Biology subjects

Cytryn, E.

Publications and source records attributed to Cytryn, E..

9 recordsLinked to original sources

bioRxiv2026

Site, Fertilization and Season Structure the Soil Microbiome and its Interactions with Bdellovibrio and Like Organisms Predators

The contribution of predation between bacteria to microbial community dynamics in agricultural fields has hardly been investigated. Here. dynamics of general prokaryotes (GEP) and of the predators Bdellovibrionales (Bd) and Bacteriovoracales (Bac) (Bdellovibrio-and-Like Organisms, BALOs) were studied in two agricultural fields differing in organic and mineral input regimes, for one year. Season, but not fertilization, affected absolute sizes of GEP and of BALO communities. 16S rRNA gene community analysis identified numerous novel Bd and Bac lineages, with none of the dominant BALOs related to characterized isolates. A few dominant BALO amplicon sequence variants (ASVs) persisted year-round, whereas others showed seasonal- or treatment specific responses. GEP, Bd, and Bac ASV -diversity was mostly influenced by season, with some changes due to fertilization in Bd, and Bac communities. Seasonal changes, site, and fertilization regimes influenced {beta}-diversity of GEP, Bd and Bac communities and determined the structure of BALO-gram-negative bacteria interaction networks, signaling that niche segregation acts at the microbiome-BALO interface. Accordingly, we suggest that shifts in GEP community structure triggered by environmental changes and agricultural practices cascade to BALO predators, in turn affecting BALO-microbiome interactions. These dynamics may be harnessed to manipulate the soil microbiome to benefit sustainable environmental and agricultural outcomes. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=121 SRC="FIGDIR/small/735237v1_ufig1.gif" ALT="Figure 1"> View larger version (29K): org.highwire.dtl.DTLVardef@ee25dcorg.highwire.dtl.DTLVardef@f79940org.highwire.dtl.DTLVardef@16e48a2org.highwire.dtl.DTLVardef@1628c9e_HPS_FORMAT_FIGEXP M_FIG The soil microbiome and the microbial predators Bdellovibrio and Like Organisms (BALOs) are influenced by environmental parameters (season) and agricultural practice (fertilization) in their population dynamics, diversity and interactions. BALO diversity is high, and novel clades are found with BALOs differing in abundance and persistence. Microbiome-BALO interactions suggest environment and agricultural practice-dependence of niche segregation in BALOs. BALOs - and other micro-predators-may thus be integrated in the development of soil microbiome manipulations for environmental and agricultural applications. C_FIG

microbiology↗

bioRxiv2026

Deciphering temporal antifungal dynamics of a rare actinomycete via integrated omics

Fungal phytopathogens pose a persistent threat to global crop production, and widespread use of chemical fungicides has driven resistance development and environmental concerns, necessitating sustainable alternatives. Actinomycetes produce diverse bioactive metabolites, yet natural product discovery has disproportionately focused on Streptomyces, leaving rare actinomycete taxa underexplored. Saccharomonospora xinjiangensis XJ-54 is a rare actinomycete exhibiting strong antifungal activity against Fusarium phytopathogens, including Fusarium oxysporum f. sp. cucumerinum (FORC), and harbors numerous biosynthetic gene clusters (BGCs) of unknown function. However, as in many rare actinomycetes, BGCs may be transcriptionally silent under standard laboratory conditions, and their expression dynamics remain poorly understood. To elucidate the molecular basis of antifungal activity in S. xinjiangensis XJ-54, we integrated genomic, transcriptomic, and metabolomic analyses. Cell-free supernatants inhibited FORC after 5 days of fermentation, with activity increasing by day 7. Time-resolved RNA sequencing demonstrated that all genomically-identified BGCs were transcriptionally active but exhibited distinct growth-phase-dependent expression patterns, with approximately half upregulated during exponential growth, and the remainder following transition to stationary phase. We observed temporal variations in transcriptional coupling between cluster-specific regulators and biosynthetic genes. LC-MS-based metabolomics showed growth-phase-dependent metabolite shifts, including stationary phase accumulation of secoiridoid-like monoterpenoids, N-acyl amines, and alkaloids (imidazoles, pyridines, indoles), correlating with the observed antifungal phenotype. Bioactivity-guided fractionation subsequently yielded an active fraction containing a predicted halogenated alkaloid that induced hyphal damage in FORC. These findings indicate that antifungal activity in S. xinjiangensis XJ-54 arises from temporally coordinated biosynthetic programs, providing a framework for optimizing growth conditions and prioritizing BGCs for functional characterization. ImportanceThe discovery of new antifungal compounds is critical for sustainable agriculture and medicine, yet most natural product research has focused on screening a narrow range of well-studied microorganisms. Rare actinomycetes represent an untapped reservoir of chemical diversity, but their biosynthetic potential is predominantly unknown. By integrating time-resolved transcriptomics with metabolomics, we show that the rare actinomycete Saccharomonospora xinjiangensis XJ-54 produces antifungal metabolites through temporally coordinated biosynthetic programs. Contrary to the prevailing assumption that the majority of biosynthetic gene clusters (BGCs) are silent, all BGCs in this strain were transcriptionally active under standard cultivation conditions, with expression patterns that were strongly growth-phase dependent. This work provides a roadmap for unlocking the biosynthetic potential of rare actinomycetes and accelerating the discovery of antifungal natural products that can be applied in agriculture and human health.

microbiology↗

bioRxiv2026

Extended-Spectrum and Last-Resort β-Lactams Exert Increasing Impacts on Chicken Manure-Derived Copiotrophic Microbiomes and Resistomes

Understanding the environmental dissemination of antimicrobial resistance (AMR) is crucial for mitigating its spread and for reducing the clinical burden of resistant infections. Within a One Health framework, animal husbandry systems, and particularly animal gut microbiomes, are widely used as models for agricultural environments, because their high densities and recurrent antibiotic exposure create strong selective pressures that can impact both environmental and human resistomes. In a previous study, we demonstrated that copiotrophic enrichment in medium that stimulates growth of gut-associated bacteria, can reveal clinically associated bacterial populations and associated antibiotic resistance genes (ARGs) that are not detected by direct environmental sampling. In the present study, we applied this enrichment approach to poultry manure to examine how {beta}-lactamase-resistant antibiotics (cefotaxime and meropenem) shape copiotrophic gut-like microbial community composition and resistance profiles relative to an earlier {beta}-lactam (ampicillin) and to antibiotic-free controls. Our results show that {beta}-lactamase-resistant antibiotics induced more pronounced shifts in both microbial diversity and ARG profiles than the early {beta}-lactam. When focusing on specific taxa, differential responses were observed correlating to antimicrobial range of action. Together, these findings underline how the diversity of pathogen and AMR indicators in gut microbiomes may be shaped by different selective pressures imposed by {beta}-lactamase-resistant antibiotics.

microbiology↗

bioRxiv2026

Biosynthetic diversity and antifungal potential of soil-derived Saccharomonospora strains

Soilborne fungal pathogens pose persistent challenges to sustainable agriculture, driving demand for biological alternatives to synthetic fungicides. While actinomycetes, particularly Streptomyces have yielded numerous antifungal compounds, less-explored genera, such as Saccharomonospora represent untapped sources of novel bioactive metabolites for plant protection. Our previous work identified Saccharomonospora as strongly associated with plant disease suppression in organically-amended soils and harbored numerous uncharacterized biosynthetic gene clusters (BGCs). Here, we investigated the biosynthetic capacity and antifungal potential of Saccharomonospora using comparative genomics, untargeted metabolomics, and in vitro bioassays. Cell-free supernatants from six strains (five soil-derived type strains and one novel isolate) were evaluated against three Fusarium phytopathogens. All strains inhibited at least one pathogen, with S. xinjiangensis and S. viridis R81 exhibiting the highest and broad-spectrum activity. Metabolomic profiling of the two most bioactive strains and one moderately active strain (S. cyanea) revealed that [~]40% of detected metabolites were shared across the three strains although their relative abundances varied. S. xinjiangensis and S. viridis R81 displayed higher abundances of shared metabolite classes than S. cyanea, including alkaloids, polyketides, and peptide derivatives. Comparative genomics across the genus revealed that most BGCs, particularly those encoding non-ribosomal peptides synthetases and polyketides synthases, were strain-specific and had low sequence similarity to characterized BGCs. In contrast, BGCs encoding, indole, ectoine, arylpolyene, and terpene were ubiquitous across the genus. Collectively, these findings demonstrate that Saccharomonospora produce antifungal metabolites and harbor diverse, uncharacterized BGCs, positioning this "less-explored" actinomycete genus as a promising source of bioactive compounds for managing soilborne fungal pathogens. ImportanceActinomycetes have historically been rich sources of antifungal metabolites for agriculture and pharmaceuticals, but discovery efforts have focused largely on Streptomyces, leaving other genera underexplored. This study demonstrates that Saccharomonospora, a rare actinomycete genus, produces antifungal metabolites active against major Fusarium pathogens and harbors largely uncharacterized biosynthetic gene clusters, indicating a reservoir of novel chemistry. These findings establish Saccharomonospora as a promising yet underutilized resource for discovering new antifungal agents, expanding the toolkit for sustainable plant disease management beyond traditional actinomycete sources.

microbiology↗

bioRxiv2024

Occurrence of "under-the-radar" antibiotic resistance in anthropogenically affected produce

With global climate change, treated-wastewater (TWW) irrigation and manure amendment are becoming increasingly important in sustainable agriculture in water- and nutrient-stressed regions. Yet, these practices can potentially disseminate pathogens and antimicrobial resistance (AMR) determinants to crops, resulting in serious health risks to humans through the food chain. Previous studies demonstrated that pathogen and AMR indicators from wastewater and manure survive poorly in the environment, suggesting that ecological barriers prevent their dissemination. However, we recently found that these elements can persist below detection levels in low quality TWW-irrigated soil, and potentially proliferate under favorable conditions. This "under the radar" phenomenon was further investigated here, in TWW irrigated- and poultry litter-amended lettuce plants, using an enrichment platform that resembles gut conditions, and an analytical approach that combined molecular and cultivation-based techniques. Enrichment uncovered clinically-relevant multidrug resistant pathogen indicators and a myriad of antibiotic resistance genes in the litter amended and TWW-irrigated lettuce that were not detected by direct analyses, or in the enriched freshwater irrigated samples. Selected resistant E. coli isolates were capable of horizontally transferring plasmids carrying multiple resistance genes to a susceptible strain. Overall, our study underlines the hidden risks of under-the-radar pathogen and AMR determinants in anthropogenically affected agroenvironments, providing a novel platform to improve quantitative microbial risk assessment models in the future.

microbiology↗

bioRxiv2022

Microbiome and resistome dynamics along a sewage-effluent-reservoir continuum underline the role of natural attenuation in effluent receiving reservoirs

This study assessed temporal dynamics of total and antibiotic resistant fecal bacterial indicators and antibiotic resistance genes (ARG) along a sewage-effluent-reservoir continuum, in an experimental system consisting of a sewage-fed membrane-aerated bioreactor (MABR) whose effluent fed a 4500 L polypropylene basin that mimicked an effluent storage reservoir. We applied a multidisciplinary approach that coupled physicochemical analyses, cultivation of total and cefotaxime-resistant E. coli, microbiome (bacterial and eukaryotic) analysis and qPCR/ddPCR quantification of selected ARGs. Total and cefotaxime-resistant E. coli loads dropped by approximately 1.5 log units in both the MABR and the reservoir, but the relative reduction (normalized to 16S rRNA genes) in both E. coli and ARGs was higher in the reservoir. Reservoir microbiomes were significantly different from those in the MABR, and were characterized by temporal shifts and periodic algal (Chlorophyta) blooms that were coupled to oxygen and pH fluctuations. Collectively, the data indicates that the decrease in E. coli and ARGs in the MABR was primarily facilitated by sludge removal, whereas in the reservoir, it was predominantly associated with microbial community shifts. The study highlights the capacity of ecological interactions in mitigating antibiotic resistance in both engineered and natural ecosystems. ImportanceAntibiotic resistance is considered one of the most significant public health predicaments of the 21st century, and there is growing evidence that anthropogenically impacted environments such as those receiving raw and treated sewage can contribute to this phenomenon. In this study, we evaluated the dynamics of total and antibiotic resistant fecal pathogen indicators and antibiotic resistance genes along a sewage-treated wastewater-effluent reservoir continuum, concurrent to evaluation of microbial community composition and physicochemical parameters. Results indicate that both the treatment bioreactor and the effluent storage reservoir removed resistant bacteria and antibiotic resistance encoding genes. However, in the reactor removal was primarily linked to physical processes, whereas in the storage reservoir it appeared to be strongly facilitated by ecological interactions. The study highlights the capacity of aquatic ecosystems to alleviate antibiotic resistance, and suggests that ecological processes in aquatic ecosystems can be harnessed to mitigate antibiotic resistance.

microbiology↗

bioRxiv2021

Seasonal dynamics are the major driver of microbial diversity and composition in intensive freshwater aquaculture

Aquaculture facilities such as fishponds are one of the most anthropogenically impacted freshwater ecosystems. The high fish biomass reared in aquaculture is associated with an intensive input into the water of fish-feed and fish excrements. This nutrients load may affect the microbial community in the water, which in turn can impact the fish health. To determine to what extent aquaculture practices and natural seasonal cycles affect the microbial populations, we characterized the microbiome of an inter-connected aquaculture system at monthly resolution, over three years. The system comprised two fishponds, where fish are grown, and a "control" operational water reservoir in which fish are not actively stocked. Clear natural seasonal cycles of temperature and inorganic nutrients concentration, as well as recurring cyanobacterial blooms during summer, were observed in both the fishponds and the reservoir. The structure of the aquatic bacterial communities in the system, characterized using 16S rRNA sequencing, was explained primarily by the natural seasonality, whereas aquaculture-related parameters had only a minor explanatory power. However, the cyanobacterial blooms were characterized by different cyanobacterial clades dominating at each fishpond, possibly in response to distinct nitrogen and phosphate ratios. In turn, nutrient ratios may have been by the magnitude of fish feed input. Taken together, our results show that, even in strongly anthropogenically impacted aquatic ecosystems, the structure of bacterial communities is mainly driven by the natural seasonality, with more subtle effects if aquaculture-related factors. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=114 SRC="FIGDIR/small/433039v1_ufig1.gif" ALT="Figure 1"> View larger version (39K): org.highwire.dtl.DTLVardef@154d693org.highwire.dtl.DTLVardef@d35ae9org.highwire.dtl.DTLVardef@1f5a7a2org.highwire.dtl.DTLVardef@d07fbc_HPS_FORMAT_FIGEXP M_FIG C_FIG HighlightsO_LIWe present three years of monthly microbiome data from an aquaculture facility. C_LIO_LIThe microbiome changes seasonally, likely driven by temperature and rainwater runoff. C_LIO_LISummer blooms of toxin-producing cyanobacteria are repeatedly observed. C_LIO_LIFish food may impact microbiome through changes in nutrient ratios. C_LI

ecology↗

bioRxiv2020

Plant cell wall polysaccharides induce colony expansion of soil-derived Flavobacterium spp.

The genus Flavobacterium is characterized by the capacity to metabolize complex organic compounds and a unique gliding motility mechanism. They are often abundant in root microbiomes of various plants, but the factors contributing to this high abundance are currently unknown. In this study, we evaluated the effect of various plant-associated poly- and mono-saccharides on colony expansion of two Flavobacterium strains. Both strains were able to spread on pectin and other polysaccharides such as microcrystalline cellulose. However, only pectin (but not pectin monomers), a component of plant cell walls, enhanced colony expansion on solid surfaces in a dose- and substrate-dependent manner. On pectin, flavobacteria exhibited bi-phasic motility, with an initial phase of rapid expansion, followed by growth within the colonized area. Proteomic and gene expression analyses revealed significant induction of carbohydrate metabolism related proteins when flavobacteria were grown on pectin, including selected SusC/D, TonB-dependent glycan transport operons. Our results show a positive correlation between colony expansion and the upregulation of proteins involved in sugar uptake, suggesting an unknown linkage between specific operons encoding for glycan uptake and metabolism and flavobacterial expansion. Furthermore, within the context of flavobacterial-plant interactions, they suggest that pectin may facilitate flavobacterial expansion on plant surfaces in addition to serving as an essential carbon source. Contribution to the field statementMembers of the Flavobacterium genus are frequently rhizosphere competent, i.e. abundant and generally enriched on root surfaces relative to surrounding bulk soil, and previous studies suggest that they may play a role in plant health and ecosystem functioning. However, little is known about genetic and physiological factors that facilitate flavobacterial colonization and proliferation in this highly competitive environment. In this study we found that pectin stimulates flavobacterial colonies in a bi-phasic manner, initially characterized by rapid expansion on agar followed by increased biomass production. This appears to be linked to pectin-stimulated induction of specific TonB-associated proteins evidentially involved in the binding and uptake of complex sugars. Given the fact that pectin and other glycans are a primary component of plant cell walls, we hypothesize that these mechanisms are at least partially responsible for the rhizosphere competence of flavobacteria.

microbiology↗

bioRxiv2020

Elucidating the diversity and potential function of nonribosomal peptide and polyketide biosynthetic gene clusters in the root microbiome

Polyketides (PKs) and nonribosomal peptides (NRPs) are two microbial secondary metabolite (SM) families known for their variety of functions, including antimicrobials, siderophores and others. Despite their involvement in bacteria-bacteria and bacteria-plant interactions, root-associated SMs are largely unexplored due to the limited cultivability of bacteria. Here, we analyzed the diversity and expression of SM-encoding biosynthetic gene clusters (BGCs) in root microbiomes by culture-independent amplicon sequencing, shotgun metagenomics and metatranscriptomics. Roots (tomato and lettuce) harbored distinct compositions of nonribosomal peptide synthetases (NRPSs) and polyketide synthases (PKSs) relative to the adjacent bulk soil, and specific BGC markers were both enriched and highly expressed in the root microbiomes. While several of the highly abundant and expressed sequences were remotely associated with known BGCs, the low similarity to characterized genes suggests their potential novelty. Low similarity genes were screened against a large set of soil-derived cosmid libraries, from which five whole BGCs of unknown function were retrieved. Three clusters were taxonomically affiliated with Actinobacteria, while the remaining were not associated with known bacteria. One Streptomyces-derived BGC was predicted to encode for a polyene with potential antifungal activity, while the others were too novel to predict chemical structure. Screening against a suite of metagenomic datasets revealed a higher abundance of retrieved clusters in roots and soil samples. In contrast, they were almost completely absent in aquatic and gut environments, supporting the notion that they might play an important role in root ecosystems. Overall, our results indicate that root microbiomes harbor a specific assemblage of undiscovered SMs. ImportanceWe identified distinct secondary metabolite (polyketide and nonribosomal peptide) encoding genes that are enriched (relative to adjacent bulk soil) and expressed in root ecosystems, yet almost completely absent in human gut and aquatic environments. Several of the genes were distantly related to genes encoding for antimicrobials and siderophores, and their high sequence variability relative to known sequences suggests that they may encode for novel metabolites and may have unique ecological functions. This study demonstrates that plant roots harbor a diverse array of unique secondary metabolite encoding genes that are highly enriched and expressed in the root ecosystem. The secondary metabolites encoded by these genes might assist the bacteria that produce them in colonization and persistence in the root environment. To explore this hypothesis, future investigations should assess their potential role in inter-bacterial and bacterial-plant interactions.

microbiology↗