Dynamic polyphosphate metabolism in cyanobacteria responding to phosphorus availability

Quantification of Polyphosphate in Environmental Planktonic Samples Using a Novel Fluorescence Dye JC-D7

Polyphosphate (polyP) is found in plankton of diverse aquatic ecosystems and is important for plankton ecology and biogeochemical cycling. However, our knowledge of polyP in aquatic environments is hindered by a lack of data due to the limitations of quantification methods. The estimate of polyP in model organisms using phenol-chloroform extraction followed by enzymatic hydrolysis is complicated and fails for environmental samples. The commonly used 4',6-diamidino-2-phenylindole (DAPI) fluorescence method for environmental studies, on the contrary, severely overestimates polyP due to interference. In this paper, we develop a plankton lysis buffer to extract polyP and a quantification method using a novel polyP-specific fluorescence dye JC-D7. We test the methods using cultured algae and bacteria, as well as natural samples from marine and freshwater environments. We show that our plankton lysis extracts polyP with high recovery while requiring substantially less time and effort. Subsequent polyP quantification using JC-D7 fluorescence overcomes the interference encountered by the DAPI method and provides an accurate measurement of polyP down to <0.5 μmol L-1. This novel method enables more accurate quantification of polyP in aquatic environments and will profoundly enhance our knowledge of polyP, plankton ecology, and biogeochemistry.

Polyphosphate-kinase-1 dependent polyphosphate hyperaccumulation for acclimation to nutrient loss in the cyanobacterium, Synechocystis sp. PCC 6803

Polyphosphate is prevalent in living organisms. To obtain insights into polyphosphate synthesis and its physiological significance in cyanobacteria, we characterize sll0290, a homolog of the polyphosphate-kinase-1 gene, in the freshwater cyanobacterium Synechocystis sp. PCC 6803. The Sll0290 protein structure reveals characteristics of Ppk1. A Synechocystis sll0290 disruptant and sll0290-overexpressing Escherichia coli transformant demonstrated loss and gain of polyphosphate synthesis ability, respectively. Accordingly, sll0290 is identified as ppk1. The disruptant (Δppk1) grows normally with aeration of ordinary air (0.04% CO2), consistent with its photosynthesis comparable to the wild type level, which contrasts with a previously reported high-CO2 (5%) requirement for Δppk1 in an alkaline hot spring cyanobacterium, Synechococcus OS-B'. Synechocystis Δppk1 is defective in polyphosphate hyperaccumulation and survival competence at the stationary phase, and also under sulfur-starvation conditions, implying that sulfur limitation is one of the triggers to induce polyphosphate hyperaccumulation in stationary cells. Furthermore, Δppk1 is defective in the enhancement of total phosphorus contents under sulfur-starvation conditions, a phenomenon that is only partially explained by polyphosphate hyperaccumulation. This study therefore demonstrates that in Synechocystis, ppk1 is not essential for low-CO2 acclimation but plays a crucial role in dynamic P-metabolic regulation, including polyP hyperaccumulation, to maintain physiological fitness under sulfur-starvation conditions.

Structural Evolution of Bacterial Polyphosphate Degradation Enzyme for Phosphorus Cycling

Living organisms ranging from bacteria to animals have developed their own ways to accumulate and store phosphate during evolution, in particular as the polyphosphate (polyP) granules in bacteria. Degradation of polyP into phosphate is involved in phosphorus cycling, and exopolyphosphatase (PPX) is the key enzyme for polyP degradation in bacteria. Thus, understanding the structure basis of PPX is crucial to reveal the polyP degradation mechanism. Here, it is found that PPX structure varies in the length of ɑ-helical interdomain linker (ɑ-linker) across various bacteria, which is negatively correlated with their enzymatic activity and thermostability - those with shorter ɑ-linkers demonstrate higher polyP degradation ability. Moreover, the artificial DrPPX mutants with shorter ɑ-linker tend to have more compact pockets for polyP binding and stronger subunit interactions, as well as higher enzymatic efficiency (kcat/Km) than that of DrPPX wild type. In Deinococcus-Thermus, the PPXs from thermophilic species possess a shorter ɑ-linker and retain their catalytic ability at high temperatures (70 °C), which may facilitate the thermophilic species to utilize polyP in high-temperature environments. These findings provide insights into the interdomain linker length-dependent evolution of PPXs, which shed light on enzymatic adaption for phosphorus cycling during natural evolution and rational design of enzyme.

Toward nitrogen recovery: Co-cultivation of microalgae and bacteria enhances the production of high-value nitrogen-rich cyanophycin

The algal-bacterial wastewater treatment process has been proven to be highly efficient in removing nutrients and recovering nitrogen (N). However, the recovery of the valuable N-rich biopolymer, cyanophycin, remains limited. This research explored the synthesis mechanism and recovery potential of cyanophycin within two algal-bacterial symbiotic reactors. The findings reveal that the synergy between algae and bacteria enhances the removal of N and phosphorus. The crude contents of cyanophycin in the algal-bacterial consortia reached 115 and 124 mg/g of mixed liquor suspended solids (MLSS), respectively, showing an increase of 11.7 %-20.4 % (p < 0.001) compared with conventional activated sludge. Among the 170 metagenome-assembled genomes (MAGs) analyzed, 50 were capable of synthesizing cyanophycin, indicating that cyanophycin producers are common in algal-bacterial systems. The compositions of cyanophycin producers in the two algal-bacterial reactors were affected by different lighting initiation time. The study identified two intracellular synthesis pathways for cyanophycin. Approximately 36 MAGs can synthesize cyanophycin de novo using ammonium and glucose, while the remaining 14 MAGs require exogenous arginine for production. Notably, several MAGs with high abundance are capable of assimilating both nitrate and ammonium into cyanophycin, demonstrating a robust N utilization capability. This research also marks the first identification of potential horizontal gene transfer of the cyanophycin synthase encoding gene (cphA) within the wastewater microbial community. This suggests that the spread of cphA could expand the population of cyanophycin producers. The study offers new insights into recycling the high-value N-rich biopolymer cyanophycin, contributing to the advancement of wastewater resource utilization.

Characterization of polyphosphate dynamics in the widespread freshwater diatom Achnanthidium minutissimum under varying phosphorus supplies

Polyphosphates (polyP) are ubiquitous biomolecules that play a multitude of physiological roles in many cells. We have studied the presence and role of polyP in a unicellular alga, the freshwater diatom Achnanthidium minutissimum. This diatom stores up to 2.0 pg·cell-1 of polyP, with chain lengths ranging from 130 to 500 inorganic phosphate units (Pi). We applied energy dispersive X-ray spectroscopy, Raman/fluorescence microscopy, and biochemical assays to localize and characterize the intracellular polyP granules that were present in large apical vacuoles. We investigated the fate of polyP in axenic A. minutissimum cells grown under phosphorus (P), replete (P(+)), or P deplete (P(-)) cultivation conditions and observed that in the absence of exogenous P, A. minutissimum rapidly utilizes their internal polyP reserves, maintaining their intrinsic growth rates for up to 8 days. PolyP-depleted A. minutissimum cells rapidly took up exogenous P a few hours after Pi resupply and generated polyP three times faster than cells that were not initially subjected to P limitation. Accordingly, we propose that A. minutissimum deploys a succession of acclimation strategies regarding polyP dynamics where the production or consumption of polyP plays a central role in the homeostasis of the diatom.

Preferential phosphatidylglycerol synthesis via phosphorus supply through rRNA degradation in the cyanobacterium, Synechocystis sp. PCC 6803, under phosphate-starved conditions

Photosynthetic organisms often encounter phosphorus (P) limitation in natural habitats. When faced with P limitation, seed plants degrade nucleic acids and extra-plastid phospholipids to remobilize P, thereby enhancing their internal-P utilization efficiency. Although prokaryotic and eukaryotic photosynthetic organisms decrease the content of phosphatidylglycerol (PG) under P-limited conditions, it remains unclear whether PG is degraded for P remobilization. Moreover, information is limited on internal-P remobilization in photosynthetic microbes. This study investigates internal-P remobilization under P-starvation (-P) conditions in a cyanobacterium, Synechocystis sp. PCC 6803, focusing on PG and nucleic acids. Our results reveal that the PG content increases by more than double in the -P culture, indicating preferential PG synthesis among cellular P compounds. Simultaneously, the faster increases of glycolipids counteract this PG increase, which decreases the PG proportion in total lipids. Two genes, glpD and plsX, contribute to the synthesis of diacylglycerol moieties in glycerolipids, with glpD also responsible for the polar head group synthesis in PG. The mRNA levels of both glpD and plsX are upregulated during -P, which would cause the preferential metabolic flow of their P-containing substrates toward glycerolipid synthesis, particularly PG synthesis. Meanwhile, we find that RNA accounts for 62% of cellular P, and that rRNA species, which makes up the majority of RNA, are degraded under -P conditions to less than 30% of their initial levels. These findings emphasize the importance of PG in -P-acclimating cell growth and the role of rRNA as a significant internal-P source for P remobilization, including preferential PG synthesis.

Efficient modulation of cellular phosphorus components in response to phosphorus deficiency in the dinoflagellate Karenia mikimotoi

IMPORTANCE

Dinoflagellates are the most common phytoplankton group and account for more than 75% of harmful algal blooms in coastal waters. In recent decades, dinoflagellates seem to prevail in phosphate-depleted waters. However, the underlying acclimation mechanisms and competitive strategies of dinoflagellates in response to phosphorus deficiency are poorly understood, especially in terms of intracellular phosphorus modulation and recycling. Here, we focused on the response of intracellular phosphorus metabolism to phosphorus deficiency in the model dinoflagellate Karenia mikimotoi. Our work reveals the strong capability of K. mikimotoi to efficiently regulate intracellular phosphorus resources, particularly through membrane phospholipid remodeling and miRNA regulation of energy metabolism. Our research improved the understanding of intracellular phosphorus metabolism in marine phytoplankton and underscored the advantageous strategies of dinoflagellates in the efficient modulation of internal phosphorus resources to maintain active physiological activity and growth under unsuitable phosphorus conditions, which help them outcompete other species in coastal phosphate-depleted environments.

Variation in intracellular polyphosphate and associated gene expression in response to different phosphorus conditions in the dinoflagellate Karenia mikimotoi

Polyphosphate (polyP) has long been recognized as a crucial intracellular reservoir for phosphorus in microorganisms. However, the dynamics of polyP and its regulatory mechanism in eukaryotic phytoplankton in response to variations in external phosphorus conditions remain poorly understood. A comprehensive investigation was conducted to examine the intracellular polyP-associated metabolic response of the dinoflagellate Karenia mikimotoi, a harmful algal bloom species, through integrated physiological, biochemical, and transcriptional analyses under varying external phosphorus conditions. Comparable growth curves and Fv/Fm between phosphorus-replete conditions and phosphorus-depleted conditions suggested that K. mikimotoi has a strong capability to mobilize the intracellular phosphorus pool for growth under phosphorus deficiency. Intracellular phosphate (IPi) and polyP contributed approximately 6-23 % and 1-3 %, respectively, to the overall particulate phosphorus (PP) content under different phosphorus conditions. The significant decrease in PP and increase in polyP:PP suggested that cellular phosphorus components other than polyP are preferred for utilization under phosphorus deficiency. Genes involved in polyP synthesis and hydrolysis were upregulated to maintain phosphorus homeostasis in K. mikimotoi. These findings provide novel insights into the specific cellular strategies for phosphorus storage and the transcriptional response in intracellular polyP metabolism in K. mikimotoi. Additionally, these results also indicate that polyP may not play a crucial role in cellular phosphorus storage in phytoplankton, at least in dinoflagellates.

Stringent Response of Cyanobacteria and Other Bacterioplankton during Different Stages of a Harmful Cyanobacterial Bloom

We conducted a field study to investigate the role of stringent response in cyanobacteria and coexisting bacterioplankton during nutrient-deprived periods at various stages of bloom in a freshwater lake (Utah Lake) for the first time. Using metagenomics and metatranscriptomics analyses, we examined the cyanobacterial ecology and expression of important functional genes related to stringent response, N and P metabolism, and regulation. Our findings mark a significant advancement in understanding the mechanisms by which toxic cyanobacteria survive and proliferate during nitrogen (N) and phosphorus (P) limitations. We successfully identified and analyzed the metagenome-assembled genomes (MAGs) of the dominant bloom-forming cyanobacteria, namely, Dolichospermum circinale, Aphanizomenon flos-aquae UKL13-PB, Planktothrix agardhii, and Microcystis aeruginosa. By mapping RNA-seq data to the coding sequences of the MAGs, we observed that these four prevalent cyanobacteria species activated multiple functions to adapt to the depletion of inorganic nutrients. During and after the blooms, the four dominant cyanobacteria species expressed high levels of transcripts related to toxin production, such as microcystins (mcy), anatoxins (ana), and cylindrospermopsins (cyr). Additionally, genes associated with polyphosphate (poly-P) storage and the stringent response alarmone (p)ppGpp synthesis/hydrolysis, including ppk, relA, and spoT, were highly activated in both cyanobacteria and bacterioplankton. Under N deficiency, the main N pathways shifted from denitrification and dissimilatory nitrate reduction in bacterioplankton toward N2-fixing and assimilatory nitrate reduction in certain cyanobacteria with a corresponding shift in the community composition. P deprivation triggered a stringent response mediated by spoT-dependent (p)ppGpp accumulation and activation of the Pho regulon in both cyanobacteria and bacterioplankton, facilitating inorganic and organic P uptake. The dominant cyanobacterial MAGs exhibited the presence of multiple alkaline phosphatase (APase) transcripts (e.g., phoA in Dolichospermum, phoX in Planktothrix, and Microcystis), suggesting their ability to synthesize and release APase enzymes to convert ambient organic P into bioavailable forms. Conversely, transcripts associated with bacterioplankton-dominated pathways like denitrification were low and did not align with the occurrence of intense cyanoHABs. The strong correlations observed among N, P, stringent response metabolisms and the succession of blooms caused by dominant cyanobacterial species provide evidence that the stringent response, induced by nutrient limitation, may activate unique N and P functions in toxin-producing cyanobacteria, thereby sustaining cyanoHABs.

Phosphorus Accumulation in Extracellular Polymeric Substances (EPS) of Colony-Forming Cyanobacteria Challenges Imbalanced Nutrient Reduction Strategies in Eutrophic Lakes

Extracellular polymeric substances (EPS) are crucial for cyanobacterial proliferation; however, certain queries, including how EPS affects cellular nutrient processes and what are the implications for nutrient management in lakes, are not well documented. Here, the dynamics of cyanobacterial EPS-associated phosphorus (EPS-P) were examined both in a shallow eutrophic lake (Lake Taihu, China) and in laboratory experiments with respect to nitrogen (N) and phosphorus (P) availability. Results indicated that 40-65% of the total cyanobacterial aggregate/particulate P presented as EPS-P (mainly labile P and Fe/Al-P). Phosphorus-starved cyanobacteria rapidly replenished their EPS-P pools after the P was resupplied, and the P concentration in this pool was stable for long afterward, although the environmental P concentration decreased dramatically. A low-N treatment enhanced the EPS production alongside two-fold EPS-P accumulation (particularly labile P) higher than the control. Such patterns occurred in the lake where EPS and EPS-P contents were high under N limitation. EPS-P enrichment increased the P content in cyanobacteria; subsequently, it could hold the total P concentration higher for longer and make bloom mitigation harder. The findings outline a new insight into EPS functions in the P process of cyanobacterial aggregates and encourage consideration of both N and P reductions in nutrient management.

Response of cyanobacterial mats to ambient phosphate fluctuations: phosphorus cycling, polyphosphate accumulation and stoichiometric flexibility

Cyanobacterial mats inhabit a variety of aquatic habitats, including the most extreme environments on Earth. They can thrive in a wide range of phosphorus (P) levels and are thus important players for ecosystem primary production and P cycling at the sediment-water interface. Polyphosphate (polyP), the major microbial P storage molecule, is assigned a critical role in compensating for phosphate fluctuations in planktonic cyanobacteria, but little is known about potentially analogous mechanisms of mat-forming cyanobacteria. To investigate acclimation strategies of cyanobacterial mats to fluctuating phosphate concentrations, laboratory batch experiments were conducted, in which the cosmopolitan mat-forming, marine cyanobacterium Sodalinema stali was exposed to low dissolved P concentrations, followed by a P pulse. Our results show that the cyanobacteria dynamically adjusted cellular P content to ambient phosphate concentrations and that they had accumulated polyP during periods of high phosphate availability, which was subsequently recycled to sustain growth during phosphate scarcity. However, following the depletion of dispensable cellular P sources, including polyP, we observed a reallocation of P contained in DNA into polyP, accompanied by increasing alkaline phosphatase activity. This suggests a change of the metabolic focus from growth towards maintenance and the attempt to acquire organic P, which would be naturally contained in the sediment. P overplus uptake following a simulated P pulse further suggests that Sodalinema-dominated mats exhibit elaborated mechanisms to cope with severe P fluctuations to overcome unfavourable environmental conditions, and potentially modulate critical P fluxes in the aquatic cycle.

The effects of light regime on carbon cycling, nutrient removal, biomass yield, and polyhydroxybutyrate (PHB) production by a constructed photosynthetic consortium

Microalgae can add value to biological wastewater treatment processes by capturing carbon and nutrients and producing valuable biomass. Harvesting small cells from liquid media is a challenge easily addressed with biofilm cultivation. Three experimental photobioreactors were constructed from inexpensive materials (e.g. plexiglass, silicone) for hybrid liquid/biofilm cultivation of a microalgal-bacterial consortia in aquaculture effluent. Three light regimes (full-spectrum, blue-white, and red) were implemented to test light spectra as a process control. High-intensity full-spectrum light caused photoinhibition and low biomass yield, but produced the most polyhydroxybutyrate (PHB) (0.14 mg g^-1); a renewable bioplastic polymer. Medium-intensity blue-white light was less effective for carbon capture, but removed up to 82 % of phosphorus. Low-intensity red light was the only net carbon-negative regime, but increased phosphorus (+4.98 mg/L) in the culture medium. Light spectra and intensity have potential as easily-implemented process controls for targeted wastewater treatment, biomass production, and PHB synthesis using photosynthetic consortia.

Transcriptomic response of the harmful algae Heterosigma akashiwo to polyphosphate utilization and phosphate stress

Phosphorus (P) is one of the major macronutrients necessary for phytoplankton growth. In some parts of the ocean, however, P is frequently scarce, hence, there is limited phytoplankton growth. To cope with P deficiency, phytoplankton evolved a variety of strategies, including, utilization of different P sources. Polyphosphate (polyP) is ubiquitously present and serves an essential function in aquatic environments, but it is unclear if and how this polymer is utilized by phytoplankton. Here, we examined the physiological and molecular responses of the widely present harmful algal bloom (HAB) species, Heterosigma akashiwo in polyP utilization, and in coping with P-deficiency. Our results revealed that two forms of inorganic polyP, namely, sodium tripolyphosphate and sodium hexametaphosphate, support H. akashiwo growth as efficiently as orthophosphate. However, few genes involved in polyP utilization have been identified. Under P-deficient conditions, genes associated with P transport, dissolved organic P utilization, sulfolipid synthesis, and energy production, were markedly elevated. In summary, our results indicate that polyP is bioavailable to H. akashiwo, and this HAB species have evolved a comprehensive strategy to cope with P deficiency.

Schindler's legacy: from eutrophic lakes to the phosphorus utilization strategies of cyanobacteria

David Schindler and his colleagues pioneered studies in the 1970s on the role of phosphorus in stimulating cyanobacterial blooms in North American lakes. Our understanding of the nuances of phosphorus utilization by cyanobacteria has evolved since that time. We review the phosphorus utilization strategies used by cyanobacteria, such as use of organic forms, alternation between passive and active uptake, and luxury storage. While many aspects of physiological responses to phosphorus of cyanobacteria have been measured, our understanding of the critical processes that drive species diversity, adaptation and competition remains limited. We identify persistent critical knowledge gaps, particularly on the adaptation of cyanobacteria to low nutrient concentrations. We propose that traditional discipline-specific studies be adapted and expanded to encompass innovative new methodologies and take advantage of interdisciplinary opportunities among physiologists, molecular biologists, and modellers, to advance our understanding and prediction of toxic cyanobacteria, and ultimately to mitigate the occurrence of blooms.

Biogeochemical Niche of Magnetotactic Cocci Capable of Sequestering Large Polyphosphate Inclusions in the Anoxic Layer of the Lake Pavin Water Column

Magnetotactic bacteria (MTB) are microorganisms thriving mostly at oxic–anoxic boundaries of aquatic habitats. MTB are efficient in biomineralising or sequestering diverse elements intracellularly, which makes them potentially important actors in biogeochemical cycles. Lake Pavin is a unique aqueous system populated by a wide diversity of MTB with two communities harbouring the capability to sequester not only iron under the form of magnetosomes but also phosphorus and magnesium under the form of polyphosphates, or calcium carbonates, respectively. MTB thrive in the water column of Lake Pavin over a few metres along strong redox and chemical gradients representing a series of different microenvironments. In this study, we investigate the relative abundance and the vertical stratification of the diverse populations of MTB in relation to environmental parameters, by using a new method coupling a precise sampling for geochemical analyses, MTB morphotype description, and in situ measurement of the physicochemical parameters. We assess the ultrastructure of MTB as a function of depth using light and electron microscopy. We evidence the biogeochemical niche of magnetotactic cocci, capable of sequestering large PolyP inclusions below the oxic–anoxic transition zone. Our results suggest a tight link between the S and P metabolisms of these bacteria and pave the way to better understand the implication of MTB for the P cycle in stratified environmental conditions.

Cyanobacteria and Cyanotoxins in a Changing Environment: Concepts, Controversies, Challenges

Concern is widely being published that the occurrence of toxic cyanobacteria is increasing in consequence of climate change and eutrophication, substantially threatening human health. Here, we review evidence and pertinent publications to explore in which types of waterbodies climate change is likely to exacerbate cyanobacterial blooms; whether controlling blooms and toxin concentrations requires a balanced approach of reducing not only the concentrations of phosphorus (P) but also those of nitrogen (N); how trophic and climatic changes affect health risks caused by toxic cyanobacteria. We propose the following for further discussion: (i) Climate change is likely to promote blooms in some waterbodies—not in those with low concentrations of P or N stringently limiting biomass, and more so in shallow than in stratified waterbodies. Particularly in the latter, it can work both ways—rendering conditions for cyanobacterial proliferation more favourable or less favourable. (ii) While N emissions to the environment need to be reduced for a number of reasons, controlling blooms can definitely be successful by reducing only P, provided concentrations of P can be brought down to levels sufficiently low to stringently limit biomass. Not the N:P ratio, but the absolute concentration of the limiting nutrient determines the maximum possible biomass of phytoplankton and thus of cyanobacteria. The absolute concentrations of N or P show which of the two nutrients is currently limiting biomass. N can be the nutrient of choice to reduce if achieving sufficiently low concentrations has chances of success. (iii) Where trophic and climate change cause longer, stronger and more frequent blooms, they increase risks of exposure, and health risks depend on the amount by which concentrations exceed those of current WHO cyanotoxin guideline values for the respective exposure situation. Where trophic change reduces phytoplankton biomass in the epilimnion, thus increasing transparency, cyanobacterial species composition may shift to those that reside on benthic surfaces or in the metalimnion, changing risks of exposure. We conclude that studying how environmental changes affect the genotype composition of cyanobacterial populations is a relatively new and exciting research field, holding promises for understanding the biological function of the wide range of metabolites found in cyanobacteria, of which only a small fraction is toxic to humans. Overall, management needs case-by-case assessments focusing on the impacts of environmental change on the respective waterbody, rather than generalisations.

Periphytic microbial response to environmental phosphate bioavailability - relevance to P management in paddy fields

Periphyton occurs widely in shallow-water ecosystems such as paddy fields and plays critical parts in regulating local phosphorus cycling. As such, understanding the mechanisms of the biofilm's response to environmental P variability may lead to better perceptions of P utilization and retention in rice farms. Present study aims at exploring the biological and biochemical processes underlying periphyton's P buffering capability through examining changes in community structure, phosphorus uptake and storage, and molecular makeup of exometabolome at different levels of P availability. Under stressed (both excessive and scarce) phosphorus conditions, we found increased populations of the bacterial genus capable of transforming orthophosphate to polyphosphate, as well as mixotrophic algae who can survive through phagotrophy. These results were corroborated by observed polyphosphate buildup under low and high P treatment. Exometabolomic analyses further revealed that periphytic organisms may substitute S-containing lipids for phospholipids, use siderophores to dissolve iron (hydr)oxides to scavenge adsorbed P, and synthesize auxins to resist phosphorus starvation. These findings not only shed light on the mechanistic insights responsible for driving the periphytic P buffer but attest to the ecological roles of periphyton in aiding plants such as rice to overcome P limitations in natural environment. Importance The ability of periphyton to buffer environmental P in shallow aquatic ecosystems may be a natural lesson on P utilization and retention in paddy fields. This work revealed the routes and tools through which periphytic organisms adapt to and regulate ambient P fluctuation. The mechanistic understanding further implicates that the biofilm may serve rice plants to alleviate P stress. Additional results from extracellular metabolite analyses suggest the dissolved periphytic exometabolome can be a valuable nutrient source for soil microbes and plants to reduce biosynthetic costs. These discoveries have the potential to improve our understanding of biogeochemical cycling of phosphorus in general and to refine P management strategies for rice farm in particular.

Remote Detection of Cyanobacterial Blooms and Chlorophyll-a Analysis in a Eutrophic Reservoir Using Sentinel-2

Harmful cyanobacterial blooms have been one of the most challenging ecological problems faced by freshwater bodies for more than a century. The use of satellite images as a tool to analyze these blooms is an innovative technology that will facilitate water governance and help develop measures to guarantee water security. To assess the viability of Sentinel-2 for identifying cyanobacterial blooms and chlorophyl-a, different bands of the Sentinel-2 satellite were considered, and those most consistent with cyanobacteria analysis were analyzed. This analysis was supplemented by an assessment of different indices and their respective correlations with the field data. The indices assessed were the following: Normalized Difference Water Index (NDWI), Normalized Differences Vegetation Index (NDVI), green Normalized Difference Vegetation Index (gNDVI), Normalized Soil Moisture Index (NSMI), and Toming’s Index. The green band (B3) obtained the best correlating results for both chlorophyll (R2 = 0.678) and cyanobacteria (R2 = 0.931). The study by bands of cyanobacteria composition can be a powerful tool for assessing the physiology of strains. NDWI gave an R2 value of 0.849 for the downstream point with the concentration of cyanobacteria. Toming’s Index obtained a high R2 of 0.859 with chlorophyll-a and 0.721 for the concentration of cyanobacteria. Notable differences in correlation for the upstream and downstream points were obtained with the indices. These results show that Sentinel-2 will be a valuable tool for lake monitoring and research, especially considering that the data will be routinely available for many years and the images will be frequent and free.

Responses of Rhodotorula mucilaginosa under Pb(II) stress: carotenoid production and budding

Rhodotorula mucilaginosa resists heavy metal (HM) stress because of its abundant extracellular polymeric substances and functional vesicles. In this study, we provided new insights into its survival strategies at both biochemical and genetic levels. After lead exposure, carotenoid biosynthesis was initiated within 24 h incubation and then increased to the maximum after 96 h of incubation. Raman analysis confirmed that carotenoids (primarily β-carotene) were the major identifiable chemical substances on the cell surface. Moreover, the increased carotenoid production was accompanied by a rising budding rate, ~40% higher than that in the cultures without Pb. During the 96 h of incubation, the driving force for Pb accumulation was assigned to this elevated budding rate. After 96 h, biosorption was primarily attributed to the enhanced antioxidant ability of the single cells during carotenoid production. Furthermore, the yeast budding cells demonstrated an evidently heterogeneous biosorption of Pb, i.e., the rejuvenated daughters had a relatively lower Pb level than the mother cells. This resulted in the protection of the buds from Pb stress. After investigating phosphorus uptake and the RNA sequencing data, we finally confirmed two tightly correlated pathways that resist HM stress, i.e., biochemical (carotenoid production) and reproductive (healthy buds) pathways.

Microfluidic and mathematical modeling of aquatic microbial communities

Aquatic microbial communities contribute fundamentally to biogeochemical transformations in natural ecosystems, and disruption of these communities can lead to ecological disasters such as harmful algal blooms. Microbial communities are highly dynamic, and their composition and function are tightly controlled by the biophysical (e.g., light, fluid flow, and temperature) and biochemical (e.g., chemical gradients and cell concentration) parameters of the surrounding environment. Due to the large number of environmental factors involved, a systematic understanding of the microbial community-environment interactions is lacking. In this article, we show that microfluidic platforms present a unique opportunity to recreate well-defined environmental factors in a laboratory setting in a high throughput way, enabling quantitative studies of microbial communities that are amenable to theoretical modeling. The focus of this article is on aquatic microbial communities, but the microfluidic and mathematical models discussed here can be readily applied to investigate other microbiomes.

Critical Review of Polyphosphate and Polyphosphate Accumulating Organisms for Agricultural Water Quality Management

Despite ongoing management efforts, phosphorus (P) loading from agricultural landscapes continues to impair water quality. Wastewater treatment research has enhanced our knowledge of microbial mechanisms influencing P cycling, especially regarding microbes known as polyphosphate accumulating organisms (PAOs) that store P as polyphosphate (polyP) under oxic conditions and release P under anoxic conditions. However, there is limited application of PAO research to reduce agricultural P loading and improve water quality. Herein, we conducted a meta-analysis to identify articles in Web of Science on polyP and its use by PAOs across five disciplines (i.e., wastewater treatment, terrestrial, freshwater, marine, and agriculture). We also summarized research that provides preliminary support for PAO-mediated P cycling in natural habitats. Terrestrial, freshwater, marine, and agriculture disciplines had fewer polyP and PAO articles compared to wastewater treatment, with agriculture consistently having the least. Most meta-analysis articles did not overlap disciplines. We found preliminary support for PAOs in natural habitats and identified several knowledge gaps and research opportunities. There is an urgent need for interdisciplinary research linking PAOs, polyP, and oxygen availability with existing knowledge of P forms and cycling mechanisms in natural and agricultural environments to improve agricultural P management strategies and achieve water quality goals.

Requirement of the exopolyphosphatase gene for cellular acclimation to phosphorus starvation in a cyanobacterium, Synechocystis sp. PCC 6803

Polyphosphate, which is ubiquitous in cells in nature, is involved in a myriad of cellular functions, and has been recently focused on its metabolism related with microbial acclimation to phosphorus-source fluctuation. In view of the ecological importance of cyanobacteria as the primary producers, this study investigated the responsibility of polyphosphate metabolism for cellular acclimation to phosphorus starvation in a cyanobacterium, Synechocystis sp. PCC 6803, with the use of a disruptant (Δppx) as to the gene of exopolyphosphatase that is responsible for polyphosphate degradation. Δppx was similar to the wild type in the cellular content of polyphosphate to show no defect in cell growth under phosphorus-replete conditions. However, under phosphorus-starved conditions, Δppx cells were defective in a phosphorus-starvation dependent decrease of polyphosphate to show deleterious phenotypes as to their survival and the stabilization of the photosystem complexes. These results demonstrated some crucial role of exopolyphosphatase to degrade polyP in the acclimation of cyanobacterial cells to phosphorus-starved conditions. Besides, it was found that ppx expression is induced in Synechocystis cells in response to phosphorus starvation through the action of the two-component system, SphS and SphR, in the phosphate regulon. The information will be a foundation for a fuller understanding of the process of cyanobacterial acclimation to phosphorus fluctuation.

Nutrient-imbalanced conditions shift the interplay between zooplankton and gut microbiota

Background

Nutrient stoichiometry of phytoplankton frequently changes with aquatic ambient nutrient concentrations, which is mainly influenced by anthropogenic water treatment and the ecosystem dynamics. Consequently, the stoichiometry of phytoplankton can markedly alter the metabolism and growth of zooplankton. However, the effects of nutrient-imbalanced prey on the interplay between zooplankton and their gut microbiota remain unknown. Using metatranscriptome, a 16 s rRNA amplicon-based neutral community model (NCM) and experimental validation, we investigated the interactions between Daphnia magna and its gut microbiota in a nutrient-imbalanced algal diet.

Results

Our results showed that in nutrient-depleted water, the nutrient-enriched zooplankton gut stimulated the accumulation of microbial polyphosphate in fecal pellets under phosphorus limitation and the microbial assimilation of ammonia under nitrogen limitation. Compared with the nutrient replete group, both N and P limitation markedly promoted the gene expression of the gut microbiome for organic matter degradation but repressed that for anaerobic metabolisms. In the nutrient limited diet, the gut microbial community exhibited a higher fit to NCM (R² = 0.624 and 0.781, for N- and P-limitation, respectively) when compared with the Control group (R² = 0.542), suggesting increased ambient-gut exchange process favored by compensatory feeding. Further, an additional axenic grazing experiment revealed that the growth of D. magna can still benefit from gut microbiota under a nutrient-imbalanced diet.

Conclusions

Together, these results demonstrated that under a nutrient-imbalanced diet, the microbes not only benefit themselves by absorbing excess nutrients inside the zooplankton gut but also help zooplankton to survive during nutrient limitation.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12864-020-07333-z.

A self-sustaining synergetic microalgal-bacterial granular sludge process towards energy-efficient and environmentally sustainable municipal wastewater treatment

Globally increasing concerns have been raised on the high energy consumption and greenhouse gas emissions in conventional municipal wastewater treatment processes over the past decades. In this study, a self-sustaining synergetic microalgal-bacterial granular sludge process was thus developed to address these challenges. The results showed that the microalgal-bacterial granular sludge process was capable of removing 92.69%, 96.84% and 87.16% of influent organics, ammonia and phosphorus under non-aeration conditions over a short time of 6 h. The effluent could meet the increasingly stringent discharge standards in many countries worldwide. A tight synergetic interrelationship effect between microalgae and bacteria in granules was essential for such excellent process performance. The stoichiometric and functional genes analyses further revealed that most of organic matter and nutrients were removed through microalgal and bacterial assimilations. Moreover, it was found that there existed a desirable distribution of functional species of microalgae and bacteria in microalgal-bacterial granules, which appeared to be essential for the self-sustaining synergetic reactions and stability of microalgal-bacterial granules. Consequently, this work may offer a promising engineering alternative with great potential to achieve energy-efficient and environmentally sustainable municipal wastewater treatment.

Linking regional shifts in microbial genome adaptation with surface ocean biogeochemistry

Linking 'omics measurements with biogeochemical cycles is a widespread challenge in microbial community ecology. Here, we propose applying genomic adaptation as 'biosensors' for microbial investments to overcome nutrient stress. We then integrate this genomic information with a trait-based model to predict regional shifts in the elemental composition of marine plankton communities. We evaluated this approach using metagenomic and particulate organic matter samples from the Atlantic, Indian and Pacific Oceans. We find that our genome-based trait model significantly improves our prediction of particulate C : P (carbon : phosphorus) across ocean regions. Furthermore, we detect previously unrecognized ocean areas of iron, nitrogen and phosphorus stress. In many ecosystems, it can be very challenging to quantify microbial stress. Thus, a carefully calibrated genomic approach could become a widespread tool for understanding microbial responses to environmental changes and the biogeochemical outcomes. This article is part of the theme issue 'Conceptual challenges in microbial community ecology'.

Isolation and Characterization of Phosphorus Solubilizing Bacteria With Multiple Phosphorus Sources Utilizing Capability and Their Potential for Lead Immobilization in Soil

Phosphorus solubilizing bacteria (PSB) can promote the level of plant-absorbable phosphorus (P) in agro-ecosystems. However, little attention has been paid to PSB harboring abilities in utilizing multiple phosphorus sources and their potentials for heavy metal immobilization. In this study, we applied the strategy of stepwise acclimation by using Ca₃(PO₄)₂, phytate, FePO₄, and AlPO₄ as sole P source. We gained 18 PSB possessing abilities of multiple P sources utilization, and these bacteria belonged to eight genera (Acinetobacter, Pseudomonas, Massilia, Bacillus, Arthrobacter, Stenotrophomonas, Ochrobactrum, and Cupriavidus), and clustered to two apparent parts: Gram-positive bacteria and Gram-negative bacteria. The isolate of Acinetobacter pittii gp-1 presented good performance for utilizing Ca₃(PO₄)₂, FePO₄, AlPO₄, and phytate, with corresponding P solubilizing levels were 250.77, 46.10, 81.99, and 7.91 mg/L PO₄^3–-P, respectively. The PSB A. pittii gp-1 exhibited good performance for solubilizing tricalcium phosphate in soil incubation experiments, with the highest values of water soluble P and available P were 0.80 and 1.64 mg/L, respectively. Additionally, the addition of A. pittii gp-1 could promote the immobilization of lead (Pb), and the highest Pb immobilization efficiency reached 23%. Simultaneously, we found the increases in abundances of both alkaline phosphatase gene (phoD) and β-propeller phytase gene (bpp) in strain gp-1 added soils. Besides, we observed the expression up-regulation of both pyrroloquinoline quinone gene (pqq) and polyphosphate kinases gene (ppk), with the highest relative expression levels of 18.18 and 5.23, respectively. We also found the polyphosphate particles using granule staining. To our knowledge, our findings first suggest that the solubilizing of tricalcium phosphate by phosphorus solubilizing bacterium belonging to Acinetobacter is coupled with the synthesis of polyphosphate. Taken together, A. pittii gp-1 could be a good candidate in improving soil fertility and quality.

Picoplankton accumulate and recycle polyphosphate to support high primary productivity in coastal Lake Ontario

Phytoplankton can accumulate polyphosphate (polyP) to alleviate limitation of essential nutrient phosphorus (P). Yet polyP metabolisms in aquatic systems and their roles in P biogeochemical cycle remain elusive. Previously reported polyP enrichment in low-phosphorus oligotrophic marine waters contradicts the common view of polyP as a luxury P-storage molecule. Here, we show that in a P-rich eutrophic bay of Lake Ontario, planktonic polyP is controlled by multiple mechanisms and responds strongly to seasonal variations. Plankton accumulate polyP as P storage under high-P conditions via luxury uptake and use it under acute P stress. Low phosphorus also triggers enrichment of polyP that can be preferentially recycled to attenuate P lost. We discover that picoplankton, despite their low production rates, are responsible for the dynamic polyP metabolisms. Picoplankton store and liberate polyP to support the high primary productivity of blooming algae. PolyP mechanisms enable efficient P recycling on ecosystem and even larger scales.

Adaptation of Synechococcus sp. PCC 7942 to phosphate starvation by glycolipid accumulation and membrane lipid remodeling

Organisms use various adaptive strategies against phosphate stress, including lipid remodeling. Here, the response of major membrane lipids to phosphate stress was analyzed in Synechococcus sp. PCC 7942. Unlike plants and eukaryotic microalgae, no significant increases in neutral lipids were found, whereas glycolipids content increased to as high as 6.13% (of dry cell weight, DCW) and phospholipids decreased to 0.34% (of DCW) after 16 days of cultivation without phosphate. Glycolipids accumulation were mainly attributed to the significant increase of digalactosyldiacylglycerol (DGDG) by 50% and sulfoquinovosyldiaclglycerol (SQDG) by 90%, both of which acted as complementary lipids for phosphatidylglycerol (PG) in the cyanobacterial membrane. Also, a notable increase in content (by 48%) of C18 fatty acids (especially C18:1) was observed in all glycolipids at the expense of C12 and C14 (72%). These changes may contribute to membrane fluidity and photosynthetic activity for basic cell metabolism and phosphate stress adaptation. Lipidomic analyses showed the reduction of PG 18:1/16: 0 (by 52%) with the increase of DGDG 18:1/16:0 (133%) and SQDG 18:1/16:0 (245%), strongly suggesting a direct conversion of PG to DGDG and SQDG. Moreover, the decreasing amount of monogalactosyldiacylglycerol (MGDG) 16:1/16:0 (22%) was consistent with the increase of free fatty acids (125%) on day 2 of phosphate absence, which suggested that MGDG is more likely to provide a pool of fatty acids for de novo synthesis of glycolipids. This study provides valuable insight into cyanobacteria adaptation strategies to phosphate stress by membrane lipid remodeling and unveils the underlying acyl chain fluxes into glycolipids.