Natural Microbial Communities Research Articles

Modelling the dispersion of infectious salmon anemia virus from Atlantic salmon farms in the Quoddy Region of New Brunswick, Canada and Maine, USA

Pathogen dispersal from infected aquaculture sites into the surrounding ocean poses risks of infection to wild and farmed species, but is difficult to predict. This study aimed to build a framework using an ocean circulation and a particle tracking model in conjunction with a dynamic infection model and a virus inactivation model to simulate the dispersal of the infectious salmon anemia virus (ISAV) from Atlantic salmon farms. Simulated particles were released from hypothetically infected farms and advected by modelled currents. Inactivation of viral cohorts by ambient ultraviolet radiation and natural microbial communities was simulated during advection. Simulations showed that ISAV concentration varied spatiotemporally with the progression of the outbreak, current speed and direction, tidal elevation amplitude, and environmental decay. Connectivity among aquaculture sites varied in relation to seaway distances, though simulations showed that connectivity can also be asymmetrical between farm sites. Sensitivity analyses showed that the dispersal of ISAV was moderately sensitive to uncertainty associated with the viral decay model, highlighting the importance of obtaining accurate estimates of inactivation rates of ISAV. This framework provides an approach to simulate waterborne viral transmission that considers the biology and epidemic features of significance for pathogens and the dynamic conditions of the ocean.

Poultry Residual Biomass as Substrate to Generate Bioelectricity using a dual Chamber Microbial Fuel Cell “MFC” with Graphite and Copper Electrodes

Microbial fuel cells (MFC) are electrochemical systems through which sustainable energy can be produced due to the degradation of organic matter using substrates with a varied chemical composition. The bioprocess that takes place inside the MFC takes advantage of the oxidation of organic matter. This process releases protons and electrons extracellularly, and the latter are transferred from the anode to the cathode generating bioelectricity. The MFC operating system produces energy due to the bacterial metabolism, through an electron transfer phenomenon that reflects into a bio energy conversion with minimal impacts on the environment. With the MFC system, it is possible to investigate the use of new residual substrates for energy production, the types of native microbial communities that develop during the degradation of specific compounds and the design of more efficient cells. In this research, copper and graphite were evaluated as low-cost electrodes using batch microbial fuel cells for 208 hours of operation, a data logger was used, and physicochemical parameters were taken during this period. The maximum power density presented was 14 mW/m2 with the graphite electrode and 6.7 mW/m2 with the copper electrode. Electrogenic bacteria were identified through biochemical and molecular tests such as bacterial culture, strain purification, DNA extraction and sequencing of microorganisms. The bacteria were uploaded to the NCBI gene data bank and the identity of these strains was identified: avian graphite 1 “Av_A1” (Pseudomonas aureginosa), avian graphite 2 “Av_A2” (Bacillus cereus) and avian copper 1 “AV_C1” (Bacillus tropicus). A dual chamber MFC was assembled, so each microbial cell can contain the residual substrate and the corresponding electron acceptor, both for the anodic and cathodic cell. These cells were separated by a Nafion® or Ultrex® membrane cation exchange membrane. The results showed us that optimal conditions for the generation of bioelectricity can be established in MFC cells, adding information to the literature on the behavior of bacteria that thrive in stressful environments such as copper and simple materials such as the graphite.

Syntrophy between bacteria and archaea enhances methane production in an EGSB bioreactor fed by cheese whey wastewater

The cheese-making process generates large amounts of cheese whey wastewater (CWW), which is abundant in nutrients but difficult to dispose of, contributing to the eutrophication of natural environments due to inadequate waste management. Here we show the anaerobic digestion of CCW by syntrophy between bacteria and archaea in an expanded granular sludge bed (EGSB) bioreactor as a low-cost alternative for bioremediation and biofuel production. The performance of the EGSB bioreactor and the composition of the natural microbial community were evaluated. During the operation of the EGSB bioreactor, physicochemical parameters such as alkalinity ratio (0.25), pH (7.5), and temperature (26°C) were attained and maintained, as well as light- and oxygen-free conditions, which favored the metabolism of oxygen-sensitive bacteria and methane-producing archaea (methanogens). Under these conditions, the chemical oxygen demand (COD) removal rate was highly efficient (> 89%). Methane (CH4) was produced from organic matter degradation by a few methanogens, mainly from Methanosaeta spp., and was enhanced by the metabolic interaction between bacteria and archaea. The biochemical methane potential (BMP) was >335 mL CH4/gCOD, indicating that the syntrophic microbial community is very efficient in removing organic matter and CH4 produced from CWW. Our results suggest that CWW could be treated in EGSB bioreactors and used as a sustainable alternative to CH4 production and also provide insights for the design of synthetic microbial communities (SynComs) for bioremediation, biogas production, and other biotechnological processes.

Long-term presence of microplastics in aerobic and anaerobic sequential batch reactors: Effect on treatment, microbial diversity, and microplastics morphology

Sewage treatment plants (STPs) are identified as the significant sink and source of microplastics (MPs) in aquatic bodies and terrestrial systems. A major fraction of MPs gets retained in STPs for a longer duration, and their potentiality for secondary MPs generation and additives leaching remain under investigated. Therefore, this study focussed on the effect of long-term exposure of aerobic and anaerobic biological sewage treatment units on MPs, along with the effect of MPs on treatment efficiency and microbial consortium. A mixture of polyvinyl chloride, polystyrene, and nylon MPs at 262 MPs/L was spiked in the aerobic and anaerobic sequential batch reactors (SBRs) for 120 days at the start of study. The study revealed a release of noteworthy fraction of secondary MPs into the reactors from spiked MPs. At the end of 120th day, the presence of secondary generated MPs was estimated as 1000 ± 71 MPs/L and 650±141 MPs/L in aerobic and anaerobic SBRs respectively. Most of the observed secondary MPs were of size < 300 µm. Leaching of additives, i.e. cyclohexylamine, cyclotetradecane, octadecanol, pipericine etc., into the SBR effluents were also observed. The depuration capacities of the reactors were not affected with the presence of MPs during the study. While the microbial diversity and abundance were negatively impacted in aerobic SBRs, no such impacts were observed in anaerobic SBRs due to MPs. These results do suggest such exposures to potentially cause secondary MPs and chemical pollution in receiving matrices for the treated effluent, as well as effect on the native microbial community.

Exploring the potential of a new marine bacterium associated with plastisphere to metabolize dibutyl phthalate and bis(2-ethylhexyl) phthalate by enrichment cultures combined with multi-omics analysis

Phthalic acid esters (PAEs) plasticizers are virulent endocrine disruptors that are mixed into plastics while fabricating and can filter out once they release into the surrounding environments. Plastic surfaces serve as new habitats for microorganisms, referred to as ‘plastisphere’. Previous metagenomic investigations of the ‘plastisphere’ indicated that marine plastic surfaces may harbor microbes that degrade PAEs plasticizers. To our knowledge, the potential of microorganisms in the marine ‘plastisphere’ to metabolize PAEs is poorly understood. In this study, by screening the natural microbial community on plastic debris that had been deployed in situ for up to 20 months, a novel marine bacterium, Microbacterium esteraromaticum DEHP-1, was successfully isolated, which could degrade and mineralize 10–200 mg/L dibutyl phthalate (DBP) and bis(2-ethylhexyl) phthalate (DEHP). According to the results of gas chromatography-mass spectrometry (GC-MS) and whole genome mining of strain DEHP-1, we found that strain DEHP-1 may metabolize DBP by successive removal of the ester side chain by esterase 2518 to produce mono-butyl phthalate (MBP) and phthalic acid (PA), whereas the degradation of DEHP may take place by the direct action of monooxygenase 0132 on the fatty acid side chain of the DEHP molecule to produce di-n-hexyl phthalate (DnHP) and DBP, and then the subsequent hydrolysis of DBP by de-esterification to PA and finally into the tricarboxylic acid (TCA) cycle. Non-targeted metabolomics results showed that intracellular degradation of PAEs did not happen. However, exposure to PAEs was found to significantly affect pathways such as arginine and proline, riboflavin, glutathione and lysine degradation. Therefore, the intracellular metabolic behavior of strain DEHP-1 exposed to PAEs was proposed for the first time. This study sheds light on the metabolic capacity and strategies of bacteria in the marine ‘plastisphere’ to effectively degrade PAEs and highlights the importance of marine microbes in mitigating plastic poisonousness.

Microbial defluorination of TFA, PFOA, and HFPO-DA by a native microbial consortium under anoxic conditions

In this study, the biodegradability of trifluoroacetate (TFA), perfluorooctanoic acid (PFOA), and perfluoro-2-methyl-3-oxahexanoic acid (HFPO-DA) by a native microbial community was evaluated over a 10-month incubation period. The observed microbial defluorination ratios and removal efficiency were 3.46 ( ± 2.73) % and 8.03 ( ± 3.03) %, 8.44 ( ± 1.88) % and 13.52 ( ± 4.96) %, 3.02 ( ± 0.62) % and 5.45 ( ± 2.99) % for TFA, PFOA and HFPO-DA, respectively. The biodegradation intermediate products, TFA and pentafluoropropionic acid (PFA), of PFOA and HFPO-DA were detected in their biodegradation treatment groups. Furthermore, the concentrations of the PFOA metabolites, perfluorohexanoic acid (PFHxA) and perfluoroheptanoic acid (PFHpA), in the aqueous solutions after incubation were quantified to be 0.21 and 4.14 µg/L. TFA, PFOA and HFPO-DA significantly reduced the microbial diversity and changed the structure of the community. The co-occurrence network analysis showed that low abundance species, such as Flexilinea flocculi, Bacteriovorax stolpii, and g_Sphingomonas, are positively correlated with the generation of fluoride ion, implying their potential collaborative functions contributing to the observed biodefluorination. The findings in this study can provide insights for the biodegradation of perfluoroalkyl carboxylic acids and their emerging alternatives by indigenous microorganisms in the environment.

Turnover of strain-level diversity modulates functional traits in the honeybee gut microbiome between nurses and foragers

BackgroundStrain-level diversity is widespread among bacterial species and can expand the functional potential of natural microbial communities. However, to what extent communities undergo consistent shifts in strain composition in response to environmental/host changes is less well understood.ResultsHere, we used shotgun metagenomics to compare the gut microbiota of two behavioral states of the Western honeybee (Apis mellifera), namely nurse and forager bees. While their gut microbiota is composed of the same bacterial species, we detect consistent changes in strain-level composition between nurses and foragers. Single nucleotide variant profiles of predominant bacterial species cluster by behavioral state. Moreover, we identify strain-specific gene content related to nutrient utilization, vitamin biosynthesis, and cell–cell interactions specifically associated with the two behavioral states.ConclusionsOur findings show that strain-level diversity in host-associated communities can undergo consistent changes in response to host behavioral changes modulating the functional potential of the community.

Biomineralization To Prevent Microbially Induced Corrosion on Concrete for Sustainable Marine Infrastructure.

Microbially induced corrosion (MIC) on concrete represents a serious issue impairing the lifespan of coastal/marine infrastructure. However, currently developed concrete corrosion protection strategies have limitations in wide applications. Here, a biomineralization method was proposed to form a biomineralized film on concrete surfaces for corrosion inhibition. Laboratory seawater corrosion experiments were conducted under different conditions [e.g., chemical corrosion (CC), MIC, and biomineralization for corrosion inhibition]. A combination of chemical and mechanical property measurements of concrete (e.g., sulfate concentrations, permeability, mass, and strength) and a genotypic-based investigation of formed concrete biofilms was conducted to evaluate the effectiveness of the biomineralization approach on corrosion inhibition. The results show that MIC resulted in much higher corrosion rates than CC. However, the biomineralization treatment effectively inhibited corrosion because the biomineralized film decreased the total and relative abundance of sulfate-reducing bacteria (SRB) and acted as a protective layer to control the diffusion of sulfate and isolate the concrete from the corrosive SRB communities, which helps extend the lifespan of concrete structures. Moreover, this technique had no negative impact on the native marine microbial communities. Our study contributes to the potential application of biomineralization for corrosion inhibition to achieve long-term sustainability for major marine concrete structures.

Establishment of microbial model communities capable of removing trace organic chemicals for biotransformation mechanisms research

BackgroundRemoval of trace organic chemicals (TOrCs) in aquatic environments has been intensively studied. Some members of natural microbial communities play a vital role in transforming chemical contaminants, however, complex microbial interactions impede us from gaining adequate understanding of TOrC biotransformation mechanisms. To simplify, in this study, we propose a strategy of establishing reduced-richness model communities capable of removing diverse TOrCs via pre-adaptation and dilution-to-extinction.ResultsMicrobial communities were adapted from tap water, soil, sand, sediment deep and sediment surface to changing concentrations of 27 TOrCs mixture. After adaptation, the communities were further diluted to reduce diversity into 96 deep well plates for high-throughput cultivation. After characterizing microbial structure and TOrC removal performance, thirty taxonomically non-redundant model communities with different removal abilities were obtained. The pre-adaptation process was found to reduce the microbial richness but to increase the evenness and phylogenetic diversity of resulting model communities. Moreover, phylogenetic diversity showed a positive effect on the number of TOrCs that can be transformed simultaneously. Pre-adaptation also improved the overall TOrC removal rates, which was found to be positively correlated with the growth rates of model communities.ConclusionsThis is the first study that investigated a wide range of TOrC biotransformation based on different model communities derived from varying natural microbial systems. This study provides a standardized workflow of establishing model communities for different metabolic purposes with changeable inoculum and substrates. The obtained model communities can be further used to find the driving agents of TOrC biotransformation at the enzyme/gene level.

Biohydrogen production from lactic acid: Use of food waste as substrate and evaluation of pretreated sludge and native microbial community as inoculum

Nowadays, lactic acid (HLa) has caught the eye as a precursor of H2 production from substrates that harbor a significant amount of lactic acid bacteria (LAB), such as Lactobacillus and Lactococcus. Since the native microbial community of food waste (FW) is dominated by LAB, the production of H2 during dark fermentation might be inhibited by the displacement of H2-producing bacteria by LAB. Therefore, lactate-driven dark fermentation in two steps is an alternative to overcome the overproliferation of LAB. In this process, FW is converted into HLa, which can subsequently be transformed into H2 by HLa-consuming bacteria during a cross-feeding mechanism with H2-producing bacteria. In the present study, FW was evaluated for HLa production at different organic loading rates (OLR) (12.5, 25.0, 37.5, and 50.0 gVS/L/d) in a semi-continuous reactor, and the HLa obtained was used for the H2 production. Results showed that OLR significantly influences HLa production during the self-fermentation of FW (p < 0.05). The highest ORL of 50.0 gVS/L/d and an HRT of 1.25 days generated the net maximum HLa production of 10.8 g/L. The HLa production was companied by the presence of acetate, propionate, and succinate, which accounted for only 20 % of the total organic acids produced. Then, effluent with HLa concentrations of 5.0, 10.0, 15.0, 20.0, and 25.0 g/L was evaluated for H2 production in batch tests using thermally pretreated sludge and the native microbial community of the effluent as inoculum. Even though different metabolic pathways for H2 production can be noted during the fermentation, which differs from one inoculum to another, the highest value of H2 production of 596.3 mL/Lreactor was obtained with the native microbial community at the highest concentration of HLa (25.0 g/L). During the fermentation process for H2 production, HLa and propionate were mainly transformed into butyrate and acetate. The present study demonstrated the feasibility of obtaining H2 from a complex substrate, such as effluent from a previous fermentation, using different inocula.

Alternative Starter Fertilization Strategies in Maize (Zea mays L.) Cultivation: Agronomic Potential of Microgranular Fertilizer and Plant Growth-Promoting Microorganisms and Their Impact on the Soil Native Microbial Community

Phosphorous (P) starter fertilization can increase maize (Zea mays L.) yield. Widespread application in soils with sufficient P availability leads to environmental risks. Subsequently, alternative strategies to support the maize plant’s early development are needed to lower P surpluses. Here, we conducted field experiments comparing standard starter fertilizer diammonium phosphate (DAP) (20.1 kg P ha−1) to microgranular fertilizer (MG) (2.4 kg P ha−1) and combined in-furrow inoculation with Bacillus atrophaeus and mycorrhizal fungi (Rhizoglomus irregulare, Funneliformis mosseae, and Funneliformis caledonium), alone and in combination. The soil microbial community inside and between the maize rows was monitored by quantitative PCR (qPCR)-based quantification of eight fungal and bacterial groups. The yield did not vary between fertilization with DAP or MG and no fertilizer control. The combined microorganism inoculum (MO), however, enhanced the yield by 4.2%. The soil microbial community composition was not affected by the MO application. However, on one field site and inside the rows, it leads to a significant increase in overall microbial gene copy numbers by 9.3% and a significant decrease in the relative abundance of the bacterial phylum of Bacillota (Firmicutes) by 18%. The in-furrow MO application is thus a promising option for starter fertilizer replacement.

A host‐derived chimeric peptide protects citrus against Huanglongbing without threatening the native microbial community of the phyllosphere

AbstractIntroductionThe application of host‐derived antibacterial peptides has been highlighted as a potential efficacious and safe tool for the treatment of Huanglongbing (HLB), the most devastating disease of citrus. However, pathogenic bacteria such as HLB‐causing Candidatus liberibacter asiaticus (CLas) often develop resistance against the host antibacterial peptides. We showed that chimeras containing two different host antibacterial peptides not only retain antibacterial activity but also overcome bacterial resistance and enhance plant defence responses. Also, chimeric peptides can have an off‐target impact on the structure and function of plant‐associated microbiomes. However, there is a lack of understanding of the impact of the chimeric peptide therapy on the microbial structure in the citrus phyllosphere while reducing the CLas titre. Here, we aim to evaluate the efficacy of a chimeric peptide (UGK17) to reduce CLas titre, inducing plant defence response and impacting the microbiome associated with the citrus phyllosphere.Material and MethodLeaf samples were collected from orange and grapefruit trees in Texas and identified as old and young leaves according to their maturity. We collected three different types of leaves based on their infection and symptoms: healthy, symptomatic (infected with typical symptoms), and asymptomatic (infected without symptoms). In planta assay was performed by dipping the leaves in the 0, 5 and 25 μM of UGK17 solutions for 48 h. The quantifications of CLas titre and pathogenesis‐related (PR) gene expression were done by quantitative polymerase chain reaction (qPCR) and reverse transcription‐qPCR, respectively. Amplicon sequencing was done to evaluate the impact of UGK17 on individual bacterial community structures. In addition, we performed an ex planta assay to assess the effect of UGK17 on the growth of bacterial isolates including Liberibacter crescens instead of unculturable CLas predominant in the phyllosphere.ResultThe UGK17 treatment reduced the CLas titre in both asymptomatic and symptomatic citrus leaves, regardless of the age of the leaves. The UGK17 application augmented the PR gene expression. In ex planta assay, the growth of L. crescens along with four other strains belonging to the family Rhizobiaceae, was significantly inhibited by the UGK17 while the growth of 74 strains were unaffected. Additionally, there was no statistically significant changes in the microbial community structure with UGK17 treatment.ConclusionOur results suggest that the chimeric peptide therapy is a promising solution to combat HLB by targeting mainly Gram‐negative pathogens and enhancing the plant immune responses without impairing the indigenous microbial community in the citrus phyllosphere.

Metabolic exchanges are ubiquitous in natural microbial communities.

Microbial communities drive global biogeochemical cycles and shape the health of plants and animals-including humans. Their structure and function are determined by ecological and environmental interactions that govern the assembly, stability and evolution of microbial communities. A widely held view is that antagonistic interactions such as competition predominate in microbial communities and are ecologically more important than synergistic interactions-for example, mutualism or commensalism. Over the past decade, however, a more nuanced picture has emerged, wherein bacteria, archaea and fungi exist within interactive networks in which they exchange essential and non-essential metabolites. These metabolic interactions profoundly impact not only the physiology, ecology and evolution of the strains involved, but are also central to the functioning of many, if not all, microbiomes. Therefore, we advocate for a balanced view of microbiome ecology that encompasses both synergistic and antagonistic interactions as key forces driving the structure and dynamics within microbial communities.

Designing a synthetic microbial community through genome metabolic modeling to enhance plant–microbe interaction

BackgroundManipulating the rhizosphere microbial community through beneficial microorganism inoculation has gained interest in improving crop productivity and stress resistance. Synthetic microbial communities, known as SynComs, mimic natural microbial compositions while reducing the number of components. However, achieving this goal requires a comprehensive understanding of natural microbial communities and carefully selecting compatible microorganisms with colonization traits, which still pose challenges. In this study, we employed multi-genome metabolic modeling of 270 previously described metagenome-assembled genomes from Campos rupestres to design a synthetic microbial community to improve the yield of important crop plants.ResultsWe used a targeted approach to select a minimal community (MinCom) encompassing essential compounds for microbial metabolism and compounds relevant to plant interactions. This resulted in a reduction of the initial community size by approximately 4.5-fold. Notably, the MinCom retained crucial genes associated with essential plant growth-promoting traits, such as iron acquisition, exopolysaccharide production, potassium solubilization, nitrogen fixation, GABA production, and IAA-related tryptophan metabolism. Furthermore, our in-silico selection for the SymComs, based on a comprehensive understanding of microbe-microbe-plant interactions, yielded a set of six hub species that displayed notable taxonomic novelty, including members of the Eremiobacterota and Verrucomicrobiota phyla.ConclusionOverall, the study contributes to the growing body of research on synthetic microbial communities and their potential to enhance agricultural practices. The insights gained from our in-silico approach and the selection of hub species pave the way for further investigations into the development of tailored microbial communities that can optimize crop productivity and improve stress resilience in agricultural systems.

PGPR-Soil Microbial Communities' Interactions and Their Influence on Wheat Growth Promotion and Resistance Induction against Mycosphaerella graminicola.

The efficiency of plant-growth-promoting rhizobacteria (PGPR) may not be consistently maintained under field conditions due to the influence of soil microbial communities. The present study aims to investigate their impact on three PGPR-based biofertilizers in wheat. We used the PGPR Paenibacillus sp. strain B2 (PB2), PB2 in co-inoculation with Arthrobacter agilis 4042 (Mix 2), or with Arthrobacter sp. SSM-004 and Microbacterium sp. SSM-001 (Mix 3). Inoculation of PB2, Mix 2, and Mix 3 into non-sterile field soil had a positive effect on root and aboveground dry biomass, depending on the wheat cultivar. The efficiency of the PGPR was further confirmed by the protection they provided against Mycosphaerella graminicola, the causal agent of Septoria leaf blotch disease. PB2 exhibited protection of ≥37.8%, while Mix 2 showed ≥47.9% protection in the four cultivars tested. These results suggest that the interactions between PGPR and native soil microbial communities are crucial for promoting wheat growth and protection. Additionally, high-throughput sequencing of microbial communities conducted 7 days after PGPR inoculations revealed no negative effects of PB2, Mix 2, and Mix 3 on the soil microbial community structure. Interestingly, the presence of Arthrobacter spp. appeared to mitigate the potential negative effect of PB2 on bacterial community and foster root colonization by other beneficial bacterial strains.

Microbiota of maize kernels as influenced by Aspergillus flavus infection in susceptible and resistant inbreds.

Nearly everything on Earth harbors a microbiome. A microbiome is a community of microbes (bacteria, fungi, and viruses) with potential to form complex networks that involve mutualistic and antagonistic interactions. Resident microbiota on/in an organism are determined by the external environment, both biotic and abiotic, and the intrinsic adaptability of each organism. Although the maize microbiome has been characterized, community changes that result from the application of fungal biocontrol strains, such as non-aflatoxigenic Aspergillus flavus, have not. We silk channel inoculated field-grown maize separately with a non-aflatoxigenic biocontrol strain (K49), a highly toxigenic strain (Tox4), and a combination of both A. flavus strains. Two maize inbreds were treated, A. flavus-susceptible B73 and A. flavus-resistant CML322. We then assessed the impacts of A. flavus introduction on the epibiota and endobiota of their maize kernels. We found that the native microbial communities were significantly affected, irrespective of genotype or sampled tissue. Overall, bacteriomes exhibited greater diversity of genera than mycobiomes. The abundance of certain genera was unchanged by treatment, including genera of bacteria (e.g., Enterobacter, Pantoea) and fungi (e.g., Sarocladium, Meyerozyma) that are known to be beneficial, antagonistic, or both on plant growth and health. Beneficial microbes like Sarocladium that responded well to A. flavus biocontrol strains are expected to enhance biocontrol efficacy, while also displacing/antagonizing harmful microbes.

Effects of water environmental factors and antibiotics on bacterial community in urban landscape lakes

The presence of antibiotics can affect the natural microbial community and exert selective pressure on the environment's microorganisms. This study focused on three types of urban landscape lakes in Xi'an that were closely related to human activities. By combining basic water quality indicators, antibiotic occurrence status, bacterial communities and their potential metabolic functions, Spearman correlation coefficient and redundancy analysis were used to explore the relationship between them, and further explore the impact mechanism of environmental factors and antibiotics on bacterial community structure. The results showed that ofloxacin, erythromycin, and roxithromycin were the main types of antibiotics in the three landscape lakes, with low ecological risks, and there was a clear clustering of antibiotic occurrence. Proteobacteria was the most abundant bacterial phylum, and each lake had its own unique dominant bacteria, which indicates that they are influenced by varying water sources, pollution, and other nearby environments. Statistical analysis showed that pH and nitrogen nutrients were the most critical environmental factors affecting bacterial communities (P<0.01), while tetracyclines and lincomycins were the antibiotics that had a significant impact on bacterial communities (P<0.05). Antibiotics mainly promote defense- and signal transduction-related functions, and inhibit the metabolic activity of bacterial communities. However, the impact of antibiotics on bacterial diversity, community structure, and potential metabolic function in the three urban lakes was less than that of environmental factors. These results help to clarify the mechanism and degree of impact of different interference factors (environmental factors, conventional pollutants, and antibiotics) on bacterial communities in the water environment and are important for the management of urban landscape lake water environments.

Food for all? Wildfire ash fuels growth of diverse eukaryotic plankton.

In December 2017, one of the largest wildfires in California history, the Thomas Fire, created a large smoke and ash plume that extended over the northeastern Pacific Ocean. Here, we explore the impact of Thomas Fire ash deposition on seawater chemistry and the growth and composition of natural microbial communities. Experiments conducted in coastal California waters during the Thomas Fire revealed that leaching of ash in seawater resulted in significant additions of dissolved nutrients including inorganic nitrogen (nitrate, nitrite and ammonium), silicic acid, metals (iron, nickel, cobalt and copper), organic nitrogen and organic carbon. After exposure to ash leachate at high (0.25 g ash l-1) and low (0.08 g ash l-1) concentrations for 4 days, natural microbial communities had 59-154% higher particulate organic carbon concentrations than communities without ash leachate additions. Additionally, a diverse assemblage of eukaryotic microbes (protists) responded to the ash leachate with taxa from 11 different taxonomic divisions increasing in relative abundance compared with control treatments. Our results suggest that large fire events can be important atmospheric sources of nutrients (particularly nitrogen) to coastal marine systems, where, through leaching of various nutrients, ash may act as a 'food for all' in protist communities.

How might bacteriophages shape biological invasions?

Invasions by eukaryotes dependent on environmentally acquired bacterial mutualists are often limited by the ability of bacterial partners to survive and establish free-living populations. Focusing on the model legume-rhizobium mutualism, we apply invasion biology hypotheses to explain how bacteriophages can impact the competitiveness of introduced bacterial mutualists. Predicting how phage-bacteria interactions affect invading eukaryotic hosts requires knowing the eco-evolutionary constraints of introduced and native microbial communities, as well as their differences in abundance and diversity. By synthesizing research from invasion biology, as well as bacterial, viral, and community ecology, we create a conceptual framework for understanding and predicting how phages can affect biological invasions through their effects on bacterial mutualists.

Prebiotics: A Solution for Improving Plant Growth, Soil Health, and Carbon Sequestration?

Soil fertility and productivity are severely impacted by exploitation and degradation processes. These threats, coupled with population growth and climatic changes, compel us to search for innovative agroecological solutions. Prebiotics, a type of soil biostimulant, are used to enhance soil conditions and plant growth and may play a role in carbon (C) sequestration. Two commercial prebiotics, K1® and NUTRIGEO L® (referred to as SPK and SPN, respectively), were assessed for their effects on agricultural soil cultivated with Zea mays L., compared to untreated soil or control (SP). Analyses were performed at two harvesting dates: three weeks (D1) and ten weeks (D2) after the application of prebiotics. Plant growth parameters and soil characteristics were measured, focusing on soil organic matter, soil bacterial and fungal communities, and plant root mycorrhization. Regarding physicochemical parameters, both prebiotic treatments increased soil electrical conductivity, cation exchange capacity, and soluble phosphorus (P) while decreasing nitrates. Meanwhile, the SPN treatment was distinct in elevating specific cationic minerals, such as calcium (Ca) and boron (B), at D2. At the microbial level, each prebiotic induced a unique shift in the indigenous bacterial and fungal communities’ abundance and diversity, evident at D2. Simultaneously, specific microbial taxa were recruited by each prebiotic treatment, such as Caulobacter, Sphingobium, and Massilia from bacteria and Mortierella globalpina and Schizothecium carpinicola from fungi in SPK as well as Chitinophaga, Neobacillus, and Rhizomicrobium from bacteria and Sordariomycetes and Mortierella minutissima from fungi in SPN. These biomarkers were identified as (a) saprotrophs, (b) plant growth-promoting bacteria and fungi, (c) endohyphal bacteria, and (d) endophytic and symbiotic microbiota. This result was reflected in the increase in glomalin content and mycorrhization rate in the treated soils, especially by SPN. We observed that these effects led to an increase in plant biomass (shoots by 19% and 22.8% and roots by 47.8% and 35.7% dry weights for SPK and SPN, respectively) and contributed to an increase in soil C content (organic C by 8.4% and total C by 8.9%), particularly with SPN treatment. In light of these findings, the use of prebiotics ten weeks after application not only increased plant growth by improving soil characteristics and shaping its native microbial community but also demonstrated the potential to enhance C sequestration.