Biology subjects

Szitenberg, A.

Publications and source records attributed to Szitenberg, A..

9 recordsLinked to original sources

bioRxiv2026

Intracellular carbon storage enables starvation survival in marine bacteria

Heterotrophic marine bacteria frequently experience fluctuations in carbon availability driven by phytoplankton dynamics. As a result, bacteria undergo repeated cycles of rapid growth during brief resource pulses followed by prolonged starvation. Yet the mechanisms that support bacterial survival during nutrient limitation remain poorly understood. Here, we investigate starvation survival in the algal-associated bacterium Phaeobacter inhibens. We show that cells remain viable for extended periods under carbon depletion while undergoing physiological and morphological changes. Using electron microscopy, metabolomics, and genetic approaches, we identify intracellular polyhydroxybutyrate (PHB) granules as a key factor supporting survival during starvation. PHB accumulates during growth and is progressively consumed under carbon limitation. Deletion of the PHB synthase gene (phaC) eliminates granule formation and reduces long-term viability. Comparative analyses show that the genetic capacity for PHB biosynthesis is widespread among members of the Roseobacter group, suggesting a conserved strategy among algal-associated bacteria. However, species lacking PHB also survive starvation, indicating that additional mechanisms contribute to persistence under nutrient limitation. Together, our results identify intracellular carbon storage as a central mechanism linking bacterial physiology to survival in fluctuating marine environments, and highlight the diversity of strategies shaping microbial community dynamics and carbon cycling in the ocean.

microbiology↗

bioRxiv2026

Pex9 regulates TORC2 during the cellular response to oxidative stress

Peroxisomes are known for their detoxification role in cellular reactive oxygen species (ROS) homeostasis, yet their regulatory roles in cellular recovery from oxidative stress remain unclear. Here, using yeast, we systematically screened a panel of fluorescently tagged peroxisome-related proteins and identified widespread stress-induced changes in their localization. Notably, we discovered that the peroxisomal import receptor, Pex9, rapidly enters the nucleus upon H2O2 exposure, independently of the canonical oxidative stress regulators-Yap1 and Skn7, suggesting a non-canonical signaling function. We further show that Pex9 nuclear entry is modulated by Avo1, an essential Tor complex 2 (TORC2) subunit. In turn, Pex9 downregulates the essential TOR complexes kinase, Tor2, at both the transcriptional and protein levels. Finally, we show that this Pex9-TORC2 regulatory loop during oxidative stress is facilitated by the cellular envelope stress response. Our findings uncover an unexpected peroxisome-TORC2 signaling axis and highlight the importance of organelles in shaping global cellular responses to stress.

cell biology↗

bioRxiv2021

Teasing apart the host-related, nutrient-related and temperature-related effects shaping the phenology and microbiome of the tropical seagrass Halophila stipulacea

BackgroundHalophila stipulacea seagrass meadows are an ecologically important and threatened component of the ecosystem in the Gulf of Aqaba. Recent studies have demonstrated correlated geographic patterns for leaf endophytic community composition and leaf morphology, also coinciding with different levels of water turbidity and nutrient concentrations. Based on these observations, workers have suggested an environmental microbial fingerprint, which may reflect various environmental stress factors seagrasses have experienced, and may add a holobiont level of plasticity to seagrasses, assisting their acclimation to changing environments and through range expansion. However, it is difficult to tease apart environmental effects from host-diversity dependent effects, which have covaried in field studies, although this is required in order to establish that differences in microbial community compositions among sites are driven by environmental conditions rather than by features governed by the host. ResultsIn this study we carried out a mesocosm experiment, in which we studied the effects of warming and nutrient stress on the composition of epiphytic bacterial communities and on some phenological traits. We studied H. stipulacea collected from two different meadows in the Gulf of Aqaba, representing differences in the host and the environment alike. We found that the source site from which seagrasses were collected was the major factor governing seagrass phenology, although heat increased shoot mortality and nutrient loading delayed new shoot emergence. Bacterial diversity, however, mostly depended on the environmental conditions. The most prominent pattern was the increase in Rhodobacteraceae under nutrient stress without heat stress, along with an increase in Microtrichaceae. Together, the two taxa have the potential to maintain nitrate reduction followed by an anammox process, which can together buffer the increase in nutrient concentrations across the leaf surface. ConclusionsOur results thus corroborate the existence of environmental microbial fingerprints, which are independent from the host diversity, and support the notion of a holobiont level plasticity, both important to understand and monitor H. stipulacea ecology under the changing climate.

microbiology↗

bioRxiv2021

Hillslope geodiversity shapes ammonia-oxidizing communities and other microbial regulators in a semi-arid shrubland

The determinants and consequences of drought-related shrub mortality were studied for over a decade, as a model for desertification processes, in a semi-arid long-term ecological research station. Recent studies have shown that geodiversity is an important spatial predictor of plant viability under extreme drought conditions. Homogeneous hillslopes, with a deep soil profile and lack of stoniness, could not support shrubs under long term drought conditions due to low water storage in their soil. Conversely, heterogeneous hillslopes, with shallow soil profiles and high stoniness, supported shrub communities under similar conditions, due to the comparatively greater soil-water content. In the current study, we investigated the effect of hillslope geodiversity on the soil microbial diversity. Using DNA metabarcoding, we found small but consistent differences in the microbial community compositions of the homogeneous and heterogeneous hillslopes; more ammonia oxidizing and reducing-sugar degrading bacteria are found in the homogeneous hillslopes, possibly dwindling the ammonia supply to shrubs. Additionally, based on functional metagenomic reconstruction, we suggest that homogeneous hillslopes have lower superoxide and antibiotics production, leading to reduced protection against pathogens. In fungi, we observed an increase in possible pathogens, at the expense of lichen forming fungi. Lichens are considered to support soil-water by slowly releasing intercepted raindrops. In conclusion, we show that not only plant-diversity but also microbial-diversity is shaped by geodiversity, and that the community shift in homogeneous hillslopes may further promote shrub mortality in this drought-prone, water limited ecosystem. HIGHLIGHTSO_LIHomogeneous hillslopes reduce soil water storage and increase aeration. C_LIO_LIAmmonia oxidizers and reducing-sugar degraders dwindle ammonia supply for plants. C_LIO_LIHomogenous hillslopes do not support moisture providing lichens. C_LIO_LIReduced antibiotics and superoxide secretion capacitate pathogens. C_LIO_LIGeodiversity facilitates microbial regulation during drought. C_LI GRAPHICAL ABSTRACT O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=87 SRC="FIGDIR/small/434393v2_ufig1.gif" ALT="Figure 1"> View larger version (36K): org.highwire.dtl.DTLVardef@1503208org.highwire.dtl.DTLVardef@4c589org.highwire.dtl.DTLVardef@144d17dorg.highwire.dtl.DTLVardef@1159040_HPS_FORMAT_FIGEXP M_FIG C_FIG

microbiology↗

bioRxiv2020

The bacterial community structure dynamics in Meloidogyne incognita infected roots and its role in worm-microbiome interactions

BackgroundPlant parasitic nematodes such as Meloidogyne incognita have a complex life cycle, occurring sequentially in various niches of the root and rhizosphere. They are known to form a range of interactions with bacteria and other microorganisms, that can affect their densities and virulence. High throughput sequencing can reveal these interactions in high temporal, and geographic resolutions, although thus far we have only scratched the surface. We have carried out a longitudinal sampling scheme, repeatedly collecting rhizosphere soil, roots, galls and second stage juveniles from 20 plants to provide a high resolution view of bacterial succession in these niches, using 16S rRNA metabarcoding. ResultsWe find that a structured community develops in the root, in which gall communities diverge from root segments lacking a gall, and that this structure is maintained throughout the crop season. We detail the successional process leading toward this structure, which is driven by interactions with the nematode and later by an increase in bacteria often found in hypoxic and anaerobic environments. We show evidence that this structure may play a role in the nematodes chemotaxis towards uninfected root segments. Finally, we describe the J2 epibiotic microenvironment as ecologically deterministic, in part, due to active bacterial attraction of second stage juveniles. ConclusionsHigh density sampling, both temporally and across adjacent microniches, coupled with the power and relative low cost of metabarcoding, has provided us with a high resolution description of our study system. Such an approach can advance our understanding of holobiont ecology. Meloidogyne spp., with their relatively low genetic diversity, large geographic range and the simplified agricultural ecosystems they occupy, can serve as a model organism. Additionally, the perspective this approach provides could promote the efforts toward biological control efficacy.

microbiology↗

bioRxiv2019

Dissecting the factors shaping fish skin microbiomes in a heterogenous inland water system

Fish skin microbiomes are rarely studied in inland water systems, in spite of their importance for fish health and ecology. This is mainly because fish species distribution often covaries with other biotic and abiotic factors, complicating the study-design. We tackled this issue in the northern part of the Jordan River system, in which a few fish species geographically overlap, across a steep gradients of water temperature and salinity. Using 16S rRNA metabarcoding, we studied the water properties that shape the skin bacterial communities, and their interaction with fish taxonomy. We found that considering the skin-community contamination by water microbial community is important, even when the water and skin communities are apparently different. With this in mind, we found alpha diversity of the skin-communities to be stable across sites, but higher in bentic loaches, compared to other fish. Beta diversity was found to be different among sites and to weakly covary with the dissolved oxygen, when treated skin-communities were considered. In contrast, water temperature and conductivity were strong factors explaining beta diversity in the untreated skin-communities. Beta diversity differences between co-occurring fish species emerged only for the treated skin-communities. Metagenomics predictions highlighted the microbiome functional implications of excluding the water-communities contamination from the fish skin-communities. Finally, we found that human induced eutrophication promotes dysbiosis of the fish skin-community, with signatures relating to fish health. This finding was in line with recent studies, showing that biofilms capture sporadic pollution events, undetectable by interspersed water monitoring.

microbiology↗

bioRxiv2019

Isolation and characterization of live yeast cells from ancient vessels as a tool in bio-archeology

Ancient fermented food has been studied based on recipes, residue analysis and ancient-DNA techniques and reconstructed using modern domesticated yeast. Here, we present a novel approach. We hypothesize that enriched yeast populations in fermented beverages could have become the dominant species in storage vessels and the descendants of these yeast could be isolated and studied long after. To this end, using a pipeline of yeast isolation from clay vessels developed here, we screened for yeast cells in beverage-related and non-related ancient vessels and sediments, from several archeological sites. We found that yeast cells could be successfully isolated specifically from clay containers of fermented beverages. Genomic analysis revealed that these yeast are similar to those found in traditional African beverages. Phenotypically, they grow similar to modern-beer producing yeast. Both strongly suggesting that they are descendants of the original fermenting yeast. These findings provide modern microorganisms as a new tool in bio-archeology. ImportanceSo far, most of the study of ancient organisms was based mainly on the analysis of ancient DNA. Here we show that it is possible to isolate and study microorganisms, yeast in this case, from thousands of years old clay vessels, used for fermentation. We demonstrate that it is highly likely that these cells are descendants of the original yeast strains which participated in the fermentation process and were absorbed into the pottery vessels. Moreover, we characterize the isolated yeast their genome and the beer they produce. These results open new and exciting avenues in the study of domesticated microorganisms and contribute significantly to the fields of bio and experimental -archeology that aims to reconstruct ancient artifacts and products.

ecology↗

bioRxiv2018

Temporal and spatial variation in distribution of fish environmental DNA in England’s largest lake

Environmental DNA offers great potential as a biodiversity monitoring tool. Previous work has demonstrated that eDNA metabarcoding provides reliable information for lake fish monitoring, but important questions remain about temporal and spatial repeatability, which is critical for understanding the ecology of eDNA and developing effective sampling strategies. Here, we carried out comprehensive spatial sampling of Englands largest lake, Windermere, during summer and winter to 1) examine repeatability of the method, 2) compare eDNA results with contemporary gill-net survey data, 3) test the hypothesis of greater spatial structure of eDNA in summer compared to winter due to differences in water mixing between seasons, and 4) compare the effectiveness of shore and offshore sampling for species detection. We find broad consistency between results from three sampling events in terms of species detection and abundance, with eDNA detecting more species than established methods and being significantly correlated to rank abundance determined by long-term data. As predicted, spatial structure was much greater in the summer, reflecting less mixing of eDNA than in the winter. For example Arctic charr, a deep-water species, was only detected in deep, mid-lake samples in the summer, while littoral or benthic species such as minnow and stickleback were more frequently detected in shore samples. By contrast in winter, the eDNA of these species was more uniformly distributed. This has important implications for design of sampling campaigns, for example, deep-water species could be missed and littoral/benthic species overrepresented by focusing exclusively on shoreline samples collected in the summer.

ecology↗

bioRxiv2017

Comparative Genomics Of Apomictic Root-Knot Nematodes: Hybridization, Ploidy, And Dynamic Genome Change

The Root-Knot Nematodes (RKN; genus Meloidogyne) are important plant parasites causing substantial agricultural losses. The Meloidogyne incognita group (MIG) of species, most of which are obligatory apomicts (mitotic parthenogens), are extremely polyphagous and important problems for global agriculture. While understanding the genomic basis for their variable success on different crops could benefit future agriculture, analyses of their genomes pose challenges due to complex evolutionary histories that may incorporate hybridization, ploidy changes, and chromosomal fragmentation. Here we sequence 19 genomes, representing five species of key RKN collected from different geographic origins. We show that a hybrid origin that predated speciation within the MIG has resulted in each species possessing two divergent genomic copies. Additionally, the MIG apomicts are hypotriploids, with a proportion of one genome present in a second copy, and this proportion varies among species. The evolutionary history of the MIG genomes is revealed to be very dynamic, with non-crossover recombination both homogenising the genomic copies, and acting as a mechanism for generating divergence between species. Interestingly, the automictic MIG species M. floridensis differs from the apomict species in that it has become homozygous throughout much of its genome.

evolutionary biology↗