first time that MCDB can induce and up-regulate the MC production and transcriptional response of the mcyD gene of toxic Microcystis. On day 4 of the culturing experiment, the intracellular MC concentration and transcriptional response of mcyD of FACHB1325 were up-regulated 1.9 and 5.3-fold over that of the control, and for FACHB905 were up-regulated 1.8 and 4.2-fold over that of the control, respectively. On day 10, the transcriptional response of mcyD was up-regulated 21.3-fold in PCC7806. These results indicate that there are interactions between toxic Microcystis and MCDB, and MCDB may play a role in regulating mcyD expression in toxic Microcystis.

Metagenomic Analysis Reveals Symbiotic Relationship among Bacteria in Microcystis-Dominated Community

Microcystis bloom, a cyanobacterial mass occurrence often found in eutrophicated water bodies, is one of the most serious threats to freshwater ecosystems worldwide. In nature, Microcystis forms aggregates or colonies that contain heterotrophic bacteria. The Microcystis-bacteria colonies were persistent even when they were maintained in lab culture for a long period. The relationship between Microcystis and the associated bacteria was investigated by a metagenomic approach in this study. We developed a visualization-guided method of binning for genome assembly after total colony DNA sequencing. We found that the method was effective in grouping sequences and it did not require reference genome sequence. Individual genomes of the colony bacteria were obtained and they provided valuable insights into microbial community structures. Analysis of metabolic pathways based on these genomes revealed that while all heterotrophic bacteria were dependent upon Microcystis for carbon and energy, Vitamin B12 biosynthesis, which is required for growth by Microcystis, was accomplished in a cooperative fashion among the bacteria. Our analysis also suggests that individual bacteria in the colony community contributed a complete pathway for degradation of benzoate, which is inhibitory to the cyanobacterial growth, and its ecological implication for Microcystis bloom is discussed.

Are freshwater bacterioplankton indifferent to variable types of amino acid substrates?

A wide range of carbon compounds sustain bacterial activity and growth in freshwater ecosystems and the amount and quality of these substrates influence bacterial diversity and metabolic function. Biologically labile low-molecular-weight compounds, such as dissolved free amino acids, are particularly important substrates and can fuel as much as 20% of the total heterotrophic production. In this study, we show that extensive laboratory incubations with variable amino acids as substrates caused only minimal differences in bacterial growth rate, growth yield, quantitative amino acid usage, community composition and diversity. This was in marked contrast to incubations under dark or light regimes, where significant responses were observed in bacterial community composition and with higher diversity in the dark incubations. While a few individual taxa still responded to amendment with specific amino acids, our results suggest that compositional shifts in the specific supply of amino acids and possibly also other labile organic substrates have a minor impact on heterotrophic bacterioplankton communities, at least in nutrient rich lakes and compared to other prevailing environmental factors.

Microbial communities reflect temporal changes in cyanobacterial composition in a shallow ephemeral freshwater lake

The frequency of freshwater cyanobacterial blooms is at risk of increasing as a consequence of climate change and eutrophication of waterways. It is increasingly apparent that abiotic data are insufficient to explain variability within the cyanobacterial community, with biotic factors such as heterotrophic bacterioplankton, viruses and protists emerging as critical drivers. During the Australian summer of 2012-2013, a bloom that occurred in a shallow ephemeral lake over a 6-month period was comprised of 22 distinct cyanobacteria, including Microcystis, Dolichospermum, Oscillatoria and Sphaerospermopsis. Cyanobacterial cell densities, bacterial community composition and abiotic parameters were assessed over this period. Alpha-diversity indices and multivariate analysis were successful at differentiating three distinct bloom phases and the contribution of abiotic parameters to each. Network analysis, assessing correlations between biotic and abiotic variables, reproduced these phases and assessed the relative importance of both abiotic and biotic factors. Variables possessing elevated betweeness centrality included temperature, sodium and operational taxonomic units belonging to the phyla Verrucomicrobia, Planctomyces, Bacteroidetes and Actinobacteria. Species-specific associations between cyanobacteria and bacterioplankton, including the free-living Actinobacteria acI, Bacteroidetes, Betaproteobacteria and Verrucomicrobia, were also identified. We concluded that changes in the abundance and nature of freshwater cyanobacteria are associated with changes in the diversity and composition of lake bacterioplankton. Given this, an increase in the frequency of cyanobacteria blooms has the potential to alter nutrient cycling and contribute to long-term functional perturbation of freshwater systems.

Integrated 'Omics', Targeted Metabolite and Single-cell Analyses of Arctic Snow Algae Functionality and Adaptability

Snow algae are poly-extremophilic microalgae and important primary colonizers and producers on glaciers and snow fields. Depending on their pigmentation they cause green or red mass blooms during the melt season. This decreases surface albedo and thus further enhances snow and ice melting. Although the phenomenon of snow algal blooms has been known for a long time, large aspects of their physiology and ecology sill remain cryptic. This study provides the first in-depth and multi-omics investigation of two very striking adjacent green and red snow fields on a glacier in Svalbard. We have assessed the algal community composition of green and red snow including their associated microbiota, i.e., bacteria and archaea, their metabolic profiles (targeted and non-targeted metabolites) on the bulk and single-cell level, and assessed the feedbacks between the algae and their physico-chemical environment including liquid water content, pH, albedo, and nutrient availability. We demonstrate that green and red snow clearly vary in their physico-chemical environment, their microbial community composition and their metabolic profiles. For the algae this likely reflects both different stages of their life cycles and their adaptation strategies. Green snow represents a wet, carbon and nutrient rich environment and is dominated by the algae Microglena sp. with a metabolic profile that is characterized by key metabolites involved in growth and proliferation. In contrast, the dry and nutrient poor red snow habitat is colonized by various Chloromonas species with a high abundance of storage and reserve metabolites likely to face upcoming severe conditions. Combining a multitude of techniques we demonstrate the power of such complementary approaches in elucidating the function and ecology of extremophiles such as green and red snow algal blooms, which play crucial roles in glacial ecosystems.

A snapshot of microbial communities from the Kutch: one of the largest salt deserts in the World

Here we present the first report on the taxonomic diversity of the microbial communities of the saline desert of the Great Rann of Kutch, Gujarat, India, using a metagenomic approach. Seven samples, differing in salinity levels and covering different seasons, were analysed to investigate the dynamics of microbial communities in relation to salinity and season. Metagenomic data generated using whole metagenome sequencing revealed that despite its very high salinity (4.11-30.79 %), the saline desert's microbiota had a rich microbial diversity that included all major phyla. Notably, 67 archaeal genera, representing more than 60 % of all known archaeal genera, were present in this ecosystem. A strong positive correlation (0.85) was observed between the presence of the extremely halophilic bacterium Salinibacter and salinity level. Taxonomic and functional comparisons of the saline desert metagenome with those of other publicly available metagenomes (i.e. sea, hypersaline lagoon, solar saltern, brine, hot desert) was carried out. The microbial community of the Kutch was found to be unique yet more similar to the sea biomes followed by hypersaline lagoon.

A novel alphaproteobacterial ectosymbiont promotes the growth of the hydrocarbon-rich green alga Botryococcus braunii

Botryococcus braunii is a colony-forming green alga that accumulates large amounts of liquid hydrocarbons within the colony. The utilization of B. braunii for biofuel production is however hindered by its low biomass productivity. Here we describe a novel bacterial ectosymbiont (BOTRYCO-2) that confers higher biomass productivity to B. braunii. 16S rDNA analysis indicated that the sequence of BOTRYCO-2 shows low similarity (<90%) to cultured bacterial species and located BOTRYCO-2 within a phylogenetic lineage consisting of uncultured alphaproteobacterial clones. Fluorescence in situ hybridization (FISH) studies and transmission electric microscopy indicated that BOTRYCO-2 is closely associated with B. braunii colonies. Interestingly, FISH analysis of a water bloom sample also found BOTRYCO-2 bacteria in close association with cyanobacterium Microcystis aeruginosa colonies, suggesting that BOTRYCO-2 relatives have high affinity to phytoplankton colonies. A PCR survey of algal bloom samples revealed that the BOTRYCO-2 lineage is commonly found in Microcystis associated blooms. Growth experiments indicated that B. braunii Ba10 can grow faster and has a higher biomass (1.8-fold) and hydrocarbon (1.5-fold) yield in the presence of BOTRYCO-2. Additionally, BOTRYCO-2 conferred a higher biomass yield to BOT-22, one of the fastest growing strains of B. braunii. We propose the species name 'Candidatus Phycosocius bacilliformis' for BOTRYCO-2.

Bacterial biogeography in the coastal waters of northern Zhejiang, East China Sea is highly controlled by spatially structured environmental gradients

The underlying mechanisms of microbial community assembly in connective coastal environments are unclear. The coastal water area of northern Zhejiang, East China Sea, is a complex marine ecosystem with multiple environmental gradients, where the distributions and determinants of bacterioplankton communities remain unclear. We collected surface water samples from 95 sites across eight zones in this area for investigating bacterial community with 16S rRNA gene high-throughput sequencing. Bacterial alpha-diversity exhibits strong associations with water chemical parameters and latitude, with 75.5% of variation explained by suspended particle. The composition of dominant phyla can group the sampling sites into four bacterial provinces, and most key discriminant phyla and families/genera of each province strongly associate with specific environmental features, suggesting that local environmental conditions shape the biogeographic provincialism of bacterial taxa. At a broader and finer phylogenetic scale, bacterial beta-diversity is dominantly explained by the shared variation of environmental and spatial factors (63.3%); meanwhile, the environmental determinants of bacterial β-diversity generally exhibit spatially structured patterns, suggesting that bacterial assembly in surface water is highly controlled by spatially structured environmental gradients in this area. This study provides evidence for the unique biogeographic pattern of bacterioplankton communities at an entire scale of this marine ecosystem.

Bacterial Community Composition in Oligosaline Lake Bosten: Low Overlap of Betaproteobacteria and Bacteroidetes with Freshwater Ecosystems

Oligosaline lakes in arid regions provide indispensable water resources for humans; however, information on the bacterial community composition (BCC) of this ecosystem is limited. In the present study, we explored seasonal and vertical variations in BCC in Lake Bosten, a unique oligosaline lake (1.2‰ salinity) in arid, northwestern China, using denaturing gradient gel electrophoresis and 16S rRNA gene sequencing. We obtained 544 clones and 98 operational taxonomic units (OTUs) from six clone libraries. The top 10 OTUs represented 59.4% of the entire bacterial community. Betaproteobacteria (22.1%), Gammaproteobacteria (19.9%), Bacteroidetes (18.8%), and Firmicutes (11.4%) dominated in Lake Bosten. Although seasonal variations were recorded in BCC, the vertical changes observed were not significant. Water temperature and salinity were the most important factors shaping the dynamics of BCC. A low degree of overlap was observed in BCC between Lake Bosten and freshwater ecosystems, especially for Betaproteobacteria and Bacteroidetes. An RDP seqmatch analysis showed that 169 sequences (31%) were novel bacterial sequences (<97% similarity to the closest sequences in GenBank), which suggested that specific indigenous bacteria inhabit this oligosaline environment. Our results support bacterial endemicity being more common than previously considered, particularly in oligosaline lakes. An analysis of these communities may reveal how bacteria respond to increases in salinity and nutrients in the early stage of salinization and eutrophication.

The ecology of pelagic freshwater methylotrophs assessed by a high-resolution monitoring and isolation campaign

Methylotrophic planktonic bacteria fulfill a particular role in the carbon cycle of lakes via the turnover of single-carbon compounds. We studied two planktonic freshwater lineages (LD28 and PRD01a001B) affiliated with Methylophilaceae (Betaproteobacteria) in Lake Zurich, Switzerland, by a combination of molecular and cultivation-based approaches. Their spatio-temporal distribution was monitored at high resolution (n=992 samples) for 4 consecutive years. LD28 methylotrophs constituted up to 11 × 10(7) cells l(-1) with pronounced peaks in spring and autumn-winter, concomitant with blooms of primary producers. They were rare in the warm water layers during summer but abundant in the cold hypolimnion, hinting at psychrophilic growth. Members of the PRD01a001B lineage were generally less abundant but also had maxima in spring. More than 120 axenic strains from these so far uncultivated lineages were isolated from the pelagic zone by dilution to extinction. Phylogenetic analysis separated isolates into two distinct genotypes. Isolates grew slowly (μmax=0.4 d(-1)), were of conspicuously small size, and were indeed psychrophilic, with higher growth yield at low temperatures. Growth was enhanced upon addition of methanol and methylamine to sterile lake water. Genomic analyses of two strains confirmed a methylotrophic lifestyle with a reduced set of genes involved in C1 metabolism. The very small and streamlined genomes (1.36 and 1.75 Mb) shared several pathways with the marine OM43 lineage. As the closest described taxa (Methylotenera sp.) are only distantly related to either set of isolates, we propose a new genus with two species, that is, 'Candidatus Methylopumilus planktonicus' (LD28) and 'Candidatus Methylopumilus turicensis' (PRD01a001B).

Multivariate and phylogenetic analyses assessing the response of bacterial mat communities from an ancient oligotrophic aquatic ecosystem to different scenarios of long-term environmental disturbance

Understanding the response of bacterial communities to environmental change is extremely important in predicting the effect of biogeochemical modifications in ecosystem functioning. The Cuatro Cienegas Basin is an ancient oasis in the Mexican Chihuahuan desert that hosts a wide diversity of microbial mats and stromatolites that have survived in extremely oligotrophic pools with nearly constant conditions. However, thus far, the response of these unique microbial communities to long-term environmental disturbances remains unexplored. We therefore studied the compositional stability of these bacterial mat communities by using a replicated (3x) mesocosm experiment: a) Control; b) Fluct: fluctuating temperature; c) 40C: increase to 40 ºC; d) UVplus: artificial increase in UV radiation; and f) UVmin: UV radiation protection. In order to observe the changes in biodiversity, we obtained 16S rRNA gene clone libraries from microbial mats at the end of the experiment (eight months) and analyzed them using multivariate and phylogenetic tools. Sequences were assigned to 13 major lineages, among which Cyanobacteria (38.8%) and Alphaproteobacteria (25.5%) were the most abundant. The less extreme treatments (Control and UVmin) had a more similar composition and distribution of the phylogenetic groups with the natural pools than the most extreme treatments (Fluct, 40C, and UVplus), which showed drastic changes in the community composition and structure, indicating a different community response to each environmental disturbance. An increase in bacterial diversity was found in the UVmin treatment, suggesting that protected environments promote the establishment of complex bacterial communities, while stressful environments reduce diversity and increase the dominance of a few Cyanobacterial OTUs (mainly Leptolyngbya sp) through environmental filtering. Mesocosm experiments using complex bacterial communities, along with multivariate and phylogenetic analyses of molecular data, can assist in addressing questions about bacterial responses to long-term environmental stress.

Comparative analysis of alkaline phosphatase-encoding genes (phoX) in two contrasting zones of Lake Taihu

Limnetic habitats that are dominated by either algae or macrophytes represent the 2 dominant ecosystems in shallow lakes. We assessed seasonal variations in the diversity and abundance of alkaline phosphate-encoding genes (phoX) in these 2 zones of Lake Taihu, which is a large, shallow, eutrophic lake in China. There was no significant difference in seasonal mean phoX diversity between the 2 zones, whereas the seasonal mean phoX abundance in the macrophyte-dominated region was higher than that in the algae-dominated region. The bulk of the genotypes in the 2 regions were most similar to the alphaproteobacterial and betaproteobacterial phoX. Genotypes most similar to phoX affiliated with Betaproteobacteria were present with greater diversity in the macrophyte-dominated zone than in the algae-dominated zone. In the algae-dominated zone, the relative proportion of genotypes most similar to cyanobacterial phoX was highest (38.8%) in summer. In addition to the different genotype structures and environmental factors between the 2 stable states, the lower gene abundances and higher alkaline phosphatase activities in Meiliang Bay in summer than those in Xukou Bay reveals different organophosphate-mineralizing modes in these 2 contrasting habitats.