Complete genome sequences of six duckweed-associated bacterial strains for studying community assembly in synthetic plant microbiome.

We report the complete genome sequences of six bacterial strains isolated from a floating macrophyte, duckweed. These six strains, representing the six dominant families of the natural duckweed microbiome, establish a simple model ecosystem when inoculated onto sterilized duckweed. Their genomes would provide insights into community assembly in plant microbiome.

Learning beyond-pairwise interactions enables the bottom-up prediction of microbial community structure.

Understanding the assembly of multispecies microbial communities represents a significant challenge in ecology and has wide applications in agriculture, wastewater treatment, and human healthcare domains. Traditionally, studies on the microbial community assembly focused on analyzing pairwise relationships among species; however, neglecting higher-order interactions, i.e., the change of pairwise relationships in the community context, may lead to substantial deviation from reality. Herein, we have proposed a simple framework that incorporates higher-order interactions into a bottom-up prediction of the microbial community assembly and examined its accuracy using a seven-member synthetic bacterial community on a host plant, duckweed. Although the synthetic community exhibited emergent properties that cannot be predicted from pairwise coculturing results, our results demonstrated that incorporating information from three-member combinations allows the acceptable prediction of the community structure and actual interaction forces within it. This reflects that the occurrence of higher-order effects follows consistent patterns, which can be predicted even from trio combinations, the smallest unit of higher-order interactions. These results highlight the possibility of predicting, explaining, and understanding the microbial community structure from the bottom-up by learning interspecies interactions from simple beyond-pairwise combinations.

Potential of Predatory Bacteria to Colonize the Duckweed Microbiome and Change Its Structure: A Model Study Using the Obligate Predatory Bacterium, Bacteriovorax sp. HI3.

Modifying the duckweed microbiome is a major challenge for enhancing the effectiveness of duckweed-based wastewater treatment and biomass production technologies. We herein examined the potential of the exogenous introduction of predatory bacteria to change the duckweed microbiome. Bacteriovorax sp. HI3, a model predatory bacterium, colonized the core of the Lemna microbiome, and its predatory behavior changed the microbiome structure, which correlated with colonization density. These results reveal that bacterial predatory interactions may be important drivers that shape the duckweed microbiome, suggesting their potential usefulness in modifying the microbiome.

Enhancement of nutrient removal in an activated sludge process using aerobic granular sludge augmentation strategy with ammonium-based aeration control.

To enhance nutrient removal from low-strength municipal wastewater in a continuous-flow activated sludge (CFAS) process using aerobic granular sludge (AGS) augmentation strategy, a pilot-scale demonstration was configured with a mainstream reactor (anaerobic/aerobic process) and a sidestream sequencing batch reactor for AGS production. The aeration of the mainstream reactor was controlled based on dissolved oxygen (DO) and ammonium concentrations during Phases I and II-III, respectively. During Phase III, an anoxic zone was created in the mainstream aerobic tank. Throughout the demonstration period, excellent sludge settleability in the mainstream reactor (SVI30 ≤ 80 mL g-1) under long sludge retention time conditions (≥12 d) allowed the maintenance of a high mixed liquor suspended solids concentration (≥3000 mg L-1). The total nitrogen (TN) removal ratio improved significantly during Phases II and III (49.3 ± 4.1% and 50.1 ± 10.2%, respectively) compared to Phase I (43.2 ± 5.5%). Low DO concentration (< 0.5 mg L-1) by the ammonium-based aeration tended to increase the simultaneous nitrification and denitrification efficiency (> 40%), enhancing TN removal (> 50%). The reduction of DO and nitrate concentrations in the returning sludge liquor can stabilize phosphorus removal (approximately 80% of the 25th percentile). In addition, the aeration efficiency during Phase III decreased by 26-29% compared to Phase I. These results suggest that the introduction of ammonium-based aeration control to the CFAS using the AGS augmentation strategy could contribute to superior sewerage treatment, including nutrient removal and a low carbon footprint.

Bioaugmentation with marine sediment-derived microbial consortia in mesophilic anaerobic digestion for enhancing methane production under ammonium or salinity stress.

Ammonium (NH4+) and salinity (NaCl) inhibit CH4 production in anaerobic digestion. However, whether bioaugmentation using marine sediment-derived microbial consortia can relieve the inhibitory effects of NH4+ and NaCl stresses on CH4 production remains unclear. Thus, this study evaluated the effectiveness of bioaugmentation using marine sediment-derived microbial consortia in alleviating the inhibition of CH4 production under NH4+ or NaCl stress and elucidated the underlying mechanisms. Batch anaerobic digestion experiments under 5 gNH4-N/L or 30 g/L NaCl were performed with or without augmentation using two marine sediment-derived microbial consortia pre-acclimated to high NH4+ and NaCl. Compared with non-bioaugmentation, bioaugmentation reinforced CH4 production. Network analysis revealed the joint effects of microbial connections by Methanoculleus, which promoted the efficient consumption of propionate accumulated under NH4+ and NaCl stresses. In conclusion, bioaugmentation with pre-acclimated marine sediment-derived microbial consortia can mitigate the inhibition under NH4+ or NaCl stress and enhance CH4 production in anaerobic digestion.

Draft Genome Sequence of Stutzerimonas stutzeri NT-I, Which Reduces Selenium Oxyanions into Elemental Selenium and Volatile Selenium Species.

Stutzerimonas stutzeri strain NT-I effectively reduces selenate and selenite into elemental selenium and volatile selenium species. It is thus a promising biological agent for treatment of selenium-contaminated wastewater. We here report the draft genome sequence of this strain.

Complete Genome Sequences of Two Predatory Bacterial Strains, Bacteriovorax sp. HI3 and Myxococcus sp. MH1, Isolated from a Freshwater Pond.

We report the complete genome sequences of two predatory bacterial strains, Bacteriovorax sp. HI3 and Myxococcus sp. MH1, which were isolated from a freshwater pond. These two strains are grouped with the Bdellovibrio and like organisms and myxobacteria, respectively. Their genomes expand our knowledge of the characteristics of predatory bacteria.

Effectiveness of tetrahydrofuran at enhancing the 1,4-dioxane degradation ability of activated sludge lacking prior exposure to 1,4-dioxane.

1,4-dioxane (DX) is a contaminant of emerging concern in water environments. The enrichment of DX-degrading bacteria indigenous to activated sludge is key for the efficient biological removal of DX in wastewater. To identify an effective substrate, which enables the selective enrichment of DX-degrading bacteria and has lower toxicity and persistence than DX, this study explored the effectiveness of tetrahydrofuran (THF) at enhancing the DX degradation ability of activated sludge without historical exposure to DX. Although the activated sludge initially exhibited negligible ability to degrade DX (100 mg-C/L) as the sole carbon source, the repeated batch cultivation on THF could enrich bacterial populations capable of degrading DX, inducing the DX degradation ability in activated sludge as effectively as DX did. The THF-enrichment culture after 4 weeks degraded 100 mg-C/L DX almost completely within 21 d. Sequencing analyses revealed that soluble di-iron monooxygenase group 5C, including THF/DX monooxygenase, would play a dominant role in the initial oxidation of DX in THF-enrichment culture, which completely differed from the enrichment culture cultivated on DX. The results indicate that THF can be applied as an effective substrate to enhance the DX degradation ability of microbial consortia, irrespective of the intrinsic ability.

Characterization of Two Novel Predatory Bacteria, Bacteriovorax stolpii HI3 and Myxococcus sp. MH1, Isolated from a Freshwater Pond: Prey Range, and Predatory Dynamics and Efficiency.

Predatory bacteria, which prey on other bacteria, have significant functions in microbial ecosystems and have attracted increasing attention for their biotechnological use. However, knowledge of the characteristics of wild-type environmental predatory bacteria remains limited. This study isolated two predatory bacteria, Bacteriovorax stolpii HI3 and Myxococcus sp. MH1, from a freshwater pond and characterized their predation capabilities. Determination of the prey range using 53 potential prey strains, including 52 environmental strains, revealed that B. stolpii HI3 and Myxococcus sp. MH1 could prey on a wide spectrum of Gram-negative bacteria and a broader range of bacteria, irrespective of phylogeny, in accordance with the common characteristics of Bdellovibrio and like organisms and myxobacteria, respectively. Liquid culture assays also found that although predation by B. stolpii HI3 rapidly and largely occurred, the prey bacteria regrew, possibly through plastic phenotypic resistance to predation. In contrast, predation by Myxococcus sp. MH1 occurred at relatively low efficiency but was longer lasting. The two strains exhibited slightly distinct temperature preferences but commonly preferred slightly alkaline pH. The novel findings of this study provide evidence for the coexistence of predatory bacteria with diverse predation capabilities in the natural aquatic environment.

Isolation of Aquatic Plant Growth-Promoting Bacteria for the Floating Plant Duckweed (Lemna minor).

Plant growth-promoting bacteria (PGPB) can exert beneficial growth effects on their host plants. Little is known about the phylogeny and growth-promoting mechanisms of PGPB associated with aquatic plants, although those of terrestrial PGPB have been well-studied. Here, we report four novel aquatic PGPB strains, MRB1-4 (NITE P-01645-P-01648), for duckweed Lemna minor from our rhizobacterial collection isolated from Lythrum anceps. The number of L. minor fronds during 14 days co-culture with the strains MRB1-4 increased by 2.1-3.8-fold, compared with an uninoculated control; the plant biomass and chlorophyll content in co-cultures also increased. Moreover, all strains possessed an indole-3-acetic acid production trait in common with a plant growth-promoting trait of terrestrial PGPB. Phylogenetic analysis showed that three strains, MRB-1, -3, and -4, were affiliated with known proteobacterial genera (Bradyrhizobium and Pelomonas); this report is the first to describe a plant-growth promoting activity of Pelomonas members. The gammaproteobacterial strain MRB2 was suggested to be phylogenetically novel at the genus level. Under microscopic observation, the Pelomonas strain MRB3 was epiphytic and adhered to both the root surfaces and fronds of duckweed. The duckweed PGPB obtained here could serve as a new model for understanding unforeseen mechanisms behind aquatic plant-microbe interactions.

Identification of key steps and associated microbial populations for efficient anaerobic digestion under high ammonium or salinity conditions.

Ammonium (NH4+) and salinity are major inhibitors of CH4 production in anaerobic digestion. This study evaluated their inhibitory effects on CH4 production and explored the key populations for efficient CH4 production under high NH4+ and NaCl concentrations to understand their inhibition mechanisms. Comparative batch experiments for mesophilic anaerobic digestion were conducted using three seeding sludges under different concentrations of NH4+ (1-5 gNH4-N/L) and NaCl (10-30 g/L). Although all sludges tolerated 3 gNH4-N/L and 10 g/L NaCl, NH4+ or NaCl concentrations higher than these substantially reduced CH4 production, depending on the seeding sludge, primarily by impairing the initial hydrolysis and methanogenesis steps. In addition, propionate was found to be a deterministic factor affecting CH4 production. Based on microbial community analysis, Candidatus Brevefilum was identified as a potential syntrophic propionate-oxidizing bacterium that facilitates the mitigation of propionate accumulation, allowing the maintenance of unaffected CH4 production under high inhibitory conditions.

Complete Genome Sequence of Luteitalea sp. Strain TBR-22.

We report a complete genome sequence of a novel bacterial isolate, strain TBR-22, belonging to the class Vicinamibacteria of the phylum Acidobacteria, which was isolated from duckweed fronds. The genome expands our knowledge of the lifestyle of this abundant but rarely characterized phylum.

Draft Genome Sequence of Bryobacteraceae Strain F-183.

Here, we report a draft genome sequence of a bacterial strain, F-183, isolated from a duckweed frond. Strain F-183 belongs to the family Bryobacteraceae of the phylum Acidobacteria, and its genomic information would contribute to understanding the ecophysiology of this abundant but rarely characterized phylum.

Genome-wide identification of bacterial colonization and fitness determinants on the floating macrophyte, duckweed.

Bacterial communities associated with aquatic macrophytes largely influence host primary production and nutrient cycling in freshwater environments; however, little is known about how specific bacteria migrate to and proliferate at this unique habitat. Here, we separately identified bacterial genes involved in the initial colonization and overall fitness on plant surface, using the genome-wide transposon sequencing (Tn-seq) of Aquitalea magnusonii H3, a plant growth-promoting bacterium of the floating macrophyte, duckweed. Functional annotation of identified genes indicated that initial colonization efficiency might be simply explained by motility and cell surface structure, while overall fitness was associated with diverse metabolic and regulatory functions. Genes involved in lipopolysaccharides and type-IV pili biosynthesis showed different contributions to colonization and fitness, reflecting their metabolic cost and profound roles in host association. These results provide a comprehensive genetic perspective on aquatic-plant-bacterial interactions, and highlight the potential trade-off between bacterial colonization and proliferation abilities on plant surface.

Microalgal transformation of food processing byproducts into functional food ingredients.

Large amounts of food processing byproducts (FPBs) are generated from food manufacturing industries, the second-largest portion of food waste generation. FPBs may require additional cost for post-treatment otherwise cause environmental contamination. Valorization of FPBs into food ingredients by microalgae cultivation can save a high cost for organic carbon sources and nutrients from medium cost. This study reviews FPBs generation categorized by industry and traditional disposal. In contrast with the low-value production, FPBs utilization as the nutrient-abundant medium for microalgae can lead to high-value production. Due to the complex composition in FPBs, various pretreatment methods have been applied to extract the desired compounds and medium preparation. Using the FPB-based medium resulted in cost reduction and a productivity enhancement in previous literature. Although there are still challenges to overcome to achieve economic viability and environmental sustainability, the microalgal transformation of FPBs is attractive for functional food ingredients production.

Temperature dependence of sequential chlorinated ethenes dechlorination and the dynamics of dechlorinating microorganisms.

Thermally enhanced bioremediation is a promising approach to shorten the bioremediation period of tetrachloroethene (PCE) and trichloroethene (TCE). To clarify the influence that temperature has on stepwise PCE dechlorination and associated microorganisms, this study conducted dechlorination experiments using contaminated soil and groundwater under five distinct temperature conditions (i.e., 15, 20, 25, 30, and 35 °C). PCE and TCE were dechlorinated most rapidly at 25-35 °C, whereas the preferable temperatures for the dechlorination of cis-1,2- dichloroethene (cis-1,2-DCE) and vinyl chloride (VC) were 25-30 °C and 25 °C, respectively. Microbial community analysis revealed that Sulfurospirillum and Geobacter may have a dominant contribution to the dechlorination of PCE to cis-1,2-DCE, whereas Dehalococcoides harboring VC reductase genes are likely major contributors to the dechlorination of cis-1,2-DCE and VC. These results suggest that temperature influences various microbial groups, including major dechlorinating microorganisms, resulting in the different extent of PCE dechlorination. In addition, the microbial community structure greatly changed after the onset of the experiment, whereas the temperature influence of 15-30 °C on the microbial community structure was minor; however, the microbial community was significantly impacted at 35 °C. Collectively, these results suggest that thermally enhanced anaerobic dechlorination at 25 °C is useful for successful dechlorination of chlorinated ethenes in a short period.

Growth Promotion of Giant Duckweed Spirodela polyrhiza (Lemnaceae) by Ensifer sp. SP4 Through Enhancement of Nitrogen Metabolism and Photosynthesis.

Duckweeds (Lemnaceae) are representative producers in fresh aquatic ecosystems and also yield sustainable biomass for animal feeds, human foods, and biofuels, and contribute toward effective wastewater treatment; thus, enhancing duckweed productivity is a critical challenge. Plant-growth-promoting bacteria (PGPB) can improve the productivity of terrestrial plants; however, duckweed-PGPB interactions remain unclear and no previous study has investigated the molecular mechanisms underlying duckweed-PGPB interaction. Herein, a PGPB, Ensifer sp. strain SP4, was newly isolated from giant duckweed (Spirodela polyrhiza), and the interactions between S. polyrhiza and SP4 were investigated through physiological, biochemical, and metabolomic analyses. In S. polyrhiza and SP4 coculture, SP4 increased the nitrogen (N), chlorophyll, and ribulose-1,5-bisphosphate carboxylase/oxygenase (RuBisCO) contents and the photosynthesis rate of S. polyrhiza by 2.5-, 2.5-, 2.7-, and 2.4-fold, respectively. Elevated photosynthesis increased the relative growth rate and biomass productivity of S. polyrhiza by 1.5- and 2.7-fold, respectively. Strain SP4 significantly altered the metabolomic profile of S. polyrhiza, especially its amino acid profile. N stable isotope analysis revealed that organic N compounds were transferred from SP4 to S. polyrhiza. These N compounds, particularly glutamic acid, possibly triggered the increase in photosynthetic and growth activities. Accordingly, we propose a new model for the molecular mechanism underlying S. polyrhiza growth promotion by its associated bacteria Ensifer sp. SP4, which occurs through enhanced N compound metabolism and photosynthesis. Our findings show that Ensifer sp. SP4 is a promising PGPB for increasing biomass yield, wastewater purification activity, and CO2 capture of S. polyrhiza.[Formula: see text] Copyright © 2021 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.

Effects of selection and compiling strategy of substrates in column-type vertical-flow constructed wetlands on the treatment of synthetic landfill leachate containing bisphenol A.

A constructed wetland (CW) is a low-cost, eco-friendly, easy-to-maintain, and widely applicable technology for treating various pollutants in the waste landfill leachate. This study determined the effects of the selection and compiling strategy of substrates used in CWs on the treatment performance of a synthetic leachate containing bisphenol A (BPA) as a representative recalcitrant pollutant. We operated five types of lab-scale vertical-flow CWs using only gravel (CW1), a sandwich of gravel with activated carbon (CW2) or brick crumbs (CW3), and two-stage hybrid CWs using gravel in one column and activated carbon (CW4) or brick crumbs (CW5) in another to treat synthetic leachate containing BPA in a 7-d sequential batch mode for 5 weeks. CWs using activated carbon (CW2 and CW4) effectively removed ammonium nitrogen (NH4-N) (99-100%), chemical oxygen demand (COD) (93-100%), and BPA (100%), indicating that the high adsorption capacity of activated carbon was the main mechanism involved in their removal. CW5 also exhibited higher pollutant removal efficiencies (NH4-N: 94-99%, COD: 89-98%, BPA: 89-100%) than single-column CWs (CW1 and CW3) (NH4-N: 76-100%, COD: 84-100%, BPA: 51-100%). This indicates the importance of the compiling strategy along with the selection of an appropriate substrate to improve the pollutant removal capability of CWs.

Isolation and Characterization of Euglena gracilis-Associated Bacteria, Enterobacter sp. CA3 and Emticicia sp. CN5, Capable of Promoting the Growth and Paramylon Production of E. gracilis under Mixotrophic Cultivation.

Euglena gracilis produces paramylon, which is a feedstock for high-value functional foods and nutritional supplements. The enhancement of paramylon productivity is a critical challenge. Microalgae growth-promoting bacteria (MGPB) can improve microalgal productivity; however, the MGPB for E. gracilis remain unclear. This study isolated bacteria capable of enhancing E. gracilis growth and paramylon production under mixotrophic conditions. Enterobacter sp. CA3 and Emticicia sp. CN5 were isolated from E. gracilis grown with sewage-effluent bacteria under mixotrophic conditions at pH 4.5 or 7.5, respectively. In a 7-day E. gracilis mixotrophic culture with glucose, CA3 increased E. gracilis biomass and paramylon production 1.8-fold and 3.5-fold, respectively (at pH 4.5), or 1.9-fold and 3.5-fold, respectively (at pH 7.5). CN5 increased E. gracilis biomass and paramylon production 2.0-fold and 4.1-fold, respectively (at pH 7.5). However, the strains did not show such effects on E. gracilis under autotrophic conditions without glucose. The results suggest that CA3 and CN5 promoted both E. gracilis growth and paramylon production under mixotrophic conditions with glucose at pH 4.5 and 7.5 (CA3) or pH 7.5 (CN5). This study also provides an isolation method for E. gracilis MGPB that enables the construction of an effective E. gracilis-MGPB-association system for increasing the paramylon yield of E. gracilis.

Novel Plant-Associated Acidobacteria Promotes Growth of Common Floating Aquatic Plants, Duckweeds.

Duckweeds are small, fast growing, and starch- and protein-rich aquatic plants expected to be a next generation energy crop and an excellent biomaterial for phytoremediation. Despite such an importance, very little is known about duckweed-microbe interactions that would be a key biological factor for efficient industrial utilization of duckweeds. Here we first report the duckweed growth promoting ability of bacterial strains belonging to the phylum Acidobacteria, the members of which are known to inhabit soils and terrestrial plants, but their ecological roles and plant-microbe interactions remain largely unclear. Two novel Acidobacteria strains, F-183 and TBR-22, were successfully isolated from wild duckweeds and phylogenetically affiliated with subdivision 3 and 6 of the phylum, respectively, based on 16S rRNA gene sequence analysis. In the co-culture experiments with aseptic host plants, the F-183 and TBR-22 strains visibly enhanced growth (frond number) of six duckweed species (subfamily Lemnoideae) up to 1.8-5.1 times and 1.6-3.9 times, respectively, compared with uninoculated controls. Intriguingly, both strains also increased the chlorophyll content of the duckweed (Lemna aequinoctialis) up to 2.4-2.5 times. Under SEM observation, the F-183 and TBR-22 strains were epiphytic and attached to the surface of duckweed. Taken together, our findings suggest that indigenous plant associated Acidobacteria contribute to a healthy growth of their host aquatic plants.