Seasonal changes in microbial community structure and activity imply winter production is linked to summer hypoxia in a large lake

Microbial difference and its influencing factors in ice-covered lakes on the three poles

Most lakes in the world are permanently or seasonally covered with ice. However, little is known about the distribution of microbes and their influencing factors in ice-covered lakes worldwide. Here we analyzed the microbial community composition in the waters of 14 ice-covered lakes in the Hoh Xil region of northern Qing-Tibetan Plateau (QTP), and conducted a meta-analysis by integrating published microbial community data of ice-covered lakes in the tripolar regions (the Arctic, Antarctica and QTP). The results showed that there were significant differences in microbial diversity, community composition and distribution patterns in the ice-covered tripolar lakes. Microbial diversity and richness were lower in the ice-covered QTP lakes (including the studied lakes in the Hoh Xil region) than those in the Arctic and Antarctica. In the ice-covered lakes of Hoh Xil, prokaryotes are mainly involved in S-metabolic processes, making them more adaptable to extreme environmental conditions. In contrast, prokaryotes in the ice-covered lakes of the Arctic and Antarctica were predominantly involved in carbon/nitrogen metabolic processes. Deterministic (salinity and nutrients) and stochastic processes (dispersal limitation, homogenizing dispersal and drift) jointly determine the geographical distribution patterns of microorganisms in ice-covered lakes, with stochastic processes dominating. These results expand the understanding of microbial diversity, distribution patterns, and metabolic processes in polar ice-covered lakes.

Strategies for regulating the intensity of different cyanobacterial blooms: Insights from the dynamics and stability of bacterioplankton communities

The occurrence of cyanobacterial blooms is increasing in frequency and magnitude due to climate change and human activities, which poses a direct threat to drinking water security. The impacts of abiotic and biotic factors on the development of blooms have been well studied; however, control strategies for different bloom intensities have rarely been explored from the perspective of the dynamics and stability of bacterioplankton communities. Here, a network analysis was used to investigate the interactions and stability of microbial communities during different periods of R. raciborskii bloom in an inland freshwater lake. The abundance and diversity of rare taxa were significantly higher than that of abundant taxa throughout the bloom cycle. At the pre-bloom (PB) stage, microbial interactions among the different bacterial groups were weak but strongly negatively correlated, indicating low robustness and weak disturbance resistance within the community. However, community stability was better, and microbial interactions became more complicated at the high-bloom (HB) and low-bloom (LB) stages. Interestingly, rare taxa were significantly responsible for community stability and connectivity despite their low relative abundance. The Mantel test revealed that Secchi depth (SD), orthophosphate (PO43--P), and dissolved oxygen (DO) were significantly positively correlated with abundant taxa, rare taxa and PB. DO was significantly positively correlated with HB, intermediate taxa, and rare taxa, while water temperature (WT), N/P and total nitrogen (TN) were significantly positively correlated with LB, abundant taxa, intermediate taxa, and rare taxa. These findings suggest that reducing the PO43--P concentration at the PB stage may be an effective approach to preventing the development of R. raciborskii blooms, while regulating rare taxa at the HB and LB stages may be a key factor in controlling R. raciborskii blooms.

Declines in ice cover are accompanied by light limitation responses and community change in freshwater diatoms

The rediscovery of diatom blooms embedded within and beneath the Lake Erie ice cover (2007-2012) ignited interest in psychrophilic adaptations and winter limnology. Subsequent studies determined the vital role ice plays in winter diatom ecophysiology as diatoms partition to the underside of ice, thereby fixing their location within the photic zone. Yet, climate change has led to widespread ice decline across the Great Lakes, with Lake Erie presenting a nearly "ice-free" state in several recent winters. It has been hypothesized that the resultant turbid, isothermal water column induces light limitation amongst winter diatoms and thus serves as a competitive disadvantage. To investigate this hypothesis, we conducted a physiochemical and metatranscriptomic survey that spanned spatial, temporal, and climatic gradients of the winter Lake Erie water column (2019-2020). Our results suggest that ice-free conditions decreased planktonic diatom bloom magnitude and altered diatom community composition. Diatoms increased their expression of various photosynthetic genes and iron transporters, which suggests that the diatoms are attempting to increase their quantity of photosystems and light-harvesting components (a well-defined indicator of light limitation). We identified two gene families which serve to increase diatom fitness in the turbid ice-free water column: proton-pumping rhodopsins (a potential second means of light-driven energy acquisition) and fasciclins (a means to "raft" together to increase buoyancy and co-locate to the surface to optimize light acquisition). With large-scale climatic changes already underway, our observations provide insight into how diatoms respond to the dynamic ice conditions of today and shed light on how they will fare in a climatically altered tomorrow.

Spatial scale impacts microbial community composition and distribution within and across stream ecosystems in North and Central America

A mechanistic understanding of factors that structure spatiotemporal community composition is a major challenge in microbial ecology. Our study of microbial communities in the headwaters of three freshwater stream networks showed significant community changes at the small spatial scale of benthic habitats when compared to changes at mid- and large-spatial scales associated with stream order and catchment. Catchment (which included temperate and tropical catchments) had the strongest influence on community composition followed by habitat type (epipsammon or epilithon) and stream orders. Alpha diversity of benthic microbiomes resulted from interactions between catchment, habitat, and canopy. Epilithon contained relatively more Cyanobacteria and algae while Acidobacteria and Actinobacteria proportions were higher in epipsammic habitats. Turnover from replacement created ~60%-95% of beta diversity differences among habitats, stream orders, and catchments. Turnover within a habitat type generally decreased downstream indicating longitudinal linkages in stream networks while between habitat turnover also shaped benthic microbial community assembly. Our study suggests that factors influencing microbial community composition shift in dominance across spatial scales, with habitat dominating locally and catchment dominating globally.

Exploring the Impacts of Full-Scale Distribution System Orthophosphate Corrosion Control Implementation on the Microbial Ecology of Hydrologically Connected Urban Streams

Many cities across the nation are plagued by lead contamination in drinking water. As such, many drinking water utilities have undertaken lead service line (LSL) replacement to prevent further lead contamination. However, given the urgency of lead mitigation, and the socioeconomic challenges associated with LSL replacement, cities have used phosphate-based corrosion inhibitors (i.e., orthophosphate) alongside LSL replacement. While necessary to ensure public health protection from lead contamination, the addition of orthophosphate into an aging and leaking drinking water system may increase the concentration of phosphate leaching into urban streams characterized by century-old failing water infrastructure. Such increases in phosphate availability may cascade into nutrient and microbial community composition shifts. The purpose of this study was to determine how this occurs and to understand whether full-scale distribution system orthophosphate addition impacts the microbial ecology of urban streams. Through monthly collection of water samples from five urban streams before and after orthophosphate addition, significant changes in microbial community composition (16S rRNA amplicon sequencing) and in the relative abundance of typical freshwater taxa were observed. In addition, key microbial phosphorus and nitrogen metabolism genes (e.g., two component regulatory systems) were predicted to change via BugBase. No significant differences in the absolute abundances of total bacteria, Cyanobacteria, and "Candidatus Accumulibacter" were observed. Overall, the findings from this study provide further evidence that urban streams are compromised by unintentional hydrologic connections with drinking water infrastructure. Moreover, our results suggest that infiltration of phosphate-based corrosion inhibitors can impact urban streams and have important, as-yet-overlooked impacts on urban stream microbial communities. IMPORTANCE Elevated lead levels in drinking water supplies are a public health risk. As such, it is imperative for cities to urgently address lead contamination from aging drinking water supplies by way of lead service line replacements and corrosion control methods. However, when applying corrosion control methods, it is also important to consider the chemical and microbiological effects that can occur in natural settings, given that our water infrastructure is aging and more prone to leaks and breaks. Here, we examine the impacts on the microbial ecology of five urban stream systems before and after full-scale distribution system orthophosphate addition. Overall, the results suggest that infiltration of corrosion inhibitors may impact microbial communities; however, future work should be done to ascertain the true impact to protect both public and environmental health.

The skin microbiota of the axolotl Ambystoma altamirani is highly influenced by metamorphosis and seasonality but not by pathogen infection

BACKGROUND

Microbiomes have been increasingly recognized as major contributors to host health and survival. In amphibians, bacterial members of the skin microbiota protect their hosts by inhibiting the growth of the fungal pathogen Batrachochytrium dendrobatidis (Bd). Even though several studies describe the influence of biotic and abiotic factors over the skin microbiota, it remains unclear how these symbiotic bacterial communities vary across time and development. This is particularly relevant for species that undergo metamorphosis as it has been shown that host physiology and ecology drastically influence diversity of the skin microbiome.

RESULTS

We found that the skin bacterial communities of the axolotl A. altamirani are largely influenced by the metamorphic status of the host and by seasonal variation of abiotic factors such as temperature, pH, dissolved oxygen and conductivity. Despite high Bd prevalence in these samples, the bacterial diversity of the skin microbiota did not differ between infected and non-infected axolotls, although relative abundance of particular bacteria were correlated with Bd infection intensity.

CONCLUSIONS

Our work shows that metamorphosis is a crucial process that shapes skin bacterial communities and that axolotls under different developmental stages respond differently to environmental seasonal variations. Moreover, this study greatly contributes to a better understanding of the factors that shape amphibian skin microbiota, especially in a largely underexplored group like axolotls (Mexican Ambystoma species).

Variability of Microbial Communities in Two Long-Term Ice-Covered Freshwater Lakes in the Subarctic Region of Yakutia, Russia

Although under-ice microbial communities are subject to a cold environment, low concentrations of nutrients, and a lack of light, they nevertheless take an active part in biogeochemical cycles. However, we still lack an understanding of how high their diversity is and how these communities are distributed during the long-term ice-cover period. Here, we assessed for the first time the composition and distribution of microbial communities during the ice-cover period in two subarctic lakes (Labynkyr and Vorota) located in the area of the lowest temperature in the Northern Hemisphere. The diversity distribution and abundance of main bacterial taxa as well as the composition of microalgae varied by time and habitat. The 16S rRNA gene sequencing method revealed, in general, a high diversity of bacterial communities where Proteobacteria (~ 45%) and Actinobacteria (~ 21%) prevailed. There were significant differences between the communities of the lakes: Chthoniobacteraceae, Moraxellaceae, and Pirellulaceae were abundant in Lake Labynkyr, while Cyanobiaceae, Oligoflexales, Ilumatobacteraceae, and Methylacidiphilaceae were more abundant in Lake Vorota. The most abundant families were evenly distributed in April, May, and June their contribution was different in different habitats. In April, Moraxellaceae and Ilumatobacteraceae were the most abundant in the water column, while Sphingomonadaceae was abundant both in water column and on the ice bottom. In May, the abundance of Comamonadaceae increased and reached the maximum in June, while Cyanobiaceae, Oxalobacteraceae, and Pirellulaceae followed. We found a correlation of the structure of bacterial communities with snow thickness, pH, N_min concentration, and conductivity. We isolated psychrophilic heterotrophic bacteria both from dominating and minor taxa of the communities studied. This allowed for specifying their ecological function in the under-ice communities. These findings will advance our knowledge of the under-ice microbial life.

Opportunities for combining data of Estonian and Russian monitoring to reflect on water quality in large transboundary Lake Peipsi

Lake Peipsi, one of the world's largest lakes, is shared between Estonia and Russia. The water quality in different parts of the lake has so far been assessed independently. Here we explore opportunities for combining data of Estonian and Russian monitoring. For that, we 1) analysed the compatibility of data for some water quality variables; 2) estimated the potential effects of the differences in sampling frequency; 3) provided a few regression models to calculate the missing data for months not sampled by the Russian side. Data of the concurrent Estonian and Russian sampling indicated a good compatibility. Estonian data analysis suggested that water quality assessment results are sensitive to sampling frequency. For example, total phosphorus (TP) in the largest basin showed a long-term decreasing trend in three month data that disappeared when data for other months were added. Disregarding some months may lead to under- or overestimation of certain factors with no consistency in the response of different basins. Hence, data of the whole ice-free period are recommended for an adequate water quality assessment. Furthermore, we demonstrated that monthly values of the water quality variables of the same year are autocorrelated. Based on this, we filled the gaps in the long-term data and compiled a dataset for the whole lake that enables its most comprehensive use in water quality assessment and management. Long-term data revealed no water quality improvement of Lake Peipsi. Further reduction of the external nutrient load is needed. Eutrophication is sustained by high internal phosphorus load.

Metatranscriptomic Sequencing of Winter and Spring Planktonic Communities from Lake Erie, a Laurentian Great Lake

Previous reports suggest planktonic and under-ice winter microbial communities in Lake Erie are dominated by diatoms. Here, we report the assembled metatranscriptomes of 79 Lake Erie surface water microbial communities spanning both the winter (28 samples) and spring (51 samples) months over spatial, temporal, and climatic gradients in 2019 through 2020.

Microbial Community Structure and Bacterial Lineages Associated with Sulfonamides Resistance in Anthropogenic Impacted Larut River

Anthropogenic activities often contribute to antibiotic resistance in aquatic environments. Larut River Malaysia is polluted with both organic and inorganic pollutants from domestic and industrial wastewater that are probably treated inadequately. The river is characterized by high biochemical oxygen demand, chemical oxygen demand, total suspended solids, ammonia, and heavy metals. In our previous study, sulfonamides (SAs) and sulfonamide resistance genes (sul) were detected in the Larut River. Hence, in this study, we further examined the microbial community structure, diversity of sulfonamide-resistant bacteria (SARB), and their resistance genes. The study also aimed at identifying cultivable bacteria potential carriers of sul genes in the aquatic environment. Proteobacteria (22.4–66.0%), Firmicutes (0.8–41.6%), Bacteroidetes (2.0–29.4%), and Actinobacteria (5.5–27.9%) were the most dominant phyla in both the effluents and river waters. SARB isolated consisted only 4.7% of the total genera identified, with SAR Klebsiella as the most dominant (38.0–61.3%) followed by SAR Escherichia (0–22.2%) and Acinetobacter (3.2–16.0%). The majority of the SAR Klebsiella isolated from the effluents and middle downstream were positive for sul genes. Sul genes-negative SAR Escherichia and Acinetobacter were low (<20%). Canonical-correlation analysis (CCA) showed that SAs residues and inorganic nutrients exerted significant impacts on microbial community and total sul genes. Network analysis identified 11 SARB as potential sul genes bacterial carriers. These findings indicated that anthropogenic activities exerted impacts on the microbial community structure and SAs resistance in the Larut River.

Spatio-temporal variation of bacterioplankton community structure in the Pearl River: impacts of artificial fishery habitat and physicochemical factors

Background

Artificial fishery habitat has been widely used in fishery resource protection and water habitat restoration. Although the bacterioplankton plays an important ecological role in fisheries ecosystems, the effect of artificial fishery habitat on bacterioplankton is not clear. In this study, high-throughput sequencing based on the 16S rRNA gene was carried out to study the characteristics of bacterioplankton community structure in artificial fishery habitat and to determine the principal environmental factors that shaped the composition, structure and function of bacterioplankton communities in an unfed aquaculture system.

Results

The results indicated that the most dominant phyla were Proteobacteria (Alphaproteobacteria and Gammaproteobacteria), Actinobacteria, Cyanobacteria, and Bacteroidetes, which accounted for 28.61%, 28.37%, 19.79%, and 10.25% of the total abundance, respectively. The factors that cause the differences in bacterioplankton community were mainly manifested in three aspects, including the diversity of the community, the role of artificial fishery habitat, and the change of environmental factors. The alpha diversity analysis showed that the diversity and richness index of the bacterioplankton communities were the highest in summer, which indicated that the seasonal variation characteristics had a great influence on it. The CCA analysis identified that the dissolved oxygen, temperature, and ammonium salt were the dominant environmental factors in an unfed aquaculture system. The LEfSe analysis founded 37 indicator species in artificial structure areas (AS group), only 9 kinds existing in the control areas of the open-water group (CW group). Meanwhile, the KEGG function prediction analysis showed that the genes which were related to metabolism in group AS were significantly enhanced.

Conclusions

This study can provide reference value for the effect of artificial habitat on bacterioplankton community and provide fundamental information for the follow-up study of ecological benefits of artificial fishery habitat. It may be contributed to apply artificial fishery habitat in more rivers.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12862-022-01965-3.

Transformations from specialists to generalists cause bacterial communities are more stable than micro-eukaryotic communities under anthropogenic activity disturbance

Different microbial components have different responses to environmental disturbances. Here, we found that the planktonic bacterial and micro-eukaryotic communities had different responses to anthropogenic activity disturbance in a subtropical river, because they had different survival strategies (generalist and specialist). We used nutrients (nitrogen and phosphorus) as indicators of anthropogenic activities. We found that river stretch 1 showed low nutrient concentrations from October 2018 to September 2019. However, a nutrient disturbance was observed in river stretch 2. The nutrient concentrations increased largely in December and January but recovered to low values in June. Bacterial communities had higher resilience under this disturbance than micro-eukaryotic communities in river stretch 2. The bacterial community composition were quite different between the two river stretches in December and January but were similar in June and July. However, the differences of micro-eukaryotic community composition between the two river stretches were always high during the study period. The bacterial communities in river stretch 2 contained more generalists and nutrient tolerant specialists. The bacterial nutrient tolerant specialists rapidly decreased in the low nutrient months and were replaced by the generalists. Bacteria which were involved in this shifts accounted for 29.3% of the total abundance. However, the micro-eukaryotic communities in river stretch 2 contained more moderate generalists. These moderate generalists were insensitive to the variation of nutrients and only 19.56% of the micro-eukaryotes had significant responses to the disturbance. The survival strategies caused bacterial communities had higher adaptability than eukaryotes to environmental fluctuation.

Spatio-temporal dynamics of bacterial communities in the shoreline of Laurentian great Lake Erie and Lake St. Clair's large freshwater ecosystems

Background

Long-term trends in freshwater bacterial community composition (BCC) and dynamics are not yet well characterized, particularly in large lake ecosystems. We addressed this gap by temporally (15 months) and spatially (6 sampling locations) characterizing BCC variation in lakes Erie and St. Clair; two connected ecosystems in the Laurentian Great Lakes.

Results

We found a spatial variation of the BCC between the two lakes and among the sampling locations (significant changes in the relative abundance of 16% of the identified OTUs at the sampling location level). We observed five distinct temporal clusters (UPGMA broad-scale temporal variation) corresponding to seasonal variation over the 15 months of sampling. Temporal variation among months was high, with significant variation in the relative abundance of 69% of the OTUs. We identified significant differences in taxonomic composition between summer months of 2016 and 2017, with a corresponding significant reduction in the diversity of BCC in summer 2017.

Conclusions

As bacteria play a key role in biogeochemical cycling, and hence in healthy ecosystem function our study defines the scope for temporal and spatial variation in large lake ecosystems. Our data also show that freshwater BCC could serve as an effective proxy and monitoring tool to access large lake health.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12866-021-02306-y.

Response and oil degradation activities of a northeast Atlantic bacterial community to biogenic and synthetic surfactants

BACKGROUND

Biosurfactants are naturally derived products that play a similar role to synthetic dispersants in oil spill response but are easily biodegradable and less toxic. Using a combination of analytical chemistry, 16S rRNA amplicon sequencing and simulation-based approaches, this study investigated the microbial community dynamics, ecological drivers, functional diversity and robustness, and oil biodegradation potential of a northeast Atlantic marine microbial community to crude oil when exposed to rhamnolipid or synthetic dispersant Finasol OSR52.

RESULTS

Psychrophilic Colwellia and Oleispira dominated the community in both the rhamnolipid and Finasol OSR52 treatments initially but later community structure across treatments diverged significantly: Rhodobacteraceae and Vibrio dominated the Finasol-amended treatment, whereas Colwellia, Oleispira, and later Cycloclasticus and Alcanivorax, dominated the rhamnolipid-amended treatment. Key aromatic hydrocarbon-degrading bacteria, like Cycloclasticus, was not observed in the Finasol treatment but it was abundant in the oil-only and rhamnolipid-amended treatments. Overall, Finasol had a significant negative impact on the community diversity, weakened the taxa-functional robustness of the community, and caused a stronger environmental filtering, more so than oil-only and rhamnolipid-amended oil treatments. Rhamnolipid-amended and oil-only treatments had the highest functional diversity, however, the overall oil biodegradation was greater in the Finasol treatment, but aromatic biodegradation was highest in the rhamnolipid treatment.

CONCLUSION

Overall, the natural marine microbial community in the northeast Atlantic responded differently to crude oil dispersed with either synthetic or biogenic surfactants over time, but oil degradation was more enhanced by the synthetic dispersant. Collectively, our results advance the understanding of how rhamnolipid biosurfactants and synthetic dispersant Finasol affect the natural marine microbial community in the FSC, supporting their potential application in oil spills. Video abstract.

Spatial distribution of sediment archaeal and bacterial communities relates to the source of organic matter and hypoxia - a biogeographical study on Lake Remoray (France)

Bottom waters hypoxia spreads in many lakes worldwide causing severe consequences on whole lakes trophic network. Here, we aimed at understanding the origin of organic matter stored in the sediment compartment and the related diversity of sediment microbial communities in a lake with deoxygenated deep water layers. We used a geostatistical approach to map and compare both the variation of organic matter and microbial communities in sediment. Spatialisation of C/N ratio and δ13C signature of sediment organic matter suggested that Lake Remoray was characterized by an algal overproduction which could be related to an excess of nutrient due to the close lake-watershed connectivity. Three spatial patterns were observed for sediment microbial communities after the hypoxic event, each characterized by specific genetic structure, microbial diversity and composition. The relative abundance variation of dominant microbial groups across Lake Remoray such as Cyanobacteria, Gammaproteobacteria, Deltaproteobacteria and Chloroflexi provided us important information on the lake areas where hypoxia occurs. The presence of methanogenic species in the deeper part of the lake suggests important methane production during hypoxia period. Taken together, our results provide an extensive picture of microbial communities' distribution related to quantity and quality of organic matter in a seasonally hypoxic lake.

The bacterial community composition and its environmental drivers in the rivers around eutrophic Chaohu Lake, China

Background

Bacterial community play a key role in environmental and ecological processes in river ecosystems. Rivers are used as receiving body for treated and untreated urban wastewaters that brings high loads of sewage and excrement bacteria. However, little is known about the bacterial community structure and functional files in the rivers around the eutrophic Chaohu Lake, the fifth largest freshwater lake in China, has been subjected to severe eutrophication and cyanobacterial blooms over the past few decades. Therefore, understanding the taxonomic and functional compositions of bacterial communities in the river will contribute to understanding aquatic microbial ecology. The main aims were to (1) examine the structure of bacterial communities and functional profiles in this system; (2) find the environmental factors of bacterial community variations.

Results

We studied 88 sites at rivers in the Chaohu Lake basin, and determined bacterial communities using Illumina Miseq sequencing of the 16 S rRNA gene, and predicted functional profiles using PICRUSt2. A total of 3,390,497 bacterial 16 S rRNA gene sequences were obtained, representing 17 phyla, and 424 genera; The dominant phyla present in all samples were Bacteroidetes (1.4-82.50 %), followed by Proteobacteria (12.6–97.30 %), Actinobacteria (0.1–17.20 %). Flavobacterium was the most numerous genera, and accounted for 0.12–80.34 % of assigned 16 S reads, followed by Acinetobacter (0.33–49.28 %). Other dominant bacterial genera including Massilia (0.06–25.40 %), Psychrobacter (0-36.23 %), Chryseobacterium (0.01–22.86 %), Brevundimonas (0.01–12.82 %), Pseudomonas (0-59.73 %), Duganella (0.08–23.37 %), Unidentified Micrococcaceae (0-8.49 %). The functional profiles of the bacterial populations indicated an relation with many human diseases, including infectious diseases. Overall results, using the β diversity measures, coupled with heatmap and RDA showed that there were spatial variations in the bacterial community composition at river sites, and Chemical oxygen demand (COD_Mn) and (NH₄⁺ )were the dominant environmental drivers affecting the bacterial community variance.

Conclusions

The high proportion of the opportunistic pathogens (Acinetobacter, Massilia, Brevundimonas) indicated that the discharge of sewage without adequate treatment into the rivers around Chaohu Lake. We propose that these bacteria could be more effective bioindicators for long-term sewage monitoring in eutrophic lakes.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12866-021-02252-9.

Changes in the Community Structure of Under-Ice and Open-Water Microbiomes in Urban Lakes Exposed to Road Salts

Salinization of freshwater is increasingly observed in regions where chloride de-icing salts are applied to the roads in winter, but little is known about the effects on microbial communities. In this study, we analyzed the planktonic microbiomes of four lakes that differed in degree of urbanization, eutrophication and salinization, from an oligotrophic reference lake with no surrounding roads, to a eutrophic, salinized lake receiving runoff from a highway. We tested the hypothesis that an influence of road salts would be superimposed on the effects of season and trophic status. We evaluated the microbial community structure by 16S rRNA sequencing for Bacteria, and by four methods for eukaryotes: 16S rRNA chloroplast analysis, 18S rRNA sequencing, photosynthetic pigment analysis and microscopy. Consistent with our hypothesis, chloride and total nitrogen concentrations were among the most important statistical factors explaining the differences in taxonomic composition. These factors were positively correlated with the abundance of cryptophytes, haptophytes, and cyanobacteria. Ice-cover was also a major structuring factor, with clear differences between the winter communities and those of the open-water period. Nitrifying and methane oxidizing bacteria were more abundant in winter, suggesting the importance of anaerobic sediment processes and release of reduced compounds into the ice-covered water columns. The four methods for eukaryotic analysis provided complementary information. The 18S rRNA observations were strongly influenced by the presence of ribosome-rich ciliates, but revealed a much higher degree of taxonomic richness and greater separation of lakes, seasonal changes and potential salinity effects than the other methods.

Seasonal effects of river flow on microbial community coalescence and diversity in a riverine network

Terrestrial microbial communities may take advantage of running waters and runoff to enter rivers and mix with aquatic microorganisms. However, the environmental factors governing the interchange of the microbial community within a watercourse and its surrounding environment and the composition of the resulting community are often underestimated. The present study investigated the effect of flow rate on the mixing of water, soil, sediment and biofilm at four sites along the Lancang River and one branch of the river in winter and summer and, in turn, the resultant changes in the microbial community within each habitat. 16S rRNA gene-based Illumina high-throughput sequencing illustrated that bacterial communities were apparently distinct among biofilm, water, soil and sediment. Biofilms had the lowest richness, Shannon diversity and evenness indices compared with other habitats, and those three indices in all habitats increased significantly from winter to summer. SourceTracker analysis showed a significant coalescence between the bacterial communities of sediment, water and biofilm samples at lower flow rates. Additionally, the proportion of Betaproteobacteria in sediment and biofilms increased with a decrease in flow rate, suggesting the flow rate had a strong impact on microbial community composition and exchange among aquatic habitats. These results were further confirmed by a Mantel test and linear regression analysis. Microbial communities in all samples exhibited a significant but very weak distance-decay relationship (r = 0.093, P = 0.024). Turbidity played a much more important role on water bacterial community structure in summer (i.e. rainy season) (BIOENV, r = 0.92). Together, these results suggest that dispersal is an important factor affecting bacterial community structure in this system.

Unravelling winter diatom blooms in temperate lakes using high frequency data and ecological modeling

In temperate lakes, it is generally assumed that light rather than temperature constrains phytoplankton growth in winter. Rapid winter warming and increasing observations of winter blooms warrant more investigation of these controls. We investigated the mechanisms regulating a massive winter diatom bloom in a temperate lake. High frequency data and process-based lake modeling demonstrated that phytoplankton growth in winter was dually controlled by light and temperature, rather than by light alone. Water temperature played a further indirect role in initiating the bloom through ice-thaw, which increased light exposure. The bloom was ultimately terminated by silicon limitation and sedimentation. These mechanisms differ from those typically responsible for spring diatom blooms and contributed to the high peak biomass. Our findings show that phytoplankton growth in winter is more sensitive to temperature, and consequently to climate change, than previously assumed. This has implications for nutrient cycling and seasonal succession of lake phytoplankton communities. The present study exemplifies the strength in integrating data analysis with different temporal resolutions and lake modeling. The new lake ecological model serves as an effective tool in analyzing and predicting winter phytoplankton dynamics for temperate lakes.

Impact of algal organic matter on the performance, cyanotoxin removal, and biofilms of biologically-active filtration systems

The occurrence of harmful algal blooms dominated by toxic cyanobacteria has induced continuous loadings of algal organic matter (AOM) and toxins in drinking water treatment plants. However, the impact of AOM on the active biofilms and microbial community structures of biologically-active filtration (BAF), which directly affects the contaminant removal, is not well understood. In this study, we systematically examined the effects of AOM on BAF performance and bacterial biofilm formation over 240 days, tracing the removal of specific AOM components, a cyanotoxin [microcystin-LR (MC-LR)], and microbial community responses. The component analysis (excitation and emission matrix analysis) results for AOM revealed that terrestrial humic-like substances showed the highest removal among all the identified components and were strongly correlated to MC-LR removal. In addition, reduced empty bed contact time and deactivation of biofilms significantly decreased BAF performances for both AOM and MC-LR. The active biofilm, bacterial community structure, and mlrA gene (involved in microcystin degradation) abundance demonstrated that bacterial biofilm composition responded to AOM and MC-LR, in which Rhodocyclaceae, Saprospiraceae, and Comamonadaceae were dominant. In addition, MC-LR biodegradation appeared to be more active at the top than at the bottom layer in BAF. Overall, this study provides deeper insights into the role of biofilms and filter operation on the fate of AOM and MC-LR in BAF.

Microbial community evolution during the aerobic biodegradation of petroleum hydrocarbons in marine sediment microcosms: Effect of biostimulation and seasonal variations

Evolution of the microbial community structure in crude oil contaminated marine sediments was assessed under aerobic biodegradation during wet (18 °C) and dry (28 °C) seasons experiments, to account for seasonal variations in nutrients and temperature, under biostimulation and natural attenuation conditions. NMDS showed significant variation in the microbial communities between the wet and the dry season experiments, and between the biostimulation and the natural attenuation treatments in the dry season microcosms. No significant variation in the microbial community and oil biodegradation was observed during the wet season experiments due to high background nitrogen levels eliminating the effect of biostimulation. Larger variations were observed in the dry season experiments and were correlated to enhanced alkanes removal in the biostimulated microcosms, where Alphaproteobacteria dominated the total microbial community by the end of biodegradation (54%). Many hydrocarbonoclastic bacterial genera showed successive dominance during the operation affecting the ultimate performance of the microcosms.

Marked variations in gut microbiota and some innate immune responses of fresh water crayfish, marron (Cherax cainii, Austin 2002) fed dietary supplementation of Clostridium butyricum

This study aimed to investigate the effects of Clostridium butyricum as a dietary probiotic supplement in fishmeal based diet on growth, gut microbiota and immune performance of marron (Cherax cainii). Marron were randomly distributed into two different treatment groups, control and probiotic fed group. After 42 days of feeding trial, the results revealed a significant (P < 0.05) increase in growth due to increase in number of moults in marron fed probiotics. The probiotic diet also significantly enhanced the total haemocyte counts (THC), lysozyme activity in the haemolymph and protein content of the tail muscle in marron. Compared to control, the 16S rRNA sequences data demonstrated an enrichment of bacterial diversity in the probiotic fed marron where significant increase of Clostridium abundance was observed. The abundance for crayfish pathogen Vibrio and Aeromonas were found to be significantly reduced post feeding with probiotic diet. Predicted metabolic pathway revealed an increased activity for the metabolism and absorption of carbohydrate, degradation of amino acid, fatty acid and toxic compounds, and biosynthesis of secondary metabolites. C. butyricum supplementation also significantly modulated the expression level of immune-responsive genes of marron post challenged with Vibrio mimicus. The overall results suggest that C. butyricum could be used as dietary probiotic supplement in marron aquaculture.

Microbial Community Dynamics During Lake Ice Freezing

Many freshwater environments experience dramatic seasonal changes with some systems remaining ice-covered for most of the winter. Freshwater systems are also highly sensitive to environmental change. However, little is known about changes in microbial abundance and community composition during lake ice formation and times of persistent ice cover. The goal of this study is to characterize temporal dynamics of microbial communities during ice formation and persistent ice cover. Samples were collected in triplicate, five days per week from surface water in the Keweenaw Waterway between November and April. Environmental conditions along with microbial abundance and microbial community composition was determined. Distinct community composition was found between ice-free and ice-covered time periods with significantly different community composition between months. The microbial community underwent dramatic shifts in microbial abundance and diversity during the transitions into and out of ice cover. The richness of the microbial community increased during times of ice cover. Relatives of microbes involved in nitrogen cycling bloomed during times of ice cover as sequences related to known nitrifying taxa were significantly enriched during ice cover. These results help to elucidate how microbial abundance and diversity change over drastic seasonal transitions and how ice cover may affect microbial abundance and diversity.

Pseudomonas Diversity Within Urban Freshwaters

Freshwater lakes are home to bacterial communities with 1000s of interdependent species. Numerous high-throughput 16S rRNA gene sequence surveys have provided insight into the microbial taxa found within these waters. Prior surveys of Lake Michigan waters have identified bacterial species common to freshwater lakes as well as species likely introduced from the urban environment. We cultured bacterial isolates from samples taken from the Chicago nearshore waters of Lake Michigan in an effort to look more closely at the genetic diversity of species found there within. The most abundant genus detected was Pseudomonas, whose presence in freshwaters is often attributed to storm water or runoff. Whole genome sequencing was conducted for 15 Lake Michigan Pseudomonas strains, representative of eight species and three isolates that could not be resolved with named species. These genomes were examined specifically for genes encoding functionality which may be advantageous in their urban environment. Antibiotic resistance, amidst other known virulence factors and defense mechanisms, were identified in the genome annotations and verified in the lab. We also tested the Lake Michigan Pseudomonas strains for siderophore production and resistance to the heavy metals mercury and copper. As the study presented here shows, a variety of pseudomonads have inhabited the urban coastal waters of Lake Michigan.

Hypoxic conditions in stormwater retention ponds: potential for hydrogen sulfide emission

Improper design and maintenance of stormwater ponds (SWPs) may lead to hypoxic conditions, poor water quality and the production of hydrogen sulfide (H₂S). The objective of this study is to develop a comprehensive understanding of hypoxic conditions of SWPs, with a focus on the potential for H₂S production and emission. This study was conducted at two retention SWPs in Ottawa, Canada; a problematic pond with the propensity for H₂S emission and a reference pond that did not demonstrate H₂S emission. The investigation illustrated a significant impact of low dissolved oxygen (DO) concentrations, hypoxic conditions, on the concentration of total sulfides in the water column. Both ponds were shown to periodically experience hypoxic conditions at depth, especially during summer periods with less precipitation and across longer periods of winter, ice-covered conditions. The problem pond, however, was shown to experience lower DO and longer hypoxic conditions than the reference pond in both non-ice-covered and ice-covered conditions due to greater depth and a longer hydraulic retention time. Hypoxic conditions were initiated at the deepest locations in the problem pond and subsequently were spread across the entirety of the pond under winter, ice-covered conditions. Algal biomass (Chlorophyll-a) and soluble biochemical oxygen demand concentrations were shown to not likely be significant factors in the development of hypoxia in the H₂S-generating pond. Algal blooms of colonial Chrysophyceae, Synura, a known mixotroph, were observed during ice-covered conditions in the problem pond possibly due to stress-coping mechanisms of algae.

Variations in Soil Bacterial Composition and Diversity in Newly Formed Coastal Wetlands

Coastal ecosystems experience some of the most active land–ocean interactions in the world, and they are characterized by high primary productivity and biological diversity in the sediment. Given the roles of microorganisms in soil biogeochemical cycling and their multifaceted influence on soil ecosystems, it is critical to understand the variations and drivers of soil microbial communities across coastal ecosystems. Here, we studied soil bacterial community dynamics at different sites (from seawater to freshwater) in the Yellow River Delta, China. Bacterial community composition and diversity over four seasons were analyzed through 16S rRNA genes. Notably, the bacterial community near the ocean had the lowest alpha-diversity when compared with the other sites. No significant differences in bacterial communities among seasons were found, indicating that seasonal variation in temperature had little influence on bacterial community in the newly formed wetlands in the Yellow River Delta. Bacterial community structure changed substantially along the salinity gradient, revealing a clear ecological replacement along the gradual transformation gradient from freshwater to seawater environment. Redundancy analysis revealed that salinity was the main driver of variations in bacterial community structure and explained 17.5% of the variability. Our study provides a better understanding of spatiotemporally determined bacterial community dynamics in coastal ecosystems.

Taxa-function robustness in microbial communities

BACKGROUND

The species composition of a microbial community is rarely fixed and often experiences fluctuations of varying degrees and at varying frequencies. These perturbations to a community's taxonomic profile naturally also alter the community's functional profile-the aggregate set of genes encoded by community members-ultimately altering the community's overall functional capacities. The magnitude of such functional changes and the specific shift that will occur in each function, however, are strongly dependent on how genes are distributed across community members' genomes. This gene distribution, in turn, is determined by the taxonomic composition of the community and would markedly differ, for example, between communities composed of species with similar genomic content vs. communities composed of species whose genomes encode relatively distinct gene sets. Combined, these observations suggest that community functional robustness to taxonomic perturbations could vary widely across communities with different compositions, yet, to date, a systematic study of the inherent link between community composition and robustness is lacking.

RESULTS

In this study, we examined how a community's taxonomic composition influences the robustness of that community's functional profile to taxonomic perturbation (here termed taxa-function robustness) across a wide array of environments. Using a novel simulation-based computational model to quantify this taxa-function robustness in host-associated and non-host-associated communities, we find notable differences in robustness between communities inhabiting different body sites, including significantly higher robustness in gut communities compared to vaginal communities that cannot be attributed solely to differences in species richness. We additionally find between-site differences in the robustness of specific functions, some of which are potentially related to site-specific environmental conditions. These taxa-function robustness differences are most strongly associated with differences in overall functional redundancy, though other aspects of gene distribution also influence taxa-function robustness in certain body environments, and are sufficient to cluster communities by environment. Further analysis revealed a correspondence between our robustness estimates and taxonomic and functional shifts observed across human-associated communities.

CONCLUSIONS

Our analysis approach revealed intriguing taxa-function robustness variation across environments and identified features of community and gene distribution that impact robustness. This approach could be further applied for estimating taxa-function robustness in novel communities and for informing the design of synthetic communities with specific robustness requirements.

Remote collection of microorganisms at two depths in a freshwater lake using an unmanned surface vehicle (USV)

Microorganisms are ubiquitous in freshwater aquatic environments, but little is known about their abundance, diversity, and transport. We designed and deployed a remote-operated water-sampling system onboard an unmanned surface vehicle (USV, a remote-controlled boat) to collect and characterize microbes in a freshwater lake in Virginia, USA. The USV collected water samples simultaneously at 5 and 50 cm below the surface of the water at three separate locations over three days in October, 2016. These samples were plated on a non-selective medium (TSA) and on a medium selective for the genus Pseudomonas (KBC) to estimate concentrations of culturable bacteria in the lake. Mean concentrations ranged from 134 to 407 CFU/mL for microbes cultured on TSA, and from 2 to 8 CFU/mL for microbes cultured on KBC. There was a significant difference in the concentration of microbes cultured on KBC across three sampling locations in the lake (P = 0.027), suggesting an uneven distribution of Pseudomonas across the locations sampled. There was also a significant difference in concentrations of microbes cultured on TSA across the three sampling days (P = 0.038), demonstrating daily fluctuations in concentrations of culturable bacteria. There was no significant difference in concentrations of microbes cultured on TSA (P = 0.707) and KBC (P = 0.641) across the two depths sampled, suggesting microorganisms were well-mixed between 5 and 50 cm below the surface of the water. About 1 percent (7/720) of the colonies recovered across all four sampling missions were ice nucleation active (ice+) at temperatures warmer than −10 °C. Our work extends traditional manned observations of aquatic environments to unmanned systems, and highlights the potential for USVs to understand the distribution and diversity of microbes within and above freshwater aquatic environments.

Seasonality Affects the Diversity and Composition of Bacterioplankton Communities in Dongjiang River, a Drinking Water Source of Hong Kong

Water quality ranks the most vital criterion for rivers serving as drinking water sources, which periodically changes over seasons. Such fluctuation is believed associated with the state shifts of bacterial community within. To date, seasonality effects on bacterioplankton community patterns in large rivers serving as drinking water sources however, are still poorly understood. Here we investigated the intra-annual bacterial community structure in the Dongjiang River, a drinking water source of Hong Kong, using high-throughput pyrosequencing in concert with geochemical property measurements during dry, and wet seasons. Our results showed that Proteobacteria, Actinobacteria, and Bacteroidetes were the dominant phyla of bacterioplankton communities, which varied in composition, and distribution from dry to wet seasons, and exhibited profound seasonal changes. Actinobacteria, Bacteroidetes, and Cyanobacteria seemed to be more associated with seasonality that the relative abundances of Actinobacteria, and Bacteroidetes were significantly higher in the dry season than those in the wet season (p < 0.01), while the relative abundance of Cyanobacteria was about 10-fold higher in the wet season than in the dry season. Temperature and NO3--N concentration represented key contributing factors to the observed seasonal variations. These findings help understand the roles of various bacterioplankton and their interactions with the biogeochemical processes in the river ecosystem.

Bacterial community structure and function shift along a successional series of tidal flats in the Yellow River Delta

Coastal ecosystems play significant ecological and economic roles but are threatened and facing decline. Microbes drive various biogeochemical processes in coastal ecosystems. Tidal flats are critical components of coastal ecosystems; however, the structure and function of microbial communities in tidal flats are poorly understood. Here we investigated the seasonal variations of bacterial communities along a tidal flat series (subtidal, intertidal and supratidal flats) and the factors affecting the variations. Bacterial community composition and diversity were analyzed over four seasons by 16S rRNA genes using the Ion Torrent PGM platform. Bacterial community composition differed significantly along the tidal flat series. Bacterial phylogenetic diversity increased while phylogenetic turnover decreased from subtidal to supratidal flats. Moreover, the bacterial community structure differed seasonally. Canonical correspondence analysis identified salinity as a major environmental factor structuring the microbial community in the sediment along the successional series. Meanwhile, temperature and nitrite concentration were major drivers of seasonal microbial changes. Despite major compositional shifts, nitrogen, methane and energy metabolisms predicted by PICRUSt were inhibited in the winter. Taken together, this study indicates that bacterial community structure changed along the successional tidal flat series and provides new insights on the characteristics of bacterial communities in coastal ecosystems.

The re-eutrophication of Lake Erie: Harmful algal blooms and hypoxia

Lake Erie supplies drinking water to more than 11 million consumers, processes millions of gallons of wastewater, provides important species habitat and supports a substantial industrial sector, with >$50 billion annual income to tourism, recreational boating, shipping, fisheries, and other industries. These and other key ecosystem services are currently threatened by an excess supply of nutrients, manifested in particular by increases in the magnitude and extent of harmful planktonic and benthic algal blooms (HABs) and hypoxia. Widespread concern for this important international waterbody has been manifested in a strong focus of scientific and public material on the subject, and commitments for Canada-US remedial actions in recent agreements among Federal, Provincial and State agencies. This review provides a retrospective synthesis of past and current nutrient inputs, impairments by planktonic and benthic HABs and hypoxia, modelling and Best Management Practices in the Lake Erie basin. The results demonstrate that phosphorus reduction is of primary importance, but the effects of climate, nitrogen and other factors should also be considered in the context of adaptive management. Actions to reduce nutrient levels by targeted Best Management Practices will likely need to be tailored for soil types, topography, and farming practices.

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.

Examining the impact of acetylene on N-fixation and the active sediment microbial community

Here we examined the impact of a commonly employed method used to measure nitrogen fixation, the acetylene reduction assay (ARA), on a marine sediment community. Historically, the ARA technique has been broadly employed for its ease of use, in spite of numerous known artifacts. To gauge the severity of these effects in a natural environment, we employed high-throughput 16S rRNA gene sequencing to detect differences in acetylene-treated sediments vs. non-treated control sediments after a 7 h incubation. Within this short time period, significant differences were seen across all activity of microbes identified in the sediment, implying that the changes induced by acetylene occur quickly. The results have important implications for our understanding of marine nitrogen budgets. Moreover, because the ARA technique has been widely used in terrestrial and freshwater habitats, these results may be applicable to other ecosystems.

Ice cover extent drives phytoplankton and bacterial community structure in a large north-temperate lake: implications for a warming climate

Mid-winter limnological surveys of Lake Erie captured extremes in ice extent ranging from expansive ice cover in 2010 and 2011 to nearly ice-free waters in 2012. Consistent with a warming climate, ice cover on the Great Lakes is in decline, thus the ice-free condition encountered may foreshadow the lakes future winter state. Here, we show that pronounced changes in annual ice cover are accompanied by equally important shifts in phytoplankton and bacterial community structure. Expansive ice cover supported phytoplankton blooms of filamentous diatoms. By comparison, ice free conditions promoted the growth of smaller sized cells that attained lower total biomass. We propose that isothermal mixing and elevated turbidity in the absence of ice cover resulted in light limitation of the phytoplankton during winter. Additional insights into microbial community dynamics were gleaned from short 16S rRNA tag (Itag) Illumina sequencing. UniFrac analysis of Itag sequences showed clear separation of microbial communities related to presence or absence of ice cover. Whereas the ecological implications of the changing bacterial community are unclear at this time, it is likely that the observed shift from a phytoplankton community dominated by filamentous diatoms to smaller cells will have far reaching ecosystem effects including food web disruptions.