Mixed-species Cultures Research Articles

Environmental dependency of ectomycorrhizal fungi as soil organic matter oxidizers.

Forest soils play a pivotal role as global carbon (C) sinks, where the dynamics of soil organic matter (SOM) are significantly influenced by ectomycorrhizal (ECM) fungi. While correlations between ECM fungal community composition and soil C storage have been documented, the underlying mechanisms behind this remain unclear. Here, we conducted controlled experiments using pure cultures growing on naturally complex SOM extracts to test how ECM fungi regulate soil C and nitrogen (N) dynamics in response to varying inorganic N availability, in both monoculture and mixed culture conditions. ECM species dominant in N-poor soils exhibited superior SOM decay capabilities compared with those prevalent in N-rich soils. Inorganic N addition alleviated N limitation for ECM species but exacerbated their C limitation, reflected by reduced N compound decomposition and increased C compound decomposition. In mixed cultures without inorganic N supplementation, ECM species with greater SOM decomposition potential facilitated the persistence of less proficient SOM decomposers. Regardless of inorganic N availability, ECM species in mixed cultures demonstrated a preference for C over N, intensifying relatively labile C compound decomposition. This study highlights the complex interactions between ECM species, their nutritional requirements, the nutritional environment of their habitat, and their role in modifying SOM.

Different responses of soil bacterial community to plant-plant interactions under organic-inorganic fertilizers affect seedling establishment during subalpine forest succession.

Rhizosphere bacterial community as a valuable indicator of soil quality and function, has been widespread studied. However, little knowledge is about the response of bacterial communities to plant-plant interaction and different fertilizers during secondary forest succession. We conducted a field pot experiment applying organic and inorganic fertilizers to monocultures and mixed cultures of dominant plant species from mid- to late-successional stages (Salix oritrepha, Betula albosinensis, and Picea asperata), and investigated the responses of plant growth and rhizosphere bacterial communities. Results indicated that growth rate of plant height varied among plant species, but no significant differences were observed in soil bacterial diversity and composition among plant species or inter-specific interactions under control. Compared to control, inorganic fertilizer resulted in increases in plant growth and the relative abundance of Proteobacteria, Patescibacteria, Bacteroidetes and Gemmatimonadetes, while simultaneously leading to decrease in the relative abundance of Acidobacteria, Actinobacteria, Chloroflexi, Rokubacteria and Planctomycetes. When grown with other species, the bacterial communities in the mixture resembled those of S. oritrepha in singular monoculture under inorganic fertilizer treatment, but plant growth was not affected by interspecific interaction. Unlike inorganic fertilizer, organic fertilizer significantly affected bacterial communities and increased bacterial diversity, but did not alter the effects of plant-plant interactions on bacterial communities. It was also observed that organic fertilizer facilitated later successional species' growth (P. asperata and B. albosinensis) by the mid-successional species (S. oritrepha), ultimately facilitating secondary forest succession. In addition, plants at different successional stages harbor specific bacterial communities to affect their growth, and the bacterial communities contributed more than soil properties to the variations in the plant growth of S. oritrepha and P. asperata though the bacterial communities were regulated by soil factors. This finding highlights the significance of the rhizosphere bacteria on plant growth and plant community succession. It also emphasize the importance of considering both plant-plant interactions and diverse fertilizer types in forest restoration efforts and provide valuable insights into optimizing agronomic practices for secondary forest succession.

Do ferrous iron-oxidizing acidophiles (Leptospirillum spp.) disturb aerobic bioleaching of laterite ores by sulfur-oxidizing acidophiles (Acidithiobacillus spp.)?

The extraction of nickel, cobalt, and other metals from laterite ores via bioleaching with sulfur-oxidizing and ferric iron-reducing, autotrophic, acidophilic bacteria (e.g. Acidithiobacillus species) has been demonstrated under anaerobic as well as aerobic conditions in experiments in different laboratories. This study demonstrated the bioleaching of laterites from Brazil with the addition of elemental sulfur in 2-L stirred-tank bioreactors with pure and mixed cultures of Acidithiobacillus and Sulfobacillus species under aerobic conditions. In particular, a potential disturbance of mineral dissolution under aerobic conditions by ferrous iron-oxidizing acidophiles likely introduced as contaminants in an applied bioleaching process was investigated with Leptospirillum ferrooxidans at 30°C and Leptospirillum ferriphilum at 40°C, at maintained pH 1.5 or without maintained pH leading to an increase in acidity (with pH values <1.0) due to the biological production of sulfuric acid. Despite the proportion of ferrous iron to the total amount of extracted iron in the solution being drastically reduced in the presence of Leptospirillum species, there was a negligible effect on the extraction efficiency of nickel and cobalt, which is positive news for laterite bioleaching under aerobic conditions.

Bacillus Species with Dye-remediation Potential – A Mini Review

Dyes are either natural or synthetic pigments used as colour for different items including textile materials, leather, cosmetics, plastic, paper, printing ink, food, human hair or paintings. The persisting colour and toxic compounds contained in most dyes leads to serious environmental pollution which is unsuitable for the survival of many ecologically important organisms. A wide range of bacterial species have been reported to effectively remediate dyes of various types and classes. This paper reviews bacterial species from the genus Bacillus with the potentiality to remediate synthetic dyes based on published literatures. Bacillus species remediate dyes basically through biosorption and enzymatic active. The most commonly used Bacillus species are Bacillus subtilis, B. cereus, B. megaterium, B. fusiformis, B. odysseyi, B. mycoides, B. paramycoides, B. pseudomycoides, B. flexus, B. cohnii, B. licheniformis, B. spizizenii, B. algicola, B. vallismortis, B. vietnamensis, B. stratosphericus, B. halodurans, B. albus, B. aryabhattai and B. velezensis. Other researches have also proven that mixed cultures of Bacillus species and species from other microbial genera display significant efficiency in the remediation of various dyes. These species produce enzymes and compounds that aid in the breakdown of dyes, thus, reducing their impact to the environment. The use of the aforementioned Bacillus species in the remediation of other dye related environmental pollutants is highly recommended.

Epithelial responses and Candida albicans pathogenicity are enhanced in the presence of oral streptococci.

Experimental models that consider host-pathogen interactions are relevant for improving knowledge about oral candidiasis. The aim of this study was to assess the epithelial immune responses, Candida penetration of cell monolayers, and virulence during mixed species culture infections. Single species cultures of Candida albicans and mixed cultures (C. albicans, Streptococcus mutans, and Streptococcus sanguinis) were used to infect monolayers of HaCaT and FaDu ATCC HTB-43 cells for 12 h. After infection, IL-18 and IL-34 gene expression was measured to assess epithelial cell immune responses, and lactate dehydrogenase (LDH) activity was measured as an indicator of cell damage. Microscopy determined C. albicans morphology and penetration of fungal cells through the keratinocyte monolayer. Monolayers devoid of infection served as controls. Data were analyzed by an ANOVA one-way test followed by Tukey's post-hoc test (α = 0.05). The results found that IL-18 and IL-34 gene expression and LDH activity were significantly (p < 0.05) upregulated for both cell lines exposed to mixed species cultures compared with C. albicans alone. Candida albicans yeast and hyphae were evident in C. albicans only infections. In contrast, monolayers infected by C. albicans, S. mutans, and S. sanguinis exhibited higher microbial invasion with several hyphal aggregates detected. The presence of streptococci in C. albicans infection enhances the virulence and pathogenicity of the fungus with associated increased immune responses and tissue damage. Extrapolation of these findings to oral infection would indicate the added potential benefit of managing bacterial components of biofilms during treatment.

Sweet potato (Ipomoea batatas) and hyacinth bean (Lablab purpureus) in combination provide greater suppression of mile-a-minute (Mikania micrantha) than either crop alone.

In natural systems, diverse plant communities tend to prevent a single species from dominating. Similarly, management of invasive alien plants may be achieved through various combinations of competing species. We used a de Wit replacement series to compare different combinations of sweet potato (Ipomoea batatas (L.) Lam), hyacinth bean (Lablab purpureus (L.) Sweet) and mile-a-minute (Mikania micrantha Kunth) through measures of photosynthesis, plant growth, nutrient levels in plant tissue and soil, and competitive ability. Cultured alone sweet potato and hyacinth beans exhibited higher total biomass, leafstalk length, and leaf area than mile-a-minute. In mixed culture, either sweet potato or hyacinth bean or both together significantly suppressed the mile-a-minute parameters, i.e., plant height, branch, leaf, adventitious root, and biomass (P<0.05). Based on a significantly lower than 1.0 relative yield of the three plant species in mixed culture, we showed intraspecific competition to be less than interspecific competition. Calculated indices (relative yield, relative yield total, competitive balance index, and change in contribution) demonstrated a higher competitive ability and higher influence of either crop compared to mile-a-minute. The presence of sweet potato and hyacinth bean, especially with both species in combination, significantly reduced (P<0.05) mile-a-minute's net photosynthetic rate (Pn), antioxidant enzyme activities (superoxide dismutase, peroxidase, catalase, and malondialdehyde), chlorophyll content, and nutrient content (N, P, and K). In soil with mile-a-minute in monoculture soil organic matter, total and available N, total and available K, and available P were significantly greater (P<0.05) than in soil with sweet potato grown in monoculture, but less than in soil with hyacinth bean grown in monoculture soil. Nutrient soil content was comparatively reduced for plant mixtures. Plant height, leaf, biomass, Pn, antioxidant enzyme activities, and plant and soil nutrient contents of sweet potato and hyacinth bean tended to be much greater when grown with two crops compared to in mixture with just sweet potato or hyacinth bean. Our results suggest that the competitive abilities of both sweet potato and hyacinth bean were greater than that of mile-a-minute, and also that mile-a-minute suppression was significantly improved via a combination of the two crops compared to either sweet potato or hyacinth bean alone.

Antibacterial and antibiofilm activities of nanoemulsion coating prepared by using caraway oil and chitosan prolongs the shelf life and quality of bananas

IntroductionBananas are a popular and nutritious fruit that are prone to rapid deterioration and microbial spoilage. Nanoemulsion coatings based on essential oils and chitosan have been proposed as a natural and effective way to preserve the quality and safety of fruits. ObjectivesThe aim of this study was to evaluate the effects of a nanoemulsion coating incorporating caraway essential oil and chitosan (CH-CANE) on the shelf life and attributes of bananas. MethodsThe CH-CANE nanoemulsion was prepared and characterized by DLS (Dynamic Light Scattering), PDI (polydispersity index), ζ potential, whiteness index, and pH. The antibacterial and antibiofilm activities of CH-CANE were tested against Escherichia coli and Salmonella typhi using broth dilution assay and biofilm quantification methods. The quality parameters of banana fruit coated with CH-CANE were measured during 7 days of storage at 25°C, including weight loss, firmness, color, MDA (malondialdehyde) levels, CAT (catalase) and SOD (superoxide dismutase) enzyme activities, total soluble sugar, titratable acidity, and microbial counts. ResultsThe CH-CANE nanoemulsion showed nanometric size (105 ± 8.4 nm), low PDI (0.269 ± 2.7), high ζ potential (+32.43 ± 1.92 mV), high whiteness index (84.39 ± 2.7), and neutral pH (6.8). The CH-CANE nanoemulsion exhibited strong antibacterial and antibiofilm activities against E. coli and S. typhi, with MIC values of 8% and biofilm reduction of 3.5 and 4-log (CFU/ml) under mono and mixed-species culture. The CH-CANE coating significantly improved the quality and safety of bananas during storage, by reducing weight loss, firmness, total soluble sugar, and titratable acidity, maintaining color, increasing antioxidant enzyme activity, and inhibiting microbial growth. ConclusionThe CH-CANE nanoemulsion coating is a promising natural and effective method to extend the shelf life and enhance the attributes of bananas.

Analysis of Industrial Bacillus Species as Potential Probiotics for Dietary Supplements.

So far, Bacillus species bacteria are being used as bacteria concentrates, supplementing cleaning preparations in order to reduce odor and expel pathogenic bacteria. Here, we discuss the potential of Bacillus species as 'natural' probiotics and evaluate their microbiological characteristics. An industrially used microbiological concentrates and their components of mixed Bacillus species cultures were tested, which may be a promising bacteria source for food probiotic preparation for supplementary diet. In this study, antagonistic activities and probiotic potential of Bacillus species, derived from an industrial microbiological concentrate, were demonstrated. The cell free supernatants (CFS) from Bacillus licheniformis mostly inhibited the growth of foodborne pathogenic bacteria, such as Escherichia coli O157:H7 ATCC 35150, Salmonella Enteritidis KCCM 12021, and Staphylococcus aureus KCCM 11335, while some of Bacillus strains showed synergistic effect with foodborne pathogenic bacteria. Moreover, Bacillus strains identified by the MALDI TOF-MS method were found sensitive to chloramphenicol, kanamycin, and rifampicin. B. licheniformis and B. cereus displayed the least sensitivity to the other tested antibiotics, such as ampicillin, ampicillin and sulfbactam, streptomycin, and oxacillin and bacitracin. Furthermore, some of the bacterial species detected extended their growth range from the mesophilic to moderately thermophilic range, up to 54 °C. Thus, their potential sensitivity to thermophilic TP-84 bacteriophage, infecting thermophilic Bacilli, was tested for the purpose of isolation a new bacterial host for engineered bionanoparticles construction. We reason that the natural environmental microflora of non-pathogenic Bacillus species, especially B. licheniformis, can become a present probiotic remedy for many contemporary issues related to gastrointestinal tract health, especially for individuals under metabolic strain or for the increasingly growing group of lactose-intolerant people.

The allelopathic algicides sanguinarine and berberine reduced the dominance of Microcystis in competition with Chlorella

Gramine, sanguinarine and berberine are potential algicides that can significantly inhibit the growth of cyanobacteria. Their effects on other phytoplankton have to be considered, because other phytoplankton species and cyanobacteria usually co-exist. In this study, we have established the relationships between phytoplankton biomasses and their marker pigments. Afterwards, we have assessed the allelopathic effects of three algicides (gramine, sanguinarine and berberine) on the mono-cultured and mixed-cultured cyanobacteria Microcystis and green algae Chlorella. Our results showed that zeaxanthine and lutein can be used to determine the cell densities of Microcystis and Chlorella in the mixed cultures, respectively. Our study also demonstrated that the inhibitory effects of these three allelopathic algicides on the growths of both Microcystis and Chlorella were sanguinarine > gramine > berberine. The concentrations for 50% of the maximal effect (EC50) of sanguinarine against Microcystis and Chlorella were 0.065 and 0.09 mg L−1, respectively; the EC50 values of gramine against Microcystis and Chlorella were 1.687 and 0.870 mg L−1, respectively; and the EC50 values of berberine against Microcystis and Chlorella were 1.969 and 2.397, respectively. The inhibitory effect of allelopathic algicides on the multiple phytoplankton species in mixed cultures was significantly greater than that in monocultures. In mixed cultures without allelopathic addition or in cultures with gramine (0.5–3 mg L−1), the dominant species was Microcystis. However, Chlorella became the dominant species when the concentration of sanguinarine was 0.1 mg L−1 or that of berberine was greater than 0.5 mg L−1. Both species of phytoplankton died completely when sanguinarine levels were greater than 0.1 mg L−1. Our results suggested that the allelopathic algicides sanguinarine and berberine reduced the dominance of Microcystis in competition with Chlorella.

Effect of Saccharomyces cerevisiae and Saccharomyces pastorianus Co-Inoculation on Alcoholic Fermentation Behavior and Aromatic Profile of Sauvignon Blanc Wine

Enhancing the sensory profile of wines by exposing the aromas of the grape variety through the involvement of microorganisms has always been a challenge in winemaking. The aim of our work was to evaluate the impact of different fermentation schemes by using mixed and pure cultures of different Saccharomyces species to Sauvignon blanc wine chemical composition and sensory profile. The Sauvignon blanc must has been inoculated with mixed and pure cultures of S. pastorianus and S. cerevisiae strains. For the mixed fermentation schemes, one strain of S. pastorianus has been inoculated with different proportions of S. cerevisiae (S. pastorianus to S. cerevisiae: 99%–1%, 95%–5%, 90%–10%, 80%–20% and 70%–30% w/w) in co-inoculation with two commercial strains of S. cerevisiae. A total of 13 fermentations trials, three monocultures and 10 mixed cultures were performed in biological triplicate. The fermentation kinetics have been controlled by density measurement and classical oenological analyses were performed based on the International Organisation of Vine and Wine (OIV) analytical methods. The population dynamics were evaluated by the specific interdelta PCR reaction of the Saccharomyces species at the beginning and at the end of the fermentation process. The volatile compounds of the wine aroma, such as the esters, higher alcohols and thiols were analyzed by GC/MS. Sensory assessment by trained panel was carried out for all produced wines. Complete depletion of the sugars was achieved between 10 and 13 days for all the fermentation trials. The population dynamics analysis revealed that the S. cerevisiae strain was the most predominant at the end of the fermentation process in all inoculation ratios that were tested. The wines that were fermented with S. pastorianus, either in pure or mixed cultures, were characterized by significantly lower acetic acid production and higher malic acid degradation when compared to the wines that were fermented only with S. cerevisiae strains. The aroma profile of the produced wines was highly affected by both inoculation ratio and the S. cerevisiae strain that was used. The presence of S. pastorianus strain enhanced the production of the varietal thiols when compared to the samples that were fermented with the S. cerevisiae pure cultures. The mixed inoculation cultures of Saccharomyces species could lead to wines with unique character which can nicely express the varietal character of the grape variety.

Screening of mixed-species starter cultures for increasing flavour during fermentation of milk

Flavour is an important factor determining the quality of fermented dairy products. Three L.delbrueckii subsp. bulgaricus isolates and five Streptococcus thermophilus isolates with good fermentation characteristics were selected for evaluation as starter cultures when used in ten different combinations, and in comparison with a commercial starter. Using solid phase micro extraction-gas chromatography-mass spectrometry (SPME-GC-MS) analysis, a total of 55 volatile compounds and nine odour-active compounds were detected in milk fermented by mixed-species starter cultures C5 (L. delbrueckii subsp. bulgaricus IMAU62081: S. thermophilus IMAU40133). The results from partial least squares-discriminant analysis (PLS-DA), electronic nose (E-nose) analysis and sensory evaluation indicated that flavor composition and content of fermentation samples from the C5 mixture were closer to the commercial control than the other mixtures. These results help understand how volatile flavour compounds in yoghurt are affected by the starter culture; this will be useful in the development of value-added fermented dairy products.

Carboxymethyl cellulose and cardamom oil in a nanoemulsion edible coating inhibit the growth of foodborne pathogens and extend the shelf life of tomatoes

A nanoemulsion edible coating solution was prepared using carboxymethyl cellulose (CMC) and cardamom essential oil (CEO) with satisfactory physical properties like size (87 ± 2.3 nm), polydispersity index (0.154 ± 0.07), ζ-potential (−27.30 ± 3.2 mV), whiteness index (86.32 ± 0.34) and pH (7.3 ± 0.48). The minimum inhibitory concentrations (MICs) of Carboxymethyl cellulose-based cardamom essential oil nanoemulsion against Escherichia coli, and Listeria monocytogenes were found to be nearly 10%. It reduced the biofilm formation by inhibiting the EPS production of both of these bacteria under both single and mixed-species culture conditions. The nanoemulsion edible coating significantly reduced the loss of fruit weight (7.32 ± 2.4%), firmness (1.3 times), total soluble solids, and titratable acidity of tomatoes by reducing oxidative stress and increasing antioxidant enzymes during 15 days of storage. By maintaining the levels of antioxidant enzymes, the nanoemulsion edible coating prevented oxidative damage-induced senescence of tomatoes. The microbial load was found to be lower in coated tomatoes, indicating that microbial spoilage was prevented. Hence, the nanoemulsion (CMC-CEONE) edible coating appears to have a high potential to extend the shelf life of fresh tomatoes during storage at 25 ± 2 °C temperature.

Candida Albicans and Streptococcus Mutans Biofilms Suppression by Bioactive Compounds Isolated from Ruta Angustifolia

Ruta angustifolia is one of the species of Ruta genus that is widely used in Asia as traditional natural medicine, but scientific research related to this plant is still limited. Several studies have stated that this plant has an antimicrobial effect, but no studies have discussed the antibiofilm effect of bioactive compounds isolated from R. angustifolia. This study is the first to address this issue. This study aims to see whether the bioactive compounds isolated from R. angustifolia can inhibit the formation of biofilms on oral microbes that play the most important role in the construction of dental caries, namely Candida albicans and Streptococcus mutans. Isolation and identification of bioactive compounds is achieved through Thin Layer Chromatography, Liquid Chromatography with tandem mass spectrometry, and proton nuclear magnetic resonance, respectively. Crystal Violet (CV) method is used to see the total biomass of biofilm, and 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyl tetrazolium bromide (MTT) method is used for the viability test. The morphological visualization of C. albicans has also been carried out using a light microscope and a scanning electron microscope. Three compounds that have been isolated are kokusaginine, chalepin, and lindelofine. The CV and MTT data were compared with the control data using an analysis of variance test followed by the Tukey honestly significant difference test, while the morphological data is qualitatively analyzed. From the results of the biofilm test, it was concluded that the three compounds could significantly inhibit the formation of biofilms produced by C. albicans and S. mutans in mixed species cultures.

Effects of monochloramine on culturability, viability and persistence of Pseudomonas putida and tap water mixed bacterial community

Bacterial biofilms are able to persist in drinking water distribution systems (DWDS) even if disinfectants such as monochloramine are used to inhibit bacterial colonization and biofilm formation. While studies have determined the monochloramine concentrations required to inhibit bacterial biofilms, not much is known about how bacterial biofilms develop resistance towards monochloramine. This study covers the development of resistance to monochloramine in both single species and mixed bacterial biofilms. Through culturability tests and flow cytometry, exposing bacterial biofilms to monochloramine disinfection using a sub-lethal concentration (1.5 mg/L Cl2, experimentally determined) was sufficient to cause an increase of the monochloramine's inhibitory concentrations by as much as two times than what is initially required to inhibit biofilm growth. Through persister cultures and 16S rRNA next generation sequencing (NGS) studies, mixed bacterial biofilms experienced to monochloramine exposure resulted in more bacterial genera becoming persistent and resistant towards monochloramine. Through this study, bacterial genera that were persistent towards monochloramine were suggested to share common traits including the ability (1) to readily enter a persister or viable but non-culturable (VBNC) state and (2) to form biofilms primarily comprising proteinaceous extra-polymeric substances (EPS). Both of these traits also suggested that selected bacterial genera tended to be more persistent to monochloramine and produce EPS. This study advances our understanding of bacterial biofilm resistance towards monochloramine and showed the importance of maintaining monochloramine concentrations in DWDS to prevent the development of bacterial resistance towards monochloramine. KEY POINTS: • Monochloramine-resistant biofilm was developed after sub-lethal disinfection. • Mixed-species culture experienced monochloramine showed more persistence to monochloramine. • Ability to enter a persister/VBNC state is a common trait of persistent bacteria genera.

Allelopathy and micropredation paradigms reconcile with system stoichiometry

AbstractAllelopathy, a type of interference competition involving exuded chemicals, has been documented for several types of organisms including terrestrial plants, aquatic macrophytes, microbes, and planktonic algae. However, due to the dynamic nature of the aquatic environment it is unclear whether allelopathy is an evolutionarily stable competition mechanism in such a setting. In this research, we consider a cosmopolitan harmful algae species, Prymnesium parvum, for which multiple ecological roles of its produced deleterious chemicals have been suggested, including broadcast allelopathy (chemicals produced and exuded) and micropredation via cell–cell interactions (chemicals produced and held within the cell). To further investigate the ecological role of the deleterious chemicals, bioassays (with phytoplankton and zooplankton target organisms) were conducted using various fractions of a P. parvum culture grown under balanced N:P stoichiometry or imbalanced, P‐reduced stoichiometry. In addition, time‐series counts were generated with cell density enumerations and observations of behavior of a mixed species culture at intervals over a 24‐h period. Our results suggest that the apparent ecological role of the chemicals in a relatively high‐density population shifts depending on system stoichiometry in regard to nitrogen and phosphorus. We show that under balanced N:P conditions, deleterious chemical production is low and cell contact mediates mortality of prey. Differently, under imbalanced, P‐reduced conditions chemical effect is high and mass mortality occurs independent of cell contact. Thus, imbalanced N:P ratios shift the apparent ecological role of the deleterious chemicals from one of micropredation to one of broadcast allelopathy. These differences likely influence bloom dynamics and result in different ecological outcomes for systems affected by blooms. Further, we suggest that these differences indicate the importance of predatory mixotrophic feeding in the evolutionary maintenance of deleterious chemical production and the occurrence of allelopathic effects as a byproduct.

One-pot synthesis of 6-aminohexanoic acid from cyclohexane using mixed-species cultures.

6-Aminohexanoic acid (6AHA) is a vital polymer building block for Nylon 6 production and an FDA-approved orphan drug. However, its production from cyclohexane is associated with several challenges, including low conversion and yield, and severe environmental issues. We aimed at overcoming these challenges by developing a bioprocess for 6AHA synthesis. A mixed-species approach turned out to be most promising. Thereby, Pseudomonas taiwanensis VLB120 strains harbouring an upstream cascade converting cyclohexane to either є-caprolactone (є-CL) or 6-hydroxyhexanoic acid (6HA) were combined with Escherichia coli JM101 strains containing the corresponding downstream cascade for the further conversion to 6AHA. ε-CL was found to be a better 'shuttle molecule' than 6HA enabling higher 6AHA formation rates and yields. Mixed-species reaction performance with 4g l-1 biomass, 10mM cyclohexane, and an air-to-aqueous phase ratio of 23 combined with a repetitive oxygen feeding strategy led to complete substrate conversion with 86% 6AHA yield and an initial specific 6AHA formation rate of 7.7±0.1UgCDW -1 . The same cascade enabled 49% 7-aminoheptanoic acid yield from cycloheptane. This combination of rationally engineered strains allowed direct 6AHA production from cyclohexane in one pot with high conversion and yield under environmentally benign conditions.

Low-Level Mouse DNA in Conditioned Medium Generates False Positive Cross-Species Contamination Results in Human Organoid Cultures.

Cell line authentication is critical for preventing the use of mixed or misidentified cell lines in research. Current efforts include short tandem repeat (STR) analysis and PCR-based assays to detect mixed species cultures. Using PCR analysis with mouse-specific primers, we identified contaminating mouse DNA in growth factor conditioned medium (CM) derived from the L-WRN cell line (L-WRN CM), as well as in human organoid cultures maintained in the L-WRN CM. DNA isolated from L-WRN CM matched the L-WRN cell signature by STR analysis. Organoid lines that were positive for murine DNA by PCR were further analyzed via bulk RNA-sequencing and transcripts were aligned to the human and mouse genomes. RNA analysis failed to detect mouse-specific gene expression above background levels, suggesting no viable murine cells were present in the organoid cultures. We interpret our data to show conclusive evidence that mouse cell-derived CM can be a source of contaminating murine DNA detected in human organoid cultures, even though live, transcriptionally-active murine cells are not present. Together, our findings suggest that multiple methods may be required to authenticate human organoid or cell lines and urges cautious interpretation of DNA-based PCR cell line authentication results.

Monoculture-based consumer-resource models predict species dominance in mixed batch cultures of dinoflagellates

Global change will disturb the frequency, scale and distribution of harmful algal blooms (HABs), but we are unable to predict future HABs due to our limited understanding of how physicochemical changes in the environment affect interspecific competition between dinoflagellates. Trait-based mechanistic modelling is an important tool to unravel and quantify various direct and indirect interactions between species. The present study explores whether MacArthur's consumer-resource model can be used as a viable base model to predict dinoflagellate growth in closed multispecies systems. To this end, two batch culture experiments (294 cultures in total) with monocultures and multispecies cultures of Alexandrium minutum, Prorocentrum lima, P. micans, Protoceratium reticulatum and Scrippsiella trochoidea were performed. Despite changes to the relative (different nitrate concentrations) and absolute nutrient availability (dilutions of L1 medium), P. micans outcompeted all other species in mixed cultures. Consumer-resource modelling parameterized using monoculture growth correctly predicted this species dominance (R² between 0.80 and 0.95). Parameter estimates revealed that P. micans had a faster uptake of nitrogen when compared to its competitors, but did not differ in resource efficiency and natural mortality rate. Yet, while the model accurately predicted community dynamics during the growth phase, it was not able to predict their dynamics beyond the point of quiescence. Consumer-resource modelling was shown to differentiate the roles of resource assimilation, resource efficiency, and natural mortality rates in batch culture experiments with minimal data requirements beyond common measurements. The results suggest that consumer-resource models provide a promising basis for trait-based modelling of interspecific competition between (harmful) algae.

Nitrite production by ammonia-oxidizing bacteria mediates chloramine decay and resistance in a mixed-species community.

As water distribution centres increasingly switch to using chloramine to disinfect drinking water, it is of paramount importance to determine the interactions of chloramine with potential biological contaminants, such as bacterial biofilms, that are found in these systems. For example, ammonia-oxidizing bacteria (AOB) are known to accelerate the decay of chloramine in drinking water systems, but it is also known that organic compounds can increase the chloramine demand. This study expanded upon our previously published model to compare the decay of chloramine in response to alginate, Pseudomonas aeruginosa, Nitrosomonas europaea and a mixed-species nitrifying culture, exploring the contributions of microbial by-products, heterotrophic bacteria and AOBs to chloramine decay. Furthermore, the contribution of AOBs to biofilm stability during chloramination was investigated. The results demonstrate that the biofilm matrix or extracellular polymeric substances (EPS), represented by alginate in these experiments, as well as high concentrations of dead or inactive cells, can drive chloramine decay rather than any specific biochemical activity of P. aeruginosa cells. Alginate was shown to reduce chloramine concentrations in a dose-dependent manner at an average rate of 0.003mgl-1 h-1 per mgl-1 of alginate. Additionally, metabolically active AOBs mediated the decay of chloramine, which protected members of mixed-species biofilms from chloramine-mediated disinfection. Under these conditions, nitrite produced by AOBs directly reacted with chloramine to drive its decay. In contrast, biofilms of mixed-species communities that were dominated by heterotrophic bacteria due to either the absence of ammonia, or the addition of nitrification inhibitors and glucose, were highly sensitive to chloramine. These results suggest that mixed-species biofilms are protected by a combination of biofilm matrix-mediated inactivation of chloramine as well as the conversion of ammonia to nitrite through the activity of AOBs present in the community.

Superior growth, N uptake and NH4+ tolerance in the giant bamboo Phyllostachys edulis over the broad-leaved tree Castanopsis fargesii at elevated NH4+ may underlie community succession and favor the expansion of bamboo.

The unbridled expansion of bamboo has imposed serious threats on ecosystem processes and functions. Considerable evidence indicates that bamboo invasions can alter plant-available soil nitrogen (N) pools and rates of N cycling, but the consequences of altered N availability for plant growth and community structure have thus far been poorly characterized. The primary soil-accessible N forms for most plants are ammonium (NH4+) and nitrate (NO3-), but plants differ in their ability to use the different N forms, and these differences can be related to their ecological characteristics and drive community structure. In this context, we evaluated the growth response, N uptake and interspecific competition in two subtropical species, Phyllostachys edulis (Carrière) J. Houzeau (Synonym Phyllostachys heterocycla Carrière) and Castanopsis fargesii Franch., dominant species of bamboo and secondary evergreen broad-leaved forests, respectively, under changing N availability in seedlings supplied with different N concentrations and NH4+/NO3- proportions, in vermiculite culture, in a controlled environment. The results show that (i) both species display an NH4+ preference at elevated N concentrations. The growth of P. edulis seedlings was strongly enhanced at increased ratios of NH4+ to NO3- especially at higher N concentrations, but to a much lesser extent in C. fargesii. (ii) NH4+ preference at the level of N uptake in both species was confirmed by the Non-invasive Micro-test Technology and by examining 15N signatures. Phyllostachys edulis had higher NH4+ net fluxes and N concentration under NH4+ treatments than C. fargesii. (iii) NH4+ at higher concentrations caused toxicity in both species as it inhibited root growth and even caused seedling death, but P. edulis had a higher NH4+-tolerance threshold (24mM) than C. fargesii (16mM). (iv) When mixed-species cultures were examined in an NH4+-rich medium, the growth of C. fargesii, but not P. edulis, was significantly inhibited compared with growth in monoculture. Therefore, P. edulis exhibited stronger plasticity and adaptation to changing N availability, whereas C. fargesii had low responsiveness and capacity to acclimate to soil N changes. Phyllostachys edulis displayed a significant competitive growth advantage compared with C. fargesii on NH4+-dominated substrates.