Nutrient Dependent Cross-Kingdom Interactions: Fungi and Bacteria From an Oligotrophic Desert Oasis

Mechanisms and implications of bacterial-fungal competition for soil resources

Elucidating complex interactions between bacteria and fungi that determine microbial community structure, composition, and functions in soil, as well as regulate carbon (C) and nutrient fluxes, is crucial to understand biogeochemical cycles. Among the various interactions, competition for resources is the main factor determining the adaptation and niche differentiation between these two big microbial groups in soil. This is because C and energy limitations for microbial growth are a rule rather than an exception. Here, we review the C and energy demands of bacteria and fungi-the two major kingdoms in soil-the mechanisms of their competition for these and other resources, leading to niche differentiation, and the global change impacts on this competition. The normalized microbial utilization preference showed that bacteria are 1.4-5 times more efficient in the uptake of simple organic compounds as substrates, whereas fungi are 1.1-4.1 times more effective in utilizing complex compounds. Accordingly, bacteria strongly outcompete fungi for simple substrates, while fungi take advantage of complex compounds. Bacteria also compete with fungi for the products released during the degradation of complex substrates. Based on these specifics, we differentiated spatial, temporal, and chemical niches for these two groups in soil. The competition will increase under the main five global changes including elevated CO2, N deposition, soil acidification, global warming, and drought. Elevated CO2, N deposition, and warming increase bacterial dominance, whereas soil acidification and drought increase fungal competitiveness.

Nitrogen transfer and cross-feeding between Azotobacter chroococcum and Paracoccus aminovorans promotes pyrene degradation

Nitrogen is a limiting nutrient for degraders function in hydrocarbon-contaminated environments. Biological nitrogen fixation by diazotrophs is a natural solution for supplying bioavailable nitrogen. Here, we determined whether the diazotroph Azotobacter chroococcum HN can provide nitrogen to the polycyclic aromatic hydrocarbon-degrading bacterium Paracoccus aminovorans HPD-2 and further explored the synergistic interactions that facilitate pyrene degradation in nitrogen-deprived environments. We found that A. chroococcum HN and P. aminovorans HPD-2 grew and degraded pyrene more quickly in co-culture than in monoculture. Surface-enhanced Raman spectroscopy combined with 15N stable isotope probing (SERS - 15N SIP) demonstrated that A. chroococcum HN provided nitrogen to P. aminovorans HPD-2. Metabolite analysis and feeding experiments confirmed that cross-feeding occurred between A. chroococcum HN and P. aminovorans HPD-2 during pyrene degradation. Transcriptomic and metabolomic analyses further revealed that co-culture significantly upregulated key pathways such as nitrogen fixation, aromatic compound degradation, protein export, and the TCA cycle in A. chroococcum HN and quorum sensing, aromatic compound degradation and ABC transporters in P. aminovorans HPD-2. Phenotypic and fluorescence in situ hybridization (FISH) assays demonstrated that A. chroococcum HN produced large amounts of biofilm and was located at the bottom of the biofilm in co-culture, whereas P. aminovorans HPD-2 attached to the surface layer and formed a bridge-like structure with A. chroococcum HN. This study demonstrates that distinct syntrophic interactions occur between A. chroococcum HN and P. aminovorans HPD-2 and provides support for their combined use in organic pollutant degradation in nitrogen-deprived environments.

Exploring the Frequency and Distribution of Ecological Non-monotonicity in Associations among Ecosystem Constituents

Complex links between biotic and abiotic constituents are fundamental for the functioning of ecosystems. Although non-monotonic interactions and associations are known to increase the stability, diversity, and productivity of ecosystems, they are frequently ignored by community-level standard statistical approaches. Using the copula-based dependence measure qad, capable of quantifying the directed and asymmetric dependence between variables for all forms of (functional) relationships, we determined the proportion of non-monotonic associations between different constituents of an ecosystem (plants, bacteria, fungi, and environmental parameters). Here, we show that up to 59% of all statistically significant associations are non-monotonic. Further, we show that pairwise associations between plants, bacteria, fungi, and environmental parameters are specifically characterized by their strength and degree of monotonicity, for example, microbe-microbe associations are on average stronger than and differ in degree of non-monotonicity from plant-microbe associations. Considering directed and non-monotonic associations, we extended the concept of ecosystem coupling providing more complete insights into the internal order of ecosystems. Our results emphasize the importance of ecological non-monotonicity in characterizing and understanding ecosystem patterns and processes.

Supplementary Information

The online version contains supplementary material available at 10.1007/s10021-023-00867-9.

Vertical variations in microbial diversity, composition, and interactions in freshwater lake sediments on the Tibetan plateau

Microbial communities in freshwater lake sediments exhibit a distinct depth-dependent variability. Further exploration is required to understand their biodiversity pattern and microbial interactions in vertical sediments. In this study, sediment cores from two freshwater lakes, Mugecuo (MGC) and Cuopu (CP), on the Tibetan plateau were sampled and subsequently sliced into layers at a depth of every centimeter or half a centimeter. Amplicon sequencing was used to analyze the composition, diversity, and interaction of microbial communities. Results showed that sediment samples of both lakes could be clustered into two groups at a sediment depth of about 20 cm, with obvious shifts in microbial community compositions. In lake MGC, the richness component dominated β-diversity and increased with depth, indicating that the microbial communities in the deep layer of MGC was selected from the surface layer. Conversely, the replacement component dominated β-diversity in CP, implying a high turnover rate in the surface layer and inactive seed banks with a high variety in the deep layer. A co-occurrence network analysis showed that negative microbial interactions were prevalent in the surface layers with high nutrient concentrations, while positive microbial interactions were more common in the deep layers with low nutrient concentrations, suggesting that microbial interactions are influenced by nutrient conditions in the vertical sediments. Additionally, the results highlight the significant contributions of abundant and rare taxa to microbial interactions and vertical fluctuations of β-diversity, respectively. Overall, this work deepens our understanding of patterns of microbial interactions and vertical fluctuation in β-diversity in lake sediment columns, particularly in freshwater lake sediments from the Tibetan plateau.

Identifying Eukaryotes and Factors Influencing Their Biogeography in Drinking Water Metagenomes

The biogeography of eukaryotes in drinking water systems is poorly understood relative to that of prokaryotes or viruses, limiting the understanding of their role and management. A challenge with studying complex eukaryotic communities is that metagenomic analysis workflows are currently not as mature as those that focus on prokaryotes or viruses. In this study, we benchmarked different strategies to recover eukaryotic sequences and genomes from metagenomic data and applied the best-performing workflow to explore the factors affecting the relative abundance and diversity of eukaryotic communities in drinking water distribution systems (DWDSs). We developed an ensemble approach exploiting k-mer- and reference-based strategies to improve eukaryotic sequence identification and identified MetaBAT2 as the best-performing binning approach for their clustering. Applying this workflow to the DWDS metagenomes showed that eukaryotic sequences typically constituted small proportions (i.e., <1%) of the overall metagenomic data with higher relative abundances in surface water-fed or chlorinated systems with high residuals. The α and β diversities of eukaryotes were correlated with those of prokaryotic and viral communities, highlighting the common role of environmental/management factors. Finally, a co-occurrence analysis highlighted clusters of eukaryotes whose members' presence and abundance in DWDSs were affected by disinfection strategies, climate conditions, and source water types.

Different sulfide to arsenic ratios driving arsenic speciation and microbial community interactions in two alkaline hot springs

Arsenic (As) is ubiquitous in geothermal fluids, which threatens both water supply safety and local ecology. The co-occurrence of sulfur (S) and As increases the complexity of As migration and transformation in hot springs. Microorganisms play important roles in As-S transformation processes. In the present study, two Tibetan alkaline hot springs (designated Gulu [GL] and Daba [DB]) with different total As concentrations (0.88 mg/L and 12.42 mg/L, respectively) and different sulfide/As ratios (3.97 and 0.008, respectively) were selected for investigating interactions between As-S geochemistry and microbial communities along the outflow channels. The results showed that As-S transformation processes were similar, although concentrations and percentages of As and S species differed between the two hot springs. Thioarsenates were detected at the vents of the hot springs (18% and 0.32%, respectively), and were desulfurized to arsenite along the drainage channel. Arsenite was finally oxidized to arsenate (532 μg/L and 12,700 μg/L, respectively). Monothioarsenate, total As, and sulfate were the key factors shaping the changes in microbial communities with geochemical gradients. The relative abundances of sulfur reduction genes (dsrAB) and arsenate reduction genes (arsC) were higher in upstream portions of GL explaining high thiolation. Arsenite oxidation genes (aoxAB) were relatively abundant in downstream parts of GL and at the vent of DB explaining low thiolation. Sulfur oxidation genes (soxABXYZ) were abundant in GL and DB. Putative sulfate-reducing bacteria (SRB), such as Desulfuromusa and Clostridium, might be involved in forming thioarsenates by producing reduced S for chemical reactions with arsenite. Sulfur-oxidizing bacteria (SOB), such as Elioraea, Pseudoxanthomonas and Pseudomonas, and arsenite-oxidizing bacteria (AsOB) such as Thermus, Sulfurihydrogenibium and Hydrogenophaga, may be responsible for the oxidation of As-bound S, thereby desulfurizing thioarsenates, forming arsenite and, by further abiotic or microbial oxidation, arsenate. This study improves our understanding of As and S biogeochemistry in hot springs.

Determining the contribution of microbiome complexity to the soil nutrient heterogeneity of fertile islands in a desert ecosystem

"Fertile islands" are known as hotspots of soil nutrient spatial heterogeneity in dryland ecosystems. Although soil microorganisms play critical functional roles in nutrient capture and cycling within fertile islands, our understanding of polymicrobial community roles in regulating soil nutrient distribution in fertile islands remains limited. Herein, we aim to clarify the relationships between the complexity of soil microbial (bacterial, archaeal and fungal) communities and the nutrient distribution around fertile islands. Soil samples were collected along vertical profiles at varying depths in three patches under the canopy of Hedysarum scoparium (CENTRE), at the edge (EDGE) of the canopy and outside (OUTSIDE) the canopy in an area of flowing sand. All the three microbiota have showed spatial heterogeneity around the fertile islands. Among them, bacteria had the most significant heterogeneity, and bacterial community assembly was dominated by deterministic processes. Microbial interaction patterns also showed spatial heterogeneity among different patches. More interaction complexity within microbiota was found in the bacteria in the CENTRE patch and in the fungi in the OUTSIDE patch. In addition, the proportions of among-kingdom connections were reduced under the canopies. Bacteria had the highest connectivity and centrality in the polymicrobial networks and were the most important predictor of polymicrobial interaction complexity, which may have contributed to the distribution of soil nutrients. The random forest (RF) model provided evidence that bacterial beta-diversity and the polymicrobial network complexity index can be optimal predictors of the soil multinutrient cycling index. Our study highlighted the responses of bacteria and polymicrobial interactions to fertile islands and their importance in driving soil nutrient heterogeneity. This information will help in managing soil microorganisms to provide dryland ecosystem services.

Cross-habitat distribution pattern of Bacillus communities and their capacities of producing industrial hydrolytic enzymes in Paracel Islands: Habitat-dependent differential contributions of the environment

Bacillus as a predominant genus of enzyme-producing bacteria presents desirable features to fulfill the vast demand of specific industries, whereas the knowledge of the Bacillus communities and their capacities of producing industrial hydrolytic enzymes across the microhabitats of the Paracel Islands is limited. Herein, a total of 193 culturable Bacillus strains belonging to 19 species were isolated across the microhabitats of seawater, sediment, coral and seagrass, covering 39 stations of the Paracel Islands. Each microhabitat displayed its unique species, while the species of Bacillus paramycoides besides being the dominant species with an abundance of 54.94% also was the only species shared by all microhabitats of the Paracel Islands. Of the Bacillus communities, 97.41% of the isolates exhibited the capacity of producing one-or-more types of enzymes with comparatively higher and broader ranges of enzyme activities, including 163 protease-, 27 cellulase-, 118 alginate lyase-, 140 K-carrageenase- and 158 agarose-producing strains. By the correlation analyses of "Bacillus-environmental factors" and "Enzyme-producing Bacillus-environmental factors", the cross-habitat distribution and enzyme-producing capacity pattern of the Bacillus communities were strongly driven by habitat type, and the environmental factors made habitat-dependent differential contributions to that in the Paracel Islands. It's worth noting that the cellulase-producing strain wasn't detected in seagrass due to its survival strategy to prevent cellulose degradation by inhibiting cellulase-producing bacteria, while coral contained more stable microbial metabolic functions to protect against environmental fluctuations. These findings besides providing large quantities of promising enzyme-producing candidates for specific industrial desires, also facilitate the development and utilization of marine microbial resources and the environmental policy- and/or law-making according to environmental features across the microhabitats of the Paracel Islands.

Co-occurrence networks reveal more complexity than community composition in resistance and resilience of microbial communities

Plant response to drought stress involves fungi and bacteria that live on and in plants and in the rhizosphere, yet the stability of these myco- and micro-biomes remains poorly understood. We investigate the resistance and resilience of fungi and bacteria to drought in an agricultural system using both community composition and microbial associations. Here we show that tests of the fundamental hypotheses that fungi, as compared to bacteria, are (i) more resistant to drought stress but (ii) less resilient when rewetting relieves the stress, found robust support at the level of community composition. Results were more complex using all-correlations and co-occurrence networks. In general, drought disrupts microbial networks based on significant positive correlations among bacteria, among fungi, and between bacteria and fungi. Surprisingly, co-occurrence networks among functional guilds of rhizosphere fungi and leaf bacteria were strengthened by drought, and the same was seen for networks involving arbuscular mycorrhizal fungi in the rhizosphere. We also found support for the stress gradient hypothesis because drought increased the relative frequency of positive correlations.

Mycelial Growth-promoting Potential of Extracellular Metabolites of Paraburkholderia spp. Isolated from Rhizopogon roseolus Sporocarp

This study aimed to investigate the effect of potential metabolite(s) produced by Paraburkholderia spp. isolated from the Rhizopogon roseolus (shouro mushroom) sporocarp on the mycelial growth of R. roseolus. For this purpose, we selected two molecularly identified bacteria: P. fungorum GIB024 and P. caledonica KN1. Direct confrontation assay at three different distances, a pour plate method that sampled bacterial spent broth either with and without agitation at 25 °C, and an indirect confrontation assay was carried out in order to assess the R. roseolus growth-promoting ability of Paraburkholderia spp. These assessments were carried out in a 1:5 diluted Melin-Norkran-modified medium with glucose (hs-dMMN) and without glucose (ls-dMMN). GIB024 promoted the growth of R. roseolus in ls-dMMN in short distance, whereas KN1 inhibited the growth of the fungus in that condition. In hs-dMMN, both bacteria have neutral or slightly promotion effect toward R. roseolus. We determined from the spent broth analysis that Paraburkholderia spp. that grew axenically under static conditions had a more pronounced mycelial growth-promoting effect on R. roseolus than under agitation conditions. We also found that high concentration of spent broth resulted in a decrease in mycelial growth-promoting ability. Volatile metabolite(s) produced by both bacteria did not promote the mycelial growth of R. roseolus. In conclusion, Paraburkholderia spp. exhibited a species- and nutrient (sugar)-dependent ability to promote the mycelial growth of R. roseolus, and the bacterial soluble metabolite(s) play a crucial role in their growth-promoting ability.

Colonization by the Mycorrhizal Helper Bacillus pumilus HR10 Is Enhanced During the Establishment of Ectomycorrhizal Symbiosis Between Hymenochaete sp. Rl and Pinus thunbergii

There are complex interactions between mycorrhizal helper bacteria (MHBs) and ectomycorrhizal (ECM) fungi, with MHBs promoting mycorrhizal synthesis and ECM fungi regulating plant rhizobacterial colonization, diversity, and function. In this study, to investigate whether the ECM fungus Hymenochaete sp. Rl affects the survival and colonization of the MHB strain Bacillus pumilus HR10 in the rhizosphere, the biomass of B. pumilus HR10 was measured in the rhizosphere and mycorrhizosphere. In addition, extracts of Hymenochaete sp. Rl and Pinus thunbergii were evaluated for their effect on B. pumilus HR10 colonization (growth, sporulation, biofilm formation, extracellular polysaccharide and extracellular protein contents, flagellar motility, and expression of colonization-related genes). The results showed that inoculation of Hymenochaete sp. Rl significantly increased the biomass of B. pumilus HR10 in the rhizosphere; however, while extracts of Hymenochaete sp. Rl and P. thunbergii did not affect the biomass or spore formation of HR10, they did affect its biofilm formation, extracellular polysaccharide and extracellular protein production, and flagellar motility. Furthermore, the addition of symbiont extracts affected the expression of chemotaxis-related genes in HR10. When the extracts were added separately, the expression of srf genes in HR10 increased; when the extracts were added simultaneously, the expression of the flagellin gene fliG in HR10 increased, but there was no significant effect on the expression of srf genes, consistent with the results on biofilm production. Thus, Hymenochaete sp. Rl and P. thunbergii roots had a positive effect on colonization by B. pumilus HR10 at the rhizosphere level through their secretions.

Sculpting the soil microbiota

Soil is a living ecosystem, the health of which depends on fine interactions among its abiotic and biotic components. These form a delicate equilibrium maintained through a multilayer network that absorbs certain perturbations and guarantees soil functioning. Deciphering the principles governing the interactions within soils is of critical importance for their management and conservation. Here, we focus on soil microbiota and discuss the complexity of interactions that impact the composition and function of soil microbiota and their interaction with plants. We discuss how physical aspects of soils influence microbiota composition and how microbiota-plant interactions support plant growth and responses to nutrient deficiencies. We predict that understanding the principles determining the configuration and functioning of soil microbiota will contribute to the design of microbiota-based strategies to preserve natural resources and develop more environmentally friendly agricultural practices.

Comparative Genomics Reveals Insights into Induction of Violacein Biosynthesis and Adaptive Evolution in Janthinobacterium

Violacein has different bioactive properties conferring distinct selective advantages, such as defense from predation and interspecific competition. Adaptation of Janthinobacterium to diverse habitats likely leads to variation in violacein production among phylogenetically closely related species inhabiting different environments, yet genomic mechanisms and the influence of adaptive evolution underpinning violacein biosynthesis in Janthinobacterium are not clear. In this study, we performed genome sequencing, comparative genomic analysis, and phenotypic characterization to investigate genomic factors regulating violacein production in nine Janthinobacterium strains, including a type strain from soil and eight strains we isolated from terrestrial subsurface sediment and groundwater. Results show that although all nine Janthinobacterium strains are phylogenetically closely related and contain genes essential for violacein biosynthesis, they vary in carbon usage and violacein production. Sediment and groundwater strains are weak violacein producers and possess far fewer secondary metabolite biosynthesis genes, indicating genome adaptation compared to soil strains. Further examination suggests that quorum sensing (QS) may play an important role in regulating violacein in Janthinobacterium: the strains exhibiting strong potential in violacein production possess both N-acyl-homoserine lactone (AHL) QS and Janthinobacterium QS (JQS) systems in their genomes, while weaker violacein-producing strains harbor only the JQS system. Preliminary tests of spent media of two Janthinobacterium strains possessing both AHL QS and JQS systems support the potential role of AHLs in inducing violacein production in Janthinobacterium. Overall, results from this study reveal potential genomic mechanisms involved in violacein biosynthesis in Janthinobacterium and provide insights into evolution of Janthinobacterium for adaptation to oligotrophic terrestrial subsurface environment.

IMPORTANCE Phylogenetically closely related bacteria can thrive in diverse environmental habitats due to adaptive evolution. Genomic changes resulting from adaptive evolution lead to variations in cellular function, metabolism, and secondary metabolite biosynthesis. The most well-known secondary metabolite produced by Janthinobacterium is the purple-violet pigment violacein. To date, the mechanisms of induction of violacein biosynthesis in Janthinobacterium is not clear. Comparative genome analysis of closely related Janthinobacterium strains isolated from different environmental habitats not only reveals potential mechanisms involved in induction of violacein production by Janthinobacterium but also provides insights into the survival strategy of Janthinobacterium for adaptation to oligotrophic terrestrial subsurface environment.

Antimicrobial compounds were isolated from the secondary metabolites of Gordonia, a resident of intestinal tract of Periplaneta americana

Gordonia sp. are members of the actinomycete family, their contribution to the environment improvement and environmental protection by their biological degradation ability, but there are few studies on the antimicrobial activity of their secondary metabolites. Our team isolated and purified an actinomycete WA 4-31 from the intestinal tract of Periplaneta americana, firstly identified the strain WA 4-31 by the morphological characteristics and the phylogenetic analyses, and found it was completely homologous to the strain of Gordonia terrae from the Indian desert. Meanwhile, actinomycin D (1), actinomycin X2 (2), mojavensin A (3) and cyclic (leucine-leucne) dipeptide (4) were obtained from the EtOAc extract from the broth of WA 4-31. Compounds 1–4 showed anti-fungus activities against Candida albicans, Aspergillus niger, A. fumigatus and Trichophyton rubrum, also anti-MRSA and inhibited Escherichia coli in different degree. Interestingly, we found when 3 was mixed with 4 with ratio of 1:1, the activity of the mixture on anti-Candida albicans was better than the single. Besides, compounds 1–3 had varying degrees of antiproliferative activities on CNE-2 and HepG-2 cell lines. These indicated that Gordonia rare actinomycete from the intestinal tract of Periplaneta americana possessed a potential as a source of active secondary metabolites.

Potential use of fungal-bacterial co-cultures for the removal of organic pollutants

Fungi and bacteria coexist in a wide variety of natural and artificial environments which can lead to their association and interaction - ranging from antagonism to cooperation - that can affect the survival, colonization, spatial distribution and stress resistance of the interacting partners. The use of polymicrobial cultivation approaches has facilitated a more thorough understanding of microbial dynamics in mixed microbial communities, such as those composed of fungi and bacteria, and their influence on ecosystem functions. Mixed (multi-domain) microbial communities exhibit unique associations and interactions that could result in more efficient systems for the degradation and removal of organic pollutants. Several previous studies have reported enhanced biodegradation of certain pollutants when using combined fungal-bacterial treatments compared to pure cultures or communities of either fungi or bacteria (single domain systems). This article reviews: (i) the mechanisms of pollutant degradation that can occur in fungal-bacterial systems (e.g.: co-degradation, production of secondary metabolites, enhancement of degradative enzyme production, and transport of bacteria by fungal mycelia); (ii) case studies using fungal-bacterial co-cultures for the removal of various organic pollutants (synthetic dyes, polycyclic aromatic hydrocarbons, pesticides, and other trace or volatile organic compounds) in different environmental matrices (e.g. water, gas/vapors, soil); (iii) the key aspects of engineering artificial fungal-bacterial co-cultures, and (iv) the current challenges and future perspectives of using fungal-bacterial co-cultures for environmental remediation.

Pollinators mediate floral microbial diversity and microbial network under agrochemical disturbance

How pollinators mediate microbiome assembly in the anthosphere is a major unresolved question of theoretical and applied importance in the face of anthropogenic disturbance. We addressed this question by linking visitation of diverse pollinator functional groups (bees, wasps, flies, butterflies, beetles, true bugs and other taxa) to the key properties of the floral microbiome (microbial α- and β-diversity and microbial network) under agrochemical disturbance, using a field experiment of bactericide and fungicide treatments on cultivated strawberries that differ in flower abundance. Structural equation modelling was used to link agrochemical disturbance and flower abundance to pollinator visitation to floral microbiome properties. Our results revealed that (i) pollinator visitation influenced the α- and β-diversity and network centrality of the floral microbiome, with different pollinator functional groups affecting different microbiome properties; (ii) flower abundance influenced the floral microbiome both directly by governing the source pool of microbes and indirectly by enhancing pollinator visitation; and (iii) agrochemical disturbance affected the floral microbiome primarily directly by fungicide, and less so indirectly via pollinator visitation. These findings improve the mechanistic understanding of floral microbiome assembly, and may be generalizable to many other plants that are visited by diverse insect pollinators in natural and managed ecosystems.

Elicitation of Antimicrobial Active Compounds by Streptomyces-Fungus Co-Cultures

The bacteria of the genus Streptomyces and Basidiomycete fungi harbor many biosynthetic gene clusters (BGCs) that are at the origin of many bioactive molecules with medical or industrial interests. Nevertheless, most BGCs do not express in standard lab growth conditions, preventing the full metabolic potential of these organisms from being exploited. Because it generates biotic cues encountered during natural growth conditions, co-culture is a means to elicit such cryptic compounds. In this study, we explored 72 different Streptomyces-fungus interaction zones (SFIZs) generated during the co-culture of eight Streptomyces and nine fungi. Two SFIZs were selected because they showed an elicitation of anti-bacterial activity compared to mono-cultures. The study of these SFIZs showed that co-culture had a strong impact on the metabolic expression of each partner and enabled the expression of specific compounds. These results show that mimicking the biotic interactions present in this ecological niche is a promising avenue of research to explore the metabolic capacities of Streptomyces and fungi.

Sixty-One Volatiles Have Phylogenetic Signals Across Bacterial Domain and Fungal Kingdom

Microorganisms are diverse in their genome sequences and subsequently in their encoded metabolic pathways, which enabled them to adapt to numerous environmental conditions. They produce thousands of small molecules, many of which are volatiles in nature and play important roles in signaling in intra- and inter-species to kingdom and domain interactions, survival, or virulence. Many of these compounds have been studied, characterized, and organized in the mVOC 2.0 database. However, such dataset has not been investigated comprehensively in terms of its phylogeny to determine key volatile markers for certain taxa. It was hypothesized that some of the volatiles described in the mVOC 2.0 database could function as a phylogenetic signal since their production is conserved among certain taxa within the microbial evolutionary tree. Our meta-analysis revealed that some volatiles were produced by a large number of bacteria but not in fungal genera such as dimethyl disulfide, acetic acid, 2-nonanone, dimethyl trisulfide, 2-undecanone, isovaleric acid, 2-tridecanone, propanoic acid, and indole (common bacterial compounds). In contrast, 1-octen-3-ol, 3-octanone, and 2-pentylfuran (common fungal compounds) were produced primarily by fungal genera. Such chemical information was further confirmed by investigating genomic data of publicly available databases revealing that bacteria or fungi harbor gene families involved in these volatiles’ biosynthesis. Our phylogenetic signal testing identified 61 volatiles with a significant phylogenetic signal as demonstrated by phylogenetic D statistic P-value < 0.05. Thirty-three volatiles were phylogenetically conserved in the bacterial domain (e.g., cyclocitral) compared to 17 volatiles phylogenetically conserved in the fungal kingdom (e.g., aristolochene), whereas 11 volatiles were phylogenetically conserved in genera from both bacteria and fungi (e.g., geosmin). These volatiles belong to different chemical classes such as heterocyclic compounds, long-chain fatty acids, sesquiterpenoids, and aromatics. The performed approaches serve as a starting point to investigate less explored volatiles with potential roles in signaling, antimicrobial therapy, or diagnostics.

Oligotrophic Nitrification and Denitrification Bacterial Communities in a Constructed Sewage Treatment Ecosystem and Nitrogen Removal of Delftia tsuruhatensis NF4

Oligotrophic nitrifiers and denitrifiers play important roles in the removal of nitrogen from wastewater. Here, we studied the dominant bacterial populations of the sewage treatment ecosystem (STE) water from different processes and those of culture on oligotrophic heterotrophic nitrification (OHN) medium and oligotrophic aerobic denitrification (OAD) medium, using co-analysis of Illumina HiSeq DNA sequencing and traditional culture methods. The results showed that the STE water had no dominant population of oligotrophic nitrifiers or oligotrophic denitrifiers. However, after culturing on OHN medium and OAD medium, the core genera Pseudomonas, Aeromonas, and Acinetobacter that have the nitrogen removal capacity in oligotrophic environments, dominated in the bacterial community. The principal component analysis (PCA) showed that the bacterial community in the constructed rapid infiltration (CRI) effluent water of STE had high similarity with those of cultures on OHN medium and OAD medium, which prompt the special purification role of nitrogen in the CRI system. The sodium alginate immobilized OAD bacteria strain Delftia tsuruhatensis NF4 was isolated from the CRI system, with total nitrogen (TN) removal efficiency of 43.3% in sterilized STE influent water, and 60.1% in OAD medium on day three. The immobilization significantly influenced the TN and nitrate removal efficiency in OAD medium (p < 0.05), but not in sterilized STE influent water (p > 0.05). This study would lay the foundation for resource discovery of oligotrophic heterotrophic nitrifiers and aerobic denitrifiers in STE and further functional application of them on the bioremediation of wastewater.

Oligotrophic nitrifiers and denitrifiers play important roles in the removal of nitrogen from wastewater. Here, we studied the dominant bacterial populations of the sewage treatment ecosystem (STE) water from different processes and those of culture on oligotrophic heterotrophic nitrification (OHN) medium and oligotrophic aerobic denitrification (OAD) medium, using co-analysis of Illumina HiSeq DNA sequencing and traditional culture methods. The results showed that the STE water had no dominant population of oligotrophic nitrifiers or oligotrophic denitrifiers. However, after culturing on OHN medium and OAD medium, the core genera Pseudomonas, Aeromonas, and Acinetobacter that have the nitrogen removal capacity in oligotrophic environments, dominated in the bacterial community. The principal component analysis (PCA) showed that the bacterial community in the constructed rapid infiltration (CRI) effluent water of STE had high similarity with those of cultures on OHN medium and OAD medium, which prompt the special purification role of nitrogen in the CRI system. The sodium alginate immobilized OAD bacteria strain Delftia tsuruhatensis NF4 was isolated from the CRI system, with total nitrogen (TN) removal efficiency of 43.3% in sterilized STE influent water, and 60.1% in OAD medium on day three. The immobilization significantly influenced the TN and nitrate removal efficiency in OAD medium (p < 0.05), but not in sterilized STE influent water (p > 0.05). This study would lay the foundation for resource discovery of oligotrophic heterotrophic nitrifiers and aerobic denitrifiers in STE and further functional application of them on the bioremediation of wastewater.

Experimental Analysis of Interactions Among Saprotrophic Fungi from A Phosphorous-Poor Desert Oasis in the Chihuahuan Desert

Fungal ecological interactions play a key role in structuring community assemblages. These associations may involve both antagonistic and synergistic relationships, which are commonly influenced by abiotic factors such as nutrient conditions. However, information for extreme, oligotrophic systems remain poor. Herein, interactions among key members of the aquatic transient fungal community (Aspergillus niger, Cladosporium sp., and Coprinellus micaceus) of a low-nutrient freshwater system in the Cuatro Ciénegas Basin, Mexico were studied. Pairwise interaction bioassays were explored in vitro under different nutrient conditions, including carbohydrates-rich, carbohydrates and amino peptides-rich, and low nutrients. Our results indicated that antagonistic patterns prevail among the studied taxa. However, nutrient-dependent changes were observed in Cladosporium sp. shifting to synergy under carbohydrates-rich conditions, suggesting changes in the fungal community composition as a result of nutrient enrichment. Remarkably, our findings contrast with previous work demonstrating mainly synergistic interactions between our tested fungal isolates and co-occurring autochthonous bacteria (Aeromonas spp. and Vibrio sp.) under low-nutrient conditions. This observation may indicate that bacteria and fungi exhibit distinct community-level responses, driven by nutrient conditions. This contributes to the knowledge of fungal community dynamics and interspecific interactions in an oligotrophic ecosystem, highlighting the relevance of nutrient-based shifts and antagonistic interactions in ecosystem dynamics.