Network analysis reveals succession of Microcystis genotypes accompanying distinctive microbial modules with recurrent patterns

Response of particle-attached and free-living bacterial communities to Microcystis blooms

The massive proliferation of Microcystis threatens freshwater ecosystems and degrades water quality globally. Understanding the mechanisms that contribute to Microcystis growth is crucial for managing Microcystis blooms. The lifestyles of bacteria can be classified generally into two groups: particle-attached (PA; > 3 µm) and free-living (FL; 0.2-3.0 µm). However, little is known about the response of PA and FL bacteria to Microcystis blooms. Using 16S rRNA gene high-throughput sequencing, we investigated the stability, assembly process, and co-occurrence patterns of PA and FL bacterial communities during distinct bloom stages. PA bacteria were phylogenetically different from their FL counterparts. Microcystis blooms substantially influenced bacterial communities. The time decay relationship model revealed that Microcystis blooms might increase the stability of both PA and FL bacterial communities. A contrasting community assembly mechanism was observed between the PA and FL bacterial communities. Throughout Microcystis blooms, homogeneous selection was the major assembly process that impacted the PA bacterial community, whereas drift explained much of the turnover of the FL bacterial community. Both PA and FL bacterial communities could be separated into modules related to different phases of Microcystis blooms. Microcystis blooms altered the assembly process of PA and FL bacterial communities. PA bacterial community appeared to be more responsive to Microcystis blooms than FL bacteria. Decomposition of Microcystis blooms may enhance cooperation among bacteria. Our findings highlight the importance of studying bacterial lifestyles to understand their functions in regulating Microcystis blooms. KEY POINTS: • Microcystis blooms alter the assembly process of PA and FL bacterial communities • Microcystis blooms increase the stability of both PA and FL bacterial communities • PA bacteria seem to be more responsive to Microcystis blooms than FL bacteria.

Insights into cyanobacterial blooms through the lens of omics

Cyanobacteria are oxygen-producing photosynthetic bacteria that convert carbon dioxide into biomass upon exposure to sunlight. However, favorable conditions cause harmful cyanobacterial blooms (HCBs), which are the dense accumulation of biomass at the water surface or subsurface, posing threats to freshwater ecosystems and human health. Understanding the mechanisms underlying cyanobacterial bloom formation is crucial for effective management. In this regard, recent advancements in omics technologies have provided valuable insights into HCBs, which have raised expectations to develop more effective control methods in the near future. This literature review aims to present the genomic architecture, adaptive mechanisms, microbial interactions, and ecological impacts of HCBs through the lens of omics. Genomic analysis indicates that the genome plasticity of cyanobacteria has enabled their resilience and effective adaptation to environmental changes. Transcriptomic investigations have revealed that cyanobacteria use various strategies for adapting to environmental stress. Additionally, metagenomic and metatranscriptomic analyses have emphasized the significant role of the microbial community in regulating HCBs. Finally, we offer perspectives on potential opportunities for further research in this field.

Effect of rainfall in shaping microbial community during Microcystis bloom in Nakdong River, Korea

Various environmental factors play a role in the formation and collapse of Microcystis blooms. This study investigates the impact of heavy rainfall on cyanobacterial abundance, microbial community composition, and functional dynamics in the Nakdong River, South Korea, during typical and exceptionally rainy years. The results reveal distinct responses to rainfall variations, particularly in cyanobacterial dominance and physicochemical characteristics. In 2020, characterized by unprecedented rainfall from mid-July to August, Microcystis blooms were interrupted significantly, exhibiting lower cell densities and decreased water temperature, compared to normal bloom patterns in 2019. Moreover, microbial community composition varied, with increases in Gammaproteobacteria and notably in genera of Limnohabitans and Fluviicola. These alterations in environmental conditions and bacterial community were similar to those of the post-bloom period in late September 2019. It shows that heavy rainfall during summer leads to changes in environmental factors, consequently causing shifts in bacterial communities akin to those observed during the autumn-specific post-bloom period in typical years. These changes also accompany shifts in bacterial functions, primarily involved in the degradation of organic matter such as amino acids, fatty acids, and terpenoids, which are assumed to have been released due to the significant collapse of cyanobacteria. Our results demonstrate that heavy rainfall in early summer induces changes in the environmental factors and subsequently microbial communities and their functions, similar to those of the post-bloom period in autumn, leading to the earlier breakdown of Microcystis blooms.

Characterization of Neowestiellopsis persica A1387 (Hapalosiphonaceae) based on the cpcA, psbA, rpoC1, nifH and nifD gene sequences

BACKGROUND

Complex descriptions of new strains of cyanobacteria appear very frequently. The main importance of these descriptions concerns potential new substances that they could synthesise, as well as their different properties as a result of their different ecological niches. The main gene used for these descriptions is 16 S with ITS or whole genome sequencing. Neowestiellopsis persica represents a unique example of the influence of ecology on morphological changes, with almost identical 16 S identity. Although our previously described Neowestiellopsis persica strain A1387 was characterized by 16 S analysis, we used different molecular markers to provide a way to separate strains of this genus that are closely related at the genetic level.

MATERIALS AND METHODS

In order to conduct an in-depth study, several molecular markers, namely psbA, rpoC1, nifD, nifH and cpcA were sequenced and studied in Neowestiellopsis persica strain A1387.

RESULTS

The results of the phylogenetic analysis, based on cpcA, showed that the studied strain A 1387 falls into a separate clade than N. persica, indicating that this signature sequence could be a useful molecular marker for phylogenetic separation of similar strains isolated in the future.

CONCLUSIONS

Analysis of strain A1387 based on gene differences confirmed that it is a Neowestiellopsis strain. The morphological changes observed in the previous study could be due to different ecological and cultivation conditions compared to the type species. At the same time, the sequences obtained have increased our understanding of this species and will help in the future to better identify strains belonging to the genus Neowestiellopsis.

Impact of persistently high sea surface temperatures on the rhizobiomes of Zostera marina in a Baltic Sea benthocosms

Persistently high marine temperatures are escalating and threating marine biodiversity. The Baltic Sea, warming faster than other seas, is a good model to study the impact of increasing sea surface temperatures. Zostera marina, a key player in the Baltic ecosystem, faces susceptibility to disturbances, especially under chronic high temperatures. Despite the increasing number of studies on the impact of global warming on seagrasses, little attention has been paid to the role of the holobiont. Using an outdoor benthocosm to replicate near-natural conditions, this study explores the repercussions of persistent warming on the microbiome of Z. marina and its implications for holobiont function. Results show that both seasonal warming and chronic warming, impact Z. marina roots and sediment microbiome. Compared with roots, sediments demonstrate higher diversity and stability throughout the study, but temperature effects manifest earlier in both compartments, possibly linked to premature Z. marina die-offs under chronic warming. Shifts in microbial composition, such as an increase in organic matter-degrading and sulfur-related bacteria, accompany chronic warming. A higher ratio of sulfate-reducing bacteria compared to sulfide oxidizers was found in the warming treatment which may result in the collapse of the seagrasses, due to toxic levels of sulfide. Differentiating predicted pathways for warmest temperatures were related to sulfur and nitrogen cycles, suggest an increase of the microbial metabolism, and possible seagrass protection strategies through the production of isoprene. These structural and compositional variations in the associated microbiome offer early insights into the ecological status of seagrasses. Certain taxa/genes/pathways may serve as markers for specific stresses. Monitoring programs should integrate this aspect to identify early indicators of seagrass health. Understanding microbiome changes under stress is crucial for the use of potential probiotic taxa to mitigate climate change effects. Broader-scale examination of seagrass-microorganism interactions is needed to leverage knowledge on host-microbe interactions in seagrasses.

Loss of submerged macrophytes in shallow lakes alters bacterial and archaeal community structures, and reduces their co-occurrence networks connectivity and complexity

Introduction

Bacteria and archaea are important components in shallow lake ecosystems and are crucial for biogeochemical cycling. While the submerged macrophyte loss is widespread in shallow lakes, the effect on the bacteria and archaea in the sediment and water is not yet widely understood.

Methods

In this study, 16S rRNA gene sequencing was used to explore the bacteria and archaea in samples taken from the sediment and water in the submerged macrophyte abundant (MA) and submerged macrophyte loss (ML) areas of Caohai Lake, Guizhou, China.

Results

The results showed that the dominant bacterial phyla were Proteobacteria and Chloroflexi in the sediment; the dominant phyla were Proteobacteria, Actinobacteriota, and Bacteroidota in the water. The dominant archaea in sediment and water were the same, in the order of Crenarchaeota, Thermoplasmatota, and Halobacterota. Non-metric multidimensional scaling (NMDS) analyses showed that bacterial and archaeal community structures in the water were significantly affected by the loss of submerged macrophytes, but not by significant changes in the sediment. This suggests that the loss of submerged macrophytes has a stronger effect on the bacterial and archaeal community structures in water than in sediment. Furthermore, plant biomass (PB) was the key factor significantly influencing the bacterial community structure in water, while total nitrogen (TN) was the main factor significantly influencing the archaeal community structure in water. The loss of submerged macrophytes did not significantly affect the alpha diversity of the bacterial and archaeal communities in either the sediment or water. Based on network analyses, we found that the loss of submerged macrophytes reduced the connectivity and complexity of bacterial patterns in sediment and water. For archaea, network associations were stronger for MA network than for ML network in sediment, but network complexity for archaea in water was not significantly different between the two areas.

Discussion

This study assesses the impacts of submerged macrophyte loss on bacteria and archaea in lakes from microbial perspective, which can help to provide further theoretical basis for microbiological research and submerged macrophytes restoration in shallow lakes.

Harmful algal blooms in Cayuga lake, NY: From microbiome analysis to eDNA monitoring

The global increase in harmful algal blooms (HABs) has become a growing concern over the years, and New York State (NYS) is no exception. The Finger Lakes region in NYS has been identified as a hotspot for HABs, with Cayuga Lake having the highest number of blooms reported. The Cayuga Lake HABs Monitoring Program has been tracking cHABs (dominant bloom taxa, chlorophyll A, and microcystin levels) since 2018. However, limited research has been conducted on the microbiome of HABs in this region. In this study, the microbiome of HABs in the Cayuga Lake was surveyed and compared with non-HAB baseline samples. Using 16S rDNA community analysis, common bloom-forming cyanobacteria, were identified, with Microcystis being the dominant taxa in high toxin blooms. Further, this study evaluated the ability of Microcystis mcyA qPCR to detect elevated levels of potential toxigenic Microcystis in water samples using both benchtop and handheld qPCR devices. The results showed good performance of the qPCR assay as a screening for high toxin versus low/no toxin blooms. Additionally, the handheld qPCR device holds potential for in-field rapid (<1 h) screenings for high toxin blooms. This study provides insights into the microbiome of HABs in Cayuga Lake and offers a potential tool for rapid screening of high toxin blooms.

Dynamic response of bacterial communities to Microcystis blooms: A three-year study

Although nutrient availability is widely recognized as the driving force behind Microcystis blooms, identifying the microorganisms that play a pivotal role in their formation is a challenging task. Our understanding of the contribution of bacterial communities to the development of Microcystis blooms remains incomplete, despite the fact that the relationship between Microcystis and bacterial communities has been extensively investigated. Most studies have focused on their interaction for a single year rather than for multiple years. To determine key bacteria crucial for the formation of Microcystis blooms, we collected samples from three sites in the Daechung Reservoir (Chuso, Hoenam, and Janggye) over three years (2017, 2019, and 2020). Our results indicated that Microcystis bloom-associated bacterial communities were more conserved across stations than across years. Bacterial communities could be separated into modules corresponding to the different phases of Microcystis blooms. Dolichospermum and Aphanizomenon belonged to the same module, whereas the module of Microcystis was distinct. The microbial recurrent association network (MRAN) showed that amplicon sequence variants (ASVs) directly linked to Microcystis belonged to Pseudanabaena, Microscillaceae, Sutterellaceae, Flavobacterium, Candidatus Aquiluna, Bryobacter, and DSSD61. These ASVs were also identified as key indicators of the bloom stage, indicating that they were fundamental biological elements in the development of Microcystis blooms. Overall, our study highlights that, although bacterial communities change annually, they continue to share core ASVs that may be crucial for the formation and maintenance of Microcystis blooms.

Variation in resource competition traits among Microcystis strains is affected by their microbiomes

Freshwater harmful algal blooms are often dominated by Microcystis, a phylogenetically cohesive group of cyanobacteria marked by extensive genetic and physiological diversity. We have previously shown that this genetic diversity and the presence of a microbiome of heterotrophic bacteria influences competitive interactions with eukaryotic phytoplankton. In this study, we sought to explain these observations by characterizing Monod equation parameters for resource usage (maximum growth rate μ max, half-saturation value for growth K s, and quota) as a function of N and P levels for four strains (NIES-843, PCC 9701, PCC 7806 [WT], and PCC 7806 ΔmcyB) in presence and absence of a microbiome derived from Microcystis isolated from Lake Erie. Results indicated limited differences in maximum growth rates but more pronounced differences in half-saturation values among Microcystis strains. The largest impact of the microbiome was reducing the minimal nitrogen concentration sustaining growth and reducing half saturation values, with variable results depending on the Microcystis strain. Microcystis strains also differed from each other in their N and P quotas and the extent to which microbiome presence affected them. Our data highlight the importance of the microbiome in altering Microcystis-intrinsic traits, strain competitive hierarchies, and thus bloom dynamics. As quota, μ max, and K s are commonly used in models for harmful algal blooms, our data suggest that model improvement may be possible by incorporating genotype dependencies of resource-use parameters.

Phytoplankton interspecific interactions modified by symbiotic fungi and bacterial metabolites under environmentally relevant hydrogen peroxide concentrations stress

Hydrogen peroxide (H2O2), which accumulates in water and triggers oxidative stress for aquatic microbes, has been shown to have profound impacts on planktonic microbial community dynamics including cyanobacterial bloom formation. Yet, potential effects of H2O2 on interspecific relationships of phytoplankton-microbe symbiotic interactions remain unclear. Here, we investigated effects of environmentally relevant H2O2 concentrations on interspecific microbial relationships in algae-microbe symbiosis. Microbes play a crucial role in the competition between M. aeruginosa and Chlorella vulgaris at low H2O2 concentrations (∼400 nM), in which fungi and bacteria protect Microcystis aeruginosa from oxidative stress. Moreover, H2O2 stimulated the synthesis and release of extracellular microcystin-LR from Microcystis aeruginosa, while intracellular microcystin-LR concentrations remained at a relatively constant level. In the presence of H2O2, loss of organoheterocyclic compounds, organic acids and ketones contributed to the growth of M. aeruginosa, but the reduction of vitamins inhibited it. Regulation of interspecific relationships by H2O2 is achieved by its action on fungal species and bacterial secretory metabolites. This study explored the response of phytoplankton interspecific relationships in symbiotic phytoplankton-microbe interactions to environmentally relevant H2O2 concentrations stress, providing a theoretical basis for understanding the formation of harmful-algae blooming and impact of photochemical properties of water on aquatic ecological safety and stability.

Selection for oligotrophy among bacteria inhabiting host microbiomes

IMPORTANCE

Understanding how natural selection has historically shaped the traits of microbial populations comprising host microbiomes would help predict how the functions of these microbes may continue to evolve over space and time. Numerous host-associated microbes have been found to adapt to their host, sometimes becoming obligate symbionts, whereas free-living microbes are best known to adapt to their surrounding environment. Our study assessed the selective pressures of both the host environment and the surrounding external environment in shaping the functional potential of host-associated bacteria. Despite residing within the resource-rich microbiome of their hosts, we demonstrate that host-associated heterotrophic bacteria show evidence of trait selection that matches the nutrient availability of their broader surrounding environment. These findings illustrate the complex mix of selective pressures that likely shape the present-day function of bacteria found inhabiting host microbiomes. Our study lends insight into the shifts in function that may occur as environments fluctuate over time.

The Bacterial Microbiome of the Coral Skeleton Algal Symbiont Ostreobium Shows Preferential Associations and Signatures of Phylosymbiosis

Ostreobium, the major algal symbiont of the coral skeleton, remains understudied despite extensive research on the coral holobiont. The enclosed nature of the coral skeleton might reduce the dispersal and exposure of residing bacteria to the outside environment, allowing stronger associations with the algae. Here, we describe the bacterial communities associated with cultured strains of 5 Ostreobium clades using 16S rRNA sequencing. We shed light on their likely physical associations by comparative analysis of three datasets generated to capture (1) all algae associated bacteria, (2) enriched tightly attached and potential intracellular bacteria, and (3) bacteria in spent media. Our data showed that while some bacteria may be loosely attached, some tend to be tightly attached or potentially intracellular. Although colonised with diverse bacteria, Ostreobium preferentially associated with 34 bacterial taxa revealing a core microbiome. These bacteria include known nitrogen cyclers, polysaccharide degraders, sulphate reducers, antimicrobial compound producers, methylotrophs, and vitamin B12 producers. By analysing co-occurrence networks of 16S rRNA datasets from Porites lutea and Paragoniastrea australensis skeleton samples, we show that the Ostreobium-bacterial associations present in the cultures are likely to also occur in their natural environment. Finally, our data show significant congruence between the Ostreobium phylogeny and the community composition of its tightly associated microbiome, largely due to the phylosymbiotic signal originating from the core bacterial taxa. This study offers insight into the Ostreobium microbiome and reveals preferential associations that warrant further testing from functional and evolutionary perspectives.

Actinobacteria produce taste and odor in drinking water reservoir: Community composition dynamics, co-occurrence and inactivation models

Taste and odor (T&O) has become a significant concern for drinking water safety. Actinobacteria are believed to produce T&O during the non-algal bloom period; however, this has not been widely investigated. In this study, the seasonal dynamics of the actinobacterial community structure and inactivation of odor-producing actinobacteria were explored. The results indicated that the diversity and community composition of actinobacteria exhibited significant spatiotemporal distribution. Network analysis and structural equation modeling showed that the actinobacterial community occupied a similar environmental niche, and the major environmental attributes exhibited spatiotemporal dynamics, which affected the actinobacterial community. Furthermore, the two genera of odorous actinobacteria were inactivated in drinking water sources using chlorine. Amycolatopsis spp. have a stronger chlorine resistance ability than Streptomyces spp., indicating that chlorine inactivates actinobacteria by first destroying cell membranes and causing the release of intracellular compounds. Finally, we integrated the observed variability in the inactivation rate of actinobacteria into an expanded Chick-Watson model to estimate its effect on inactivation. These findings will deepen our understanding of the seasonal dynamics of actinobacterial community structure in drinking water reservoirs and provide a foundation for reservoir water quality management strategies.

Bimetallic Metal-Organic Frameworks as an Efficient Capture Probe in Signal On-Off-On Electrochemiluminescence Aptasensor for Microcystin-LR Detection

To ensure drinking water quality, the development of rapid and accurate analytical methods is essential. Herein, a highly sensitive electrochemiluminescence (ECL) aptasensor-based on the signal on-off-on strategy was developed to detect the water pollutant microcystin-LR (MC-LR). This strategy was based on a newly prepared ruthenium-copper metal-organic framework (RuCu MOF) as the ECL signal-transmitting probe and three types of PdPt alloy core-shell nanocrystals with different crystal structures as signal-off probes. Compounding the copper-based MOF (Cu-MOF) precursor with ruthenium bipyridyl at room temperature facilitated the retention of the intrinsic crystallinity and high porosity of the MOFs as well as afforded excellent ECL performance. Since bipyridine ruthenium in RuCu MOFs could transfer energies to the organic ligand (H₃BTC), the ultra-efficient ligand luminescent ECL signal probe was finally obtained, which greatly improved the sensitivity of the aptasensor. To further improve the sensitivity of the aptasensor, the quenching effects of noble metal nanoalloy particles with different crystal states were investigated, which contained PdPt octahedral (PdPt_Oct), PdPt rhombic dodecahedral (PdPt_RD), and PdPt nanocube (PdPt_NC). Among them, the PdPt_RD nanocrystal exhibited higher activity and excellent durability, stemming from the charge redistribution caused by the hybridization of Pt and Pd atoms. Moreover, PdPt_RD could also load more -NH₂-DNA strands because it exposed more active sites with a large specific surface area. The fabricated aptasensor exhibited outstanding sensitivity and stability in MC-LR detection, with a linear detection range of 0.0001-50 ng mL^-1. This study provides valuable directions for the application of alloy nanoparticles of noble metals and bimetallic MOFs in the field of ECL immunoassay.

Vegetation as a key driver of the distribution of microbial generalists that in turn shapes the overall microbial community structure in the low Arctic tundra

Understanding the variability of microbial niches and their interaction with abiotic and biotic factors in the Arctic can provide valuable insights into microbial adaptations to extreme environments. This study investigates the structure and diversity of soil bacterial communities obtained from sites with varying vegetation coverage and soil biogeochemical properties in the low Arctic tundra and explores how bacteria interact under different environmental parameters. Our findings reveal differences in bacterial composition and abundance among three bacterial niche breadths (specialists, common taxa, and generalists). Co-occurrence network analysis revealed Rhizobiales and Ktedonobacterales as keystone taxa that connect and support other microbes in the habitat. Low-elevation indicators, such as vascular plants and moisture content, were correlated with two out of three generalist modular hubs and were linked to a large proportion of generalists' distribution (18%). Structural equation modeling revealed that generalists' distribution, which influenced the remaining microbial communities, was mainly regulated by vegetation coverage as well as other abiotic and biotic factors. These results suggest that elevation-dependent environmental factors directly influence microbial community structure and module formation through the regulation of generalists' distribution. Furthermore, the distribution of generalists was mainly affected by macroenvironment filtering, whereas the distribution of specialists was mainly affected by microenvironment filtering (species-engineered microbial niche construction). In summary, our findings highlight the strong top-down control exerted by vegetation on generalists' distribution, which in turn shapes the overall microbial community structure in the low Arctic tundra.

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.

Viruses may facilitate the cyanobacterial blooming during summer bloom succession in Xiangxi Bay of Three Gorges Reservoir, China

The occurrence of cyanobacterial blooms in summer are frequently accompanied by the succession of phytoplankton communities in freshwater. However, little is known regarding the roles of viruses in the succession, such as in huge reservoirs. Here, we investigated the viral infection characteristics of phytoplankton and bacterioplankton during the summer bloom succession in Xiangxi Bay of Three Gorges Reservoir, China. The results indicated that three distinct bloom stages and two successions were observed. From cyanobacteria and diatom codominance to cyanobacteria dominance, the first succession involved different phyla and led to a Microcystis bloom. From Microcystis dominance to Microcystis and Anabaena codominance, the second succession was different Cyanophyta genera and resulted in the persistence of cyanobacterial bloom. The structural equation model (SEM) showed that the virus had positive influence on the phytoplankton community. Through the Spearman’s correlation and redundancy analysis (RDA), we speculated that both the increase of viral lysis in the eukaryotic community and the increase of lysogeny in cyanobacteria may contributed to the first succession and Microcystis blooms. In addition, the nutrients supplied by the lysis of bacterioplankton might benefit the second succession of different cyanobacterial genera and sustain the dominance of cyanobacteria. Based on hierarchical partitioning method, the viral variables still have a marked effect on the dynamics of phytoplankton community, although the environmental attributes were the major factors. Our findings suggested that viruses played multiple potential roles in summer bloom succession and may help the blooms success of cyanobacteria in Xiangxi Bay. Under the background of increasingly serious cyanobacterial blooms worldwide, our study may have great ecological and environmental significance for understanding the population succession in phytoplankton and controlling the cyanobacterial blooms.

Unravelling microalgal-bacterial interactions in aquatic ecosystems through 16S rRNA gene-based co-occurrence networks

Interactions between microalgae and bacteria can directly influence the global biogeochemical cycles but the majority of such interactions remain unknown. 16S rRNA gene-based co-occurrence networks have potential to help identify microalgal-bacterial interactions. Here, we used data from 10 Earth microbiome projects to identify potential microalgal-bacterial associations in aquatic ecosystems. A high degree of clustering was observed in microalgal-bacterial modules, indicating densely connected neighbourhoods. Proteobacteria and Bacteroidetes predominantly co-occurred with microalgae and represented hubs of most modules. Our results also indicated that species-specificity may be a global characteristic of microalgal associated microbiomes. Several previously known associations were recovered from our network modules, validating that biologically meaningful results can be inferred using this approach. A range of previously unknown associations were recognised such as co-occurrences of Bacillariophyta with uncultured Planctomycetes OM190 and Deltaproteobacteria order NB1-j. Planctomycetes and Verrucomicrobia were identified as key associates of microalgae due to their frequent co-occurrences with several microalgal taxa. Despite no clear taxonomic pattern, bacterial associates appeared functionally similar across different environments. To summarise, we demonstrated the potential of 16S rRNA gene-based co-occurrence networks as a hypothesis-generating framework to guide more focused research on microalgal-bacterial associations.

Coexistence of Synechococcus and Microcystis Blooms in a Tropical Urban Reservoir and Their Links with Microbiomes

Bacteria play a crucial role in driving ecological processes in aquatic ecosystems. Studies have shown that bacteria-cyanobacteria interactions contributed significantly to phytoplankton dynamics. However, information on the contribution of bacterial communities to blooms remains scarce. Here, we tracked changes in the bacterial community during the development of a cyanobacterial bloom in an equatorial estuarine reservoir. Two forms of blooms were observed simultaneously corresponding to the lotic and lentic characteristics of the sampling sites where significant spatial variabilities in physicochemical water quality, cyanobacterial biomass, secondary metabolites, and cyanobacterial/bacterial compositions were detected. Microcystis dominated the upstream sites during peak periods and were succeeded by Synechococcus when the bloom subsided. For the main body of the reservoir, a mixed bloom featuring coccoid and filamentous cyanobacteria (Microcystis, Synechococcus, Planktothricoides, Nodosilinea, Raphidiopsis, and Prochlorothrix) was observed. Concentrations of the picocyanobacteria Synechococcus remained high throughout the study, and their positive correlations with cylindrospermopsin and anatoxin-a suggested that they could produce cyanotoxins, which pose more damaging impacts than previously supposed. Succession of different cyanobacteria (Synechococcus and Microcystis) following changes in nutrient composition and ionic strength was demonstrated. The microbiomes associated with blooms were unique to the dominant cyanobacteria. Generic and specialized bloom biomarkers for the Microcystis and downstream mixed blooms were also identified. Microscillaceae, Chthoniobacteraceae, and Roseomonas were the major heterotrophic bacteria associated with Microcystis bloom, whereas Phycisphaeraceae and Methylacidiphilaceae were the most prominent groups for the Synechococcus bloom. Collectively, bacterial community can be greatly deviated by the geological condition, monsoon season, cyanobacterial density, and dominant cyanobacteria.

Microcystis pangenome reveals cryptic diversity within and across morphospecies

Microcystis, a common harmful algal bloom (HAB) taxon, threatens water supplies and human health, yet species delimitation is contentious in this taxon, leading to challenges in research and management of this threat. Historical and common morphology-based classifications recognize multiple morphospecies, most with variable and diverse ecologies, while DNA sequence-based classifications indicate a single species with multiple ecotypes. To better delimit Microcystis species, we conducted a pangenome analysis of 122 genomes. Core- and non-core gene phylogenetic analyses placed 113 genomes into 23 monophyletic clusters containing at least two genomes. Overall, genome-related indices revealed that Microcystis contains at least 16 putative genospecies. Fifteen genospecies included at least one Microcystis aeruginosa morphospecies, and 10 genospecies included two or more morphospecies. This classification system will enable consistent taxonomic identification of Microcystis and thereby aid in resolving some of the complexities and controversies that have long characterized eco-evolutionary research and management of this important HAB taxon.

Temporal and functional interrelationships between bacterioplankton communities and the development of a toxigenic Microcystis bloom in a lowland European reservoir

The cyanobacteria-associated microbiome is constantly reshaped by bloom development. However, the synergistic-antagonistic nature of the relationships between Microcystis and its microbiome still remains unclear. Therefore, temporal changes of bacterioplankton communities and their functional potential through different developing stages of a Microcystis toxigenic bloom were investigated, considering bacterioplankton assemblages as particle-attached (PAB) and free-living (FLB) bacteria. 16S rRNA sequencing revealed that PAB were represented by Proteobacteria and Cyanobacteria, while FLB by Proteobacteria and Actinobacteria. Network and ordination analyses indicated that PAB inter-relationships were more complex-numerous connections between taxa with stronger correlations, than FLB-rather influenced by physico-chemical parameters. PAB in pre-summer was diverse with Proteobacteria containing potential taxa involved in nitrogen-transforming processes. In mid-summer, PAB presented a mix-bloom dominated by Snowella, Aphanizomenon, and Microcystis, which were succeeded by toxigenic Microcystis in post-summer. Both periods were associated to potential taxa with parasitic/predatory lifestyles against cyanobacteria. In post-summer, Sutterellaceae were recognized as poor water quality indicators, and their strong association with Microcystis could have represented an increased threat for that period. Microcystis was a major factor significantly reducing PAB diversity and evenness, suggesting that it negatively influenced bacterioplankton assemblages, probably also altering the overall community functional potential.

Linking microbiomes with per- and poly-fluoroalkyl substances (PFASs) in soil ecosystems: Microbial community assembly, stability, and trophic phylosymbiosis

Microbiomes are vital in promoting nutrient cycling and plant growth in soil ecosystems. However, microbiomes face adverse effects from multiple persistent pollutants, including per- and poly-fluoroalkyl substances (PFASs). PFASs threaten the fertility and health of soil ecosystems, yet the response of microbial community stability and trophic transfer efficiencies to PFASs is still poorly understood. This study explored the spatial patterns of PFASs in topsoil environments from the West Taihu Lake Basin of China and links their presence to soil microbial community stability at compositional and functional levels. Our results revealed that PFBA (13.87%), PFTrDA (11.63%), PFDoA (11.02%), PFOA (10.99%), and PFOS (10.39%) contributed the most to the spatial occurrence of PFASs. Soil properties, including salinity (14.47%), uniformity (9.68%), dissolved inorganic carbon (8.62%), and clay content (8.18%), affected PFASs distribution the most. In soil microbiomes, eukaryotic taxa had wider niche breadths and stronger community stability than prokaryotes when exposed to PFASs (p < 0.05). The presence of PFBA and PFHpA inhibited the functional stability of archaeal and bacterial communities (p < 0.05). PFBA and PFPeA reduced the structural stability of heterotrophic bacteria and Myxobacteria, respectively (p < 0.05). Based on null modeling, PFPeA significantly regulated the assembly processes of most microbial sub-communities (p < 0.01). The trophic transferring efficiencies of autotrophic bacteria to metazoan organisms were directly stimulated by PFASs (p < 0.05), and the potential trophic transferring efficiencies of methanogenic archaea to protozoa were inhibited by PFASs (p < 0.05). This study highlighted the potential contributions of PFASs to soil microbial community stability and food webs during ecological soil management.

Evaluation of phoxim toxicity on aquatic and zebrafish intestinal microbiota by metagenomics and 16S rRNA gene sequencing analysis

Phoxim is one of the main organophosphorus pesticides used in agricultural production. However, little information is known about how it affects the aquatic microbial community and the intestinal microbiota of fish. Herein, we utilized shotgun metagenomics and 16S rRNA gene sequencing to reveal the aquatic eco-risk of phoxim. Seven days of phoxim exposure significantly changed the composition of aquatic microbial community, obliterated the interactions between microorganisms, and thus reduced the complexity and stability of the microbial community. During long-time exposure (i.e., 14 days), most of the ecological functions were restored due to the redundancy of the microbial community. However, phoxim exposure promoted the dissemination of elfamycin resistance gene. The zebrafish gut microbial community also recovered from a temporary ecological disorder of aquatic microbiota, but phoxim continually affected zebrafish growth and swimming behavior. Overall, our results demonstrated that phoxim exposure significantly changed the structure and function of the microbial community and displayed a negative impact on freshwater ecosystems in a short exposure time.

Microcystis colony formation: Extracellular polymeric substance, associated microorganisms, and its application

Microcystis sp., amongst the most prevalent bloom-forming cyanobacteria, is typically found as a colonial form with multiple microorganisms embedded in the mucilage known as extracellular polymeric substance. The colony-forming ability of Microcystis has been thoroughly investigated, as has the connection between Microcystis and other microorganisms, which is crucial for colony development. The following are the key subjects to comprehend Microcystis bloom in depth: 1) key issues related to the Microcystis bloom, 2) features and functions of extracellular polymeric substance, as well as diversity of associated microorganisms, and 3) applications of Microcystis-microorganisms interaction including bloom control, polluted water bioremediation, and bioactive compound production. Future research possibilities and recommendations regarding Microcystis-microorganism interactions and their significance in Microcystis colony formation are also explored. More information on such interactions, as well as the mechanism of Microcystis colony formation, can bring new insights into cyanobacterial bloom regulation and a better understanding of the aquatic ecosystem.

Extra benefit of microalgae in raw piggery wastewater treatment: pathogen reduction

BACKGROUND

Monitoring microbial communities especially focused on pathogens in newly developed wastewater treatment systems is recommended for public health. Thus, we investigated the microbial community shift in a pilot-scale microalgal treatment system for piggery wastewater.

RESULTS

Microalgae showed reasonable removal efficiencies for COD and ammonia, resulting in higher transparency of the final effluent. Metagenome and microbial diversity analyses showed that heterotrophic microalgal cultivation barely changed the bacterial community; however, the mixotrophic microalgal cultivation induced a sudden change. In addition, an evaluation of risk groups (RGs) of bacteria showed that raw piggery wastewater included abundant pathogens, and the microalgal treatment of the raw piggery wastewater decreased the RG2 pathogens by 63%. However, co-cultivation of microalgae and the most dominant RG2 pathogen, Oligella, showed no direct effects between them.

CONCLUSIONS

Thus, a microbial interaction network was constructed to elucidate algae-bacteria interrelationships, and the decrease in Oligella was indirectly connected with microalgal growth via Brevundimonas, Sphingopyxis, and Stenotrophomonas. In a validation test, 3 among 4 connecting bacterial strains exhibited inhibition zones against Oligella. Therefore, we showed that microalgal wastewater treatment causes a decrease in RG2 bacteria, which is an indirect impact of microalgae associated with bacteria. Video abstract.

Uptake of Phytoplankton-Derived Carbon and Cobalamins by Novel Acidobacteria Genera in Microcystis Blooms Inferred from Metagenomic and Metatranscriptomic Evidence

Interactions between bacteria and phytoplankton can influence primary production, community composition, and algal bloom development. However, these interactions are poorly described for many consortia, particularly for freshwater bloom-forming cyanobacteria. Here, we assessed the gene content and expression of two uncultivated Acidobacteria from Lake Erie Microcystis blooms. These organisms were targeted because they were previously identified as important catalase producers in Microcystis blooms, suggesting that they protect Microcystis from H₂O₂. Metatranscriptomics revealed that both Acidobacteria transcribed genes for uptake of organic compounds that are known cyanobacterial products and exudates, including lactate, glycolate, amino acids, peptides, and cobalamins. Expressed genes for amino acid metabolism and peptide transport and degradation suggest that use of amino acids and peptides by Acidobacteria may regenerate nitrogen for cyanobacteria and other organisms. The Acidobacteria genomes lacked genes for biosynthesis of cobalamins but expressed genes for its transport and remodeling. This indicates that the Acidobacteria obtained cobalamins externally, potentially from Microcystis, which has a complete gene repertoire for pseudocobalamin biosynthesis; expressed them in field samples; and produced pseudocobalamin in axenic culture. Both Acidobacteria were detected in Microcystis blooms worldwide. Together, the data support the hypotheses that uncultured and previously unidentified Acidobacteria taxa exchange metabolites with phytoplankton during harmful cyanobacterial blooms and influence nitrogen available to phytoplankton. Thus, novel Acidobacteria may play a role in cyanobacterial physiology and bloom development. IMPORTANCE Interactions between heterotrophic bacteria and phytoplankton influence competition and successions between phytoplankton taxa, thereby influencing ecosystem-wide processes such as carbon cycling and algal bloom development. The cyanobacterium Microcystis forms harmful blooms in freshwaters worldwide and grows in buoyant colonies that harbor other bacteria in their phycospheres. Bacteria in the phycosphere and in the surrounding community likely influence Microcystis physiology and ecology and thus the development of freshwater harmful cyanobacterial blooms. However, the impacts and mechanisms of interaction between bacteria and Microcystis are not fully understood. This study explores the mechanisms of interaction between Microcystis and uncultured members of its phycosphere in situ with population genome resolution to investigate the cooccurrence of Microcystis and freshwater Acidobacteria in blooms worldwide.

Gene expression in the microbial consortia of colonial Microcystis aeruginosa-a potential buoyant particulate biofilm

Microcystis spp., notorious bloom-forming cyanobacteria, are often present in colony form in eutrophic lakes worldwide. Uncovering the mechanisms underlying Microcystis colony formation and maintenance is vital to control the blooms, but it has long been a challenge. Here, bacterial communities and gene expression patterns of colonial and unicellular forms of one non-axenic strain of Microcystis aeruginosa isolated from Lake Taihu were compared. Evidently, different microbial communities between them were observed through 16S rDNA MiSeq sequencing. Metatranscriptome analyses revealed that transcripts for pathways involved in bacterial biofilm formation, such as biosynthesis of peptidoglycan and arginine by Bacteroidetes, methionine biosynthesis, alginate metabolism, flagellum, and motility, as well as widespread colonization islands by Proteobacteria, were highly enriched in the colonial form. Furthermore, transcripts for nitrogen fixation and denitrification pathways by Proteobacteria that usually occur in biofilms were significantly enriched in the colonial Microcystis. Results revealed that microbes associated with Microcystis colonies play important roles through regulation of biofilm-related genes in colony formation and maintenance. Moreover, Microcystis colony represents a potential "buoyant particulate biofilm", which is a good model for biofilm studies. The biofilm features of colonial Microcystis throw a new light on management and control of the ubiquitous blooms in eutrophic waters. This article is protected by copyright. All rights reserved.

Temporal heterogeneity of bacterial communities and their responses to Raphidiopsis raciborskii blooms

To elucidate the interspecies connectivity between cyanobacteria and other bacteria (noncyanobacteria), microbial diversity and composition were investigated through high-throughput sequencing (HTS) in a drinking water reservoir in Chongqing city, Southwest China, during Raphidiopsis raciborskii blooms. Significant temporal changes were observed in microbial community composition during the sampling period, primarily reflected by variations in relative bacterial abundance. The modularity analysis of the network demonstrated that the bacterial community forms co-occurrence/exclusion patterns in response to variations in environmental factors. Moreover, five modules involved in the dynamic phases of the R. raciborskii bloom were categorized into the Pre-Bloom, Bloom, Post-Bloom, and Non-Bloom Groups. The reservoir was eutrophic (i.e., the average concentrations of total nitrogen (TN) and total phosphorus (TP) were 2.32 and 0.07 mg L^-1, respectively) during the investigation; however, Pearson's correlation coefficient showed that R. raciborskii was not significantly correlated with nitrogen and phosphorus. However, other environmental factors, such as water temperature, pH, and the permanganate index, were positively correlated with R. raciborskii. Importantly, Proteobacteria (α-, γ-Proteobacteria), Acidobacteria, Chloroflexi, and Firmicutes were preferentially associated with increased R. raciborskii blooms. These results suggested that the transition of R. raciborskii bloom-related microbial modules and their keystone species could be crucial in the development and collapse of R. raciborskii blooms and could provide a fundamental basis for understanding the linkage between the structure and function of the microbial community during bloom dynamics.

Network-based analysis reveals differences in plant assembly between the native and the invaded ranges

Associated with the introduction of alien species in a new area, interactions with other native species within the recipient community occur, reshaping the original community and resulting in a unique assemblage. Yet, the differences in community assemblage between native and invaded ranges remain unclear. Mediterranean grasslands provide an excellent scenario to study community assembly following transcontinental naturalisation of plant species. Here, we compared the community resemblance of plant communities in Mediterranean grasslands from both the native (Spain) and invaded (Chile) ranges. We used a novel approach, based on network analysis applied to co-occurrence analysis in plant communities, allowing us to study the co-existence of native and alien species in central Chile. This useful methodology is presented as a step forward in invasion ecology studies and conservation strategies. We found that community structure differed between the native and the invaded range, with alien species displaying a higher number of connections and, therefore, acting as keystones to sustain the structure within the invaded community. Alien species acting like keystones within the Chilean grassland communities might exacerbate the threat posed by biological invasions for the native biodiversity assets. Controlling the spread of the alien species identified here as keystones should help managing potential invasion in surrounding areas. Network analyses is a free, easy-to-implement and straightforward visual tool that can be widely used to reveal shifts in native communities and elucidate the role of multiple invaders into communities.

Comparing microscopy and DNA metabarcoding techniques for identifying cyanobacteria assemblages across hundreds of lakes

Accurately identifying the species present in an ecosystem is vital to lake managers and successful bioassessment programs. This is particularly important when monitoring cyanobacteria, as numerous taxa produce toxins and can have major negative impacts on aquatic ecosystems. Increasingly, DNA-based techniques such as metabarcoding are being used for measuring aquatic biodiversity, as they could accelerate processing time, decrease costs and reduce some of the biases associated with traditional light microscopy. Despite the continuing use of traditional microscopy and the growing use of DNA metabarcoding to identify cyanobacteria assemblages, methodological comparisons between the two approaches have rarely been reported from a wide suite of lake types. Here, we compare planktonic cyanobacteria assemblages generated by inverted light microscopy and DNA metabarcoding from a 379-lake dataset spanning a longitudinal and trophic gradient. We found moderate levels of congruence between methods at the broadest taxonomic levels (i.e., Order, RV=0.40, p < 0.0001). This comparison revealed distinct cyanobacteria communities from lakes of different trophic states, with Microcystis, Aphanizomenon and Dolichospermum dominating with both methods in eutrophic and hypereutrophic sites. This finding supports the use of either method when monitoring eutrophication in lake surface waters. The biggest difference between the two methods was the detection of picocyanobacteria, which are typically underestimated by light microscopy. This reveals that the communities generated by each method currently are complementary as opposed to identical and promotes a combined-method strategy when monitoring a range of trophic systems. For example, microscopy can provide measures of cyanobacteria biomass, which are critical data in managing lakes. Going forward, we believe that molecular genetic methods will be increasingly adopted as reference databases are routinely updated with more representative sequences and will improve as cyanobacteria taxonomy is resolved with the increase in available genetic information.

Dynamic Responses of Endosymbiotic Microbial Communities Within Microcystis Colonies in North American Lakes to Altered Nitrogen, Phosphorus, and Temperature Levels

The toxic cyanobacterium, Microcystis, is a pervasive cyanobacterial harmful algal bloom (CHAB) - forming genus that naturally occurs in colonies that harbor diverse microbiomes of heterotrophic bacteria. While the effects of nutrient loading and climatic warming on CHABs are well-known, little is known regarding how these environmental drivers alter the structural and functional potential of the microbial assemblages associated with blooms that, in turn, may impact cyanobacterial growth. Here, we used next-generation sequencing of 16S ribosomal rRNA genes to characterize the dynamics of the bacterial assemblages within Microcystis colonies in two temperate North American lakes: Lake Erie and Lake Agawam (NY, United States) and quantified their responses to experimentally increased levels of nitrogen (N), phosphorus (P) and temperature. Across experiments, Microcystis populations were consistently and significantly promoted by N and, to a lesser extent, elevated temperature (p < 0.05). In contrast, bacterial assemblages within Microcystis colonies were more resilient to environmental perturbations, with the relative abundance of 7–16% of amplicon sequence variants changing and several individual taxa displaying significant (p < 0.05) increases and decreases in relative abundance, primarily in response to elevated temperature and to a lesser extent, N. In contrast to individual taxa, community diversity was not significantly altered by individual treatments during experiments but rather was inversely correlated with the intensity of Microcystis blooms (p < 0.001). While predicted metabolic function was even less impacted by environmental drivers than microbial diversity, the predicted abundance of nitrogenase (nifH), alkaline phosphatase (phoX), and urease (ure) genes significantly increased in response to N but decreased in response to increased temperature (p < 0.05). Collectively, the resilience of microbial community structure and function within colonies suggests they may support the ability of Microcystis to persist through short-term fluctuations in environmental conditions by supplying essential nutrients.

Analysis of micropollutants in a marine outfall using network analysis and decision tree

The presence of micropollutants (MPs), including pharmaceutical, industrial, and pesticidal compounds, threatens both human health and the aquatic ecosystem. The development and extensive use of new chemicals have also inevitably led to the accumulation of MPs in aquatic environments. Recreational beaches are especially vulnerable to contamination, affecting humans and aquatic animals via the absorption of MPs in water during marine activities (e.g., swimming, sailing, and windsurfing). Additionally, marine outfalls in an urbanized coastal city can cause serious chemical and microbial pollution on recreational beaches, leading to an increase in adverse effects on public health and the ecological system. Therefore, the aim of this study was to, with the use of network and decision tree analyses, identify the features and factors that influence the change in MP concentrations in a marine outfall. These analyses were conducted to inspect the relationship between each MP and its hierarchical structure as well as hydrometeorological variables. Additionally, a risk analysis was conducted in this study in which the MPs were prioritized based on their optimized risk quotient values. During our monitoring of MP concentrations over time at the marine outfall, high concentrations of pharmaceutical and industrial compounds were detected when the tide level was low after rainfall. Furthermore, results of the risk analysis and the prioritization revealed that a total of 18 substances identified in our study posed a risk to the ecosystem; these include major ecotoxicologically hazardous substances such as telmisartan, mevinphos, and methiocarb. Results of the network analysis demonstrated distinct trends for pharmaceutical and industrial substances, whilst those for pesticide compounds were irregular. Additionally, the hierarchical structures for most MPs consisted of rainfall, tide level, and antecedent dry hours; this implies that these factors influence MP dynamics. These findings will be helpful for establishing chemical contamination management plans for recreational beaches in the future.

Linkage between bacterial community-mediated hydrogen peroxide detoxification and the growth of Microcystis aeruginosa

Microcystis aeruginosa, an important cyanobloom-forming cyanobacterium, is sensitive to the high light intensity and consequent oxidative stress. Based on our genomic and transcriptomic analyses of H₂O₂-treated cells, many genes involved in photosynthesis, Calvin cycle, and microcystin synthesis were downregulated, whereas several toxin-antitoxin genes, DNA repair genes, and H₂O₂-defense systems such as peroxiredoxins and glutathione synthesis were upregulated. Axenic M. aeruginosa was then co-cultured with synthetic bacterial communities collected from 15 different freshwater samples with exhibiting different degrees of H₂O₂-production and catalase activities. Our analyses indicated that H₂O₂-resistant bacterial communities favored the growth and photosynthetic activity of M. aeruginosa cells under either H₂O₂ treatment or high light conditions. Nanopore-based bacterial community analyses indicated that these growth-promoting effects were likely attributable to a high proportion of Alphaproteobacteria (e.g., Brevundimonas and Ochrobactrum species), which protected M. aeruginosa cells from H₂O₂ toxicity. Further, these bacterial communities exhibited higher catalase activity levels and faster O₂ production rates upon H₂O₂ detoxification. Taken together, our findings newly suggest that the occurrence of catalase-less M. aeruginosa blooms is largely influenced by the surrounding microbiota during high light and organic-rich conditions.

Cyanobacterial community succession and associated cyanotoxin production in hypereutrophic and eutrophic freshwaters

Cyanobacterial harmful algal blooms (cyanoHABs) in freshwater bodies are mainly attributed to excess loading of nutrients [nitrogen (N) and phosphorus (P)]. This study provides a comprehensive review of how the existing nutrient (i.e., N and P) conditions and microbial ecological factors affect cyanobacterial community succession and cyanotoxin production in freshwaters. Different eutrophic scenarios (i.e., hypereutrophic vs. eutrophic conditions) in the presence of (i) high levels of N and P, (ii) a relatively high level of P but a low level of N, and (iii) a relatively high level of N but a low level of P, are discussed in association with cyanobacterial community succession and cyanotoxin production. The seasonal cyanobacterial community succession is mostly regulated by temperature in hypereutrophic freshwaters, where both temperature and nitrogen fixation play a critical role in eutrophic freshwaters. While the early cyanoHAB mitigation strategies focus on reducing P from water bodies, many more studies show that both N and P have a profound contribution to cyanobacterial blooms and toxin production. The availability of N often shapes the structure of the cyanobacterial community (e.g., the relative abundance of N₂-fixing and non-N₂-fixing cyanobacterial genera) and is positively linked to the levels of microcystin. Ecological aspects of cyanotoxin production and release, related functional genes, and corresponding nutrient and environmental conditions are also elucidated. Research perspectives on cyanoHABs and cyanobacterial community succession are discussed and presented with respect to the following: (i) role of internal nutrients and their species, (ii) P- and N-based control vs. solely P-based control of cyanoHABs, and (iii) molecular investigations and prediction of cyanotoxin production.

Ecological network analysis reveals distinctive microbial modules associated with heavy metal contamination of abandoned mine soils in Korea

Heavy metal pollution in soil around abandoned mine sites is one of the most critical environmental issues worldwide. Soil microbes form complex communities and perform ecological functions individually or in cooperation with other organisms to adapt to harsh environments. In this study, we investigated the distribution patterns of bacterial and fungal communities in non-contaminated and heavy metal-contaminated soil of the abandoned Samkwang mine in Korea to explore microbial interaction mechanisms and their modular structures. As expected, the bacterial and fungal community structures showed large differences depending on the degree of heavy metal contamination. The microbial network was divided into three modules based on the levels of heavy metal pollution: heavy metal-tolerant (HM-Tol), heavy metal-mid-tolerant (HM-mTol), and heavy metal-sensitive (HM-Sens) modules. Taxonomically, microbes assigned to Vicinamibacterales, Pedosphaeraceae, Nitrosomonadaceae, and Gemmatimonadales were the major groups constituting the HM-Tol module. Among the detected heavy metals (As, Pb, Cd, Cu, and Zn), copper concentrations played a key role in the formation of the HM-Tol module. In addition, filamentous fungi (Fusarium and Mortierella) showed potential interactions with bacteria (Nitrosomonadaceae) that could contribute to module stability in heavy metal-contaminated areas. Overall, heavy metal contamination was accompanied by distinct microbial communities, which could participate in the bioremediation of heavy metals. Analysis of the microbial interactions among bacteria and fungi in the presence of heavy metals could provide fundamental information for developing bioremediation mechanisms for the recovery of heavy metal-contaminated soil.

Effects of Sugarcane and Soybean Intercropping on the Nitrogen-Fixing Bacterial Community in the Rhizosphere

Intercropping between sugarcane and soybean is widely used to increase crop yield and promote the sustainable development of the sugarcane industry. However, our understanding of the soil microenvironment in intercropping systems, especially the effect of crop varieties on rhizosphere soil bacterial communities, remains poor. We selected two excellent sugarcane cultivars, Zhongzhe1 (ZZ1) and Zhongzhe9 (ZZ9), from Guangxi and the local soybean variety GUIZAO2 from Guangxi for field interplanting experiments. These two cultivars of sugarcane have good drought resistance. Rhizosphere soil samples were collected from the two intercropping systems to measure physicochemical properties and soil enzyme activities and to extract total soil DNA for high-throughput sequencing. We found that the diversity of the rhizosphere bacterial community was significantly different between the two intercropping systems. Compared with ZZ1, the ZZ9 intercropping system enriched the nitrogen-fixing bacteria, increasing the available nitrogen content by 18% compared with that with ZZ1. In addition, ZZ9 intercropping with soybean formed a more compact rhizosphere environment than ZZ1, thus providing favorable conditions for sugarcane growth. These results provide guidance for the sugarcane industry, especially for the management of sugarcane and soybean intercropping in Guangxi, China.

Seasonal succession of microbes in different size-fractions and their modular structures determined by both macro- and micro-environmental filtering in dynamic coastal waters

Microbes interact with each other in response to various environmental changes in coastal marine ecosystems. To explore how the macroenvironment (environmental filtering) and species-engineered microenvironment (niche construction) affect the ecological network of the marine microbiome in the highly dynamic coastal waters of Korea, we analyzed the modular structures of the microbial community and identified microbial interconnections in different size fractions for a year. Fluctuations in the macroenvironment, such as temperature and nutrient concentrations driven by seasonal changes, are the major factors in determining successive microbial modules. Compared to particle-associated (PA) microbes, free-living (FL) microbes seemed to be more affected by macroenvironmental filtering. Modules related to nutrients were further divided into various modules according to different lifestyles. In addition, a large transient discharge of the Changjiang (Yangtze River) in summer also formed a distinct microbial module, which was related to the high ammonia concentration arising from phytoplankton degradation. Microbes belonging to the SAR11, SAR86, and SAR116 clades, Flavobacteriaceae, and MG IIa-L showed repeated interconnections in temperature-related modules, while the SAR202 clade, Marinimicrobia, DEV007 clade, and Arctic97B-4 and Sva0996 marine groups displayed repeated connections in nutrient-related modules. These 'skeleton'-forming microbes created species-engineered microenvironments, further fine-tuning microbial modular structures. Furthermore, they serve as keystone species for module stability by linking interdependent microbial partners within their own modules through universally beneficial metabolic activities. Therefore, they could reinforce the ecological resilience of microbial communities under abiotic and biotic perturbations in dynamic coastal waters. In conclusion, both macro- and micro-environmental filtering were important for determining the seasonal succession of microbial community structures.

Reviewing Interspecies Interactions as a Driving Force Affecting the Community Structure in Lakes via Cyanotoxins

The escalating occurrence of toxic cyanobacterial blooms worldwide is a matter of concern. Global warming and eutrophication play a major role in the regularity of cyanobacterial blooms, which has noticeably shifted towards the predomination of toxic populations. Therefore, understanding the effects of cyanobacterial toxins in aquatic ecosystems and their advantages to the producers are of growing interest. In this paper, the current literature is critically reviewed to provide further insights into the ecological contribution of cyanotoxins in the variation of the lake community diversity and structure through interspecies interplay. The most commonly detected and studied cyanobacterial toxins, namely the microcystins, anatoxins, saxitoxins, cylindrospermopsins and β-N-methylamino-L-alanine, and their ecotoxicity on various trophic levels are discussed. This work addresses the environmental characterization of pure toxins, toxin-containing crude extracts and filtrates of single and mixed cultures in interspecies interactions by inducing different physiological and metabolic responses. More data on these interactions under natural conditions and laboratory-based studies using direct co-cultivation approaches will provide more substantial information on the consequences of cyanotoxins in the natural ecosystem. This review is beneficial for understanding cyanotoxin-mediated interspecies interactions, developing bloom mitigation technologies and robustly assessing the hazards posed by toxin-producing cyanobacteria to humans and other organisms.

Co-existing water and sediment bacteria are driven by contrasting environmental factors across glacier-fed aquatic systems

Glacier-fed aquatic ecosystems provide habitats for diverse and active bacterial communities. However, the environmental vulnerabilities of co-existing water and sediment bacterial communities in these ecosystems remain unclear. Here, 16S rRNA gene sequencing was used to investigate co-existing bacterial communities in paired water and sediment samples from multiple rivers and lakes that are mainly fed by glaciers from the southeast Tibetan Plateau. Overall, the bacterial communities were dissimilar between the water and sediment, which indicated that there were limited interactions between them. Bacterial diversity was greatest in the sediments, where it was mainly driven by changes in nitrogen compounds and pH. Meanwhile water bacterial diversity was more susceptible to evapotranspiration, elevation, and mean annual temperature. Water samples contained higher proportions of Proteobacteria and Bacteroidetes, while sediment harbored higher proportions of Acidobacteria, Actinobacteria, Chloroflexi, Firmicutes, Planctomycetes, Cyanobacteria, and Gemmatimonadetes. Bacterial community composition was significantly correlated with mean annual precipitation in water, but with nitrogen compounds in sediment. The co-occurrence network of water included more keystone species (e.g., CL500-29 marine group, Nocardioides spp., and Bacillus spp.) than the sediment network. These keystone species showed stronger phylogenetic signals than the species in the modular structures. Further, ecological clusters within the networks suggested that there were contrasting environmental vulnerabilities and preferences between water and sediment communities. These findings demonstrated that co-existing water and sediment bacterial communities and ecological clusters were shaped by contrasting environmental factors. This work provides a basis for understanding the importance of bacterial communities in maintaining glacier-fed aquatic ecosystems. Further, the results provide new perspectives for water resource management and water conservation in changing environments.

Covariance of Phytoplankton, Bacteria, and Zooplankton Communities Within Microcystis Blooms in San Francisco Estuary

Microcystis blooms have occurred in upper San Francisco Estuary (USFE) since 1999, but their potential impacts on plankton communities have not been fully quantified. Five years of field data collected from stations across the freshwater reaches of the estuary were used to identify the plankton communities that covaried with Microcystis blooms, including non-photosynthetic bacteria, cyanobacteria, phytoplankton, zooplankton, and benthic genera using a suite of analyses, including microscopy, quantitative PCR (qPCR), and shotgun metagenomic analysis. Coherence between the abundance of Microcystis and members of the plankton community was determined by hierarchal cluster analysis (CLUSTER) and type 3 similarity profile analysis (SIMPROF), as well as correlation analysis. Microcystis abundance varied with many cyanobacteria and phytoplankton genera and was most closely correlated with the non-toxic cyanobacterium Merismopoedia, the green algae Monoraphidium and Chlamydomonas, and the potentially toxic cyanobacteria Pseudoanabaena, Dolichospermum, Planktothrix, Sphaerospermopsis, and Aphanizomenon. Among non-photosynthetic bacteria, the xenobiotic bacterium Phenylobacterium was the most closely correlated with Microcystis abundance. The coherence of DNA sequences for phyla across trophic levels in the plankton community also demonstrated the decrease in large zooplankton and increase in small zooplankton during blooms. The breadth of correlations between Microcystis and plankton across trophic levels suggests Microcystis influences ecosystem production through bottom-up control during blooms. Importantly, the abundance of Microcystis and other members of the plankton community varied with wet and dry conditions, indicating climate was a significant driver of trophic structure during blooms.

The genetic and ecophysiological diversity of Microcystis

Microcystis is a cyanobacterium that forms toxic blooms in freshwater ecosystems around the world. Biological variation among taxa within the genus is apparent through genetic and phenotypic differences between strains and via the spatial and temporal distribution of strains in the environment, and this fine-scale diversity exerts strong influence over bloom toxicity. Yet we do not know how varying traits of Microcystis strains govern their environmental distribution, the tradeoffs and links between these traits, or how they are encoded at the genomic level. Here we synthesize current knowledge on the importance of diversity within Microcystis and on the genes and traits that likely underpin ecological differentiation of taxa. We briefly review spatial and environmental patterns of Microcystis diversity in the field and genetic evidence for cohesive groups within Microcystis. We then compile data on strain-level diversity regarding growth responses to environmental conditions and explore evidence for variation of community interactions across Microcystis strains. Potential links and tradeoffs between traits are identified and discussed. The resulting picture, while incomplete, highlights key knowledge gaps that need to be filled to enable new models for predicting strain-level dynamics, which influence the development, toxicity and cosmopolitan nature of Microcystis blooms.

Individual Microcystis colonies harbour distinct bacterial communities that differ by Microcystis oligotype and with time

Interactions between bacteria and phytoplankton in the phycosphere have impacts at the scale of whole ecosystems, including the development of harmful algal blooms. The cyanobacterium Microcystis causes toxic blooms that threaten freshwater ecosystems and human health globally. Microcystis grows in colonies that harbour dense assemblages of other bacteria, yet the taxonomic composition of these phycosphere communities and the nature of their interactions with Microcystis are not well characterized. To identify the taxa and compositional variance within Microcystis phycosphere communities, we performed 16S rRNA V4 region amplicon sequencing on individual Microcystis colonies collected biweekly via high-throughput droplet encapsulation during a western Lake Erie cyanobacterial bloom. The Microcystis phycosphere communities were distinct from microbial communities in whole water and bulk phytoplankton seston in western Lake Erie but lacked 'core' taxa found across all colonies. However, dissimilarity in phycosphere community composition correlated with sampling date and the Microcystis 16S rRNA oligotype. Several taxa in the phycosphere were specific to and conserved with Microcystis of a single oligotype or sampling date. Together, this suggests that physiological differences between Microcystis strains, temporal changes in strain phenotypes, and the composition of seeding communities may impact community composition of the Microcystis phycosphere.

Imaging mass spectrometry of interspecies metabolic exchange revealed the allelopathic interaction between Microcystis aeruginosa and its antagonist

The frequent outbreaks of cyanobacterial blooms which caused serious societal and economic loss have become a worldwide problem. Interactions between toxic cyanobacteria and heterotrophic bacteria competitors play a pivotal role in the formation of toxic cyanobacterial bloom, but the underlying mechanisms of interactions between them await further research. The antagonist activity of Pseudomonas grimontii (P.grimontii) was confirmed by reduction in chlorophyll a concentration of Microcystis aeruginosa (M. aeruginosa) in an infected culture for a 7d period. The initial concentration of P.grimontii affected the M. aeruginosa activity significantly. When the 10% (V/V) concentration of P.grimontii A01 and P.grimontii A14 cultures were infected, the reduction of M. aeruginosa reached to 91.81% and 78.25% after 7 days, respectively. While a 0.1% (v/v) concentration of P.grimontii A01 and P.grimontii A14 cultures were infected, the M. aeruginosa increased 31.13% and 16.67% occurred, respectively. The content of reactive oxygen species (ROS) and malondialdehyde (MDA) increased with increasing of P.grimontii fermentation liquid, indicating the M. aeruginosa underwent oxidative stress. Using matrix-assisted laser desorption ionization-time of flight (MALDI-TOF) imaging mass spectrometry (IMS) profiling of co-cultures of M. aeruginosa and its antagonist P.grimontii, we revealed novel interspecies allelopathic interactions and compete molecule. We showed the spatial secondary metabolites may mediate the interactions in which P.grimontii inhibits growth of M. aeruginosa. Additionally, we revealed how M. aeruginosa feedback to the P.grimontii, which stimulates secondary metabolites such as [D-Asp3]-microcystin-LR released by M. aeruginosa. IMS method highlights the significance of allelopathic interactions between a widely distributed toxic cyanobacteria and its bacteria competitors.

Genotype and host microbiome alter competitive interactions between Microcystis aeruginosa and Chlorella sorokiniana

Cyanobacterial harmful algal blooms (cyanoHABs) continue to increase in frequency and magnitude, threatening global freshwater ecosystems and services. In north-temperate lakes cyanobacteria appear in early summer, succeeding green algae as the dominant phytoplankton group, a pattern thought to be mediated by changes in temperature and bioavailable nutrients. To understand additional drivers of this successional pattern our study used reciprocal invasion experiments to examine the competitive interaction between Microcystis aeruginosa, a dominant contributor to cyanoHABs, and the green alga Chlorella sorokiniana. We considered two factors that may impact these interactions: (1) strain variation, with a specific emphasis on the presence or absence of the gene for the hepatotoxin microcystin, and (2) host-associated bacteria. We used toxic M. aeruginosa PCC 7806 (microcystin producing strain), a non-toxic mutant of PCC 7806, non-toxic M. aeruginosa PCC 9701 (non-microcystin producing strain), and C. sorokiniana. Each organism was available free of all bacteria (i.e., axenic) and with a re-introduced defined bacterial community to generate their xenic counterparts. Competitive interactions were assessed with reciprocal invasion experiments between paired xenic and paired axenic populations of C. sorokiniana and one of the two Microcystis strains, each assessed separately. Flow cytometry and random forest models were used to rapidly discriminate and quantify phytoplankton population densities with 99% accuracy. We found that M. aeruginosa PCC 7806, but not strain PCC 9701, could proliferate from low abundance in a steady-state population of C. sorokiniana. Further, the presence of bacteria allowed M. aeruginosa PCC 7806 to grow to a higher population density into an established C. sorokiniana population than when grown axenic. Conversely, when M. aeruginosa was dominant, C. sorokiniana was only able to proliferate from low density into the PCC 9701 strain, and only when axenic. The mutant of PCC 7806 lacking the ability to produce microcystin behaved similarly to the toxic wild-type, implying microcystin is not responsible for the difference in competitive abilities observed between the two wild-type strains. Quantification of microcystins (MCs) when PCC 7806 M. aeruginosa was introduced into the C. sorokiniana culture showed two-fold more MCs per cell when host-associated bacteria were absent compared to present in both species cultures. Our results show that the ability of M. aeruginosa to compete with C. sorokiniana is determined by genomic differences beyond genes involved in microcystin toxin generation and indicate an important role of host-associated bacteria in mediating phytoplankton interspecies interactions. These results expand our understanding of the key drivers of phytoplankton succession and the establishment and persistence of freshwater harmful cyanobacterial blooms.