Gene expression pattern of microbes associated with large cyanobacterial colonies for a whole year in Lake Taihu

Divergent responses of abundant and rare bacterial communities to environmental variables in highly urbanized coastal regions: N-NO2- mediates the community assembly and co-occurrence networks

Understanding how rare and abundant bacterial taxa respond to environmental shifts is essential for predicting microbial community dynamics in highly urbanized estuarine ecosystems, where anthropogenic disturbances and nutrient fluctuations significantly reshape ecological processes. Here, we investigated the responses of rare and abundant bacterial communities to the environments in densely urbanized coastal areas (i.e., EO: eight outlets; NMR: nearshore marine region) within Pearl River Estuary, subsequently exploring the relationships of assembly processes and co-occurrence networks with N-NO2-. Both taxonomic and phylogenetic divergences among abundant and rare taxa exhibited positive associations with various environmental parameters. Broader environmental thresholds in rare taxa than abundant taxa suggested greater environmental adaptability in rare bacterial communities. Null model analyses revealed disparate stochastic processes governed community assembly for rare and abundant taxa. Correlations of environmental parameters with beta-nearest taxon index (βNTI) identified temperature (T), dissolved oxygen (DO), salinity (Sal), and nitrite nitrogen (N-NO2-) as pivotal factors shaping community assembly in urbanized coastal areas. Furthermore, significant positive associations between βNTI and N-NO2- suggest that the fluctuations in N-NO2- concentrations are associated with notable transitions in abundant and rare community assembly dynamics, shifting from deterministic to stochastic processes. In the co-occurrence networks, significant correlations with N-NO2- were observed in different modules of rare and abundant taxa. In NMR, module 2 showed a significantly positive correlation, while modules 1 and 3 exhibited significantly negative correlations. In contrast, only module 1 of abundant taxa displayed a significantly positive correlation in EO. It contributes fresh perspectives on environmental adaptability, advancing the comprehension of ecological processes alongside co-occurrence patterns amid fluctuating N-NO2- levels within highly urbanized coastal regions.

Lake ecological restoration of vegetation removal mitigates algal blooms and alters landscape patterns of water and sediment bacteria

Elucidating the influences of ecological restoration measure of lakeshore vegetation removal on water quality and biological community is an important but underestimated subject. We adopted molecular and statistical tools to estimate ecological restoration performance in a plateau lake receiving vegetation removal and simultaneously investigated variabilities of bacterial communities in water and sediment. Significant decreases in lake trophic level and algal bloom degree followed notable decreases in water total nitrogen and total phosphorus after vegetation removal. Non-significant changes in sediment nutrients accompanied remarkable variabilities of abundance and composition of nutrient-cycling functional genes (NCFGs) of sediment bacteria. Taxonomic and phylogenetic α-diversities, functional redundancies, and dispersal potentials of bacteria in water and sediment decreased after vegetation removal, and community successions of water and sediment bacteria were separately significant and non-significant. There were opposite changes in ecological attributes of bacteria in water and sediment in response to vegetation removal, including niche breadth, species replacement, richness difference, community complexity, and community stability. Species replacement rather than richness difference affected more on taxonomic β-diversities of bacteria in water and sediment before and after vegetation removal, and determinism rather than stochasticity dominated bacterial community assemblage. Our results highlighted vegetation removal mitigated algal bloom and affected differently on landscapes of water and sediment bacteria. These findings point to dominant ecological mechanisms underlying landscape shifts in water and sediment bacteria in a disturbed lake receiving vegetation removal and have the potential to guide lake ecological restoration.

Contrasting but interconnecting metatranscriptome between large buoyant and small suspended particles during cyanobacterial blooming in the large shallow eutrophic Taihu Lake

Large cyanobacterial colonies as visible particles floating on the water surface provide different microbial niches from small particles suspended in the water column in eutrophic freshwaters. However, functional potential differences among microbes colonizing on these contrasting particles are not well understood. Here, the metatranscriptome of microbes inhabiting these two kinds of particles during cyanobacterial bloom (dominated by Microcystis spp.) was analyzed and compared. Community compositions of active bacteria associated with small suspended particles (SA, aggregates dominated by small cyanobacteria colonies, other algae and detritus, etc.) were much more diverse than those associated with large buoyant cyanobacterial colonies (LA), but functional diversity was not significantly different between them. Transcripts related to phosphorus and nitrogen metabolism from Proteobacteria, and respiration from Bacteroidetes were enriched in LA, whereas many more pathways such as photosynthesis from Cyanobacteria, cofactors, and protein metabolism from all dominant phyla were enriched in SA. Nevertheless, many transcripts were significantly correlated within and between LA and SA. These results indicated interconnection of bacteria between LA and SA. Moreover, many transcripts in SA were significantly correlated with transcripts from cyanobacterial phycobilisome in LA, indicating that bacterial metabolism in SA may influence cyanobacterial biomass in LA. Thus, the prediction of cyanobacterial blooms by bacterial activity in SA may be possible when there is no visible bloom on the water surface.

Human activities-impacted lake dissolved organic matter (DOM) affects phycosphere microbial diversity and DOM diversification via carbon metabolism

Photosynthetic carbon sequestration and microbial carbon metabolism are major processes of algae-bacteria interactions, affecting pollutant degradation as well as fundamental biogeochemical cycles in aquatic systems. Human-induced land-use changes greatly alter the molecular composition and input of terrestrial dissolved organic matter (DOM) in inland lakes. However, how the origin of DOM leads to varying effects on phycosphere microbial communities or molecular composition of DOM, e.g., via carbon metabolism, has been little studied in freshwater. Here, we incubated the cyanobacterium Microcystis aeruginosa and a bacterial community from natural lakes to establish an alga-bacteria model system. This allowed us to investigate how DOM from different sources affects phycosphere microbial diversity and DOM diversification. We showed that Suwannee River fulvic acid (SRFA), Suwannee River natural organic matter (SRNOM) and cropland lake DOM promote algal growth, whereas DOM from an urban lake inhibits algal growth. Algal metabolites and DOM together shaped the chemotaxis response of phycosphere communities. High-resolution mass spectrometry analysis demonstrated that DOM chemo-diversity tended to become uniform after interactions of diverse DOM sources with the algae-bacteria symbiosis system. Molecular thermodynamic analysis of DOM based on a substrate-explicit model further verified that microbial interactions render DOM less bioavailable and thus increase recalcitrant DOM formation. Metabolome analysis uncovered that DOM addition intensifies metabolic pathways related to labile and recalcitrant DOM utilization (mainly lignin/carboxyl-rich alicyclic molecule (CRAM)-like DOM, unsaturated hydrocarbon), whereby cofactor and vitamin metabolism represented an extremely strong activity in all metabolic pathways. Our results highlight covariation and interactions of DOM with microbial metabolism at the molecular level and expands our understanding of microbially mediated DOM shaping aquatic carbon cycling.

Algicidal activity synchronized with nitrogen removal by actinomycetes: Algicidal mechanism, stress response of algal cells, denitrification performance, and indigenous bacterial community co-occurrence

The harmful algal blooms (HABs) can damage the ecological equilibrium of aquatic ecosystems and threaten human health. The bio-degradation of algal by algicidal bacteria is an environmentally friendly and economical approach to control HABs. This study applied an aerobic denitrification synchronization algicidal strain Streptomyces sp. LJH-12-1 (L1) to control HABs. The cell-free filtrate of the strain L1 showed a great algolytic effect on bloom-forming cyanobacterium, Microcystis aeruginosa (M. aeruginosa). The optimal algicidal property of strain L1 was indirect light-dependent algicidal with an algicidal rate of 85.0%. The functional metabolism, light-trapping, light-transfer efficiency, the content of pigments, and inhibition of photosynthesis of M. aeruginosa decreased after the addition of the supernatant of the strain L1 due to oxidative stress. Moreover, 96.05% nitrate removal rate synchronized with algicidal activity was achieved with the strain L1. The relative abundance of N cycling functional genes significantly increased during the strain L1 effect on M. aeruginosa. The algicidal efficiency of the strain L1 in the raw water was 76.70% with nitrate removal efficiency of 81.4%. Overall, this study provides a novel route to apply bacterial strain with the property of denitrification coupled with algicidal activity in treating micro-polluted water bodies.

Aerobic anoxygenic phototrophs play important roles in nutrient cycling within cyanobacterial Microcystis bloom microbiomes

BACKGROUND

During the bloom season, the colonial cyanobacterium Microcystis forms complex aggregates which include a diverse microbiome within an exopolymer matrix. Early research postulated a simple mutualism existing with bacteria benefitting from the rich source of fixed carbon and Microcystis receiving recycled nutrients. Researchers have since hypothesized that Microcystis aggregates represent a community of synergistic and interacting species, an interactome, each with unique metabolic capabilities that are critical to the growth, maintenance, and demise of Microcystis blooms. Research has also shown that aggregate-associated bacteria are taxonomically different from free-living bacteria in the surrounding water. Moreover, research has identified little overlap in functional potential between Microcystis and members of its microbiome, further supporting the interactome concept. However, we still lack verification of general interaction and know little about the taxa and metabolic pathways supporting nutrient and metabolite cycling within Microcystis aggregates.

RESULTS

During a 7-month study of bacterial communities comparing free-living and aggregate-associated bacteria in Lake Taihu, China, we found that aerobic anoxygenic phototrophic (AAP) bacteria were significantly more abundant within Microcystis aggregates than in free-living samples, suggesting a possible functional role for AAP bacteria in overall aggregate community function. We then analyzed gene composition in 102 high-quality metagenome-assembled genomes (MAGs) of bloom-microbiome bacteria from 10 lakes spanning four continents, compared with 12 complete Microcystis genomes which revealed that microbiome bacteria and Microcystis possessed complementary biochemical pathways that could serve in C, N, S, and P cycling. Mapping published transcripts from Microcystis blooms onto a comprehensive AAP and non-AAP bacteria MAG database (226 MAGs) indicated that observed high levels of expression of genes involved in nutrient cycling pathways were in AAP bacteria.

CONCLUSIONS

Our results provide strong corroboration of the hypothesized Microcystis interactome and the first evidence that AAP bacteria may play an important role in nutrient cycling within Microcystis aggregate microbiomes. Video Abstract.

The synchronicity of bloom-forming cyanobacteria transcription patterns and hydrogen peroxide dynamics

Hydrogen peroxide is a reactive oxygen species (ROS) naturally occurring at low levels in aquatic environments and production varies widely across different ecosystems. Oxygenic photosynthesis generates hydrogen peroxide as a byproduct, of which some portion can be released to ambient water. However, few studies have examined hydrogen peroxide dynamics in relation to cyanobacterial harmful algal blooms (cHABs). A year-long investigation of algal succession and hydrogen peroxide dynamics was conducted at the Caloosahatchee River, Florida, USA. We aimed to identify potential biological mechanisms responsible for elevated hydrogen peroxide production during cHAB events through the exploration of the freshwater microbial metatranscriptome. Hydrogen peroxide concentrations were elevated from February to September of 2021 when cyanobacteria were active and abundant. We observed one Microcystis cHAB event in spring and one in winter. Both had distinct nutrient uptake and cyanotoxin gene expression patterns. While meaningful levels of microcystin were only detected during periods of elevated hydrogen peroxide, cyanopeptolin was by far the most expressed cyanotoxin during the spring bloom when hydrogen peroxide was at its yearly maxima. Gene expressions of five microbial enzymes (Rubisco, superoxide dismutase, cytochrome b559, pyruvate oxidase, and NADH dehydrogenase) positively correlated to hydrogen peroxide concentrations. Additionally, there was higher nitrogen-fixing gene (nifDKH) expression by filamentous cyanobacteria after the spring bloom but no secondary bloom formation occurred. Overall, elevated environmental hydrogen peroxide concentrations were linked to cyanobacterial dominance and greater expression of specific enzymes in the photosynthesis of cyanobacteria. This implicates cyanobacterial photosynthesis and growth results in increased hydrogen peroxide generation as reflected in measured environmental concentrations.

Potential gap in understanding cyanoHABs: Light-dependent morphological variations in colonial cyanobacterium Microcystis

Colony formation is a crucial characteristic of Microcystis, a cyanobacterium known for causing cyanobacterial harmful algal blooms (cyanoHABs). It has been observed that as Microcystis colonies grow larger, they often become less densely packed, which correlates with a decrease in light penetration. The objective of this study was to investigate the effects of light limitation on the morphological variations in Microcystis, particularly in relation to the crowded cellular environment. The results indicated that when there was sufficient light (transmittance = 100 %) to support a growth rate of 0.11±0.01 day-1, a significant increase in colony size was found, from 466±15 μm to 1030±111 μm. However, under light limitation (transmittance = 50 % - 1 %) where the growth rate was lower than 0, there was no significant improvement in colony size. Microcystis in the light limitation groups exhibited a loose cell arrangement and even the presence of holes or pores within the colony, confirming the negative correlation between colony size and cell arrangement. This pattern is driven by regional differences in growth within the colony, as internal cells have a significantly lower frequency of division compared to peripheral cells, due to intra-colony self-shading (ICSS). The research demonstrates that Microcystis can adjust its cell arrangement to avoid excessive self-shading, which has implications for predicting and controlling cyanoHABs. These findings also contribute to the understanding of cyanobacterial variations and can potentially inform future research on the diverse phycosphere.

Temperature-mediated microbial carbon utilization in China's lakes

Microbes play an important role in aquatic carbon cycling but we have a limited understanding of their functional responses to changes in temperature across large geographic areas. Here, we explored how microbial communities utilized different carbon substrates and the underlying ecological mechanisms along a space-for-time substitution temperature gradient of future climate change. The gradient included 47 lakes from five major lake regions in China spanning a difference of nearly 15°C in mean annual temperatures (MAT). Our results indicated that lakes from warmer regions generally had lower values of variables related to carbon concentrations and greater carbon utilization than those from colder regions. The greater utilization of carbon substrates under higher temperatures could be attributed to changes in bacterial community composition, with a greater abundance of Cyanobacteria and Actinobacteriota and less Proteobacteria in warmer lake regions. We also found that the core species in microbial networks changed with increasing temperature, from Hydrogenophaga and Rhodobacteraceae, which inhibited the utilization of amino acids and carbohydrates, to the CL500-29-marine-group, which promoted the utilization of all almost carbon substrates. Overall, our findings suggest that temperature can mediate aquatic carbon utilization by changing the interactions between bacteria and individual carbon substrates, and the discovery of core species that affect carbon utilization provides insight into potential carbon sequestration within inland water bodies under future climate warming.

Harmful cyanobacteria-diatom/dinoflagellate blooms and their cyanotoxins in freshwaters: A nonnegligible chronic health and ecological hazard

Human and ecological health depends on the vitality of freshwater systems, but these are increasingly threatened by cyanotoxins released from harmful algal blooms (HABs). Periodic cyanotoxin production, although undesirable, may be tolerable when there is enough time for cyanotoxins to degrade and dissipate in the environment, but the year-round presence of these toxins will be a chronic health for humans and ecosystems. The purpose of this critical review is to document the seasonal shifts of algal species and their ecophysiological acclimatation to dynamic environmental conditions. We discuss how these conditions will create successive occurrences of algal blooms and the release of cyanotoxins into freshwater. We first review the most common cyanotoxins, and evaluate the multiple ecological roles and physiological functions of these toxins for algae. Then, the annual recurring patterns HABs are considered in the context of global change, which demonstrates the capacity for algal blooms to shift from seasonal to year-round growth regimes that are driven by abiotic and biotic factors, leading to chronic loading of freshwaters with cyanotoxins. At last, we illustrate the impacts of HABs on the environment by compiling four health issues and four ecology issues emanating from their presence in the that covers atmosphere, aquatic ecosystems and terrestrial ecosystems. Our study highlights the annual patterns of algal blooms, and proposes that a "perfect storm" of events is lurking that will cause the 'seasonal toxicity' to become a full-blown, 'chronic toxicity' in the context of the deterioration of HABs, highlighting a non-negligible chronic health and ecological hazard.